Clinical Focus

  • Diagnostic Medicine
  • Undiagnosed Diseases and Medical Mysteries
  • Rare Disorders
  • Post-Acute COVID-19 Syndrome (long COVID)
  • Internal Medicine

Academic Appointments

Administrative Appointments

  • Co-Director, Stanford Post-Acute COVID-19 Syndrome Clinic (2021 - Present)
  • Director, Stanford Consultative Medicine Clinic (2019 - Present)
  • Chief Resident, Stanford Internal Medicine Residency Program (2018 - 2019)

Honors & Awards

  • Julian Wolfsohn Award (for clinical excellence, leadership, teaching, kindness), Stanford Internal Medicine Residency (2016)
  • Harold M. Weintraub Graduate Student Award (National), Fred Hutchinson Cancer Research Center (2012)
  • Alpha Omega Alpha (Medical Honor Society), Stanford University chapter (2019)
  • Phi Beta Kappa (Honor Society), Rice University chapter (2006)

Professional Education

  • Board Certification: American Board of Internal Medicine, Internal Medicine (2019)
  • Visiting scholar, NIH, Undiagnosed Diseases Program (2019)
  • Chief Resident, Stanford University Internal Medicine Residency (2019)
  • Residency: Stanford University Internal Medicine Residency (2018) CA
  • Medical Education: University of Washington School of Medicine (2015) WA
  • Ph.D., University of Washington, Molecular and Cellular Biology (2011)

Current Research and Scholarly Interests

My scholarly interests are focused on defining, studying, and improving patients' diagnostic journeys. What prolongs the journey to the correct diagnosis and how can we shorten it? With this question in mind, we are exploring crowdsourcing, informatics/AI, health data visualization, and advanced laboratory testing as ways to help tackle the toughest cases in medicine-- complex, rare, and mystery conditions.

With the COVID pandemic, the puzzling and complex illness of post-acute COVID-19 syndrome (PACS) or long COVID came to light. Together with a multidisciplinary group of physicians and researchers, we launched a program here at Stanford to advance the care and understanding of PACS. Our goal is to better understand the natural history, clinical symptomatology, immunological response, risk factors, and subgroup stratification for PACS. We are also actively assessing management strategies that may be effective for heterogeneous PACS symptoms.

Clinical Trials

  • Paxlovid for Treatment of Long Covid Not Recruiting

    The purpose of this study is to compare whether being treated with Paxlovid (nirmatrelvir plus ritonavir) for 15 days works better than being treated with placebo (plus ritonavir) to reduce severe symptoms of Long Covid (the placebo does not have any active drug). Participants will have 5 planned visits to the study clinic over 15 weeks and will take the drug (or placebo) for the first 15 days. This study uses the term post-acute sequelae of SARS-CoV-2 (PASC), which is another name for "Long Covid."

    Stanford is currently not accepting patients for this trial. For more information, please contact Study Team, 650-308-6788.

    View full details

All Publications

  • Nirmatrelvir-Ritonavir and Symptoms in Adults With Postacute Sequelae of SARS-CoV-2 Infection: The STOP-PASC Randomized Clinical Trial. JAMA internal medicine Geng, L. N., Bonilla, H., Hedlin, H., Jacobson, K. B., Tian, L., Jagannathan, P., Yang, P. C., Subramanian, A. K., Liang, J. W., Shen, S., Deng, Y., Shaw, B. J., Botzheim, B., Desai, M., Pathak, D., Jazayeri, Y., Thai, D., O'Donnell, A., Mohaptra, S., Leang, Z., Reynolds, G. Z., Brooks, E. F., Bhatt, A. S., Shafer, R. W., Miglis, M. G., Quach, T., Tiwari, A., Banerjee, A., Lopez, R. N., De Jesus, M., Charnas, L. R., Utz, P. J., Singh, U. 2024


    There is an urgent need to identify treatments for postacute sequelae of SARS-CoV-2 infection (PASC).To assess the efficacy of a 15-day course of nirmatrelvir-ritonavir in reducing the severity of select PASC symptoms.This was a 15-week blinded, placebo-controlled, randomized clinical trial conducted from November 2022 to September 2023 at Stanford University (California). The participants were adults with moderate to severe PASC symptoms of 3 months or longer duration.Participants were randomized 2:1 to treatment with oral nirmatrelvir-ritonavir (NMV/r, 300 mg and 100 mg) or with placebo-ritonavir (PBO/r) twice daily for 15 days.Primary outcome was a pooled severity of 6 PASC symptoms (fatigue, brain fog, shortness of breath, body aches, gastrointestinal symptoms, and cardiovascular symptoms) based on a Likert scale score at 10 weeks. Secondary outcomes included symptom severity at different time points, symptom burden and relief, patient global measures, Patient-Reported Outcomes Measurement Information System (PROMIS) measures, orthostatic vital signs, and sit-to-stand test change from baseline.Of the 155 participants (median [IQR] age, 43 [34-54] years; 92 [59%] females), 102 were randomized to the NMV/r group and 53 to the PBO/r group. Nearly all participants (n = 153) had received the primary series for COVID-19 vaccination. Mean (SD) time between index SARS-CoV-2 infection and randomization was 17.5 (9.1) months. There was no statistically significant difference in the model-derived severity outcome pooled across the 6 core symptoms at 10 weeks between the NMV/r and PBO/r groups. No statistically significant between-group differences were found at 10 weeks in the Patient Global Impression of Severity or Patient Global Impression of Change scores, summative symptom scores, and change from baseline to 10 weeks in PROMIS fatigue, dyspnea, cognitive function, and physical function measures. Adverse event rates were similar in NMV/r and PBO/r groups and mostly of low grade.The results of this randomized clinical trial showed that a 15-day course of NMV/r in a population of patients with PASC was generally safe but did not demonstrate a significant benefit for improving select PASC symptoms in a mostly vaccinated cohort with protracted symptom duration. Further studies are needed to determine the role of antivirals in the treatment of Identifier: NCT05576662.

