Clinical Focus

  • Autopsy
  • Gastrointestinal Pathology
  • Anatomic and Clinical Pathology

Academic Appointments

Professional Education

  • Fellowship: Oregon Health and Science University Dept of Pathology (2008) OR
  • Board Certification: American Board of Pathology, Anatomic Pathology (2009)
  • Residency: Cedars Sinai Medical Center Pathology Residency (2007) CA
  • Internship: Naval Hospital San Diego Surgery Residency (1999) CA
  • Medical Education: George Washington University Office of the Registrar (1998) DC

Current Research and Scholarly Interests

I am the Director of the Research Autopsy Collaboration at Stanford (RACS) to collect organs and tissues from decedent donors for cancer and disease research.
I have a number of research interests associated with my autopsy work, including how the time interval between death and collection (the PMI) affects the condition and research viability of the collected tissue, how valuable blood and tissue cultures behave after death, and how autopsy results affect clinical practice in an established information loop. I have projects exploring physician and family attitudes towards autopsy and the utilization of rapid autopsy tissue in characterizing cancer evolution from genetic and immunologic standpoints.

All Publications

  • Research autopsy programmes in oncology: shared experience from 14 centres across the world. The Journal of pathology Geukens, T., Maetens, M., Hooper, J. E., Oesterreich, S., Lee, A. V., Miller, L., Atkinson, J. M., Rosenzweig, M., Puhalla, S., Thorne, H., Devereux, L., Bowtell, D., Loi, S., Bacon, E. R., Ihle, K., Song, M., Rodriguez-Rodriguez, L., Welm, A. L., Gauchay, L., Murali, R., Chanda, P., Karacay, A., Naceur-Lombardelli, C., Bridger, H., Swanton, C., Jamal-Hanjani, M., Kollath, L., True, L., Morrissey, C., Chambers, M., Chinnaiyan, A. M., Wilson, A., Mehra, R., Reichert, Z., Carey, L. A., Perou, C. M., Kelly, E., Maeda, D., Goto, A., Kulka, J., Székely, B., Szasz, A. M., Tőkés, A. M., Van Den Bogaert, W., Floris, G., Desmedt, C. 2024


    While there is a great clinical need to understand the biology of metastatic cancer in order to treat it more effectively, research is hampered by limited sample availability. Research autopsy programmes can crucially advance the field through synchronous, extensive, and high-volume sample collection. However, it remains an underused strategy in translational research. Via an extensive questionnaire, we collected information on the study design, enrolment strategy, study conduct, sample and data management, and challenges and opportunities of research autopsy programmes in oncology worldwide. Fourteen programmes participated in this study. Eight programmes operated 24 h/7 days, resulting in a lower median postmortem interval (time between death and start of the autopsy, 4 h) compared with those operating during working hours (9 h). Most programmes (n = 10) succeeded in collecting all samples within a median of 12 h after death. A large number of tumour sites were sampled during each autopsy (median 15.5 per patient). The median number of samples collected per patient was 58, including different processing methods for tumour samples but also non-tumour tissues and liquid biopsies. Unique biological insights derived from these samples included metastatic progression, treatment resistance, disease heterogeneity, tumour dormancy, interactions with the tumour micro-environment, and tumour representation in liquid biopsies. Tumour patient-derived xenograft (PDX) or organoid (PDO) models were additionally established, allowing for drug discovery and treatment sensitivity assays. Apart from the opportunities and achievements, we also present the challenges related with postmortem sample collections and strategies to overcome them, based on the shared experience of these 14 programmes. Through this work, we hope to increase the transparency of postmortem tissue donation, to encourage and aid the creation of new programmes, and to foster collaborations on these unique sample collections. © 2024 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.

    View details for DOI 10.1002/path.6271

    View details for PubMedID 38551513

  • Intrathecal Gene Therapy for Giant Axonal Neuropathy. The New England journal of medicine Bharucha-Goebel, D. X., Todd, J. J., Saade, D., Norato, G., Jain, M., Lehky, T., Bailey, R. M., Chichester, J. A., Calcedo, R., Armao, D., Foley, A. R., Mohassel, P., Tesfaye, E., Carlin, B. P., Seremula, B., Waite, M., Zein, W. M., Huryn, L. A., Crawford, T. O., Sumner, C. J., Hoke, A., Heiss, J. D., Charnas, L., Hooper, J. E., Bouldin, T. W., Kang, E. M., Rybin, D., Gray, S. J., Bönnemann, C. G. 2024; 390 (12): 1092-1104


    Giant axonal neuropathy is a rare, autosomal recessive, pediatric, polysymptomatic, neurodegenerative disorder caused by biallelic loss-of-function variants in GAN, the gene encoding gigaxonin.We conducted an intrathecal dose-escalation study of scAAV9/JeT-GAN (a self-complementary adeno-associated virus-based gene therapy containing the GAN transgene) in children with giant axonal neuropathy. Safety was the primary end point. The key secondary clinical end point was at least a 95% posterior probability of slowing the rate of change (i.e., slope) in the 32-item Motor Function Measure total percent score at 1 year after treatment, as compared with the pretreatment slope.One of four intrathecal doses of scAAV9/JeT-GAN was administered to 14 participants - 3.5×1013 total vector genomes (vg) (in 2 participants), 1.2×1014 vg (in 4), 1.8×1014 vg (in 5), and 3.5×1014 vg (in 3). During a median observation period of 68.7 months (range, 8.6 to 90.5), of 48 serious adverse events that had occurred, 1 (fever) was possibly related to treatment; 129 of 682 adverse events were possibly related to treatment. The mean pretreatment slope in the total cohort was -7.17 percentage points per year (95% credible interval, -8.36 to -5.97). At 1 year after treatment, posterior mean changes in slope were -0.54 percentage points (95% credible interval, -7.48 to 6.28) with the 3.5×1013-vg dose, 3.23 percentage points (95% credible interval, -1.27 to 7.65) with the 1.2×1014-vg dose, 5.32 percentage points (95% credible interval, 1.07 to 9.57) with the 1.8×1014-vg dose, and 3.43 percentage points (95% credible interval, -1.89 to 8.82) with the 3.5×1014-vg dose. The corresponding posterior probabilities for slowing the slope were 44% (95% credible interval, 43 to 44); 92% (95% credible interval, 92 to 93); 99% (95% credible interval, 99 to 99), which was above the efficacy threshold; and 90% (95% credible interval, 89 to 90). Between 6 and 24 months after gene transfer, sensory-nerve action potential amplitudes increased, stopped declining, or became recordable after being absent in 6 participants but remained absent in 8.Intrathecal gene transfer with scAAV9/JeT-GAN for giant axonal neuropathy was associated with adverse events and resulted in a possible benefit in motor function scores and other measures at some vector doses over a year. Further studies are warranted to determine the safety and efficacy of intrathecal AAV-mediated gene therapy in this disorder. (Funded by the National Institute of Neurological Disorders and Stroke and others; number, NCT02362438.).

    View details for DOI 10.1056/NEJMoa2307952

    View details for PubMedID 38507752

  • A Large Postmortem Database of COVID-19 Patients Can Inform Disease Research and Public Policy Decision Making. Archives of pathology & laboratory medicine Hooper, J. E., Sanchez, H., Litovsky, S., Lu, Z. A., Gabrielson, E. W., Padera, R. F., Steffensen, T., Solomon, I. H., Gilbert, A., Threlkeld, K. J., Rapkiewicz, A. V., Harper, H., Kapp, M. E., Schwerdt, M. K., Mount, S., Wang, Y., Lu, R., Williamson, A. K. 2024


    Autopsies performed on COVID-19 patients have provided critical information about SARS-CoV-2's tropism, mechanisms of tissue injury, and the spectrum of disease.To provide an updated database of postmortem disease in COVID-19 patients, assess relationships among clinical and pathologic variables, evaluate the accuracy of death certification, and correlate disease variables to causes of death.The 272 postmortem examinations reported in this paper were submitted by 14 pathologists from 9 medical or forensic institutions across the United States. The study spans the eras of the 3 principal COVID-19 strains and incorporates surveyed demographic, clinical, and postmortem data from decedents infected with SARS-CoV-2, including primary and contributing causes of death. It is the largest database of its kind to date.Demographics of the decedents reported here correspond well to national statistics. Primary causes of death as determined by autopsy and official death certificates were significantly correlated. When specifically cited disease conditions found at autopsy were correlated with COVID-19 versus non-COVID-19 death, only lung findings characteristic of SARS-CoV-2 infection or the absence of lung findings were significantly associated.Changes in hospitalization and disease likely stem from longer lifespans after COVID-19 diagnosis and alteration in treatment approaches. Although Omicron variants preferentially replicate in the upper airways, autopsied patients who died of COVID-19 in that time period showed the same lung damage as earlier decedents. Most importantly, findings suggest that there are still unelucidated risk factors for death from COVID-19 including possibly genetic susceptibility.

    View details for DOI 10.5858/arpa.2023-0380-OA

    View details for PubMedID 38452801

  • Comparing anti-tumor and anti-self immunity in a patient with melanoma receiving immune checkpoint blockade. Journal of translational medicine Chen, S., McMiller, T. L., Soni, A., Succaria, F., Sidhom, J. W., Cappelli, L. C., Casciola-Rosen, L. A., Morales, I. R., Sankaran, P., Berger, A. E., Deutsch, J. S., Zhu, Q. C., Anders, R. A., Hooper, J. E., Pardoll, D. M., Lipson, E. J., Taube, J. M., Topalian, S. L. 2024; 22 (1): 241


    Tumor regression following immune checkpoint blockade (ICB) is often associated with immune-related adverse events (irAEs), marked by inflammation in non-cancerous tissues. This study was undertaken to investigate the functional relationship between anti-tumor and anti-self immunity, to facilitate irAE management while promoting anti-tumor immunity.Multiple biopsies from tumor and inflamed tissues were collected from a patient with melanoma experiencing both tumor regression and irAEs on ICB, who underwent rapid autopsy. Immune cells infiltrating melanoma lesions and inflamed normal tissues were subjected to gene expression profiling with multiplex qRT-PCR for 122 candidate genes. Subsequently, immunohistochemistry was conducted to assess the expression of 14 candidate markers of immune cell subsets and checkpoints. TCR-beta sequencing was used to explore T cell clonal repertoires across specimens.While genes involved in MHC I/II antigen presentation, IFN signaling, innate immunity and immunosuppression were abundantly expressed across specimens, irAE tissues over-expressed certain genes associated with immunosuppression (CSF1R, IL10RA, IL27/EBI3, FOXP3, KLRG1, SOCS1, TGFB1), including those in the COX-2/PGE2 pathway (IL1B, PTGER1/EP1 and PTGER4/EP4). Immunohistochemistry revealed similar proportions of immunosuppressive cell subsets and checkpoint molecules across samples. TCRseq did not indicate common TCR repertoires across tumor and inflammation sites, arguing against shared antigen recognition between anti-tumor and anti-self immunity in this patient.This comprehensive study of a single patient with melanoma experiencing both tumor regression and irAEs on ICB explores the immune landscape across these tissues, revealing similarities between anti-tumor and anti-self immunity. Further, it highlights expression of the COX-2/PGE2 pathway, which is known to be immunosuppressive and potentially mediates ICB resistance. Ongoing clinical trials of COX-2/PGE2 pathway inhibitors targeting the major COX-2 inducer IL-1B, COX-2 itself, or the PGE2 receptors EP2 and EP4 present new opportunities to promote anti-tumor activity, but may also have the potential to enhance the severity of ICB-induced irAEs.

    View details for DOI 10.1186/s12967-024-04973-7

    View details for PubMedID 38443917

  • PD-L1-expressing macrophages play a protective role in the joint during arthritis. Arthritis & rheumatology (Hoboken, N.J.) Wood, M. K., Daoud, A., Talor, M. V., Kalinoski, H. M., Hughes, D. M., Jaime, C. M., Hooper, J. E., Won, T., Čiháková, D. 2023


    Arthritis associated with immune checkpoint inhibitor (ICI) therapies highlights the importance of immune checkpoint expression for joint homeostasis. We investigated the role of programmed death ligand 1 (PD-L1) in the synovium using collagen-induced arthritis (CIA) mouse model.We blocked PD-L1 using blocking antibodies (Abs) during CIA and assessed the arthritis severity by clinical and histological scoring. PD-L1 expression and origin of synovial macrophages were investigated using flow cytometry and parabiosis. We utilized Cre-Lox mice to ascertain the protective role of PD-L1-expressing macrophages in arthritis. The immune profile of human and murine synovial PD-L1+ macrophages was determined by RT-PCR, flow cytometry, and single-cell RNA sequencing.Anti-PD-L1 Ab treatment during CIA worsened arthritis with increased immune cell infiltration compared with isotype control, supporting the regulatory role of PD-L1 in the joint. The main cells expressing PD-L1 in the synovium were macrophages. Using parabiosis, we showed that synovial PD-L1+ macrophages were both locally proliferating and partially replaced by the circulation. PD-L1+ macrophages had increased levels of MerTK and IL-10 expression during acute CIA. Genetic depletion of PD-L1 on macrophages in Lyzcre PD-L1fl/fl mice resulted in worsened CIA compared with controls. We found that human PD-L1+ macrophages in the healthy and rheumatoid arthritis synovium express MerTK and IL-10.PD-L1+ macrophages with efferocytotic and anti-inflammatory characteristics protect the synovium from severe arthritis in the CIA mouse model. Tissue-protective PD-L1-expressing macrophages are also present in the human synovium at homeostasis and during rheumatoid arthritis. This article is protected by copyright. All rights reserved.

    View details for DOI 10.1002/art.42749

    View details for PubMedID 37997621

  • Intermediate filament dysregulation in astrocytes in the human disease model of KLHL16 mutation in giant axonal neuropathy (GAN). Molecular biology of the cell Battaglia, R., Faridounnia, M., Beltran, A., Robinson, J., Kinghorn, K., Ezzell, J. A., Bharucha-Goebel, D., Bonnemann, C., Hooper, J. E., Opal, P., Bouldin, T. W., Armao, D., Snider, N. 2023: mbcE23030094


    Giant Axonal Neuropathy (GAN) is a pediatric neurodegenerative disease caused by KLHL16 mutations. KLHL16 encodes gigaxonin, which regulates intermediate filament (IF) turnover. Previous neuropathological studies and examination of postmortem brain tissue in the current study revealed involvement of astrocytes in GAN. To develop a clinically-relevant model, we reprogrammed skin fibroblasts from seven GAN patients to pluripotent stem cells (iPSCs), which were used to generate neural progenitor cells (NPCs), astrocytes, and brain organoids. Multiple isogenic control clones were derived via CRISPR/Cas9 gene editing of one patient line carrying the G332R gigaxonin mutation. All GAN iPSCs were deficient for gigaxonin and displayed patient-specific increased vimentin expression. GAN NPCs had lower nestin expression and fewer nestin-positive cells compared to isogenic controls, but nestin morphology was unaffected. GAN brain organoids were marked by the presence of neurofilament and GFAP aggregates. GAN iPSC-astrocytes displayed striking dense perinuclear vimentin and GFAP accumulations and abnormal nuclear morphology. In over-expression systems, GFAP oligomerization and perinuclear aggregation were augmented in the presence of vimentin. GAN patient cells with large perinuclear vimentin aggregates accumulated significantly more nuclear KLHL16 mRNA compared to cells without vimentin aggregates. As an early effector of KLHL16 mutations, vimentin may be a potential target in GAN.