    View details for DOI 10.1001/jamainternmed.2024.2007

    View details for PubMedID 38848477

  • Social determinants of health associated with developing long COVID in the US veteran population JOURNAL OF PUBLIC HEALTH-HEIDELBERG Van Cleve, R., Quach, T., Shaheen, M., Bell, K., Roshwalb, A., Petrin, R., Geng, L. N., Asch, S. M., Lienau, A. 2024
  • IgM N-glycosylation correlates with COVID-19 severity and rate of complement deposition. Nature communications Haslund-Gourley, B. S., Woloszczuk, K., Hou, J., Connors, J., Cusimano, G., Bell, M., Taramangalam, B., Fourati, S., Mege, N., Bernui, M., Altman, M. C., Krammer, F., van Bakel, H., IMPACC Network, Maecker, H. T., Rouphael, N., Diray-Arce, J., Wigdahl, B., Kutzler, M. A., Cairns, C. B., Haddad, E. K., Comunale, M. A., Ozonoff, A., Ehrlich, L. I., Melamed, E., Sesma, A. F., Simon, V., Pulendran, B., Nadeau, K. C., Davis, M. M., McCoey, G. A., Sekaly, R., Baden, L. R., Levy, O., Schaenman, J., Reed, E. F., Shaw, A. C., Hafler, D. A., Montgomery, R. R., Kleinstein, S. H., Becker, P. M., Augustine, A. D., Calfee, C. S., Erle, D. J., DeBakey, M. E., Corry, D. B., Kheradmand, F., Atkinson, M. A., Brakenridge, S. C., Higuita, N. I., Metcalf, J. P., Hough, C. L., Messer, W. B., Kraft, M., Bime, C., Peters, B., Milliren, C. E., Syphurs, C., McEnaney, K., Barton, B., Lentucci, C., Saluvan, M., Chang, A. C., Hoch, A., Albert, M., Shaheen, T., Kho, A. T., Liu, S., Thomas, S., Chen, J., Murphy, M. D., Cooney, M., Hayati, A. N., Bryant, R., Abraham, J., Jayavelu, N. D., Presnell, S., Jancsyk, T., Maguire, C., Qi, J., Lee, B., Fourati, S., Esserman, D. A., Guan, L., Gygi, J., Pawar, S., Brito, A., Fragiadakis, G. K., Patel, R., Overton, J. A., Vita, R., Westendorf, K., Shannon, C. P., Tebbutt, S. J., Thyagarajan, R. V., Rousseau, J. F., Wylie, D., Triplett, T. A., Kojic, E., Chinthrajah, S., Ahuja, N., Rogers, A. J., Artandi, M., Geng, L., Yendewa, G., Powell, D. L., Kim, J. N., Simmons, B., Goonewardene, I. M., Smith, C. M., Martens, M., Sherman, A. C., Walsh, S. R., Issa, N. C., Salehi-Rad, R., Dela Cruz, C., Farhadian, S., Iwasaki, A., Ko, A. I., Anderson, E. J., Mehta, A. K., Sevransky, J. E., Seyfert-Margolis, V., Leligdowicz, A., Matthay, M. A., Singer, J. P., Kangelaris, K. N., Hendrickson, C. M., Krummel, M. F., Langelier, C. R., Woodruff, P. G., Corry, D. B., Kheradmand, F., Anderson, M. L., Guirgis, F. W., Drevets, D. A., Brown, B. R., Siegel, S. A., Lu, Z., Mosier, J., Kimura, H., Khor, B., van Bakel, H., Rahman, A., Stadlbauer, D., Dutta, J., Xie, H., Kim-Schulze, S., Gonzalez-Reiche, A. S., van de Guchte, A., Carreno, J. M., Singh, G., Raskin, A., Tcheou, J., Bielak, D., Kawabata, H., Kelly, G., Patel, M., Nie, K., Yellin, T., Fried, M., Sullivan, L., Morris, S., Sieg, S., Steen, H., van Zalm, P., Fatou, B., Mendez, K., Lasky-Su, J., Hutton, S. R., Michelotti, G., Wong, K., Jha, M., Viode, A., Kanarek, N., Petrova, B., Zhao, Y., Bosinger, S. E., Boddapati, A. K., Tharp, G. K., Pellegrini, K. L., Beagle, E., Cowan, D., Hamilton, S., Ribeiro, S. P., Hodder, T., Rosen, L. B., Lee, S., Wilson, M. R., Dandekar, R., Alvarenga, B., Rajan, J., Eckalbar, W., Schroeder, A. W., Tsitsiklis, A., Mick, E., Guerrero, Y. S., Love, C., Maliskova, L., Adkisson, M., Siles, N., Geltman, J., Hurley, K., Saksena, M., Altman, D., Srivastava, K., Eaker, L. Q., Bermudez-Gonzalez, M. C., Beach, K. F., Sominsky, L. A., Azad, A. R., Mulder, L. C., Kleiner, G., Lee, A. S., Do, E., Fernandes, A., Manohar, M., Hagan, T., Blish, C. A., Din, H. N., Roque, J., Yang, S., Sigal, N., Chang, I., Tribout, H., Harris, P., Consolo, M., Edwards, C., Lee, E., Lin, E., Croen, B., Semenza, N. C., Rogowski, B., Melnyk, N., Bell, M. R., Furukawa, S., McLin, R., Schearer, P., Sheidy, J., Tegos, G. P., Nagle, C., Smolen, K., Desjardins, M., van Haren, S., Mitre, X., Cauley, J., Li, X., Tong, A., Evans, B., Montesano, C., Licona, J. H., Krauss, J., Chang, J. B., Izaguirre, N., Rooks, R., Elashoff, D., Brook, J., Ramires-Sanchez, E., Llamas, M., Rivera, A., Perdomo, C., Ward, D. C., Magyar, C. E., Fulcher, J. A., Pickering, H. C., Sen, S., Chaudhary, O., Coppi, A., Fournier, J., Mohanty, S., Muenker, C., Nelson, A., Raddassi, K., Rainone, M., Ruff, W. E., Salahuddin, S., Schulz, W. L., Vijayakumar, P., Wang, H., Wunder, E. J., Young, H. P., Rothman, J., Konstorum, A., Chen, E., Cotsapas, C., Grubaugh, N. D., Wang, X., Xu, L., Asashima, H., Bristow, L., Hussaini, L., Hellmeister, K., Samaha, H., Wimalasena, S. T., Cheng, A., Spainhour, C., Scherer, E. M., Johnson, B., Bechnak, A., Ciric, C. R., Hewitt, L., Carter, E., Mcnair, N., Panganiban, B., Huerta, C., Usher, J., Vaysman, T., Holland, S. M., Abe-Jones, Y., Asthana, S., Beagle, A., Bhide, S., Carrillo, S. A., Chak, S., Ghale, R., Gonzalez, A., Jauregui, A., Jones, N., Lea, T., Lee, D., Lota, R., Milush, J., Nguyen, V., Pierce, L., Prasad, P. A., Rao, A., Samad, B., Shaw, C., Sigman, A., Sinha, P., Ward, A., Willmore, A., Zhan, J., Rashid, S., Rodriguez, N., Tang, K., Altamirano, L. T., Betancourt, L., Curiel, C., Sutter, N., Paz, M. T., Tietje-Ulrich, G., Leroux, C., Thakur, N., Vasquez, J. J., Santhosh, L., Song, L., Nelson, E., Moldawer, L. L., Borresen, B., Roth-Manning, B., Ungaro, R. F., Oberhaus, J., Booth, J. L., Sinko, L. A., Brunton, A., Sullivan, P. E., Strnad, M., Lyski, Z. L., Coulter, F. J., Micheleti, C., Conway, M., Francisco, D., Molzahn, A., Erickson, H., Wilson, C. C., Schunk, R., Sierra, B., Hughes, T. 2024; 15 (1): 404


    The glycosylation of IgG plays a critical role during human severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, activating immune cells and inducing cytokine production. However, the role of IgM N-glycosylation has not been studied during human acute viral infection. The analysis of IgM N-glycosylation from healthy controls and hospitalized coronavirus disease 2019 (COVID-19) patients reveals increased high-mannose and sialylation that correlates with COVID-19 severity. These trends are confirmed within SARS-CoV-2-specific immunoglobulin N-glycan profiles. Moreover, the degree of total IgM mannosylation and sialylation correlate significantly with markers of disease severity. We link the changes of IgM N-glycosylation with the expression of Golgi glycosyltransferases. Lastly, we observe antigen-specific IgM antibody-dependent complement deposition is elevated in severe COVID-19 patients and modulated by exoglycosidase digestion. Taken together, this work links the IgM N-glycosylation with COVID-19 severity and highlights the need to understand IgM glycosylation and downstream immune function during human disease.

    View details for DOI 10.1038/s41467-023-44211-0

    View details for PubMedID 38195739

  • Features of acute COVID-19 associated with post-acute sequelae of SARS-CoV-2 phenotypes: results from the IMPACC study. Nature communications Ozonoff, A., Jayavelu, N. D., Liu, S., Melamed, E., Milliren, C. E., Qi, J., Geng, L. N., McComsey, G. A., Cairns, C. B., Baden, L. R., Schaenman, J., Shaw, A. C., Samaha, H., Seyfert-Margolis, V., Krammer, F., Rosen, L. B., Steen, H., Syphurs, C., Dandekar, R., Shannon, C. P., Sekaly, R. P., Ehrlich, L. I., Corry, D. B., Kheradmand, F., Atkinson, M. A., Brakenridge, S. C., Higuita, N. I., Metcalf, J. P., Hough, C. L., Messer, W. B., Pulendran, B., Nadeau, K. C., Davis, M. M., Sesma, A. F., Simon, V., van Bakel, H., Kim-Schulze, S., Hafler, D. A., Levy, O., Kraft, M., Bime, C., Haddad, E. K., Calfee, C. S., Erle, D. J., Langelier, C. R., Eckalbar, W., Bosinger, S. E., Peters, B., Kleinstein, S. H., Reed, E. F., Augustine, A. D., Diray-Arce, J., Maecker, H. T., Altman, M. C., Montgomery, R. R., Becker, P. M., Rouphael, N. 2024; 15 (1): 216


    Post-acute sequelae of SARS-CoV-2 (PASC) is a significant public health concern. We describe Patient Reported Outcomes (PROs) on 590 participants prospectively assessed from hospital admission for COVID-19 through one year after discharge. Modeling identified 4 PRO clusters based on reported deficits (minimal, physical, mental/cognitive, and multidomain), supporting heterogenous clinical presentations in PASC, with sub-phenotypes associated with female sex and distinctive comorbidities. During the acute phase of disease, a higher respiratory SARS-CoV-2 viral burden and lower Receptor Binding Domain and Spike antibody titers were associated with both the physical predominant and the multidomain deficit clusters. A lower frequency of circulating B lymphocytes by mass cytometry (CyTOF) was observed in the multidomain deficit cluster. Circulating fibroblast growth factor 21 (FGF21) was significantly elevated in the mental/cognitive predominant and the multidomain clusters. Future efforts to link PASC to acute anti-viral host responses may help to better target treatment and prevention of PASC.