    View details for DOI 10.1091/mbc.E23-03-0094

    View details for PubMedID 37672338

  • Osteopontin drives retinal ganglion cell resiliency in glaucomatous optic neuropathy. Cell reports Zhao, M., Toma, K., Kinde, B., Li, L., Patel, A. K., Wu, K. Y., Lum, M. R., Tan, C., Hooper, J. E., Kriegstein, A. R., La Torre, A., Liao, Y. J., Welsbie, D. S., Hu, Y., Han, Y., Duan, X. 2023; 42 (9): 113038


    Chronic neurodegeneration and acute injuries lead to neuron losses via diverse processes. We compared retinal ganglion cell (RGC) responses between chronic glaucomatous conditions and the acute injury model. Among major RGC subclasses, αRGCs and intrinsically photosensitive RGCs (ipRGCs) preferentially survive glaucomatous conditions, similar to findings in the retina subject to axotomy. Focusing on an αRGC intrinsic factor, Osteopontin (secreted phosphoprotein 1 [Spp1]), we found an ectopic neuronal expression of Osteopontin (Spp1) in other RGCs subject to glaucomatous conditions. This contrasted with the Spp1 downregulation subject to axotomy. αRGC-specific Spp1 elimination led to significant αRGC loss, diminishing their resiliency. Spp1 overexpression led to robust neuroprotection of susceptible RGC subclasses under glaucomatous conditions. In contrast, Spp1 overexpression did not significantly protect RGCs subject to axotomy. Additionally, SPP1 marked adult human RGC subsets with large somata and SPP1 expression in the aqueous humor correlated with glaucoma severity. Our study reveals Spp1's role in mediating neuronal resiliency in glaucoma.

    View details for DOI 10.1016/j.celrep.2023.113038

    View details for PubMedID 37624696

  • Anti-Gephyrin antibodies: A novel specificity in patients with systemic sclerosis and lower bowel dysfunction. Arthritis & rheumatology (Hoboken, N.J.) McMahan, Z. H., Kulkarni, S., Andrade, F., Perin, J., Zhang, C., Hooper, J. E., Wigley, F. M., Rosen, A., Pasricha, P. J., Casciola-Rosen, L. 2023


    OBJECTIVE: Autoantibodies are clinically useful in phenotyping patients with systemic sclerosis (SSc). GI function is regulated by the enteric nervous system (ENS) and commonly impaired in SSc suggesting that the SSc autoimmune response may target ENS antigens. We sought to identify novel anti-ENS autoantibodies with an aim to clinically phenotype SSc GI dysfunction.METHODS: Serum from a SSc patient with GI dysfunction but without defined SSc-associated autoantibodies was used for autoantibody discovery. Immunoprecipitations performed with murine myenteric plexus lysates were on-bead digested and autoantigens were identified by mass spectrometry. Prevalence was determined and clinical features associated with novel autoantibodies were evaluated in a SSc cohort using regression analyses. Expression of gephyrin in human GI tract tissue was examined by immunohistochemistry.RESULTS: We identified gephyrin as a novel SSc autoantigen. Anti-gephyrin antibodies were present in 9% of SSc patients (16/188) and absent in healthy controls (0/46). Anti-gephyrin antibody-positive patients had higher constipation scores [1.00 vs. 0.50;p=0.02] and were more likely to have severe constipation and severe distention/bloating [46% vs. 15%;p=0.005; 54% vs. 25%;p=0.023, respectively]. Anti-gephyrin antibody levels were significantly higher among patients with severe constipation [0.04 vs. 0.00;p=0.001] and severe distention and bloating [0.03 vs. 0.004;p=0.010]. Severe constipation was associated with anti-gephyrin antibodies even in the adjusted model. Importantly, gephyrin was expressed in the ENS, which regulates gut motility.CONCLUSION: Gephyrin is a novel ENS autoantigen that is expressed in human myenteric ganglia. Anti-gephyrin autoantibodies are associated with the presence and severity of constipation in SSc patients.

    View details for DOI 10.1002/art.42667

    View details for PubMedID 37530745

  • Functional neuronal circuits promote disease progression in cancer. Science advances Restaino, A. C., Walz, A., Vermeer, S. J., Barr, J., Kovacs, A., Fettig, R. R., Vermeer, D. W., Reavis, H., Williamson, C. S., Lucido, C. T., Eichwald, T., Omran, D. K., Jung, E., Schwartz, L. E., Bell, M., Muirhead, D. M., Hooper, J. E., Spanos, W. C., Drapkin, R., Talbot, S., Vermeer, P. D. 2023; 9 (19): eade4443


    The molecular and functional contributions of intratumoral nerves to disease remain largely unknown. We localized synaptic markers within tumors suggesting that these nerves form functional connections. Consistent with this, electrophysiological analysis shows that malignancies harbor significantly higher electrical activity than benign disease or normal tissues. We also demonstrate pharmacologic silencing of tumoral electrical activity. Tumors implanted in transgenic animals lacking nociceptor neurons show reduced electrical activity. These data suggest that intratumoral nerves remain functional at the tumor bed. Immunohistochemical staining demonstrates the presence of the neuropeptide, Substance P (SP), within the tumor space. We show that tumor cells express the SP receptor, NK1R, and that ligand/receptor engagement promotes cellular proliferation and migration. Our findings identify a mechanism whereby intratumoral nerves promote cancer progression.

    View details for DOI 10.1126/sciadv.ade4443

    View details for PubMedID 37163587

  • SARS-CoV-2 infection results in upregulation of Plasminogen Activator Inhibitor-1 and Neuroserpin in the lungs, and an increase in fibrinolysis inhibitors associated with disease severity. EJHaem Toomer, K. H., Gerber, G. F., Zhang, Y., Daou, L., Tushek, M., Hooper, J. E., Francischetti, I. M. 2023; 4 (2): 324-338


    Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection results in coagulation activation although it is usually not associated with consumption coagulopathy. D-dimers are also commonly elevated despite systemic hypofibrinolysis. To understand these unusual features of coronavirus disease 2019 (COVID-19) coagulopathy, 64 adult patients with SARS-CoV-2 infection (36 moderate and 28 severe) and 16 controls were studied. We evaluated the repertoire of plasma protease inhibitors (Serpins, Kunitz, Kazal, Cystatin-like) targeting the fibrinolytic system: Plasminogen Activator Inhibitor-1 (PAI-1), Tissue Plasminogen Activator/Plasminogen Activator Inhibitor-1 complex (t-PA/PAI-1), α-2-Antiplasmin, Plasmin-α2-Antiplasmin Complex, Thrombin-activatable Fibrinolysis Inhibitor (TAFI)/TAFIa, Protease Nexin-1 (PN-1), and Neuroserpin (the main t-PA inhibitor of the central nervous system). Inhibitors of the common (Antithrombin, Thrombin-antithrombin complex, Protein Z [PZ]/PZ inhibitor, Heparin Cofactor II, and α2-Macroglobulin), Protein C ([PC], Protein C inhibitor, and Protein S), contact (Kallistatin, Protease Nexin-2/Amyloid Beta Precursor Protein, and α-1-Antitrypsin), and complement (C1-Inhibitor) pathways, in addition to Factor XIII, Histidine-rich glycoprotein (HRG) and Vaspin were also investigated by enzyme-linked immunosorbent assay. The association of these markers with disease severity was evaluated by logistic regression. Pulmonary expression of PAI-1 and Neuroserpin in the lungs from eight post-mortem cases was assessed by immunohistochemistry. Results show that six patients (10%) developed thrombotic events, and mortality was 11%. There was no significant reduction in plasma anticoagulants, in keeping with a compensated state. However, an increase in fibrinolysis inhibitors (PAI-1, Neuroserpin, PN-1, PAP, and t-PA/PAI-1) was consistently observed, while HRG was reduced. Furthermore, these markers were associated with moderate and/or severe disease. Notably, immunostains demonstrated overexpression of PAI-1 in epithelial cells, macrophages, and endothelial cells of fatal COVID-19, while Neuroserpin was found in intraalveolar macrophages only. These results imply that the lungs in SARS-CoV-2 infection provide anti-fibrinolytic activity resulting in a shift toward a local and systemic hypofibrinolytic state predisposing to (immuno)thrombosis, often in a background of compensated disseminated intravascular coagulation.

    View details for DOI 10.1002/jha2.654

    View details for PubMedID 37206290

    View details for PubMedCentralID PMC10188457

  • Intermediate filament dysregulation and astrocytopathy in the human disease model of KLHL16 mutation in giant axonal neuropathy (GAN). bioRxiv : the preprint server for biology Battaglia, R., Faridounnia, M., Beltran, A., Robinson, J., Kinghorn, K., Ezzell, J. A., Bharucha-Goebel, D., Bonnemann, C., Hooper, J. E., Opal, P., Bouldin, T. W., Armao, D., Snider, N. 2023


    Giant Axonal Neuropathy (GAN) is a pediatric neurodegenerative disease caused by KLHL16 mutations. KLHL16 encodes gigaxonin, a regulator of intermediate filament (IF) protein turnover. Previous neuropathological studies and our own examination of postmortem GAN brain tissue in the current study revealed astrocyte involvement in GAN. To study the underlying mechanisms, we reprogrammed skin fibroblasts from seven GAN patients carrying different KLHL16 mutations to iPSCs. Isogenic controls with restored IF phenotypes were derived via CRISPR/Cas9 editing of one patient carrying a homozygous missense mutation (G332R). Neural progenitor cells (NPCs), astrocytes, and brain organoids were generated through directed differentiation. All GAN iPSC lines were deficient for gigaxonin, which was restored in the isogenic control. GAN iPSCs displayed patient-specific increased vimentin expression, while GAN NPCs had decreased nestin expression compared to isogenic control. The most striking phenotypes were observed in GAN iPSC-astrocytes and brain organoids, which exhibited dense perinuclear IF accumulations and abnormal nuclear morphology. GAN patient cells with large perinuclear vimentin aggregates accumulated nuclear KLHL16 mRNA. In over-expression studies, GFAP oligomerization and perinuclear aggregation were potentiated in the presence of vimentin. As an early effector of KLHL16 mutations, vimentin may serve as a potential therapeutic target in GAN.

    View details for DOI 10.1101/2023.03.13.532440

    View details for PubMedID 36993491

    View details for PubMedCentralID PMC10054982

  • Mortui vivos docent: a modern revival of temporal bone plug harvests. Frontiers in neuroscience Sagi, V., Kosaraju, N., Moore, L. S., Mulders, J. Y., Solyali, M., Ma, X., Regula, D. P., Hooper, J. E., Stankovic, K. M. 2023; 17: 1242831


    Human temporal bones (HTBs) are invaluable resources for the study of otologic disorders and for evaluating novel treatment approaches. Given the high costs and technical expertise required to collect and process HTBs, there has been a decline in the number of otopathology laboratories. Our objective is to encourage ongoing study of HTBs by outlining the necessary steps to establish a pipeline for collection and processing of HTBs. In this methods manuscript, we: (1) provide the design of a temporal bone plug sawblade that can be used to collect specimens from autopsy donors; (2) establish that decalcification time can be dramatically reduced from 9 to 3months if ethylenediaminetetraacetic acid is combined with microwave tissue processing and periodic bone trimming; (3) show that serial sections of relatively-rapidly decalcified HTBs can be successfully immunostained for key inner ear proteins; (4) demonstrate how to drill down a HTB to the otic capsule within a few hours so that subsequent decalcification time can be further reduced to only weeks. We include photographs and videos to facilitate rapid dissemination of the developed methods. Collected HTBs can be used for many purposes, including, but not limited to device testing, imaging studies, education, histopathology, and molecular studies. As new technology develops, it is imperative to continue studying HTBs to further our understanding of the cellular and molecular underpinnings of otologic disorders.

    View details for DOI 10.3389/fnins.2023.1242831

    View details for PubMedID 37886674

  • The SARS-CoV-2 spike protein binds and modulates estrogen receptors. Science advances Solis, O., Beccari, A. R., Iaconis, D., Talarico, C., Ruiz-Bedoya, C. A., Nwachukwu, J. C., Cimini, A., Castelli, V., Bertini, R., Montopoli, M., Cocetta, V., Borocci, S., Prandi, I. G., Flavahan, K., Bahr, M., Napiorkowski, A., Chillemi, G., Ooka, M., Yang, X., Zhang, S., Xia, M., Zheng, W., Bonaventura, J., Pomper, M. G., Hooper, J. E., Morales, M., Rosenberg, A. Z., Nettles, K. W., Jain, S. K., Allegretti, M., Michaelides, M. 2022; 8 (48): eadd4150


    The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike (S) protein binds angiotensin-converting enzyme 2 as its primary infection mechanism. Interactions between S and endogenous proteins occur after infection but are not well understood. We profiled binding of S against >9000 human proteins and found an interaction between S and human estrogen receptor α (ERα). Using bioinformatics, supercomputing, and experimental assays, we identified a highly conserved and functional nuclear receptor coregulator (NRC) LXD-like motif on the S2 subunit. In cultured cells, S DNA transfection increased ERα cytoplasmic accumulation, and S treatment induced ER-dependent biological effects. Non-invasive imaging in SARS-CoV-2-infected hamsters localized lung pathology with increased ERα lung levels. Postmortem lung experiments from infected hamsters and humans confirmed an increase in cytoplasmic ERα and its colocalization with S in alveolar macrophages. These findings describe the discovery of a S-ERα interaction, imply a role for S as an NRC, and advance knowledge of SARS-CoV-2 biology and coronavirus disease 2019 pathology.