    View details for DOI 10.1038/s41467-023-44090-5

    View details for PubMedID 38172101

    View details for PubMedCentralID PMC10764789

  • New Alcohol Sensitivity in Patients With Post-acute Sequelae of SARS-CoV-2 (PASC): A Case Series. Cureus Eastin, E. F., Tiwari, A., Quach, T. C., Bonilla, H. F., Miglis, M. G., Yang, P. C., Geng, L. N. 2023; 15 (12): e51286


    Post-acute sequelae of SARS-CoV-2 (PASC), or long COVID, is characterized by persistent symptoms after acute SARS-CoV-2 infection that can vary from patient to patient. Here, we present a case series of four patients with a history of SARS-CoV-2 infection referred to the Post-Acute COVID-19 Syndrome (PACS) Clinic at Stanford University for evaluation of persistent symptoms, who also experienced new-onset alcohol sensitivity. Alcohol reactions and sensitivity are not well characterized in the literature as it relates to post-viral illness. While there have been some anecdotal reports of new alcohol sensitivity in PASC patients in the media, there is a paucity of published data in the medical literature about this topic. During their medical consultation, the patients self-reported new changes in their symptoms or behaviors following the use of alcohol. A new onset of alcohol sensitivities should be assessed along with other post-COVID-19 symptoms and may provide novel avenues to explore the pathobiology of illness and potential interventions.

    View details for DOI 10.7759/cureus.51286

    View details for PubMedID 38288178

    View details for PubMedCentralID PMC10823305

  • Low-dose naltrexone use for the management of post-acute sequelae of COVID-19. International immunopharmacology Bonilla, H., Tian, L., Marconi, V. C., Shafer, R., McComsey, G. A., Miglis, M., Yang, P., Bonilla, A., Eggert, L., Geng, L. N. 2023; 124 (Pt B): 110966


    The global prevalence of Post-Acute Sequelae of SARS-CoV-2 Infection (PASC) stands at approximately 43 % among individuals who have previously had acute COVID-19. In contrast, in the United States, the National Center for Health Statistics (NCHS) estimates that around 11 % of individuals who have been infected with SARS-CoV-2 go on to experience long COVID. The underlying causes of PASC remains under investigation, and there are no currently established FDA-approved therapies. One of the leading hypotheses for the cause of PASC is the persistent activation of innate immune cells with increase systemic inflammation. Naltrexone is a medication with anti-inflammatory and immunomodulatory properties that has been used in other conditions that overlap with PASC. We performed a retrospective review of a clinical cohort of 59 patients at a single academic center who received low-dose naltrexone (LDN) off-label as a potential therapeutic intervention for PASC. The use of LDN was associated with a fewer number of symptoms, improved clinical symptoms (fatigue, post-exertional malaise, unrefreshing sleep, and abnormal sleep pattern), and a better functional status. This observation warrants testing in rigorous, randomized, placebo-controlled clinical trials.

    View details for DOI 10.1016/j.intimp.2023.110966

    View details for PubMedID 37804660

  • SARS-CoV-2 reservoir in post-acute sequelae of COVID-19 (PASC). Nature immunology Proal, A. D., VanElzakker, M. B., Aleman, S., Bach, K., Boribong, B. P., Buggert, M., Cherry, S., Chertow, D. S., Davies, H. E., Dupont, C. L., Deeks, S. G., Eimer, W., Ely, E. W., Fasano, A., Freire, M., Geng, L. N., Griffin, D. E., Henrich, T. J., Iwasaki, A., Izquierdo-Garcia, D., Locci, M., Mehandru, S., Painter, M. M., Peluso, M. J., Pretorius, E., Price, D. A., Putrino, D., Scheuermann, R. H., Tan, G. S., Tanzi, R. E., VanBrocklin, H. F., Yonker, L. M., Wherry, E. J. 2023


    Millions of people are suffering from Long COVID or post-acute sequelae of COVID-19 (PASC). Several biological factors have emerged as potential drivers of PASC pathology. Some individuals with PASC may not fully clear the coronavirus SARS-CoV-2 after acute infection. Instead, replicating virus and/or viral RNA-potentially capable of being translated to produce viral proteins-persist in tissue as a 'reservoir'. This reservoir could modulate host immune responses or release viral proteins into the circulation. Here we review studies that have identified SARS-CoV-2 RNA/protein or immune responses indicative of a SARS-CoV-2 reservoir in PASC samples. Mechanisms by which a SARS-CoV-2 reservoir may contribute to PASC pathology, including coagulation, microbiome and neuroimmune abnormalities, are delineated. We identify research priorities to guide the further study of a SARS-CoV-2 reservoir in PASC, with the goal that clinical trials of antivirals or other therapeutics with potential to clear a SARS-CoV-2 reservoir are accelerated.

    View details for DOI 10.1038/s41590-023-01601-2

    View details for PubMedID 37667052

    View details for PubMedCentralID 8755397

  • Myalgic Encephalomyelitis/Chronic Fatigue Syndrome is common in post-acute sequelae of SARS-CoV-2 infection (PASC): Results from a post-COVID-19 multidisciplinary clinic. Frontiers in neurology Bonilla, H., Quach, T. C., Tiwari, A., Bonilla, A. E., Miglis, M., Yang, P. C., Eggert, L. E., Sharifi, H., Horomanski, A., Subramanian, A., Smirnoff, L., Simpson, N., Halawi, H., Sum-Ping, O., Kalinowski, A., Patel, Z. M., Shafer, R. W., Geng, L. C. 2023; 14: 1090747


    The global prevalence of PASC is estimated to be present in 0·43 and based on the WHO estimation of 470 million worldwide COVID-19 infections, corresponds to around 200 million people experiencing long COVID symptoms. Despite this, its clinical features are not well-defined.We collected retrospective data from 140 patients with PASC in a post-COVID-19 clinic on demographics, risk factors, illness severity (graded as one-mild to five-severe), functional status, and 29 symptoms and principal component symptoms cluster analysis. The Institute of Medicine (IOM) 2015 criteria were used to determine the Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) phenotype.The median age was 47 years, 59.0% were female; 49.3% White, 17.2% Hispanic, 14.9% Asian, and 6.7% Black. Only 12.7% required hospitalization. Seventy-two (53.5%) patients had no known comorbid conditions. Forty-five (33.9%) were significantly debilitated. The median duration of symptoms was 285.5 days, and the number of symptoms was 12. The most common symptoms were fatigue (86.5%), post-exertional malaise (82.8%), brain fog (81.2%), unrefreshing sleep (76.7%), and lethargy (74.6%). Forty-three percent fit the criteria for ME/CFS, majority were female, and obesity (BMI > 30 Kg/m2) (P = 0.00377895) and worse functional status (P = 0.0110474) were significantly associated with ME/CFS.Most PASC patients evaluated at our clinic had no comorbid condition and were not hospitalized for acute COVID-19. One-third of patients experienced a severe decline in their functional status. About 43% had the ME/CFS subtype.

    View details for DOI 10.3389/fneur.2023.1090747

    View details for PubMedID 36908615

    View details for PubMedCentralID PMC9998690

  • Development of a Definition of Postacute Sequelae of SARS-CoV-2 Infection. JAMA Thaweethai, T., Jolley, S. E., Karlson, E. W., Levitan, E. B., Levy, B., McComsey, G. A., McCorkell, L., Nadkarni, G. N., Parthasarathy, S., Singh, U., Walker, T. A., Selvaggi, C. A., Shinnick, D. J., Schulte, C. C., Atchley-Challenner, R., Horwitz, L. I., Foulkes, A. S., RECOVER Consortium, Alba, G. A., Alicic, R., Altman, N., Anglin, K., Argueta, U., Ashktorab, H., Baslet, G., Bassett, I. V., Bateman, L., Bedi, B., Bhattacharyya, S., Bind, M., Blomkalns, A. L., Bonilla, H., Bush, P. A., Castro, M., Chan, J., Charney, A. W., Chen, P., Chibnik, L. B., Chu, H. Y., Clifton, R. G., Costantine, M. M., Cribbs, S. K., Davila Nieves, S. I., Deeks, S. G., Duven, A., Emery, I. F., Erdmann, N., Erlandson, K. M., Ernst, K. C., Farah-Abraham, R., Farner, C. E., Feuerriegel, E. M., Fleurimont, J., Fonseca, V., Franko, N., Gainer, V., Gander, J. C., Gardner, E. M., Geng, L. N., Gibson, K. S., Go, M., Goldman, J. D., Grebe, H., Greenway, F. L., Habli, M., Hafner, J., Han, J. E., Hanson, K. A., Heath, J., Hernandez, C., Hess, R., Hodder, S. L., Hoffman, M. K., Hoover, S. E., Huang, B., Hughes, B. L., Jagannathan, P., John, J., Jordan, M. R., Katz, S. D., Kaufman, E. S., Kelly, J. D., Kelly, S. W., Kemp, M. M., Kirwan, J. P., Klein, J. D., Knox, K. S., Krishnan, J. A., Kumar, A., Laiyemo, A. O., Lambert, A. A., Lanca, M., Lee-Iannotti, J. K., Logarbo, B. P., Longo, M. T., Luciano, C. A., Lutrick, K., Maley, J. H., Marathe, J. G., Marconi, V., Marshall, G. D., Martin, C. F., Matusov, Y., Mehari, A., Mendez-Figueroa, H., Mermelstein, R., Metz, T. D., Morse, R., Mosier, J., Mouchati, C., Mullington, J., Murphy, S. N., Neuman, R. B., Nikolich, J. Z., Ofotokun, I., Ojemakinde, E., Palatnik, A., Palomares, K., Parimon, T., Parry, S., Patterson, J. E., Patterson, T. F., Patzer, R. E., Peluso, M. J., Pemu, P., Pettker, C. M., Plunkett, B. A., Pogreba-Brown, K., Poppas, A., Quigley, J. G., Reddy, U., Reece, R., Reeder, H., Reeves, W. B., Reiman, E. M., Rischard, F., Rosand, J., Rouse, D. J., Ruff, A., Saade, G., Sandoval, G. J., Schlater, S. M., Shepherd, F., Sherif, Z. A., Simhan, H., Singer, N. G., Skupski, D. W., Sowles, A., Sparks, J. A., Sukhera, F. I., Taylor, B. S., Teunis, L., Thomas, R. J., Thorp, J. M., Thuluvath, P., Ticotsky, A., Tita, A. T., Tuttle, K. R., Urdaneta, A. E., Valdivieso, D., VanWagoner, T. M., Vasey, A., Verduzco-Gutierrez, M., Wallace, Z. S., Ward, H. D., Warren, D. E., Weiner, S. J., Welch, S., Whiteheart, S. W., Wiley, Z., Wisnivesky, J. P., Yee, L. M., Zisis, S. 2023


    Importance: SARS-CoV-2 infection is associated with persistent, relapsing, or new symptoms or other health effects occurring after acute infection, termed postacute sequelae of SARS-CoV-2 infection (PASC), also known as long COVID. Characterizing PASC requires analysis of prospectively and uniformly collected data from diverse uninfected and infected individuals.Objective: To develop a definition of PASC using self-reported symptoms and describe PASC frequencies across cohorts, vaccination status, and number of infections.Design, Setting, and Participants: Prospective observational cohort study of adults with and without SARS-CoV-2 infection at 85 enrolling sites (hospitals, health centers, community organizations) located in 33 states plus Washington, DC, and Puerto Rico. Participants who were enrolled in the RECOVER adult cohort before April 10, 2023, completed a symptom survey 6 months or more after acute symptom onset or test date. Selection included population-based, volunteer, and convenience sampling.Exposure: SARS-CoV-2 infection.Main Outcomes and Measures: PASC and 44 participant-reported symptoms (with severity thresholds).Results: A total of 9764 participants (89% SARS-CoV-2 infected; 71% female; 16% Hispanic/Latino; 15% non-Hispanic Black; median age, 47 years [IQR, 35-60]) met selection criteria. Adjusted odds ratios were 1.5 or greater (infected vs uninfected participants) for 37 symptoms. Symptoms contributing to PASC score included postexertional malaise, fatigue, brain fog, dizziness, gastrointestinal symptoms, palpitations, changes in sexual desire or capacity, loss of or change in smell or taste, thirst, chronic cough, chest pain, and abnormal movements. Among 2231 participants first infected on or after December 1, 2021, and enrolled within 30 days of infection, 224 (10% [95% CI, 8.8%-11%]) were PASC positive at 6 months.Conclusions and Relevance: A definition of PASC was developed based on symptoms in a prospective cohort study. As a first step to providing a framework for other investigations, iterative refinement that further incorporates other clinical features is needed to support actionable definitions of PASC.

    View details for DOI 10.1001/jama.2023.8823

    View details for PubMedID 37278994

  • The Use of Nirmatrelvir-ritonavir in a Case of Breakthrough Long COVID Exploratory Research and Hypothesis in Medicine Geng, L. N., Bonilla, H. F., Shafer, R. W., Miglis, M. G., Yang, P. C. 2023

    View details for DOI 10.14218/ERHM.2022.00045

  • Anti-nucleocapsid antibody levels and pulmonary comorbid conditions are linked to post-COVID-19 syndrome. JCI insight Jia, X., Cao, S., Lee, A. S., Manohar, M., Sindher, S. B., Ahuja, N., Artandi, M., Blish, C. A., Blomkalns, A. L., Chang, I., Collins, W. J., Desai, M., Din, H. N., Do, E., Fernandes, A., Geng, L. N., Rosenberg-Hasson, Y., Mahoney, M. R., Glascock, A. L., Chan, L. Y., Fong, S. Y., Phelps, M., Raeber, O., Purington, N., Röltgen, K., Rogers, A. J., Snow, T., Wang, T. T., Solis, D., Vaughan, L., Verghese, M., Maecker, H., Wittman, R., Puri, R., Kistler, A., Yang, S., Boyd, S. D., Pinsky, B. A., Chinthrajah, S., Nadeau, K. C. 2022; 7 (13)


    BACKGROUNDProlonged symptoms after SARS-CoV-2 infection are well documented. However, which factors influence development of long-term symptoms, how symptoms vary across ethnic groups, and whether long-term symptoms correlate with biomarkers are points that remain elusive.METHODSAdult SARS-CoV-2 reverse transcription PCR-positive (RT-PCR-positive) patients were recruited at Stanford from March 2020 to February 2021. Study participants were seen for in-person visits at diagnosis and every 1-3 months for up to 1 year after diagnosis; they completed symptom surveys and underwent blood draws and nasal swab collections at each visit.RESULTSOur cohort (n = 617) ranged from asymptomatic to critical COVID-19 infections. In total, 40% of participants reported at least 1 symptom associated with COVID-19 six months after diagnosis. Median time from diagnosis to first resolution of all symptoms was 44 days; median time from diagnosis to sustained symptom resolution with no recurring symptoms for 1 month or longer was 214 days. Anti-nucleocapsid IgG level in the first week after positive RT-PCR test and history of lung disease were associated with time to sustained symptom resolution. COVID-19 disease severity, ethnicity, age, sex, and remdesivir use did not affect time to sustained symptom resolution.CONCLUSIONWe found that all disease severities had a similar risk of developing post-COVID-19 syndrome in an ethnically diverse population. Comorbid lung disease and lower levels of initial IgG response to SARS-CoV-2 nucleocapsid antigen were associated with longer symptom duration.TRIAL, NCT04373148.FUNDINGNIH UL1TR003142 CTSA grant, NIH U54CA260517 grant, NIEHS R21 ES03304901, Sean N Parker Center for Allergy and Asthma Research at Stanford University, Chan Zuckerberg Biohub, Chan Zuckerberg Initiative, Sunshine Foundation, Crown Foundation, and Parker Foundation.