    View details for DOI 10.1126/sciadv.add4150

    View details for PubMedID 36449624

  • Method development for generation of PDX models from rapid autopsy samples for the NCI patient-derived models repository Evrard, Y. A., Eugeni, M., Ahalt-Gottholm, M., Bonomi, C., Borgel, S., Caffrey, T. C., Carter, J., Chang, T., Chen, L., Cooper, K., Das, B., Delaney, E., Dougherty, K., Duregon, E., Ecker, S., Geraghty, J., Gibson, M., Hicks, L., Hull, J., Veldt, S., Jiwani, S., Karlovich, C. A., Loewenstein, J., Mallow, C., McGlynn, C., Mills, J., Miner, T., Schneider, J., Shearer, T., Styers, S., Uzelac, S., Grandgenett, P., Hollingsworth, M., Hooper, J. E., Williams, P., Hollingshead, M., Doroshow, J. H. AMER ASSOC CANCER RESEARCH. 2022
  • The SARS-CoV-2 spike protein binds and modulates estrogen receptors. bioRxiv : the preprint server for biology Solis, O., Beccari, A. R., Iaconis, D., Talarico, C., Ruiz-Bedoya, C. A., Nwachukwu, J. C., Cimini, A., Castelli, V., Bertini, R., Montopoli, M., Cocetta, V., Borocci, S., Prandi, I. G., Flavahan, K., Bahr, M., Napiorkowski, A., Chillemi, G., Ooka, M., Yang, X., Zhang, S., Xia, M., Zheng, W., Bonaventura, J., Pomper, M. G., Hooper, J. E., Morales, M., Rosenberg, A. Z., Nettles, K. W., Jain, S. K., Allegretti, M., Michaelides, M. 2022


    The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike (S) protein binds angiotensin-converting enzyme 2 (ACE2) at the cell surface, which constitutes the primary mechanism driving SARS-CoV-2 infection. Molecular interactions between the transduced S and endogenous proteins likely occur post-infection, but such interactions are not well understood. We used an unbiased primary screen to profile the binding of full-length S against >9,000 human proteins and found significant S-host protein interactions, including one between S and human estrogen receptor alpha (ERα). After confirming this interaction in a secondary assay, we used bioinformatics, supercomputing, and experimental assays to identify a highly conserved and functional nuclear receptor coregulator (NRC) LXD-like motif on the S2 subunit and an S-ERα binding mode. In cultured cells, S DNA transfection increased ERα cytoplasmic accumulation, and S treatment induced ER-dependent biological effects and ACE2 expression. Noninvasive multimodal PET/CT imaging in SARS-CoV-2-infected hamsters using [ 18 F]fluoroestradiol (FES) localized lung pathology with increased ERα lung levels. Postmortem experiments in lung tissues from SARS-CoV-2-infected hamsters and humans confirmed an increase in cytoplasmic ERα expression and its colocalization with S protein in alveolar macrophages. These findings describe the discovery and characterization of a novel S-ERα interaction, imply a role for S as an NRC, and are poised to advance knowledge of SARS-CoV-2 biology, COVID-19 pathology, and mechanisms of sex differences in the pathology of infectious disease.

    View details for DOI 10.1101/2022.05.21.492920

    View details for PubMedID 35665018

    View details for PubMedCentralID PMC9164441

  • IgM anti-ACE2 autoantibodies in severe COVID-19 activate complement and perturb vascular endothelial function. JCI insight Casciola-Rosen, L., Thiemann, D. R., Andrade, F., Trejo-Zambrano, M. I., Leonard, E. K., Spangler, J. B., Skinner, N. E., Bailey, J., Yegnasubramanian, S., Wang, R., Vaghasia, A. M., Gupta, A., Cox, A. L., Ray, S. C., Linville, R. M., Guo, Z., Searson, P. C., Machamer, C. E., Desiderio, S., Sauer, L. M., Laeyendecker, O., Garibaldi, B. T., Gao, L., Damarla, M., Hassoun, P. M., Hooper, J. E., Mecoli, C. A., Christopher-Stine, L., Gutierrez-Alamillo, L., Yang, Q., Hines, D., Clarke, W. A., Rothman, R. E., Pekosz, A., Fenstermacher, K. Z., Wang, Z., Zeger, S. L., Rosen, A. 2022


    BACKGROUND: COVID-19 is a global pandemic caused by the novel coronavirus SARS-CoV-2. Some clinical features of severe COVID-19 represent blood vessel damage induced by activation of host immune responses, initiated by the virus. We hypothesized that autoantibodies against angiotensin converting enzyme-2 (ACE2), the SARS-CoV-2 receptor expressed on vascular endothelium, are generated during COVID-19, and are of mechanistic importance.METHODS: The study was done in an opportunity sample of 118 COVID-19 inpatients. Autoantibodies recognizing ACE2 were detected by ELISA. Binding properties of anti-ACE2 IgM from patients were analyzed via biolayer interferometry. The effects of anti-ACE2 IgM on complement activation and endothelial function were demonstrated in a tissue-engineered pulmonary microvessel model.RESULTS: Anti-ACE2 IgM (but not IgG) were associated with severe COVID-19, found in 18/66 (27.2%) patients with severe disease compared to 2/52 (3.8%) of patients with moderate disease (OR 9.38, 95% CI 2.38-42.0; p=0.0009, Fisher's exact test). Anti-ACE2 IgM were rare (2/50) in non-COVID-19 ventilated patients with ARDS. Unexpectedly, ACE2-reactive IgM in COVID-19 do not undergo class-switching to IgG, and have apparent KD values of 5.6-21.7nM, indicating that they are T-independent. Anti-ACE2 IgM activated complement and initiated complement-binding and functional changes in endothelial cells in microvessels, suggesting that they contribute to the angiocentric pathology of COVID-19.CONCLUSIONS: Our results identify anti-ACE2 IgM as a mechanism-based biomarker strongly associated with severe clinical outcomes in SARS-CoV-2 infection, which has therapeutic implications. We anticipate that additional IgM responses may identify other COVID-19 subgroups with severe disease, and potentially other serious pandemic illnesses.

    View details for DOI 10.1172/jci.insight.158362

    View details for PubMedID 35349483

  • Updating Normal Organ Weights Using a Large Current Sample Database. Archives of pathology & laboratory medicine Bell, M. D., Long, T., Roden, A. C., Cooper, F. I., Sanchez, H., Trower, C., Martinez, C., Hooper, J. E. 2022


    Organ weights are an essential part of autopsy analysis. Deviations from normal organ weights provide important clues to disease processes. The assessment of normal organ weights depends on reliable reference tables, but most widely available reference tables are based on data that are either decades old or derived from relatively small sample sizes.To provide an updated reference table of organ weights based on contemporary sources and a large sample size.Organ weights from 4197 carefully screened autopsies performed on adults at the Palm Beach County Medical Examiner's Office in West Palm Beach, Florida, and the Mayo Clinic Hospital in Rochester, Minnesota.Height and body weight data in this study reflect the well-recognized increases in both variables, but most particularly in body weight, seen during the last decades. The study data show a strong positive association between organ weight and body weight for the heart, liver, and spleen. There is a similar but weaker association between body weight and the weight of the lungs and kidneys. Brain weight is independent of body weight but shows a strong negative association with age. Even when controlling for body weight, men's organs are heavier, except for the weight of the liver, which is comparable in men and women. These associations are in agreement with the findings of previous studies. The current study suggests that, for some of the commonly weighed organs, there has been an increase in median organ weight when compared with existing references.The tables presented here provide an updated reference that should prove useful to autopsy pathologists in the forensic and hospital settings.

    View details for DOI 10.5858/arpa.2021-0287-OA

    View details for PubMedID 35344994

  • Endothelial thrombomodulin downregulation caused by hypoxia contributes to severe infiltration and coagulopathy in COVID-19 patient lungs. EBioMedicine Won, T., Wood, M. K., Hughes, D. M., Talor, M. V., Ma, Z., Schneider, J., Skinner, J. T., Asady, B., Goerlich, E., Halushka, M. K., Hays, A. G., Kim, D., Parikh, C. R., Rosenberg, A. Z., Coppens, I., Johns, R. A., Gilotra, N. A., Hooper, J. E., Pekosz, A., Cihakova, D. 1800; 75: 103812


    BACKGROUND: Thromboembolism is a life-threatening manifestation of coronavirus disease 2019 (COVID-19). We investigated a dysfunctional phenotype of vascular endothelial cells in the lungs during COVID-19.METHODS: We obtained the lung specimens from the patients who died of COVID-19. The phenotype of endothelial cells and immune cells was examined by flow cytometry and immunohistochemistry (IHC) analysis. We tested the presence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in the endothelium using IHC and electron microscopy.FINDINGS: The autopsy lungs of COVID-19 patients exhibited severe coagulation abnormalities, immune cell infiltration, and platelet activation. Pulmonary endothelial cells of COVID-19 patients showed increased expression of procoagulant von Willebrand factor (VWF) and decreased expression of anticoagulants thrombomodulin and endothelial protein C receptor (EPCR). In the autopsy lungs of COVID-19 patients, the number of macrophages, monocytes, and T cells was increased, showing an activated phenotype. Despite increased immune cells, adhesion molecules such as ICAM-1, VCAM-1, E-selectin, and P-selectin were downregulated in pulmonary endothelial cells of COVID-19 patients. Notably, decreased thrombomodulin expression in endothelial cells was associated with increased immune cell infiltration in the COVID-19 patient lungs. There were no SARS-CoV-2 particles detected in the lung endothelium of COVID-19 patients despite their dysfunctional phenotype. Meanwhile, the autopsy lungs of COVID-19 patients showed SARS-CoV-2 virions in damaged alveolar epithelium and evidence of hypoxic injury.INTERPRETATION: Pulmonary endothelial cells become dysfunctional during COVID-19, showing a loss of thrombomodulin expression related to severe thrombosis and infiltration, and endothelial cell dysfunction might be caused by a pathologic condition in COVID-19 patient lungs rather than a direct infection with SARS-CoV-2.FUNDING: This work was supported by the Johns Hopkins University, the American Heart Association, and the National Institutes of Health.

    View details for DOI 10.1016/j.ebiom.2022.103812

    View details for PubMedID 35033854

  • Upregulation of pulmonary tissue factor, loss of thrombomodulin and immunothrombosis in SARS-CoV-2 infection ECLINICALMEDICINE Francischetti, I. B., Toomer, K., Zhang, Y., Jani, J., Siddiqui, Z., Brotman, D. J., Hooper, J. E., Kickler, T. S. 2021; 39: 101069


    SARS-CoV-2 infection is associated with thrombotic and microvascular complications. The cause of coagulopathy in the disease is incompletely understood.A single-center cross-sectional study including 66 adult COVID-19 patients (40 moderate, 26 severe disease), and 9 controls, performed between 04/2020 and 10/2020. Markers of coagulation, endothelial cell function [angiopoietin-1,-2, P-selectin, von Willebrand Factor Antigen (WF:Ag), von Willebrand Factor Ristocetin Cofactor, ADAMTS13, thrombomodulin, soluble Endothelial cell Protein C Receptor (sEPCR), Tissue Factor Pathway Inhibitor], neutrophil activation (elastase, citrullinated histones) and fibrinolysis (tissue-type plasminogen activator, plasminogen activator inhibitor-1) were evaluated using ELISA. Tissue Factor (TF) was estimated by antithrombin-FVIIa complex (AT/FVIIa) and microparticles-TF (MP-TF). We correlated each marker and determined its association with severity. Expression of pulmonary TF, thrombomodulin and EPCR was determined by immunohistochemistry in 9 autopsies.Comorbidities were frequent in both groups, with older age associated with severe disease. All patients were on prophylactic anticoagulants. Three patients (4.5%) developed pulmonary embolism. Mortality was 7.5%. Patients presented with mild alterations in the coagulogram (compensated state). Biomarkers of endothelial cell, neutrophil activation and fibrinolysis were elevated in severe vs moderate disease; AT/FVIIa and MP-TF levels were higher in severe patients. Logistic regression revealed an association of D-dimers, angiopoietin-1, vWF:Ag, thrombomodulin, white blood cells, absolute neutrophil count (ANC) and hemoglobin levels with severity, with ANC and vWF:Ag identified as independent factors. Notably, postmortem specimens demonstrated epithelial expression of TF in the lung of fatal COVID-19 cases with loss of thrombomodulin staining, implying in a shift towards a procoagulant state.Coagulation dysregulation has multifactorial etiology in SARS-Cov-2 infection. Upregulation of pulmonary TF with loss of thrombomodulin emerge as a potential link to immunothrombosis, and therapeutic targets in the disease.John Hopkins University School of Medicine.

    View details for DOI 10.1016/j.eclinm.2021.101069

    View details for Web of Science ID 000704058900004

    View details for PubMedID 34377969

    View details for PubMedCentralID PMC8342934

  • Pathology Residency Program Special Expertise Tracks Meet the Needs of an Evolving Field ACADEMIC PATHOLOGY Wake, L. M., Allison, D. B., Ware, A. D., Hooper, J. E., Baras, A. S., Bloch, E. M., Clarke, W., Burns, K. H., Sfanos, K. S., Borowitz, M. J., Steenbergen, C., Hruban, R. H., White, M. J. 2021; 8: 23742895211037034


    Pathologists who enter the workforce must have a diverse skill set beyond that of clinical diagnostics alone. Anticipating this need, the Johns Hopkins Pathology Residency Program developed Special Expertise Tracks to enhance training in relevant subspecialty domains. Using a combination of discussions and surveys, we assessed: (1) our current resident curriculum; (2) perceived curricular strengths and needs; (3) resident career preferences and ultimate career paths; (4) perceived barriers to implementing an advanced elective curriculum; and (5) available departmental/institutional resources. Additionally, we utilized the Accreditation Council for Graduate Medical Education Pathology Milestones as a curricular guide. Six professional residency training Special Expertise Tracks were established: Education, Physician-Scientist Research, Informatics, Quality Improvement/Quality Assurance/Value-Based Care, Health Policy/Hospital Management and Global Health. After implementation in 2017, the Education track has had 4 residents complete the curriculum successfully; the Physician-Scientist Research track has had 2 residents and the Informatics and Global Health tracks have each had one resident successfully complete their respective curricula. Currently, 5 residents are pursuing the Education track, one is pursuing the Physician-Scientist Research track, one is pursuing the Informatics track, and 2 residents are pursuing the Global Health track. Five residents have completed long-term projects including developing several e-learning modules, an online free digital cytopathology atlas, peer-reviewed articles, book chapters, and books. The Johns Hopkins Pathology Resident Special Expertise Track program provides pathology residents an opportunity to gain meaningful experience and additional skills tailored to their individual career interests.