    View details for DOI 10.1172/jci.insight.156713

    View details for PubMedID 35801588

  • Diagnostic journeys: characterization of patients and diagnostic outcomes from an academic second opinion clinic. Diagnosis (Berlin, Germany) Chao, S., Lotfi, J., Lin, B., Shaw, J., Jhandi, S., Mahoney, M., Singh, B., Nguyen, L., Halawi, H., Geng, L. N. 2022


    Diagnostic programs and second opinion clinics have grown and evolved in the recent years to help patients with rare, puzzling, and complex conditions who often suffer prolonged diagnostic journeys, but there is a paucity of literature on the clinical characteristics of these patients and the efficacy of these diagnostic programs. This study aims to characterize the diagnostic journey, case features, and diagnostic outcomes of patients referred to a team-based second opinion clinic at Stanford.Retrospective chart review was performed for 237 patients evaluated for diagnostic second opinion in the Stanford Consultative Medicine Clinic over a 5 year period. Descriptive case features and diagnostic outcomes were assessed, and correlation between the two was analyzed.Sixty-three percent of our patients were women. 49% of patients had a potential precipitating event within about a month prior to the start of their illness, such as medication change, infection, or medical procedure. A single clear diagnosis was determined in 33% of cases, whereas the remaining cases were assessed to have multifactorial contributors/diagnoses (20%) or remained unclear despite extensive evaluation (47%). Shorter duration of illness, fewer prior specialties seen, and single chief symptom were associated with higher likelihood of achieving a single clear diagnosis.A single-site academic consultative service can offer additional diagnostic insights for about half of all patients evaluated for puzzling conditions. Better understanding of the clinical patterns and patient experiences gained from this study helps inform strategies to shorten their diagnostic odysseys.

    View details for DOI 10.1515/dx-2022-0029

    View details for PubMedID 35596123

  • Training Internal Medicine Residents in Difficult Diagnosis: A Novel Diagnostic Second Opinion Clinic Experience. Journal of medical education and curricular development Testa, S., Joshi, M., Lotfi, J., Lin, B., Artandi, M., Chiang, K. F., Chang, K., Singh, B., Geng, L. N. 2022; 9: 23821205221091036


    Background: In primary care clinics, time constraints and lack of exposure to highly complex cases may limit the breadth and depth of learning for internal medicine residents. To address these issues, we piloted a novel experience for residents to evaluate patients with puzzling symptoms referred by another clinician.Objective: To increase internal medicine residents' exposure to patients with perplexing presentations and foster a team-based approach to solving diagnostically challenging cases.Methods: During the academic year 2020-2021, residents participating in their 2-week primary care "block" rotation were given protected time to evaluate 1-2 patients from the Stanford Consultative Medicine clinic, an internist-led diagnostic second opinion service, and present their patients at the case conference. We assessed the educational value of the program with resident surveys including 5-point Lickert scale and open-ended questions.Results: 21 residents participated in the pilot with a survey response rate of 66.6% (14/21). Both the educational value and overall quality of the experience were rated as 4.8 out of 5 (SD 0.4, range 4-5; 1:"very poor"; 5:"excellent"). Residents learned about new diagnostic tools as well as how to approach complex presentations and diagnostic dilemmas. Residents valued the increased time devoted to patient care, the team-based approach to tackling difficult cases, and the intellectual challenge of these cases. Barriers to implementation include patient case volume, time, and faculty engagement.Conclusions: Evaluation of diagnostically challenging cases in a structured format is a highly valuable experience that offers a framework to enhance outpatient training in internal medicine.

    View details for DOI 10.1177/23821205221091036

    View details for PubMedID 35372696

  • Characterization of autonomic symptom burden in long COVID: A global survey of 2,314 adults. Frontiers in neurology Larsen, N. W., Stiles, L. E., Shaik, R., Schneider, L., Muppidi, S., Tsui, C. T., Geng, L. N., Bonilla, H., Miglis, M. G. 2022; 13: 1012668


    Background: Autonomic dysfunction is a known complication of post-acute sequelae of SARS-CoV-2 (PASC)/long COVID, however prevalence and severity are unknown.Objective: To assess the frequency, severity, and risk factors of autonomic dysfunction in PASC, and to determine whether severity of acute SARS-CoV-2 infection is associated with severity of autonomic dysfunction.Design: Cross-sectional online survey of adults with PASC recruited through long COVID support groups between October 2020 and August 2021.Participants: 2,413 adults ages 18-64 years with PASC including patients who had a confirmed positive test for COVID-19 (test-confirmed) and participants who were diagnosed with COVID-19 based on clinical symptoms alone.Main measures: The main outcome measure was the Composite Autonomic Symptom 31 (COMPASS-31) total score, used to assess global autonomic dysfunction. Test-confirmed hospitalized vs. test-confirmed non-hospitalized participants were compared to determine if the severity of acute SARS-CoV-2 infection was associated with the severity autonomic dysfunction.Key results: Sixty-six percent of PASC patients had a COMPASS-31 score >20, suggestive of moderate to severe autonomic dysfunction. COMPASS-31 scores did not differ between test-confirmed hospitalized and test-confirmed non-hospitalized participants [28.95 (15.62, 46.60) vs. 26.4 (13.75, 42.10); p = 0.06].Conclusions: Evidence of moderate to severe autonomic dysfunction was seen in 66% of PASC patients in our study, independent of hospitalization status, suggesting that autonomic dysfunction is highly prevalent in the PASC population and independent of the severity of acute COVID-19 illness.

    View details for DOI 10.3389/fneur.2022.1012668

    View details for PubMedID 36353127

  • Consultative Medicine - An Emerging Specialty for Patients with Perplexing Conditions. The New England journal of medicine Geng, L. N., Verghese, A., Tilburt, J. C. 1800; 385 (26): 2478-2484

    View details for DOI 10.1056/NEJMms2111017

    View details for PubMedID 34936744

  • Phases of the Diagnostic Journey: A Framework International Archives of Internal Medicine Geng, L. N., Sum-Ping, O., Geng, Y. 2019
  • Genomics in medicine: a novel elective rotation for internal medicine residents. Postgraduate medical journal Geng, L. N., Kohler, J. N., Levonian, P. n., Bernstein, J. A., Ford, J. M., Ahuja, N. n., Witteles, R. n., Hom, J. n., Wheeler, M. n. 2019


    It is well recognised that medical training globally and at all levels lacks sufficient incorporation of genetics and genomics education to keep up with the rapid advances and growing application of genomics to clinical care. However, the best strategy to implement these desired changes into postgraduate medical training and engage learners is still unclear. We developed a novel elective rotation in 'Genomic Medicine and Undiagnosed Diseases' for categorical Internal Medicine Residents to address this educational gap and serve as an adaptable model for training that can be applied broadly across different specialties and at other institutions. Key curriculum goals achieved include increased understanding about genetic testing modalities and tools available for diagnosis and risk analysis, the role of genetics-trained allied health professionals, and indications and limitations of genetic and genomic testing in both rare and common conditions.

    View details for DOI 10.1136/postgradmedj-2018-136355

    View details for PubMedID 31439813

  • Loss of Paneth Cell Autophagy Causes Acute Susceptibility to Toxoplasma gondii-Mediated Inflammation. Cell host & microbe Burger, E., Araujo, A., López-Yglesias, A., Rajala, M. W., Geng, L., Levine, B., Hooper, L. V., Burstein, E., Yarovinsky, F. 2018; 23 (2): 177-190.e4


    The protozoan parasite Toxoplasma gondii triggers severe small intestinal immunopathology characterized by IFN-γ- and intestinal microbiota-mediated inflammation, Paneth cell loss, and bacterial dysbiosis. Paneth cells are a prominent secretory epithelial cell type that resides at the base of intestinal crypts and releases antimicrobial peptides. We demonstrate that the microbiota triggers basal Paneth cell-specific autophagy via induction of IFN-γ, a known trigger of autophagy, to maintain intestinal homeostasis. Deletion of the autophagy protein Atg5 specifically in Paneth cells results in exaggerated intestinal inflammation characterized by complete destruction of the intestinal crypts resembling that seen in pan-epithelial Atg5-deficient mice. Additionally, lack of functional autophagy in Paneth cells within intestinal organoids and T. gondii-infected mice causes increased sensitivity to the proinflammatory cytokine TNF along with increased intestinal permeability, leading to exaggerated microbiota- and IFN-γ-dependent intestinal immunopathology. Thus, Atg5 expression in Paneth cells is essential for tissue protection against cytokine-mediated immunopathology during acute gastrointestinal infection.

    View details for DOI 10.1016/j.chom.2018.01.001

    View details for PubMedID 29358083

    View details for PubMedCentralID PMC6179445

  • COMMD1 is linked to the WASH complex and regulates endosomal trafficking of the copper transporter ATP7A. Molecular biology of the cell Phillips-Krawczak, C. A., Singla, A., Starokadomskyy, P., Deng, Z., Osborne, D. G., Li, H., Dick, C. J., Gomez, T. S., Koenecke, M., Zhang, J. S., Dai, H., Sifuentes-Dominguez, L. F., Geng, L. N., Kaufmann, S. H., Hein, M. Y., Wallis, M., McGaughran, J., Gecz, J., Sluis, B. v., Billadeau, D. D., Burstein, E. 2015; 26 (1): 91-103


    COMMD1 deficiency results in defective copper homeostasis, but the mechanism for this has remained elusive. Here we report that COMMD1 is directly linked to early endosomes through its interaction with a protein complex containing CCDC22, CCDC93, and C16orf62. This COMMD/CCDC22/CCDC93 (CCC) complex interacts with the multisubunit WASH complex, an evolutionarily conserved system, which is required for endosomal deposition of F-actin and cargo trafficking in conjunction with the retromer. Interactions between the WASH complex subunit FAM21, and the carboxyl-terminal ends of CCDC22 and CCDC93 are responsible for CCC complex recruitment to endosomes. We show that depletion of CCC complex components leads to lack of copper-dependent movement of the copper transporter ATP7A from endosomes, resulting in intracellular copper accumulation and modest alterations in copper homeostasis in humans with CCDC22 mutations. This work provides a mechanistic explanation for the role of COMMD1 in copper homeostasis and uncovers additional genes involved in the regulation of copper transporter recycling.

    View details for DOI 10.1091/mbc.E14-06-1073

    View details for PubMedID 25355947

    View details for PubMedCentralID PMC4279232

  • Behcet's disease with major vascular involvement. BMJ case reports Geng, L. N., Conway, D., Barnhart, S., Nowatzky, J. 2013; 2013


    A 40-year-old Chinese man was admitted for haemoptysis and progressive deep vein thrombosis involving the inferior vena cava (IVC) despite anticoagulation. An IVC filter had been placed earlier at an outside hospital. CT angiography revealed two pulmonary artery aneurysms. The patient was found to have a history of oral and genital ulcers, uveitis and erythema nodosum, thus meeting criteria for Behçet's disease. Other causes of the haemoptysis and thrombophilia were excluded. He underwent successful coil embolisation of the pulmonary artery aneurysms and responded well to immunosuppressive therapy with cyclophosphamide and steroids. Anticoagulation was cautiously continued to limit the long-term risk of secondary thrombosis from his IVC filter. The patient remains well 5 months after initiation of immunosuppressive therapy. Making a diagnosis of Behçet's disease in the setting of thrombosis is crucial, as treatment must include immunosuppression, and, thus, fundamentally differs from the management of most other thrombotic disorders.

    View details for DOI 10.1136/bcr-2013-200893

    View details for PubMedID 24214153

    View details for PubMedCentralID PMC3830209

  • DUX4 binding to retroelements creates promoters that are active in FSHD muscle and testis. PLoS genetics Young, J. M., Whiddon, J. L., Yao, Z., Kasinathan, B., Snider, L., Geng, L. N., Balog, J., Tawil, R., van der Maarel, S. M., Tapscott, S. J. 2013; 9 (11): e1003947


    The human double-homeodomain retrogene DUX4 is expressed in the testis and epigenetically repressed in somatic tissues. Facioscapulohumeral muscular dystrophy (FSHD) is caused by mutations that decrease the epigenetic repression of DUX4 in somatic tissues and result in mis-expression of this transcription factor in skeletal muscle. DUX4 binds sites in the human genome that contain a double-homeobox sequence motif, including sites in unique regions of the genome as well as many sites in repetitive elements. Using ChIP-seq and RNA-seq on myoblasts transduced with DUX4 we show that DUX4 binds and activates transcription of mammalian apparent LTR-retrotransposons (MaLRs), endogenous retrovirus (ERVL and ERVK) elements, and pericentromeric satellite HSATII sequences. Some DUX4-activated MaLR and ERV elements create novel promoters for genes, long non-coding RNAs, and antisense transcripts. Many of these novel transcripts are expressed in FSHD muscle cells but not control cells, and thus might contribute to FSHD pathology. For example, HEY1, a repressor of myogenesis, is activated by DUX4 through a MaLR promoter. DUX4-bound motifs, including those in repetitive elements, show evolutionary conservation and some repeat-initiated transcripts are expressed in healthy testis, the normal expression site of DUX4, but more rarely in other somatic tissues. Testis expression patterns are known to have evolved rapidly in mammals, but the mechanisms behind this rapid change have not yet been identified: our results suggest that mobilization of MaLR and ERV elements during mammalian evolution altered germline gene expression patterns through transcriptional activation by DUX4. Our findings demonstrate a role for DUX4 and repetitive elements in mammalian germline evolution and in FSHD muscular dystrophy.

    View details for DOI 10.1371/journal.pgen.1003947

    View details for PubMedID 24278031

    View details for PubMedCentralID PMC3836709

  • Deregulation of the protocadherin gene FAT1 alters muscle shapes: implications for the pathogenesis of facioscapulohumeral dystrophy. PLoS genetics Caruso, N., Herberth, B., Bartoli, M., Puppo, F., Dumonceaux, J., Zimmermann, A., Denadai, S., Lebossé, M., Roche, S., Geng, L., Magdinier, F., Attarian, S., Bernard, R., Maina, F., Levy, N., Helmbacher, F. 2013; 9 (6): e1003550


    Generation of skeletal muscles with forms adapted to their function is essential for normal movement. Muscle shape is patterned by the coordinated polarity of collectively migrating myoblasts. Constitutive inactivation of the protocadherin gene Fat1 uncoupled individual myoblast polarity within chains, altering the shape of selective groups of muscles in the shoulder and face. These shape abnormalities were followed by early onset regionalised muscle defects in adult Fat1-deficient mice. Tissue-specific ablation of Fat1 driven by Pax3-cre reproduced muscle shape defects in limb but not face muscles, indicating a cell-autonomous contribution of Fat1 in migrating muscle precursors. Strikingly, the topography of muscle abnormalities caused by Fat1 loss-of-function resembles that of human patients with facioscapulohumeral dystrophy (FSHD). FAT1 lies near the critical locus involved in causing FSHD, and Fat1 mutant mice also show retinal vasculopathy, mimicking another symptom of FSHD, and showed abnormal inner ear patterning, predictive of deafness, reminiscent of another burden of FSHD. Muscle-specific reduction of FAT1 expression and promoter silencing was observed in foetal FSHD1 cases. CGH array-based studies identified deletion polymorphisms within a putative regulatory enhancer of FAT1, predictive of tissue-specific depletion of FAT1 expression, which preferentially segregate with FSHD. Our study identifies FAT1 as a critical determinant of muscle form, misregulation of which associates with FSHD.