    View details for DOI 10.1177/23742895211037034

    View details for Web of Science ID 000709226200001

    View details for PubMedID 34485688

    View details for PubMedCentralID PMC8411632

  • Pulmonary hypoplasia correlates with the length of anhydramnios in patients with early pregnancy renal anhydramnios (EPRA) JOURNAL OF PERINATOLOGY Jelin, E. B., Hooper, J. E., Duregon, E., Williamson, A. K., Olson, S., Voegtline, K., Jelin, A. C. 2021; 41 (8): 1924-1929


    Early pregnancy renal anhydramanios (EPRA) occurs when the fetus is anuric before 22 weeks gestational age (GA) and is considered universally lethal. Serial amnioinfusions have successfully ameliorated the lethal pulmonary hypoplasia associated with EPRA and have resulted in cases of neonatal survival, peritoneal dialysis, and renal transplant.We sought to evaluate the lung pathology of untreated fetuses and neonates that had EPRA.This is a retrospective case series of all fetuses and neonates diagnosed with isolated EPRA that underwent autopsy at a single tertiary care center between 1987 and 2018. Autopsy data were correlated with ultrasound findings and GA at delivery. Fetal weights, lung weights, and lung developmental stage were recorded.Nineteen cases met criteria for analysis and ranged from 16 to 38 weeks GA at termination or birth. The observed-to-expected (O/E) lung-to-body-weight ratio was significantly associated with GA (r = -0.51, p = 0.03), such that as GA increased the O/E ratio decreased. When limited to patients >22 weeks, this relationship strengthened (r = -0.75, p = 0.01). Importantly, overall O/E body weight had no relationship with GA.This study shows that the degree of pulmonary hypoplasia in EPRA increases with the length of anhydramnios. This suggests that amnioinfusions are likely to be of most benefit the soonest they can feasibly be initiated.

    View details for DOI 10.1038/s41372-021-01128-0

    View details for Web of Science ID 000670168300003

    View details for PubMedID 34230606

  • Role of androgen receptor splice variant-7 (AR-V7) in prostate cancer resistance to 2nd-generation androgen receptor signaling inhibitors (vol 39, pg 6935, 2020) ONCOGENE Zhu, Y., Dalrymple, S. L., Coleman, I., Zheng, S., Xu, J., Hooper, J. E., Antonarakis, E. S., De Marzo, A. M., Meeker, A. K., Nelson, P. S., Isaacs, W. B., Denmeade, S. R., Luo, J., Brennen, W., Isaacs, J. T. 2021; 40 (22): 3914-3916

    View details for DOI 10.1038/s41388-021-01805-6

    View details for Web of Science ID 000648041500005

    View details for PubMedID 33958727

  • SARS-CoV-2 infection drives endothelial dysfunction indirectly through hypoxia and increased pro-inflammatory cytokine production Won, T., Wood, M. K., Hughes, D. M., Talor, M. V., Johns, R. A., Gilotra, N. A., Pekosz, A. S., Hooper, J. E., Cihakova, D. AMER ASSOC IMMUNOLOGISTS. 2021
  • Y A Postmortem Portrait of the Coronavirus Disease 2019 (COVID-19) Pandemic ARCHIVES OF PATHOLOGY & LABORATORY MEDICINE Hooper, J. E., Padera, R. F., Dolhnikoff, M., Ferraz da Silva, L., Duarte-Neto, A., Kapp, M. E., Lacy, J., Mauad, T., Nascimento Saldiva, P., Rapkiewicz, A., Wolf, D. A., Felix, J. C., Benson, P., Shanes, E., Gawelek, K. L., Marshall, D. A., McDonald, M. M., Muller, W., Priemer, D. S., Solomon, I. H., Zak, T., Bhattacharjee, M. B., Fu, L., Gilbert, A. R., Harper, H. L., Litovsky, S., Lomasney, J., Mount, S. L., Reilly, S., Sekulic, M., Steffensen, T. S., Threlkeld, K. J., Zhao, B., Williamson, A. K. 2021; 145 (5): 529-535


    This study represents the largest compilation to date of clinical and postmortem data from decedents with coronavirus disease 2019 (COVID-19). It will augment previously published small series of autopsy case reports, refine clinicopathologic considerations, and improve the accuracy of future vital statistical reporting.To accurately reflect the preexisting diseases and pathologic conditions of decedents with SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) infection through autopsy.Comprehensive data from 135 autopsy evaluations of COVID-19-positive decedents is presented, including histologic assessment. Postmortem examinations were performed by 36 pathologists at 19 medical centers or forensic institutions in the United States and Brazil. Data from each autopsy were collected through the online submission of multiple-choice and open-ended survey responses.Patients dying of or with COVID-19 had an average of 8.89 pathologic conditions documented at autopsy, spanning a combination of prior chronic disease and acute conditions acquired during hospitalization. Virtually all decedents were cited as having more than 1 preexisting condition, encompassing an average of 2.88 such diseases each. Clinical conditions during terminal hospitalization were cited 395 times for the 135 autopsied decedents and predominantly encompassed acute failure of multiple organ systems and/or impaired coagulation. Myocarditis was rarely cited.Cause-of-death statements in both autopsy reports and death certificates may not encompass the severity or spectrum of comorbid conditions in those dying of or with COVID-19. If supported by additional research, this finding may have implications for public health decisions and reporting moving forward through the pandemic.

    View details for DOI 10.5858/arpa.2020-0786-SA

    View details for Web of Science ID 000646027600002

    View details for PubMedID 33449998

  • Myosin specific T-RM cells mediate increased severity of immune checkpoint inhibitor myocarditis Kalinoski, H., Won, T., Rusinkevich, V., Talor, M. V., Hughes, D. M., Wood, M. K., Hooper, J. E., Cihakova, D. AMER ASSOC IMMUNOLOGISTS. 2021
  • Pericardial macrophages and their role in myocardial infarction Hughes, D. M., Won, T., Jurcova, I., Talor, M. V., Szarszoi, O., Curnova, L., Striz, I., Hooper, J. E., Melenovsky, V., Cihakova, D. AMER ASSOC IMMUNOLOGISTS. 2021
  • Resistance to androgen receptor signaling inhibition does not necessitate development of neuroendocrine prostate cancer JCI INSIGHT Brennen, W., Zhu, Y., Coleman, I. M., Dalrymple, S. L., Antony, L., Patel, R. A., Hanratty, B., Chikarmane, R., Meeker, A. K., Zheng, S., Hooper, J. E., Luo, J., De Marzo, A. M., Corey, E., Xu, J., Yegnasubramanian, S., Haffner, M. C., Nelson, P. S., Nelson, W. G., Isaacs, W. B., Isaacs, J. T. 2021; 6 (8)


    Resistance to AR signaling inhibitors (ARSis) in a subset of metastatic castration-resistant prostate cancers (mCRPCs) occurs with the emergence of AR- neuroendocrine prostate cancer (NEPC) coupled with mutations/deletions in PTEN, TP53, and RB1 and the overexpression of DNMTs, EZH2, and/or SOX2. To resolve whether the lack of AR is the driving factor for the emergence of the NE phenotype, molecular, cell, and tumor biology analyses were performed on 23 xenografts derived from patients with PC, recapitulating the full spectrum of genetic alterations proposed to drive NE differentiation. Additionally, phenotypic response to CRISPR/Cas9-mediated AR KO in AR+ CRPC cells was evaluated. These analyses document that (a) ARSi-resistant NEPC developed without androgen deprivation treatment; (b) ARS in ARSi-resistant AR+/NE+ double-positive "amphicrine" mCRPCs did not suppress NE differentiation; (c) the lack of AR expression did not necessitate acquiring a NE phenotype, despite concomitant mutations/deletions in PTEN and TP53, and the loss of RB1 but occurred via emergence of an AR-/NE- double-negative PC (DNPC); (d) despite DNPC cells having homogeneous genetic driver mutations, they were phenotypically heterogeneous, expressing basal lineage markers alone or in combination with luminal lineage markers; and (e) AR loss was associated with AR promoter hypermethylation in NEPCs but not in DNPCs.

    View details for DOI 10.1172/jci.insight.146827

    View details for Web of Science ID 000642643500015

    View details for PubMedID 33724955

    View details for PubMedCentralID PMC8119192

  • Muscle Biopsy Findings in a Case of SARS-CoV-2-Associated Muscle Injury JOURNAL OF NEUROPATHOLOGY AND EXPERIMENTAL NEUROLOGY Hooper, J. E., Uner, M., Priemer, D. S., Rosenberg, A., Chen, L. 2021; 80 (4): 377-378

    View details for DOI 10.1093/jnen/nlaa155

    View details for Web of Science ID 000648962000009

    View details for PubMedID 33355335

    View details for PubMedCentralID PMC7799012

  • Rapid Autopsy Programs and Research Support: The Pre- and Post-COVID-19 Environments AJSP-REVIEWS AND REPORTS Hooper, J. E. 2021; 26 (2): 100-107


    Each rapid autopsy is a powerful opportunity to supply multiple researchers with many valuable tissue specimens at the same time. Since the beginning of the development of rapid autopsy, the overriding organizing principle for all RAPs has been that the samples or organs must be removed and processed as rapidly as possible. To accomplish this some rapid autopsy programs are focused just on one tumor type, while others accept patients demonstrating all tumor types and sometimes other diseases as well. RAPs are logistically complicated and labor-intensive structures, therefore, the key to their success is program flexibility and maintaining a multidisciplinary focus. The necessary collaborations in the complex relationships between clinicians and researchers can be broken down into a series of thought and action steps that must be understood, accepted, and practiced by all participants. A crucial part of the pre-case steps (prior to death) for a rapid autopsy is the study consenting process. It is extremely important that this individualized consent is obtained for postmortem specimens and that it is written in general enough terms to be used for patients with all types of diseases and for an appropriate range of future research uses. The advent of Sars-CoV-2/COVID-19 has presented new challenges and opportunities to the field of autopsy pathology. Guidelines and practice had to be created and adapted to protect physicians and staff while maximizing diagnostic yield. However, any autopsy performed on a patient dying of or with COVID-19 represents a unique opportunity to contribute to understanding of disease mechanisms and to improve death certification, thus assisting in both clinical care and the development of health public policy.

    View details for DOI 10.1097/PCR.0000000000000435

    View details for Web of Science ID 000631939700004

    View details for PubMedID 33718610

    View details for PubMedCentralID PMC7954201

  • The Genetic Evolution of Treatment-Resistant Cutaneous, Acral, and Uveal Melanomas CLINICAL CANCER RESEARCH Makohon-Moore, A. P., Lipson, E. J., Hooper, J. E., Zucker, A., Hong, J., Bielski, C. M., Hayashi, A., Tokheim, C., Baez, P., Kappagantula, R., Kohutek, Z., Makarov, V., Riaz, N., Postow, M. A., Chapman, P. B., Karchin, R., Socci, N. D., Solit, D. B., Chan, T. A., Taylor, B. S., Topalian, S. L., Iacobuzio-Donahue, C. A. 2021; 27 (5): 1516-1525


    Melanoma is a biologically heterogeneous disease composed of distinct clinicopathologic subtypes that frequently resist treatment. To explore the evolution of treatment resistance and metastasis, we used a combination of temporal and multilesional tumor sampling in conjunction with whole-exome sequencing of 110 tumors collected from 7 patients with cutaneous (n = 3), uveal (n = 2), and acral (n = 2) melanoma subtypes.Primary tumors, metastases collected longitudinally, and autopsy tissues were interrogated. All but 1 patient died because of melanoma progression.For each patient, we generated phylogenies and quantified the extent of genetic diversity among tumors, specifically among putative somatic alterations affecting therapeutic resistance.In 4 patients who received immunotherapy, we found 1-3 putative acquired and intrinsic resistance mechanisms coexisting in the same patient, including mechanisms that were shared by all tumors within each patient, suggesting that future therapies directed at overcoming intrinsic resistance mechanisms may be broadly effective.

    View details for DOI 10.1158/1078-0432.CCR-20-2984

    View details for Web of Science ID 000625367700031

    View details for PubMedID 33323400

    View details for PubMedCentralID PMC7925434

  • Assessing Brain Capillaries in Coronavirus Disease 2019 JAMA NEUROLOGY Nauen, D. W., Hooper, J. E., Stewart, C., Solomon, I. H. 2021; 78 (6): 760-762

    View details for DOI 10.1001/jamaneurol.2021.0225

    View details for Web of Science ID 000617178200001

    View details for PubMedID 33576767

    View details for PubMedCentralID PMC7881367

  • Role of androgen receptor splice variant-7 (AR-V7) in prostate cancer resistance to 2nd-generation androgen receptor signaling inhibitors (vol 39, pg 6935, 2020) ONCOGENE Zhu, Y., Dalrymple, S. L., Coleman, I., Zheng, S., Xu, J., Hooper, J. E., Antonarakis, E. S., De Marzo, A. M., Meeker, A. K., Nelson, P. S., Isaacs, W. B., Denmeade, S. R., Luo, J., Brennen, W., Isaacs, J. T. 2021; 40 (11): 2148

    View details for DOI 10.1038/s41388-021-01640-9

    View details for Web of Science ID 000616489100008

    View details for PubMedID 33564077

  • Evaluating T-cell cross-reactivity between tumors and immune-related adverse events with TCR sequencing: pitfalls in interpretations of functional relevance JOURNAL FOR IMMUNOTHERAPY OF CANCER Cottrell, T., Zhang, J., Zhang, B., Kaunitz, G. J., Burman, P., Chan, H., Verde, F., Hooper, J. E., Hammers, H., Allaf, M. E., Ji, H., Taube, J., Smith, K. N. 2021; 9 (7)


    T-cell receptor sequencing (TCRseq) enables tracking of T-cell clonotypes recognizing the same antigen over time and across biological compartments. TCRseq has been used to test if cross-reactive antitumor T cells are responsible for development of immune-related adverse events (irAEs) following immune checkpoint blockade. Prior studies have interpreted T-cell clones shared among the tumor and irAE as evidence supporting this, but interpretations of these findings are challenging, given the constraints of TCRseq. Here we capitalize on a rare opportunity to understand the impact of potential confounders, such as sample size, tissue compartment, and collection batch/timepoint, on the relative proportion of shared T-cell clones between an irAE and tumor specimens. TCRseq was performed on tumor-involved and -uninvolved tissues, including an irAE, that were obtained throughout disease progression and at the time of rapid autopsy from a patient with renal cell carcinoma treated with programmed death-1 (PD-1) blockade. Our analyses show significant effects of these confounders on our ability to understand T-cell receptor overlap, and we present mitigation strategies and study design recommendations to reduce these errors. Implementation of these strategies will enable more rigorous TCRseq-based studies of immune responses in human tissues, particularly as they relate to antitumor T-cell cross-reactivity in irAEs following checkpoint blockade.

    View details for DOI 10.1136/jitc-2021-002642

    View details for Web of Science ID 000691845400002

    View details for PubMedID 34230111

    View details for PubMedCentralID PMC8261872

  • Fatal SARS-CoV-2 Inflammatory Syndrome and Myocarditis in an Adolescent: A Case Report. The Pediatric infectious disease journal Beaudry, J. T., Dietrick, B., Lammert, D. B., Constas, A., McCaw, J., Hammond, J., Buendia, M., Stein, J. E., Pekosz, A., Schuette, J., Mostafa, H. H., Hooper, J. E., Bernier, M., Agwu, A., Feldman, L. S. 2021; 40 (2): e72-e76


    BACKGROUND: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes coronavirus disease 2019 (COVID-19), an entity in children initially characterized by milder case presentations and better prognoses as compared with adults. Recent reports, however, raise concern for a new hyperinflammatory entity in a subset of pediatric COVID-19 patients.METHODS: We report a fatal case of confirmed COVID-19 with hyperinflammatory features concerning for both multi-inflammatory syndrome in children (MIS-C) and primary COVID-19.RESULTS: This case highlights the ambiguity in distinguishing between these two entities in a subset of pediatric patients with COVID-19-related disease and the rapid decompensation these patients may experience.CONCLUSIONS: Appropriate clinical suspicion is necessary for both acute disease and MIS-C. SARS-CoV-2 serologic tests obtained early in the diagnostic process may help to narrow down the differential but does not distinguish between acute COVID-19 and MIS-C. Better understanding of the hyperinflammatory changes associated with MIS-C and acute COVID-19 in children will help delineate the roles for therapies, particularly if there is a hybrid phenotype occurring in adolescents.

    View details for DOI 10.1097/INF.0000000000002978

    View details for PubMedID 33181783

  • End-of-Life Care: A Multimodal and Comprehensive Curriculum for Graduating Medical Students Utilizing Experiential Learning Opportunities. MedEdPORTAL : the journal of teaching and learning resources Jeffers, J. M., Bord, S., Hooper, J. E., Fleishman, C., Cayea, D., Garibaldi, B. 2021; 17: 11149


    Introduction: End-of-life (EOL) care is an essential skill for most physicians and health care providers, yet there continues to be an educational gap in medical education literature for these skills. The Johns Hopkins School of Medicine developed the Transition to Residency, Internship, and Preparation for Life Events (TRIPLE) curriculum with the primary goal of preparing graduating medical students for life after medical school.Methods: The EOL module was one of many within the TRIPLE curriculum and consisted of two half-day sessions that targeted EOL care, death, dying, and communication skills. The first half-day session focused on a standardized patient encounter where learners initiated and completed an EOL care goals conversation around a living will. The second half-day session focused on death and dying. It included didactic sessions on organ donation, autopsy/death certificates, a simulation-based learning session on ending a resuscitation, and a standardized patient encounter where learners disclosed the death of a loved one. End-of-day and end-of-course evaluations were collected via anonymous online surveys.Results: In 2019, 120 students and 26 instructors participated in TRIPLE. Students rated the EOL module overall as 4.6 of 5 (SD = 0.6) and rated instructors overall as 4.6 of 5 (SD = 0.6).Discussion: By implementing a thorough and diverse curriculum with a variety of modalities and targeted skills, learners may be better prepared to care for patients dealing with EOL care issues. Further, the generalization of these skills may assist learners in a variety of other aspects of patient and family care.

    View details for DOI 10.15766/mep_2374-8265.11149

    View details for PubMedID 33928187

  • Overview of Pathologic Findings of Vaping in the Context of an Autopsy Patient With Chronic Injury ARCHIVES OF PATHOLOGY & LABORATORY MEDICINE Priemer, D. S., Gravenmier, C., Batouli, A., Hooper, J. E. 2020; 144 (11): 1408-1413


    Electronic cigarettes are handheld devices that heat an inner liquid containing chemicals to be aerosolized and inhaled, and have become a popular alternative to conventional cigarettes. Their use, termed vaping, has been linked to severe injury, with 2711 cases of associated lung injury and 60 deaths reported to the Centers for Disease Control and Prevention at the time of writing. Published case reports and series have emerged detailing clinical and imaging characteristics of vaping-induced lung injury. However, the pathologic characteristics of these induced injuries are still being established, particularly findings occurring over time.To illustrate the autopsy findings of an older patient who died of vaping-induced injury after prolonged symptomology and to provide a review of the most recent literature regarding the basic science, epidemiology, clinical presentation, imaging characteristics, and pathology of vaping-induced lung injury.Autopsy case and peer-reviewed literature.Vaping-induced lung injury has emerged as a public health issue, and this case represents a rare opportunity to evaluate this issue at autopsy. Most commonly, the injury has been attributed to tetrahydrocannabinol product use as opposed to nicotine. This case demonstrates that as today's young and relatively healthy "vapers" grow older and develop the comorbidities that come with advanced age, there is serious risk of chronic lung damage from vaping that could result in death. Further observations and studies, particularly autopsy evidence, are clearly important to understand the possible outcomes.

    View details for DOI 10.5858/arpa.2019-0637-RA

    View details for Web of Science ID 000582675700017

    View details for PubMedID 32383974

  • IgM autoantibodies recognizing ACE2 are associated with severe COVID-19. medRxiv : the preprint server for health sciences Casciola-Rosen, L., Thiemann, D. R., Andrade, F., Trejo Zambrano, M. I., Hooper, J. E., Leonard, E., Spangler, J., Cox, A. L., Machamer, C., Sauer, L., Laeyendecker, O., Garibaldi, B. T., Ray, S. C., Mecoli, C., Christopher-Stine, L., Gutierrez-Alamillo, L., Yang, Q., Hines, D., Clarke, W., Rothman, R. E., Pekosz, A., Fenstermacher, K., Wang, Z., Zeger, S. L., Rosen, A. 2020


    SARS-CoV-2 infection induces severe disease in a subpopulation of patients, but the underlying mechanisms remain unclear. We demonstrate robust IgM autoantibodies that recognize angiotensin converting enzyme-2 (ACE2) in 18/66 (27%) patients with severe COVID-19, which are rare (2/52; 3.8%) in hospitalized patients who are not ventilated. The antibodies do not undergo class-switching to IgG, suggesting a T-independent antibody response. Purified IgM from anti-ACE2 patients activates complement. Pathological analysis of lung obtained at autopsy shows endothelial cell staining for IgM in blood vessels in some patients. We propose that vascular endothelial ACE2 expression focuses the pathogenic effects of these autoantibodies on blood vessels, and contributes to the angiocentric pathology observed in some severe COVID-19 patients. These findings may have predictive and therapeutic implications.

    View details for DOI 10.1101/2020.10.13.20211664

    View details for PubMedID 33083808

  • SARS-CoV-2 Virus Isolated From the Mastoid and Middle Ear: Implications for COVID-19 Precautions During Ear Surgery JAMA OTOLARYNGOLOGY-HEAD & NECK SURGERY Frazier, K. M., Hooper, J. E., Mostafa, H. H., Stewart, C. 2020; 146 (10): 964-966

    View details for DOI 10.1001/jamaoto.2020.1922

    View details for Web of Science ID 000604968900018

    View details for PubMedID 32701126

    View details for PubMedCentralID PMC7378866

  • Role of androgen receptor splice variant-7 (AR-V7) in prostate cancer resistance to 2nd-generation androgen receptor signaling inhibitors ONCOGENE Zhu, Y., Dalrymple, S. L., Coleman, I., Zheng, S., Xu, J., Hooper, J. E., Antonarakis, E. S., De Marzo, A. M., Meeker, A. K., Nelson, P. S., Isaacs, W. B., Denmeade, S. R., Luo, J., Brennen, W., Isaacs, J. T. 2020; 39 (45): 6935-6949


    The role of truncated androgen receptor splice variant-7 (AR-V7) in prostate cancer biology is an unresolved question. Is it simply a marker of resistance to 2nd-generation androgen receptor signaling inhibitors (ARSi) like abiraterone acetate (Abi) and enzalutamide (Enza) or a functional driver of lethal resistance via its ligand-independent transcriptional activity? To resolve this question, the correlation between resistance to ARSi and genetic chances and expression of full length AR (AR-FL) vs. AR-V7 were evaluated in a series of independent patient-derived xenografts (PDXs). While all PDXs lack PTEN expression, there is no consistent requirement for mutation in TP53, RB1, BRCA2, PIK3CA, or MSH2, or expression of SOX2 or ERG and ARSi resistance. Elevated expression of AR-FL alone is sufficient for Abi but not Enza resistance, even if AR-FL is gain-of-function (GOF) mutated. Enza resistance is consistently correlated with enhanced AR-V7 expression. In vitro and in vivo growth responses of Abi-/Enza-resistant LNCaP-95 cells in which CRISPR-Cas9 was used to knockout AR-FL or AR-V7 alone or in combination were evaluated. Combining these growth responses with RNAseq analysis demonstrates that both AR-FL- and AR-V7-dependent transcriptional complementation are needed for Abi/Enza resistance.

    View details for DOI 10.1038/s41388-020-01479-6

    View details for Web of Science ID 000573446900002

    View details for PubMedID 32989253

    View details for PubMedCentralID PMC7655549

  • Association of Impaired Spermatogenesis With the Use of Immune Checkpoint Inhibitors in Patients With Metastatic Melanoma JAMA ONCOLOGY Scovell, J. M., Benz, K., Samarska, I., Kohn, T. P., Hooper, J. E., Matoso, A., Herati, A. S. 2020; 6 (8): 1297-1299

    View details for DOI 10.1001/jamaoncol.2020.1641

    View details for Web of Science ID 000562846800022

    View details for PubMedID 32556068

    View details for PubMedCentralID PMC7303895

  • Comparison of skeletal and soft tissue pericytes identifies CXCR4(+) bone forming mural cells in human tissues BONE RESEARCH Xu, J., Li, D., Hsu, C., Tian, Y., Zhang, L., Wang, Y., Tower, R. J., Chang, L., Meyers, C. A., Gao, Y., Broderick, K., Morris, C., Hooper, J. E., Nimmagadda, S., Peault, B., James, A. W. 2020; 8 (1)
  • Comparison of skeletal and soft tissue pericytes identifies CXCR4+ bone forming mural cells in human tissues. Bone research Xu, J., Li, D., Hsu, C. Y., Tian, Y., Zhang, L., Wang, Y., Tower, R. J., Chang, L., Meyers, C. A., Gao, Y., Broderick, K., Morris, C., Hooper, J. E., Nimmagadda, S., Péault, B., James, A. W. 2020; 8 (1): 22


    Human osteogenic progenitors are not precisely defined, being primarily studied as heterogeneous multipotent cell populations and termed mesenchymal stem cells (MSCs). Notably, select human pericytes can develop into bone-forming osteoblasts. Here, we sought to define the differentiation potential of CD146+ human pericytes from skeletal and soft tissue sources, with the underlying goal of defining cell surface markers that typify an osteoblastogenic pericyte. CD146+CD31-CD45- pericytes were derived by fluorescence-activated cell sorting from human periosteum, adipose, or dermal tissue. Periosteal CD146+CD31-CD45- cells retained canonical features of pericytes/MSC. Periosteal pericytes demonstrated a striking tendency to undergo osteoblastogenesis in vitro and skeletogenesis in vivo, while soft tissue pericytes did not readily. Transcriptome analysis revealed higher CXCR4 signaling among periosteal pericytes in comparison to their soft tissue counterparts, and CXCR4 chemical inhibition abrogated ectopic ossification by periosteal pericytes. Conversely, enrichment of CXCR4+ pericytes or stromal cells identified an osteoblastic/non-adipocytic precursor cell. In sum, human skeletal and soft tissue pericytes differ in their basal abilities to form bone. Diversity exists in soft tissue pericytes, however, and CXCR4+ pericytes represent an osteoblastogenic, non-adipocytic cell precursor. Indeed, enrichment for CXCR4-expressing stromal cells is a potential new tactic for skeletal tissue engineering.

    View details for DOI 10.1038/s41413-020-0097-0

    View details for PubMedID 32509378

    View details for PubMedCentralID PMC7244476

  • Sacral protuberance with cleft lip and palate: Prenatal presentation of 3MC syndrome AMERICAN JOURNAL OF MEDICAL GENETICS PART A Lawson, C., Blakemore, K. J., Ryan, R., Hooper, J. E., Tsimis, M., Jelin, A. 2020; 182 (7): 1812-1814


    3MC syndromes are rare heterogeneous autosomal recessive conditions previously designated as Mingarelli, Malpuech, Michels, and Carnevale syndromes, characterized by dysmorphic facial features, facial clefts, growth restriction, and intellectual disability. 3MC is secondary to mutations in the MASP1, MASP3, COLEC11, and COLEC10 genes. The number of patients with 3MC syndrome with known mutations in the COLEC11 or MASP1 is, to date, less than 50. At the time this case presented (2015), the only gene identified in Online Mendelian Inheritance in Man to be associated with 3MC syndrome was MASP1. We present, to the best of our knowledge, the first prenatal report of 3MC syndrome, secondary to a homozygous variant in MASP1. Fetal findings included bilateral cleft lip and palate, abnormality of the sacral spine, a right echogenic pelvic kidney, and brachycephaly. 3MC syndrome should be considered as part of the differential diagnosis when fetal ultrasound detects facial clefts and spinal defects, as the risk of recurrence is significant and a molecularly confirmed diagnosis allows for alternate reproductive options.

    View details for DOI 10.1002/ajmg.a.61624

    View details for Web of Science ID 000534786900001

    View details for PubMedID 32441374

    View details for PubMedCentralID PMC7780158

  • Innate Lymphoid Cells Play a Pathogenic Role in Pericarditis CELL REPORTS Choi, H., Won, T., Hou, X., Chen, G., Bracamonte-Baran, W., Talor, M., Jurcova, I., Szarszoi, O., Curnova, L., Striz, I., Hooper, J. E., Melenovsky, V., Cihakova, D. 2020; 30 (9): 2989-+


    We find that cardiac group 2 innate lymphoid cells (ILC2s) are essential for the development of IL-33-induced eosinophilic pericarditis. We show a pathogenic role for ILC2s in cardiac inflammation, in which ILC2s activated by IL-33 drive the development of eosinophilic pericarditis in collaboration with cardiac fibroblasts. ILCs, not T and B cells, are required for the development of pericarditis. ILC2s transferred to the heart of Rag2-/-Il2rg-/- mice restore their susceptibility to eosinophil infiltration. Moreover, ILC2s direct cardiac fibroblasts to produce eotaxin-1. We also find that eosinophils reside in the mediastinal cavity and that eosinophils transferred to the mediastinal cavity of eosinophil-deficient ΔdblGATA1 mice following IL-33 treatment migrate to the heart. Thus, the serous cavities may serve as a reservoir of cardiac-infiltrating eosinophils. In humans, patients with pericarditis show higher amounts of ILCs in pericardial fluid than do healthy controls and patients with other cardiac diseases. We demonstrate that ILCs play a critical role in pericarditis.