    View details for DOI 10.1371/journal.pgen.1003550

    View details for PubMedID 23785297

    View details for PubMedCentralID PMC3681729

  • Generation of isogenic D4Z4 contracted and noncontracted immortal muscle cell clones from a mosaic patient: a cellular model for FSHD. The American journal of pathology Krom, Y. D., Dumonceaux, J., Mamchaoui, K., den Hamer, B., Mariot, V., Negroni, E., Geng, L. N., Martin, N., Tawil, R., Tapscott, S. J., van Engelen, B. G., Mouly, V., Butler-Browne, G. S., van der Maarel, S. M. 2012; 181 (4): 1387-401


    In most cases facioscapulohumeral muscular dystrophy (FSHD) is caused by contraction of the D4Z4 repeat in the 4q subtelomere. This contraction is associated with local chromatin decondensation and derepression of the DUX4 retrogene. Its complex genetic and epigenetic cause and high clinical variability in disease severity complicate investigations on the pathogenic mechanism underlying FSHD. A validated cellular model bypassing the considerable heterogeneity would facilitate mechanistic and therapeutic studies of FSHD. Taking advantage of the high incidence of somatic mosaicism for D4Z4 repeat contraction in de novo FSHD, we have established a clonal myogenic cell model from a mosaic patient. Individual clones are genetically identical except for the size of the D4Z4 repeat array, being either normal or FSHD sized. These clones retain their myogenic characteristics, and D4Z4 contracted clones differ from the noncontracted clones by the bursts of expression of DUX4 in sporadic nuclei, showing that this burst-like phenomenon is a locus-intrinsic feature. Consequently, downstream effects of DUX4 expression can be observed in D4Z4 contracted clones, like differential expression of DUX4 target genes. We also show their participation to in vivo regeneration with immunodeficient mice, further expanding the potential of these clones for mechanistic and therapeutic studies. These cell lines will facilitate pairwise comparisons to identify FSHD-specific differences and are expected to create new opportunities for high-throughput drug screens.

    View details for DOI 10.1016/j.ajpath.2012.07.007

    View details for PubMedID 22871573

    View details for PubMedCentralID PMC3463638

  • DUX4 activates germline genes, retroelements, and immune mediators: implications for facioscapulohumeral dystrophy. Developmental cell Geng, L. N., Yao, Z., Snider, L., Fong, A. P., Cech, J. N., Young, J. M., van der Maarel, S. M., Ruzzo, W. L., Gentleman, R. C., Tawil, R., Tapscott, S. J. 2012; 22 (1): 38-51


    Facioscapulohumeral dystrophy (FSHD) is one of the most common inherited muscular dystrophies. The causative gene remains controversial and the mechanism of pathophysiology unknown. Here we identify genes associated with germline and early stem cell development as targets of the DUX4 transcription factor, a leading candidate gene for FSHD. The genes regulated by DUX4 are reliably detected in FSHD muscle but not in controls, providing direct support for the model that misexpression of DUX4 is a causal factor for FSHD. Additionally, we show that DUX4 binds and activates LTR elements from a class of MaLR endogenous primate retrotransposons and suppresses the innate immune response to viral infection, at least in part through the activation of DEFB103, a human defensin that can inhibit muscle differentiation. These findings suggest specific mechanisms of FSHD pathology and identify candidate biomarkers for disease diagnosis and progression.

    View details for DOI 10.1016/j.devcel.2011.11.013

    View details for PubMedID 22209328

    View details for PubMedCentralID PMC3264808

  • Immunodetection of human double homeobox 4. Hybridoma (2005) Geng, L. N., Tyler, A. E., Tapscott, S. J. 2011; 30 (2): 125-30


    Double homeobox 4 (DUX4) is a candidate disease gene for facioscapulohumeral dystrophy (FSHD), one of the most common muscular dystrophies characterized by progressive skeletal muscle degeneration. Despite great strides in understanding precise genetics of FSHD, the molecular pathophysiology of the disease remains unclear. One of the major limitations has been the availability of appropriate molecular tools to study DUX4 protein. In the present study, we report the development of five new monoclonal antibodies targeted against the N- and C-termini of human DUX4, and characterize their reactivity using Western blot and immunofluorescence staining. Additionally, we show that expression of the canonical full coding DUX4 induces cell death in human primary muscle cells, whereas the expression of a shorter splice form of DUX4 results in no such toxicity. Immunostaining with these new antibodies reveals a differential effect of two DUX4 isoforms on human muscle cells. These antibodies will provide an excellent tool for investigating the role of DUX4 in FSHD pathogenesis.

    View details for DOI 10.1089/hyb.2010.0094

    View details for PubMedID 21529284

    View details for PubMedCentralID PMC3132944

  • Facioscapulohumeral dystrophy: incomplete suppression of a retrotransposed gene. PLoS genetics Snider, L., Geng, L. N., Lemmers, R. J., Kyba, M., Ware, C. B., Nelson, A. M., Tawil, R., Filippova, G. N., van der Maarel, S. M., Tapscott, S. J., Miller, D. G. 2010; 6 (10): e1001181


    Each unit of the D4Z4 macrosatellite repeat contains a retrotransposed gene encoding the DUX4 double-homeobox transcription factor. Facioscapulohumeral dystrophy (FSHD) is caused by deletion of a subset of the D4Z4 units in the subtelomeric region of chromosome 4. Although it has been reported that the deletion of D4Z4 units induces the pathological expression of DUX4 mRNA, the association of DUX4 mRNA expression with FSHD has not been rigorously investigated, nor has any human tissue been identified that normally expresses DUX4 mRNA or protein. We show that FSHD muscle expresses a different splice form of DUX4 mRNA compared to control muscle. Control muscle produces low amounts of a splice form of DUX4 encoding only the amino-terminal portion of DUX4. FSHD muscle produces low amounts of a DUX4 mRNA that encodes the full-length DUX4 protein. The low abundance of full-length DUX4 mRNA in FSHD muscle cells represents a small subset of nuclei producing a relatively high abundance of DUX4 mRNA and protein. In contrast to control skeletal muscle and most other somatic tissues, full-length DUX4 transcript and protein is expressed at relatively abundant levels in human testis, most likely in the germ-line cells. Induced pluripotent (iPS) cells also express full-length DUX4 and differentiation of control iPS cells to embryoid bodies suppresses expression of full-length DUX4, whereas expression of full-length DUX4 persists in differentiated FSHD iPS cells. Together, these findings indicate that full-length DUX4 is normally expressed at specific developmental stages and is suppressed in most somatic tissues. The contraction of the D4Z4 repeat in FSHD results in a less efficient suppression of the full-length DUX4 mRNA in skeletal muscle cells. Therefore, FSHD represents the first human disease to be associated with the incomplete developmental silencing of a retrogene array normally expressed early in development.

    View details for DOI 10.1371/journal.pgen.1001181

    View details for PubMedID 21060811

    View details for PubMedCentralID PMC2965761

  • Variability in the Androgen Response of Prostate Epithelium to 5 alpha-Reductase Inhibition: Implications for Prostate Cancer Chemoprevention CANCER RESEARCH Mostaghel, E. A., Geng, L., Holcomb, I., Coleman, I. M., Lucas, J., True, L. D., Nelson, P. S. 2010; 70 (4): 1286-1295


    Inhibitors of 5alpha-reductase (SRD5A) that lower intraprostatic levels of dihydrotestosterone (DHT) reduce the overall incidence of prostate cancer (PCa), but there is significant variation in chemopreventive activity between individual men. In seeking molecular alterations that might underlie this variation, we compared gene expression patterns in patients with localized PCa who were randomized to prostatectomy alone versus treatment with two different doses of the SRD5A inhibitor dutasteride. Prostatic levels of DHT were decreased by >90% in both dutasteride-treated patient groups versus the untreated patient group. Despite significant and uniform suppression of tissue DHT, unsupervised clustering based on prostatic gene expression did not discriminate these groups. However, subjects could be resolved into distinct cohorts characterized by high or low expression of genes regulated by the androgen receptor (AR), based solely on AR transcript expression. The higher-dose dutasteride treatment group was found to include significantly fewer cancers with TMPRSS2-ERG genetic fusions. Dutasteride treatment was associated with highly variable alterations in benign epithelial gene expression. Segregating subjects based on expression of AR and androgen-regulated genes revealed that patients are differentially sensitive to SRD5A inhibition. Our findings suggest that AR levels may predict the chemopreventive efficacy of SRD5A inhibitors.

    View details for DOI 10.1158/0008-5472.CAN-09-2509

    View details for Web of Science ID 000278485700003

    View details for PubMedID 20124490

    View details for PubMedCentralID PMC2822890

  • DNA methylation of developmental genes in pediatric medulloblastomas identified by denaturation analysis of methylation differences. Proceedings of the National Academy of Sciences of the United States of America Diede, S. J., Guenthoer, J., Geng, L. N., Mahoney, S. E., Marotta, M., Olson, J. M., Tanaka, H., Tapscott, S. J. 2010; 107 (1): 234-9


    DNA methylation might have a significant role in preventing normal differentiation in pediatric cancers. We used a genomewide method for detecting regions of CpG methylation on the basis of the increased melting temperature of methylated DNA, termed denaturation analysis of methylation differences (DAMD). Using the DAMD assay, we find common regions of cancer-specific methylation changes in primary medulloblastomas in critical developmental regulatory pathways, including Sonic hedgehog (Shh), Wingless (Wnt), retinoic acid receptor (RAR), and bone morphogenetic protein (BMP). One of the commonly methylated loci is the PTCH1-1C promoter, a negative regulator of the Shh pathway that is methylated in both primary patient samples and human medulloblastoma cell lines. Treatment with the DNA methyltransferase inhibitor 5-aza-2'-deoxycytidine (5-aza-dC) increases the expression of PTCH1 and other methylated loci. Whereas genetic mutations in PTCH1 have previously been shown to lead to medulloblastoma, our study indicates that epigenetic silencing of PTCH1, and other critical developmental loci, by DNA methylation is a fundamental process of pediatric medulloblastoma formation. This finding warrants strong consideration for DNA demethylating agents in future clinical trials for children with this disease.

    View details for DOI 10.1073/pnas.0907606106

    View details for PubMedID 19966297

    View details for PubMedCentralID PMC2806770

  • RNA transcripts, miRNA-sized fragments and proteins produced from D4Z4 units: new candidates for the pathophysiology of facioscapulohumeral dystrophy. Human molecular genetics Snider, L., Asawachaicharn, A., Tyler, A. E., Geng, L. N., Petek, L. M., Maves, L., Miller, D. G., Lemmers, R. J., Winokur, S. T., Tawil, R., van der Maarel, S. M., Filippova, G. N., Tapscott, S. J. 2009; 18 (13): 2414-30


    Deletion of a subset of the D4Z4 macrosatellite repeats in the subtelomeric region of chromosome 4q causes facioscapulohumeral muscular dystrophy (FSHD) when occurring on a specific haplotype of 4qter (4qA161). Several genes have been examined as candidates for causing FSHD, including the DUX4 homeobox gene in the D4Z4 repeat, but none have been definitively shown to cause the disease, nor has the full extent of transcripts from the D4Z4 region been carefully characterized. Using strand-specific RT-PCR, we have identified several sense and antisense transcripts originating from the 4q D4Z4 units in wild-type and FSHD muscle cells. Consistent with prior reports, we find that the DUX4 transcript from the last (most telomeric) D4Z4 unit is polyadenylated and has two introns in its 3-prime untranslated region. In addition, we show that this transcript generates (i) small si/miRNA-sized fragments, (ii) uncapped, polyadenylated 3-prime fragments that encode the conserved C-terminal portion of DUX4 and (iii) capped and polyadenylated mRNAs that contain the double-homeobox domain of DUX4 but splice-out the C-terminal portion. Transfection studies demonstrate that translation initiation at an internal methionine can produce the C-terminal polypeptide and developmental studies show that this peptide inhibits myogenesis at a step between MyoD transcription and the activation of MyoD target genes. Together, we have identified new sense and anti-sense RNA transcripts, novel mRNAs and mi/siRNA-sized RNA fragments generated from the D4Z4 units that are new candidates for the pathophysiology of FSHD.

    View details for DOI 10.1093/hmg/ddp180

    View details for PubMedID 19359275

    View details for PubMedCentralID PMC2694690

  • Type 1 diabetes promotes disruption of advanced atherosclerotic lesions in LDL receptor-deficient mice. Proceedings of the National Academy of Sciences of the United States of America Johansson, F., Kramer, F., Barnhart, S., Kanter, J. E., Vaisar, T., Merrill, R. D., Geng, L., Oka, K., Chan, L., Chait, A., Heinecke, J. W., Bornfeldt, K. E. 2008; 105 (6): 2082-7


    Cardiovascular disease, largely because of disruption of atherosclerotic lesions, accounts for the majority of deaths in people with type 1 diabetes. Recent mouse models have provided insights into the accelerated atherosclerotic lesion initiation in diabetes, but it is unknown whether diabetes directly worsens more clinically relevant advanced lesions. We therefore used an LDL receptor-deficient mouse model, in which type 1 diabetes can be induced at will, to investigate the effects of diabetes on preexisting lesions. Advanced lesions were induced by feeding mice a high-fat diet for 16 weeks before induction of diabetes. Diabetes, independently of lesion size, increased intraplaque hemorrhage and plaque disruption in the brachiocephalic artery of mice fed low-fat or high-fat diets for an additional 14 weeks. Hyperglycemia was not sufficient to induce plaque disruption. Furthermore, diabetes resulted in increased accumulation of monocytic cells positive for S100A9, a proinflammatory biomarker for cardiovascular events, and for a macrophage marker protein, without increasing lesion macrophage content. S100A9 immunoreactivity correlated with intraplaque hemorrhage. Aggressive lowering primarily of triglyceride-rich lipoproteins prevented both plaque disruption and the increased S100A9 in diabetic atherosclerotic lesions. Conversely, oleate promoted macrophage differentiation into an S100A9-positive population in vitro, thereby mimicking the effects of diabetes. Thus, diabetes increases plaque disruption, independently of effects on plaque initiation, through a mechanism that requires triglyceride-rich lipoproteins and is associated with an increased accumulation of S100A9-positive monocytic cells. These findings indicate an important link between diabetes, plaque disruption, and the innate immune system.

    View details for DOI 10.1073/pnas.0709958105

    View details for PubMedID 18252823

    View details for PubMedCentralID PMC2538884

  • Structure and enzymatic properties of a chimeric bacteriophage RB69 DNA polymerase and single-stranded DNA binding protein with increased processivity. Proteins Sun, S., Geng, L., Shamoo, Y. 2006; 65 (1): 231-8


    In vivo, replicative DNA polymerases are made more processive by their interactions with accessory proteins at the replication fork. Single-stranded DNA binding protein (SSB) is an essential protein that binds tightly and cooperatively to single-stranded DNA during replication to remove adventitious secondary structures and protect the exposed DNA from endogenous nucleases. Using information from high resolution structures and biochemical data, we have engineered a functional chimeric enzyme of the bacteriophage RB69 DNA polymerase and SSB with substantially increased processivity. Fusion of RB69 DNA polymerase with its cognate SSB via a short six amino acid linker increases affinity for primer-template DNA by sixfold and subsequently increases processivity by sevenfold while maintaining fidelity. The crystal structure of this fusion protein was solved by a combination of multiwavelength anomalous diffraction and molecular replacement to 3.2 A resolution and shows that RB69 SSB is positioned proximal to the N-terminal domain of RB69 DNA polymerase near the template strand channel. The structural and biochemical data suggest that SSB interactions with DNA polymerase are transient and flexible, consistent with models of a dynamic replisome during elongation.

    View details for DOI 10.1002/prot.21088

    View details for PubMedID 16881051

  • Structural and functional characterization of the first intracellular loop of human thromboxane A(2) receptor ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS Geng, L., Wu, J. X., So, S. P., Huang, G. X., Ruan, K. H. 2004; 423 (2): 253-265


    The conformation of a constrained peptide mimicking the putative first intracellular domain (iLP1) of thromboxane A(2) receptor (TP) was determined by (1)H 2D NMR spectroscopy. Through completed assignments of TOCSY, DQF-COSY, and NOESY spectra, a NMR structure of the peptide showed a beta-turn in residues 56-59 and a short helical structure in the residues 63-66. It suggests that residues 63-66 may be part of the second transmembrane domain (TM), and that Arg60, in an exposed position on the outer surface of the loop, may be involved in signaling through charge contact with Gq protein. The sequence alignment of Lys residue in the same position of other prostanoid receptors mediates different G protein couplings, suggesting that the chemical properties of Arg and Lys may also affect the receptor signaling activity. These hypotheses were supported by mutagenesis studies, in which the mutant of Arg60Leu completely lost activity in increasing intracellular calcium level through Gq coupling, and the mutant of Arg60Lys retained only about 35% signaling activity. The difference between the side chain functions of Lys and Arg in effecting the signaling was discussed.

    View details for DOI 10.1016/

    View details for Web of Science ID 000220164100003

    View details for PubMedID 15001390