    View details for DOI 10.1016/j.celrep.2020.02.040

    View details for Web of Science ID 000517773300012

    View details for PubMedID 32130902

    View details for PubMedCentralID PMC7332109

  • Inhibition of glutaminase to reverse fibrosis in iatrogenic laryngotracheal stenosis LARYNGOSCOPE Tsai, H., Motz, K. M., Ding, D., Lina, I., Murphy, M. K., Benner, D., Feeley, M., Hooper, J., Hillel, A. T. 2020; 130 (12): E773-E781


    Glutamine metabolism is a critical energy source for iatrogenic laryngotracheal stenosis (iLTS) scar fibroblasts, and glutaminase (GLS) is an essential enzyme converting glutamine to glutamate. We hypothesize that the GLS-specific inhibitor BPTES will block glutaminolysis and reduce iLTS scar fibroblast proliferation, collagen deposition, and fibroblast metabolism in vitro.Test-tube Lab Research.Immunohistochemistry of a cricotracheal resection (n = 1) and a normal airway specimen (n = 1) were assessed for GLS expression. GLS expression was assessed in brush biopsies of subglottic/tracheal fibrosis and normal airway from patients with iLTS (n = 6). Fibroblasts were isolated and cultured from biopsies of subglottic/tracheal fibrosis (n = 6). Fibroblast were treated with BPTES and BPTES + dimethyl α-ketoglutarate (DMK), an analogue of the downstream product of GLS. Fibroblast proliferation, gene expression, protein production, and metabolism were assessed in all treatment conditions and compared to control.GLS was overexpressed in brush biopsies of iLTS scar specimens (P = .029) compared to normal controls. In vitro, BPTES inhibited iLTS scar fibroblast proliferation (P = .007), collagen I (Col I) (P < .0001), collagen III (P = .004), and α-smooth muscle actin (P = .0025) gene expression and protein production (P = .031). Metabolic analysis demonstrated that BPTES reduced glycolytic reserve (P = .007) but had no effects on mitochondrial oxidative phosphorylation. DMK rescued BPTES inhibition of Col I gene expression (P = .0018) and protein production (P = .021).GLS is overexpressed in iLTS scar. Blockage of GLS with BPTES significantly inhibits iLTS scar fibroblasts proliferation and function, demonstrating a critical role for GLS in iLTS. Targeting GLS to inhibit glutaminolysis may be a successful strategy to reverse scar formation in the airway.NA Laryngoscope, 2020.

    View details for DOI 10.1002/lary.28493

    View details for Web of Science ID 000505636800001

    View details for PubMedID 31904876

    View details for PubMedCentralID PMC7335682

  • The problem with autopsy today may be us. Autopsy & case reports Hooper, J. E. 2020; 10 (1): e2020142

    View details for DOI 10.4322/acr.2020.142

    View details for PubMedID 32039069

  • Cancer biology as revealed by the research autopsy NATURE REVIEWS CANCER Iacobuzio-Donahue, C. A., Michael, C., Baez, P., Kappagantula, R., Hooper, J. E., Hollman, T. J. 2019; 19 (12): 686-697


    A research autopsy is a post-mortem medical procedure performed on a deceased individual with the primary goal of collecting tissue to support basic and translational research. This approach has increasingly been used to investigate the pathophysiological mechanisms of cancer evolution, metastasis and treatment resistance. In this Review, we discuss the rationale for the use of research autopsies in cancer research and provide an evidence-based discussion of the quality of post-mortem tissues compared with other types of biospecimens. We also discuss the advantages of using post-mortem tissues over other types of biospecimens, including the large amounts of tissue that can be obtained and the extent of multiregion sampling that is achievable, which is not otherwise possible in living patients. We highlight how the research autopsy has supported the identification of the clonal origins and modes of spread among metastases, the extent that selective pressures imposed by treatments cause bottlenecks leading to parallel and convergent tumour evolution, and the creation of rare tissue banks and patient-derived model systems. Finally, we comment on the future of the research autopsy as an integral component of precision medicine strategies.

    View details for DOI 10.1038/s41568-019-0199-4

    View details for Web of Science ID 000498825600006

    View details for PubMedID 31519982

    View details for PubMedCentralID PMC7453489

  • Comparing anti-tumor and anti-self immunity in a patient with melanoma receiving immune checkpoint blockade Chen, S., Soni, A., McMiller, T., Sidhom, J., Succaria, F., Berger, A., Hooper, J., Pardoll, D., Lipson, E., Taube, J., Topalian, S. BMC. 2019
  • Prenatal diagnosis of Desbuquois dysplasia Type 1: Utilization of high-density SNP array to map homozygosity and identify the gene AMERICAN JOURNAL OF MEDICAL GENETICS PART A Forster, K. R., Hooper, J. E., Blakemore, K. J., Baschat, A. A., Hoover-Fong, J. 2019; 179 (12): 2490-2493


    Desbuquois dysplasia (DBQD1 [MIM 251450]) is an autosomal recessive chondrodysplasia with micromelia, severe joint laxity and dislocations, and a characteristic radiographic "monkey wrench" appearance at the proximal femur. Type 1 Desbuquois dysplasia is caused by mutations in CANT1 and is distinct from Type 2, caused by mutations in XYLT1, in that the former has unique hand anomalies including accessory phalangeal ossification centers, advanced carpal bone maturation, and/or axial phalangeal deviation. Severe prenatal presentations have been rarely reported. We report a Pakistani female in a consanguineous relationship with a diagnosis of Type 1 Desbuquois dysplasia in three consecutive pregnancies. Multiple similar severe fetal limb anomalies were detected by ultrasound in Pregnancy 1 and 2. Regions of homozygosity within the single nucleotide polymorphism (SNP)-microarray from both terminated fetuses were compared, revealing CANT1 as a likely disease-causing candidate gene. Insufficient fetal DNA precluded confirmatory testing, therefore parents were tested; both had a previously reported heterozygous CANT1 mutation (c.643G>T; Glu215Term). The patient presented with a third pregnancy revealing similarly abnormal limb position and probable polysyndactyly by ultrasound. Targeted testing of CANT1 revealed homozygous c.643G>T CANT1 mutations and this pregnancy was terminated. In clinical situations in which ample DNA is not available or more expensive testing (e.g., whole exome sequencing) with a longer turnaround time is not feasible, utilization of SNP-microarray in consanguineous families at risk for rare autosomal recessive disorders may dramatically narrow the list of candidate genes.

    View details for DOI 10.1002/ajmg.a.61372

    View details for Web of Science ID 000491121500001

    View details for PubMedID 31587486

  • Rapid research autopsy is a stealthy but growing contributor to cancer research CANCER Duregon, E., Schneider, J., DeMarzo, A. M., Hooper, J. E. 2019; 125 (17): 2915-2919

    View details for DOI 10.1002/cncr.32184

    View details for Web of Science ID 000480603300004

    View details for PubMedID 31090935

    View details for PubMedCentralID PMC6690796

  • Mannose Receptor-positive Macrophage Infiltration Correlates with Prostate Cancer Onset and Metastatic Castration-resistant Disease EUROPEAN UROLOGY ONCOLOGY Zarif, J. C., Baena-Del Valle, J. A., Hicks, J. L., Heaphy, C. M., Vidal, I., Luo, J., Lotan, T. L., Hooper, J. E., Isaacs, W. B., Pienta, K. J., De Marzo, A. M. 2019; 2 (4): 429-436


    M2 tumor-associated macrophages (M2-TAMs) can suppress inflammation in the tumor microenvironment and have been reported to modulate cancer progression. We and others have previously reported M2-TAM infiltration in metastatic castration-resistant prostate cancer (mCRPC).To determine whether the extent of M2-TAM infiltration correlates with PC aggressiveness.Normal prostate tissue, localized PC, and mCRPC samples from 192 patients were retrospectively analyzed.We analytically validated an immunohistochemistry assay for detection of the human mannose receptor (CD206) to assess M2 macrophage involvement.Multiplex immunofluorescent staining showed that a small fraction of CD206 staining co-localized with the endothelial cells of lymphatic vessels, while the vast majority of staining occurred in CD68-positive macrophages. The area fraction of staining for CD206-positive macrophages increased in a stepwise fashion from normal (ie, no inflammation) prostate tissue, to primary untreated carcinomas, to hormone-naïve regional lymph node metastases, to mCRPC. Complementary studies using flow cytometry confirmed CD206-positive M2-TAM infiltration. Limitations include the small number of rapid autopsy samples and the lack of neuroendocrine PC samples.Our results revealed a progressive increase in CD206-positive macrophages from normal prostate to mCRPC. Given the immunosuppressive nature of macrophages and the lack of clinical success of immunotherapy for PC patients, our results provide a rationale for therapeutic targeting of macrophages in the PC microenvironment as a potential method to augment immunotherapeutic responses.In this report we used 192 prostate cancer samples to determine if M2 macrophage infiltration is correlated with castration resistance in prostate cancer.

    View details for DOI 10.1016/j.euo.2018.09.014

    View details for Web of Science ID 000474616500013

    View details for PubMedID 31277779

    View details for PubMedCentralID PMC7039332

  • Disconnect between Fibrotic Response and Right Ventricular Dysfunction AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE Crnkovic, S., Egemnazarov, B., Damico, R., Marsh, L. M., Nagy, B. M., Douschan, P., Atsina, K., Kolb, T. M., Mathai, S. C., Hooper, J. E., Ghanim, B., Klepetko, W., Fruhwald, F., Lassner, D., Olschewski, A., Olschewski, H., Hassoun, P. M., Kwapiszewska, G. 2019; 199 (12): 1550-1560


    Rationale: Remodeling and fibrosis of the right ventricle (RV) may cause RV dysfunction and poor survival in patients with pulmonary hypertension. Objectives: To investigate the consequences of RV fibrosis modulation and the accompanying cellular changes on RV function. Methods: Expression of fibrotic markers was assessed in the RV of patients with pulmonary hypertension, the murine pulmonary artery banding, and rat monocrotaline and Sugen5416/hypoxia models. Invasive hemodynamic and echocardiographic assessment was performed on galectin-3 knockout or inhibitor-treated mice. Measurements and Main Results: Established fibrosis was characterized by marked expression of galectin-3 and an enhanced number of proliferating RV fibroblasts. Galectin-3 genetic and pharmacologic inhibition or antifibrotic treatment with pirfenidone significantly diminished RV fibrosis progression in the pulmonary artery banding model, without improving RV functional parameters. RV fibrotic regions were populated with mesenchymal cells coexpressing vimentin and PDGFRα (platelet-derived growth factor receptor-α), but generally lacked αSMA (α-smooth muscle actin) positivity. Serum levels of galectin-3 were increased in patients with idiopathic pulmonary arterial hypertension but did not correlate with cardiac function. No changes of galectin-3 expression were observed in the lungs. Conclusions: We identified extrapulmonary galectin-3 as an important mediator that drives RV fibrosis in pulmonary hypertension through the expansion of PDGFRα/vimentin-expressing cardiac fibroblasts. However, interventions effectively targeting fibrosis lack significant beneficial effects on RV function.

    View details for DOI 10.1164/rccm.201809-1737OC

    View details for Web of Science ID 000471677100019

    View details for PubMedID 30557518

    View details for PubMedCentralID PMC6580669

  • Preclinical rationale for entinostat in embryonal rhabdomyosarcoma SKELETAL MUSCLE Bharathy, N., Berlow, N. E., Wang, E., Abraham, J., Settelmeyer, T. P., Hooper, J. E., Svalina, M. N., Bajwa, Z., Goros, M. W., Hernandez, B. S., Wolff, J. E., Pal, R., Davies, A. M., Ashok, A., Bushby, D., Mancini, M., Noakes, C., Goodwin, N. C., Ordentlich, P., Keck, J., Hawkins, D. S., Rudzinski, E. R., Mansoor, A., Perkins, T. J., Vakoc, C. R., Michalek, J. E., Keller, C. 2019; 9: 12


    Rhabdomyosarcoma (RMS) is the most common soft tissue sarcoma in the pediatric cancer population. Survival among metastatic RMS patients has remained dismal yet unimproved for years. We previously identified the class I-specific histone deacetylase inhibitor, entinostat (ENT), as a pharmacological agent that transcriptionally suppresses the PAX3:FOXO1 tumor-initiating fusion gene found in alveolar rhabdomyosarcoma (aRMS), and we further investigated the mechanism by which ENT suppresses PAX3:FOXO1 oncogene and demonstrated the preclinical efficacy of ENT in RMS orthotopic allograft and patient-derived xenograft (PDX) models. In this study, we investigated whether ENT also has antitumor activity in fusion-negative eRMS orthotopic allografts and PDX models either as a single agent or in combination with vincristine (VCR).We tested the efficacy of ENT and VCR as single agents and in combination in orthotopic allograft and PDX mouse models of eRMS. We then performed CRISPR screening to identify which HDAC among the class I HDACs is responsible for tumor growth inhibition in eRMS. To analyze whether ENT treatment as a single agent or in combination with VCR induces myogenic differentiation, we performed hematoxylin and eosin (H&E) staining in tumors.ENT in combination with the chemotherapy VCR has synergistic antitumor activity in a subset of fusion-negative eRMS in orthotopic "allografts," although PDX mouse models were too hypersensitive to the VCR dose used to detect synergy. Mechanistic studies involving CRISPR suggest that HDAC3 inhibition is the primary mechanism of cell-autonomous cytoreduction in eRMS. Following cytoreduction in vivo, residual tumor cells in the allograft models treated with chemotherapy undergo a dramatic, entinostat-induced (70-100%) conversion to non-proliferative rhabdomyoblasts.Our results suggest that the targeting class I HDACs may provide a therapeutic benefit for selected patients with eRMS. ENT's preclinical in vivo efficacy makes ENT a rational drug candidate in a phase II clinical trial for eRMS.

    View details for DOI 10.1186/s13395-019-0198-x

    View details for Web of Science ID 000468852800001

    View details for PubMedID 31113472

    View details for PubMedCentralID PMC6528217

  • Advancing the pathologic phenotype of giant axonal neuropathy: early involvement of the ocular lens ORPHANET JOURNAL OF RARE DISEASES Armao, D., Bouldin, T. W., Bailey, R. M., Hooper, J. E., Bharucha, D. X., Gray, S. J. 2019; 14: 27


    Giant axonal neuropathy (GAN; ORPHA: 643; OMIM# 256850) is a rare, hereditary, pediatric neurodegenerative disorder associated with intracellular accumulations of intermediate filaments (IFs). GAN knockout (KO) mouse models mirror the IF dysregulation and widespread nervous system pathology seen in human GAN. Validation of therapeutic efficacy and viral vector delivery systems with these GAN KO models has provided the springboard for the development of a viral vector being delivered intrathecally in an ongoing Phase I gene therapy clinical trial for the treatment of children with GAN ( ). During the course of a comprehensive pathologic characterization of the GAN KO mouse, we discovered the very early and unexpected involvement of the ocular lens. Light microscopy revealed the presence of intracytoplasmic inclusion bodies within lens epithelial cells. The inclusion bodies showed strong immunohistochemical positivity for glial fibrillary acidic protein (GFAP). We confirmed that intracytoplasmic inclusion bodies are also present within lens epithelial cells in human GAN. These IF inclusion bodies in lens epithelial cells are unique to GAN. Similar IF inclusion bodies in lens epithelial cells have not been reported previously in experimental animal models or human diseases. Since current paradigms in drug discovery and drug repurposing for IF-associated disorders are often hindered by lack of validated targets, our findings suggest that lens epithelial cells in the GAN KO mouse may provide a potential target, in vivo and in vitro, for evaluating drug efficacy and alternative therapeutic approaches in promoting the clearance of IF inclusions in GAN and other diseases characterized by intracellular IF accumulations.

    View details for DOI 10.1186/s13023-018-0957-5

    View details for Web of Science ID 000457462000002

    View details for PubMedID 30709364

    View details for PubMedCentralID PMC6359799

  • The HDAC3-SMARCA4-miR-27a axis promotes expression of the PAX3:FOXO1 fusion oncogene in rhabdomyosarcoma SCIENCE SIGNALING Bharathy, N., Berlow, N. E., Wang, E., Abraham, J., Settelmeyer, T. P., Hooper, J. E., Svalina, M. N., Ishikawa, Y., Zientek, K., Bajwa, Z., Goros, M. W., Hernandez, B. S., Wolff, J. E., Rudek, M. A., Xu, L., Anders, N. M., Pal, R., Harrold, A. P., Davies, A. M., Ashok, A., Bushby, D., Mancini, M., Noakes, C., Goodwin, N. C., Ordentlich, P., Keck, J., Hawkins, D. S., Rudzinski, E. R., Chatterjee, B., Bachinger, H., Barr, F. G., Liddle, J., Garcia, B. A., Mansoor, A., Perkins, T. J., Vakoc, C. R., Michalek, J. E., Keller, C. 2018; 11 (557)


    Rhabdomyosarcoma (RMS) is the most common soft tissue sarcoma of childhood with an unmet clinical need for decades. A single oncogenic fusion gene is associated with treatment resistance and a 40 to 45% decrease in overall survival. We previously showed that expression of this PAX3:FOXO1 fusion oncogene in alveolar RMS (aRMS) mediates tolerance to chemotherapy and radiotherapy and that the class I-specific histone deacetylase (HDAC) inhibitor entinostat reduces PAX3:FOXO1 protein abundance. Here, we established the antitumor efficacy of entinostat with chemotherapy in various preclinical cell and mouse models and found that HDAC3 inhibition was the primary mechanism of entinostat-induced suppression of PAX3:FOXO1 abundance. HDAC3 inhibition by entinostat decreased the activity of the chromatin remodeling enzyme SMARCA4, which, in turn, derepressed the microRNA miR-27a. This reexpression of miR-27a led to PAX3:FOXO1 mRNA destabilization and chemotherapy sensitization in aRMS cells in culture and in vivo. Furthermore, a phase 1 clinical trial (ADVL1513) has shown that entinostat is tolerable in children with relapsed or refractory solid tumors and is planned for phase 1B cohort expansion or phase 2 clinical trials. Together, these results implicate an HDAC3-SMARCA4-miR-27a-PAX3:FOXO1 circuit as a driver of chemoresistant aRMS and suggest that targeting this pathway with entinostat may be therapeutically effective in patients.

    View details for DOI 10.1126/scisignal.aau7632

    View details for Web of Science ID 000451217900005

    View details for PubMedID 30459282

    View details for PubMedCentralID PMC6432638

  • Report and Recommendations of the Association of Pathology Chairs' Autopsy Working Group ACADEMIC PATHOLOGY Davis, G. G., Winters, G. L., Fyfe, B. S., Hooper, J. E., Iezzoni, J. C., Johnson, R. L., Markwood, P. S., Naritoku, W. Y., Nashelsky, M., Sampson, B. A., Steinberg, J. J., Stubbs, J. R., Timmons, C., Hoffman, R. D. 2018; 5: 2374289518793988


    Autopsy has been a foundation of pathology training for many years, but hospital autopsy rates are notoriously low. At the 2014 meeting of the Association of Pathology Chairs, some pathologists suggested removing autopsy from the training curriculum of pathology residents to provide additional months for training in newer disciplines, such as molecular genetics and informatics. At the same time, the American Board of Pathology received complaints that newly hired pathologists recently certified in anatomic pathology are unable to perform an autopsy when called upon to do so. In response to a call to abolish autopsy from pathology training on the one hand and for more rigorous autopsy training on the other, the Association of Pathology Chairs formed the Autopsy Working Group to examine the role of autopsy in pathology residency training. After 2 years of research and deliberation, the Autopsy Working Group recommends the following:Autopsy should remain a component of anatomic pathology training.A training program must have an autopsy service director with defined responsibilities, including accountability to the program director to record every autopsy performed by every resident.Specific entrustable activities should be defined that a resident must master in order to be deemed competent in autopsy practice, as well as criteria for gaining the trust to perform the tasks without direct supervision.Technical standardization of autopsy performance and reporting must be improved.The current minimum number of 50 autopsies should not be reduced until the changes recommended above have been implemented.

    View details for DOI 10.1177/2374289518793988

    View details for Web of Science ID 000443283600001

    View details for PubMedID 30186954

    View details for PubMedCentralID PMC6117865

  • The Evolution of Earned, Transparent, and Quantifiable Faculty Salary Compensation: The Johns Hopkins Pathology Experience ACADEMIC PATHOLOGY Burns, K. H., Borowitz, M. J., Carroll, K. C., Gocke, C. D., Hooper, J. E., Amukele, T., Tobian, A. R., Valentine, A., Kahl, R., Rodas-Eral, V., Boitnott, J. K., Jackson, J., Sanfilippo, F., Hruban, R. H. 2018; 5: 2374289518777463


    Faculty value equitable and transparent policies for determining salaries and expect their compensation to compare favorably to the marketplace. Academic institutions use compensation to recruit and retain talented faculty as well as to reward accomplishment. Institutions are therefore working to decrease salary disparities that appear arbitrary or reflect long-standing biases and to identify metrics for merit-based remuneration. Ours is a large academic pathology department with 97 tenure-track faculty. Faculty salaries are comprised of 3 parts (A + B + C). Part A is determined by the type of appointment and years at rank; part B recognizes defined administrative, educational, or clinical roles; and part C is a bonus to reward and incentivize activities that forward the missions of the department and medical school. A policy for part C allocations was first codified and approved by department faculty in 1993. It rewarded performance using a semiquantitative scale, based on subjective evaluations of the department director (chair) in consultation with deputy directors (vice chairs) and division directors. Faculty could not directly calculate their part C, and distributions data were not widely disclosed. Over the last 2 years (2015-2017), we have implemented a more objective formula for quantifying an earned part C, which is primarily designed to recognize scholarship in the form of research productivity, educational excellence, and clinical quality improvement. Here, we share our experience with this approach, reviewing part C calculations as made for individual faculty members, providing a global view of the resulting allocations, and considering how the process and outcomes reflect our values.

    View details for DOI 10.1177/2374289518777463

    View details for Web of Science ID 000435829500001

    View details for PubMedID 29978019

    View details for PubMedCentralID PMC6024278

  • INSM1 over-expression in CDK4-amplified glioblastoma Ames, H., Rodriguez, F., Eberhart, C., Hooper, J., Laterra, J. OXFORD UNIV PRESS INC. 2018: 492
  • The Association of Departmental Quality Infrastructure and Positive Change: A Pathology Department Illustration ACADEMIC PATHOLOGY Hooper, J. E., Richardson, H., Maters, A. W., Carroll, K. C., Pronovost, P. J. 2018; 5: 2374289517744753


    A vertically and horizontally well-integrated quality improvement team is essential for effective quality data collection and implementation of improvement measures. We outline the quality structure of a large academic pathology department and describe successful projects across multiple divisions made possible by this tightly integrated structure. The physician vice chair for quality organizes departmental quality efforts and provides representation at the hospital level. The department has an independent continuous quality improvement unit and each laboratory of the department has a staff quality improvement representative. Faculty and staff experts have interacted to produce improvements such as accurate container labeling, efficient triage of specimens, and reduction of unnecessary testing. Specialized task forces such as the Courier Task Force are producing concrete recommendations for process improvement. All phases of pathology patient care are represented by faculty and staff who are trained in quality improvement, and each position touches and communicates actively with levels above and below itself. The key to the department's approach has been the daily attention to quality efforts in all of its activities and the close association of faculty and staff to accomplish the goals of greater efficiency, safety, and cost savings.

    View details for DOI 10.1177/2374289517744753

    View details for Web of Science ID 000433787300001

    View details for PubMedID 29376115

    View details for PubMedCentralID PMC5777549

  • The tumor suppressor phosphatase PP2A-56a regulates stemness and promotes the initiation of malignancies in a novel murine model PLOS ONE Janghorban, M., Langer, E. M., Wang, X., Zachman, D., Daniel, C. J., Hooper, J., Fleming, W. H., Agarwal, A., Sears, R. C. 2017; 12 (11): e0188910


    Protein phosphatase 2A (PP2A) is a ubiquitously expressed Serine-Threonine phosphatase mediating 30-50% of protein phosphatase activity. PP2A functions as a heterotrimeric complex, with the B subunits directing target specificity to regulate the activity of many key pathways that control cellular phenotypes. PP2A-B56α has been shown to play a tumor suppressor role and to negatively control c-MYC stability and activity. Loss of B56α promotes cellular transformation, likely at least in part through its regulation of c-MYC. Here we report generation of a B56α hypomorph mouse with very low B56α expression that we used to study the physiologic activity of the PP2A-B56α phosphatase. The predominant phenotype we observed in mice with B56α deficiency in the whole body was spontaneous skin lesion formation with hyperproliferation of the epidermis, hair follicles and sebaceous glands. Increased levels of c-MYC phosphorylation on Serine62 and c-MYC activity were observed in the skin lesions of the B56αhm/hm mice. B56α deficiency was found to increase the number of skin stem cells, and consistent with this, papilloma initiation was accelerated in a carcinogenesis model. Further analysis of additional tissues revealed increased inflammation in spleen, liver, lung, and intestinal lymph nodes as well as in the skin lesions, resembling elevated extramedullary hematopoiesis phenotypes in the B56αhm/hm mice. We also observed an increase in the clonogenicity of bone marrow stem cells in B56αhm/hm mice. Overall, this model suggests that B56α is important for stem cells to maintain homeostasis and that B56α loss leading to increased activity of important oncogenes, including c-MYC, can result in aberrant cell growth and increased stem cells that can contribute to the initiation of malignancy.

    View details for DOI 10.1371/journal.pone.0188910

    View details for Web of Science ID 000416841900166

    View details for PubMedID 29190822

    View details for PubMedCentralID PMC5708644

  • Fatal Congenital Retroperitoneal Neuroblastoma Diagnosed by Fetal Magnetic Resonance Imaging JOURNAL OF COMPUTER ASSISTED TOMOGRAPHY Snyder, E., Jelin, A. C., Huisman, T. M., Hooper, J. E., Tekes, A. 2017; 41 (4): 651-652


    Congenital extra-adrenal neuroblastoma is a rare condition, which typically has a favorable prognosis. We present a unique case of extra-adrenal retroperitoneal neuroblastoma diagnosed by fetal magnetic resonance imaging, which ultimately leads to fetal hydrops and neonatal death.

    View details for DOI 10.1097/RCT.0000000000000563

    View details for Web of Science ID 000405919000023

    View details for PubMedID 27997441

  • Postmortem Assessment of Vector Biodistribution in the First-in-Human Intrathecal scAAV9 Gene Therapy Trial for Giant Axonal Neuropathy Gray, S. J., Bailey, R. M., Bharucha-Goebel, D., Foley, A., Zaric, V., Crawford, T. O., Armao, D., Sumner, C. J., Hoke, A., Chen, L., Grieger, J. C., Samulski, R., Mohassel, P., Hooper, J. E., Bonnemann, C. CELL PRESS. 2017: 139
  • A Model for the Departmental Quality Management Infrastructure Within an Academic Health System ACADEMIC MEDICINE Mathews, S. C., Demski, R., Hooper, J. E., Biddison, L., Berry, S. A., Petty, B. G., Chen, A. R., Hill, P. M., Miller, M. R., Witter, F. R., Allen, L., Wick, E. C., Stierer, T. S., Paine, L., Puttgen, H. A., Tamargo, R. J., Pronovost, P. J. 2017; 92 (5): 608-613


    As quality improvement and patient safety come to play a larger role in health care, academic medical centers and health systems are poised to take a leadership role in addressing these issues. Academic medical centers can leverage their large integrated footprint and have the ability to innovate in this field. However, a robust quality management infrastructure is needed to support these efforts. In this context, quality and safety are often described at the executive level and at the unit level. Yet, the role of individual departments, which are often the dominant functional unit within a hospital, in realizing health system quality and safety goals has not been addressed. Developing a departmental quality management infrastructure is challenging because departments are diverse in composition, size, resources, and needs.In this article, the authors describe the model of departmental quality management infrastructure that has been implemented at the Johns Hopkins Hospital. This model leverages the fractal approach, linking departments horizontally to support peer and organizational learning and connecting departments vertically to support accountability to the hospital, health system, and board of trustees. This model also provides both structure and flexibility to meet individual departmental needs, recognizing that independence and interdependence are needed for large academic medical centers. The authors describe the structure, function, and support system for this model as well as the practical and essential steps for its implementation. They also provide examples of its early success.

    View details for DOI 10.1097/ACM.0000000000001380

    View details for Web of Science ID 000401145100029

    View details for PubMedID 27603038

  • Uses and limitations of IgG4 positive plasma cells in evaluating ulcerative colitis. Journal of gastrointestinal and liver diseases : JGLD Keyashian, K. n., Duregon, E. n., Brinkerhof, B. T., Bradley, L. n., Larson, B. n., Lim, J. n., Modiano, N. n., Collins, J. n., Morgan, T. K., Hooper, J. E. 2017; 26 (4): 428–29

    View details for DOI 10.15403/jgld.2014.1121.264.igg

    View details for PubMedID 29253063

  • PSMA-Targeted F-18-DCFPyL PET/CT Imaging of Clear Cell Renal Cell Carcinoma: Results from a Rapid Autopsy EUROPEAN UROLOGY Gorin, M. A., Rowe, S. P., Hooper, J. E., Kates, M., Hammers, H., Szabo, Z., Pomper, M. G., Allaf, M. E. 2017; 71 (1): 145-146

    View details for DOI 10.1016/j.eururo.2016.06.019

    View details for Web of Science ID 000390564400049

    View details for PubMedID 27363386

    View details for PubMedCentralID PMC5516900

  • Increased Mucosal IgG4 Infiltration Is Associated with Poor Clinical Outcomes in Ulcerative Colitis Brinkerhoff, B. T., Keyashian, K., Bradley, L., Larson, B., Lim, J., Modiano, N., Collins, J., Morgan, T. K., Hooper, J. E. NATURE PUBLISHING GROUP. 2016: 163A
  • Pulmonary Emboli and the Risk of Mortality in a Diverse Disease Environment Shabihkhani, M., Hooper, J. E. NATURE PUBLISHING GROUP. 2016: 10A
  • Hybrid Capture 2 is as Effective as PCR Testing for High-risk Human Papillomavirus in Head and Neck Cancers APPLIED IMMUNOHISTOCHEMISTRY & MOLECULAR MORPHOLOGY Hooper, J. E., Hebert, J. F., Schilling, A., Gross, N. D., Schindler, J. S., Lagowski, J. P., Kulesz-Martin, M., Corless, C. L., Morgan, T. K. 2015; 23 (4): 266-272


    High-risk human papillomavirus (HPV) infection is a common cause of oropharyngeal squamous cell carcinoma, especially in young male nonsmokers. Accurately diagnosing HPV-associated oral cancers is important, because they have a better prognosis and may be treated differently than smoking-related oral carcinomas. Various methods have been validated to test for high-risk HPV in cervical tissue samples, and they are in routine clinical use to detect dysplasia before it progresses to invasive disease. Similarly, future screening for HPV-mediated oropharyngeal dysplasia may identify patients before it progresses. Our objective was to compare 4 of these methods in a retrospective series of 87 oral and oropharyngeal squamous cell carcinomas that had archived fresh-frozen and paraffin-embedded tissue for evaluation. Patient age, sex, smoking history, and tumor location were also recorded. DNA prepared from fresh-frozen tissue was tested for HPV genotypes by multiplex polymerase chain reaction analysis, and high-risk HPV screening was carried out using Hybrid Capture 2 and Cervista. Histologic sections were immunostained for p16. HPV-positive outcome was defined as agreement between at least 2 of the 3 genetic tests and used for χ analysis and calculations of diagnostic predictive value. As expected, high-risk HPV-positive oral cancers were most common in the tonsil and base of the tongue (oropharynx) of younger male (55 vs. 65 y) (P=0.0002) nonsmokers (P=0.01). Most positive cases were HPV16 (33/36, 92%). Hybrid Capture 2 and Cervista were as sensitive as polymerase chain reaction and had fewer false positives than p16 immunohistochemical staining.

    View details for DOI 10.1097/PDM.0000000000000036

    View details for Web of Science ID 000352259500004

    View details for PubMedID 25839700

    View details for PubMedCentralID PMC4116481

  • A Patient-Derived Xenograft Model of Parameningeal Embryonal Rhabdomyosarcoma for Preclinical Studies. Sarcoma Hooper, J. E., Cantor, E. L., Ehlen, M. S., Banerjee, A., Malempati, S., Stenzel, P., Woltjer, R. L., Gandour-Edwards, R., Goodwin, N. C., Yang, Y., Kaur, P., Bult, C. J., Airhart, S. D., Keller, C. 2015; 2015: 826124


    Embryonal rhabdomyosarcoma (eRMS) is one of the most common soft tissue sarcomas in children and adolescents. Parameningeal eRMS is a variant that is often more difficult to treat than eRMS occurring at other sites. A 14-year-old female with persistent headaches and rapid weight loss was diagnosed with parameningeal eRMS. She progressed and died despite chemotherapy with vincristine, actinomycin-D, and cyclophosphamide plus 50.4Gy radiation therapy to the primary tumor site. Tumor specimens were acquired by rapid autopsy and tumor tissue was transplanted into immunodeficient mice to create a patient-derived xenograft (PDX) animal model. As autopsy specimens had an ALK R1181C mutation, PDX tumor bearing animals were treated with the pan-kinase inhibitor lestaurtinib but demonstrated no decrease in tumor growth, suggesting that single agent kinase inhibitor therapy may be insufficient in similar cases. This unique parameningeal eRMS PDX model is publicly available for preclinical study.

    View details for DOI 10.1155/2015/826124

    View details for PubMedID 26696773

  • Suprarenal retroperitoneal liposarcoma with intracaval tumor thrombus: an imaging mimic of adrenocortical carcinoma CLINICAL IMAGING Vajtai, Z., Korngold, E., Hooper, J. E., Sheppard, B. C., Foster, B. R., Coakley, F. V. 2014; 38 (1): 75-77


    We report a 57-year-old previously healthy man who presented with dull right upper quadrant pain, weight loss, fatigue, and night sweats. Computed tomography demonstrated a large, heterogeneously enhancing, soft tissue mass with no macroscopic fat above the right kidney with tumor thrombus extending into the inferior vena cava and right atrium. Positron Emission Tomography scanning demonstrated intense Fluorodeoxyglucose avidity in the primary tumor and tumor thrombus. The presumptive radiological diagnosis was adrenocortical carcinoma, but surgical pathology revealed a dedifferentiated liposarcoma. We conclude that suprarenal retroperitoneal liposarcoma should be included in the differential diagnosis for an apparent adrenal mass with venous invasion.

    View details for DOI 10.1016/j.clinimag.2013.08.016

    View details for Web of Science ID 000328314100016

    View details for PubMedID 24075490

  • Overcoming autopsy barriers in pediatric cancer research PEDIATRIC BLOOD & CANCER Alabran, J. L., Hooper, J. E., Hill, M., Smith, S. E., Spady, K. K., Davis, L. E., Peterson, L. S., Malempati, S., Ryan, C. W., Acosta, R., Spunt, S. L., Keller, C. 2013; 60 (2): 204-209


    More than 13,000 children annually in the United States and Canada under the age of 20 will be diagnosed with cancer at a mortality approaching 20% 1,2. Tumor samples obtained by autopsy provide an innovative way to study tumor progression, potentially aiding in the discovery of new treatments and increased survival rates. The purpose of this study was to identify barriers to autopsies and develop guidelines for requesting autopsies for research purposes.Families of children treated for childhood cancer were referred by patient advocacy groups and surveyed about attitudes and experiences with research autopsies. From 60 interviews, barriers to autopsy and tumor banking were identified. An additional 14 interviews were conducted with medical and scientific experts.Ninety-three percent of parents of deceased children did or would have consented to a research autopsy if presented with the option; however, only half of these families were given the opportunity to donate autopsy tissue for research. The most significant barriers were the physicians' reluctance to ask a grieving family and lack of awareness about research opportunities.The value of donating tumor samples to research via an autopsy should be promoted to all groups managing pediatric cancer patients. Not only does autopsy tumor banking offer a potentially important medical and scientific impact, but the opportunity to contribute this Legacy Gift of autopsy tumor tissue also creates a positive outlet for the grieving family. Taking these findings into account, our multidisciplinary team has developed a curriculum addressing key barriers.

    View details for DOI 10.1002/pbc.24320

    View details for PubMedID 23015377

  • MDM2 Amplification and PI3KCA Mutation in a Case of Sclerosing Rhabdomyosarcoma. Sarcoma Kikuchi, K., Wettach, G. R., Ryan, C. W., Hung, A., Hooper, J. E., Beadling, C., Warrick, A., Corless, C. L., Olson, S. B., Keller, C., Mansoor, A. 2013; 2013: 520858


    A rare sclerosing variant of rhabdomyosarcoma characterized by prominent hyalinization and pseudovascular pattern has recently been described as a subtype biologically distinct from embryonal, alveolar, and pleomorphic forms. We present cytogenetic and molecular findings as well as experimental studies of an unusual case of sclerosing rhabdomyosarcoma. The primary lesion arose within the plantar subcutaneous tissue of the left foot of an otherwise healthy 23-year-old male who eventually developed pulmonary nodules despite systemic chemotherapy. Two genetic abnormalities identified in surgical and/or autopsy samples of the tumor were introduced into 10T1/2 murine fibroblasts to determine whether these genetic changes cooperatively facilitated transformation and growth. Cytogenetic analysis revealed a complex abnormal hyperdiploid clone, and MDM2 gene amplification was confirmed by fluorescence in situ hybridization. Cancer gene mutation screening using a combination of multiplexed PCR and mass spectroscopy revealed a PIK3CA exon 20 H1047R mutation in the primary tumor, lung metastasis, and liver metastasis. However, this mutation was not cooperative with MDM2 overexpression in experimental assays for transformation or growth. Nevertheless, MDM2 and PIK3CA are genes worthy of further investigation in patients with sclerosing rhabdomyosarcoma and might be considered in the enrollment of these patients into clinical trials of targeted therapeutics.

    View details for DOI 10.1155/2013/520858

    View details for PubMedID 23766666

  • The novel monoclonal antibody HPC2 and N-cadherin distinguish pancreatic ductal adenocarcinoma from cholangiocarcinoma HUMAN PATHOLOGY Hooper, J. E., Morgan, T. K., Grompe, M., Sheppard, B. C., Troxell, M. L., Corless, C. L., Streeter, P. R. 2012; 43 (10): 1583-1589


    Metastatic pancreatic ductal adenocarcinoma and primary cholangiocarcinoma are morphologically very similar and, therefore, challenging to distinguish in liver biopsies. The distinction is important because surgical management and prognosis differ significantly. Several immunohistochemical markers have been evaluated to aid this diagnosis, but aside from N-cadherin, which labels cholangiocarcinoma, few provide the combination of good sensitivity and specificity. Our laboratory recently developed the novel monoclonal antibody human pancreatic cancer fusion #2 (HPC2) that recognizes pancreatic cancer. We hypothesized that the combination of our new marker and N-cadherin can assist in distinguishing metastatic pancreatic cancer from cholangiocarcinoma. We immunostained resections of 60 pancreatic ductal adenocarcinomas and 31 cholangiocarcinomas for the HPC2 and N-cadherin antigens. We also stained 24 gallbladder adenocarcinomas, 11 ampullary adenocarcinomas, and 10 metastatic colonic adenocarcinomas to the liver. Sections were independently scored by 2 pathologists with good agreement using both markers (κ statistics, 0.62-0.64; P < .0001). HPC2 was observed in 80% of pancreatic cancers (48/60), 82% of ampullary (9/11), and 32% (10/31) of cholangiocarcinomas. N-cadherin stained 27% (16/60) of the pancreas cases and 58% (18/31) of the cholangiocarcinomas. Gallbladder and colon cancers were usually double negative (18/24 and 8/10, respectively). Each marker provided significant likelihood ratios to separate pancreatic cancer (HPC2, 2.48 [1.46-4.19]; P < .0001) from cholangiocarcinoma (N-cadherin, 2.17 [1.3-3.64]; P < .01). The combination of both markers provided even better specificity and positive likelihood ratios. We conclude that HPC2 and N-cadherin significantly improve accurate classification of pancreatic cancer and cholangiocarcinoma.

    View details for DOI 10.1016/j.humpath.2011.11.012

    View details for PubMedID 22406361

  • Polyoma virus nephropathy-related mass lesion in an apparently immunocompetent patient INTERNATIONAL UROLOGY AND NEPHROLOGY Go, S., Conlin, M., Hooper, J. E., Troxell, M. L. 2012; 44 (5): 1585-1588


    Polyoma virus is a recognized cause of hemorrhagic cystitis, viral nephropathy, and ureteral stricture in renal and stem cell transplant recipients. Rarely, polyoma virus causes native kidney and bladder pathology in heavily immunosuppressed patients. We report a unique case of native kidney polyoma virus nephropathy, urothelial ulceration, and renal pelvic fibrosis presenting as a mass lesion in a non-debilitated, apparently immunocompetent man. Based on radiologic, ureterorenoscopic, and urine cytologic findings, a laparoscopic nephrectomy was performed. However, nephrectomy revealed a hemorrhagic scar-like lesion, with urothelial ulceration, but no neoplasm or malignancy. Histopathologic evaluation and immunostaining revealed polyoma viral infection in the nearby renal medulla. This case adds polyoma virus nephropathy to the differential diagnosis of non-neoplastic and reactive masses, which may mimic renal malignancy.

    View details for DOI 10.1007/s11255-011-9985-y

    View details for PubMedID 21559788

  • Disseminated coccidioidomycosis in pregnancy ARCHIVES OF PATHOLOGY & LABORATORY MEDICINE Hooper, J. E., Lu, Q., Pepkowitz, S. H. 2007; 131 (4): 652-655


    Coccidioidomycosis is a fungal infection contracted through the inhalation of airborne spores, which are most frequently present in desert areas of the southwestern United States and Mexico. Primary immune response to infection is by T(H)1, a subset of helper T cells. Although pulmonary symptoms are most common, hematogenous systemic spread can also occur. Pregnancy is a well-noted risk factor for disseminated Coccidioides infection. The objective of this review is to provide an overview of coccidioidomycosis and to review immunologic and hormonal factors that increase risk of dissemination in pregnancy. Dissemination may occur more frequently in pregnant patients than in nonpregnant women because of shifts in T-cell immunity, changes in cytokine production, and increased hormone levels. There is disagreement regarding the precise incidence of systemic spread in pregnancy, but most sources agree that risk is substantially increased and vigilance must be high in patients with exposures in endemic areas.

    View details for Web of Science ID 000245610500028

    View details for PubMedID 17425401

  • Relevance of the autopsy as a medical tool - A large database of physician attitudes ARCHIVES OF PATHOLOGY & LABORATORY MEDICINE Hooper, J. E., Geller, S. A. 2007; 131 (2): 268-274


    Autopsy rates for patients dying in hospitals have declined from approximately 50% in the 1950s to 5% or less today.To investigate the nature of physician attitudes about autopsy in a large and varied population and to relate these attitudes to certain physician demographic variables.A 10-question, anonymous, multiple-choice format questionnaire was distributed to all attending physicians at 4 hospitals: 2 that were university-affiliated (1 private and 1 public), 1 military, and 1 private nonuniversity-affiliated medical center. A total of 2608 surveys were distributed.Three hundred eighty-eight (15%) physicians responded to the survey. Respondents agreed (77%) that autopsy results could affect their future medical practice, and disagreed (73%) that the accuracy of modern diagnostic procedures makes autopsy unnecessary. Most respondents (72%) disagreed that litigation concerns play a role in the decision to request autopsy. Spearman correlation coefficients found 9 significant relationships among the survey items, with many correlations reflecting statistically significant relationships between demographic and attitudinal variables.The survey data and statistical analysis confirm that respondents value the autopsy as a relevant clinical tool, in spite of declining requests. One of the most crucial factors influencing attitudes is the physician's level of experience with autopsy in training and practice. Among other interesting results was that strength of belief in autopsy relevancy correlates significantly (P = .003) with greater prior exposure to the autopsy. In a sense, the current low autopsy rates may be self-perpetuating because of the paucity of and decreasing experience with autopsy by succeeding generations of clinicians.

    View details for Web of Science ID 000244317700014

    View details for PubMedID 17284112