Jeff Nirschl

All Publications

• A pathologist-AI collaboration framework for enhancing diagnostic accuracies and efficiencies. Nature biomedical engineering Huang, Z., Yang, E., Shen, J., Gratzinger, D., Eyerer, F., Liang, B., Nirschl, J., Bingham, D., Dussaq, A. M., Kunder, C., Rojansky, R., Gilbert, A., Chang-Graham, A. L., Howitt, B. E., Liu, Y., Ryan, E. E., Tenney, T. B., Zhang, X., Folkins, A., Fox, E. J., Montine, K. S., Montine, T. J., Zou, J. 2024

  Abstract

  In pathology, the deployment of artificial intelligence (AI) in clinical settings is constrained by limitations in data collection and in model transparency and interpretability. Here we describe a digital pathology framework, nuclei.io, that incorporates active learning and human-in-the-loop real-time feedback for the rapid creation of diverse datasets and models. We validate the effectiveness of the framework via two crossover user studies that leveraged collaboration between the AI and the pathologist, including the identification of plasma cells in endometrial biopsies and the detection of colorectal cancer metastasis in lymph nodes. In both studies, nuclei.io yielded considerable diagnostic performance improvements. Collaboration between clinicians and AI will aid digital pathology by enhancing accuracies and efficiencies.

  View details for DOI 10.1038/s41551-024-01223-5

  View details for PubMedID 38898173

  View details for PubMedCentralID 6345440

• The fasciola cinereum of the hippocampal tail as an interventional target in epilepsy. Nature medicine Jamiolkowski, R. M., Nguyen, Q. A., Farrell, J. S., McGinn, R. J., Hartmann, D. A., Nirschl, J. J., Sanchez, M. I., Buch, V. P., Soltesz, I. 2024

  Abstract

  Targeted tissue ablation involving the anterior hippocampus is the standard of care for patients with drug-resistant mesial temporal lobe epilepsy. However, a substantial proportion continues to suffer from seizures even after surgery. We identified the fasciola cinereum (FC) neurons of the posterior hippocampal tail as an important seizure node in both mice and humans with epilepsy. Genetically defined FC neurons were highly active during spontaneous seizures in epileptic mice, and closed-loop optogenetic inhibition of these neurons potently reduced seizure duration. Furthermore, we specifically targeted and found the prominent involvement of FC during seizures in a cohort of six patients with epilepsy. In particular, targeted lesioning of the FC in a patient reduced the seizure burden present after ablation of anterior mesial temporal structures. Thus, the FC may be a promising interventional target in epilepsy.

  View details for DOI 10.1038/s41591-024-02924-9

  View details for PubMedID 38632391

  View details for PubMedCentralID 3712982

• CDC42BPA::BRAF represents a novel fusion in desmoplastic infantile ganglioglioma/desmoplastic infantile astrocytoma. Neuro-oncology advances Barros Guinle, M. I., Nirschl, J. J., Xing, Y. L., Nettnin, E. A., Arana, S., Feng, Z. P., Nasajpour, E., Pronina, A., Garcia, C. A., Grant, G. A., Vogel, H., Yeom, K. W., Prolo, L. M., Petritsch, C. K. 2024; 6 (1): vdae050

  View details for DOI 10.1093/noajnl/vdae050

  View details for PubMedID 38741773

  View details for PubMedCentralID PMC11089409

• Uncovering microstructural architecture from histology. bioRxiv : the preprint server for biology Georgiadis, M., Auf der Heiden, F., Abbasi, H., Ettema, L., Nirschl, J., Taghavi, H. M., Wakatsuki, M., Liu, A., Ho, W. H., Carlson, M., Doukas, M., Koppes, S. A., Keereweer, S., Sobel, R. A., Setsompop, K., Liao, C., Amunts, K., Axer, M., Zeineh, M., Menzel, M. 2024

  Abstract

  Microstructural tissue organization underlies the complex connectivity of the brain and controls properties of connective, muscle, and epithelial tissue. However, discerning microstructural architecture with high resolution for large fields of view remains prohibitive. We address this challenge with computational scattered light imaging (ComSLI), which exploits the anisotropic light scattering of aligned structures. Using a rotating lightsource and a high-resolution camera, ComSLI determines fiber architecture with micrometer resolution from histological sections across preparation and staining protocols. We show complex fiber architecture in brain and non-brain sections, including histological paraffin-embedded sections with various stains, and demonstrate its applicability on animal and human tissue, including disease cases with altered microstructure. ComSLI opens new avenues for investigating fiber architecture in new and archived sections across organisms, tissues, and diseases.One Sentence Summary: We uncover microstructural architecture of new or archived human and animal histological sections in health and disease.

  View details for DOI 10.1101/2024.03.26.586745

  View details for PubMedID 38585744

• Orientation-invariant autoencoders learn robust representations for shape profiling of cells and organelles. Nature communications Burgess, J., Nirschl, J. J., Zanellati, M. C., Lozano, A., Cohen, S., Yeung-Levy, S. 2024; 15 (1): 1022

  Abstract

  Cell and organelle shape are driven by diverse genetic and environmental factors and thus accurate quantification of cellular morphology is essential to experimental cell biology. Autoencoders are a popular tool for unsupervised biological image analysis because they learn a low-dimensional representation that maps images to feature vectors to generate a semantically meaningful embedding space of morphological variation. The learned feature vectors can also be used for clustering, dimensionality reduction, outlier detection, and supervised learning problems. Shape properties do not change with orientation, and thus we argue that representation learning methods should encode this orientation invariance. We show that conventional autoencoders are sensitive to orientation, which can lead to suboptimal performance on downstream tasks. To address this, we develop O2-variational autoencoder (O2-VAE), an unsupervised method that learns robust, orientation-invariant representations. We use O2-VAE to discover morphology subgroups in segmented cells and mitochondria, detect outlier cells, and rapidly characterise cellular shape and texture in large datasets, including in a newly generated synthetic benchmark.

  View details for DOI 10.1038/s41467-024-45362-4

  View details for PubMedID 38310122

  View details for PubMedCentralID 9119736

• MORPHOLOGY, MOLECULAR FEATURES, AND CLINICAL BEHAVIOR OF METHYLATION CLASS PLEOMORPHIC XANTHOASTROCYTOMA Dampier, C., Shah, N., Galbraith, K., Rajan, S., Vaubel, R., Ketchum, C., Costa, F., Ferman, S., Neto, O., Wadhwani, N., Lee, H., Mao, Q., Robinson, L., Marshall, M., Baker, T., Cathcart, S., Alexandrescu, S., Fernandes, I., Cotter, J., Gilani, A., McCord, M., Thomas, D., Thomas-Ogunniyi, J., Pytel, P., Lopes, B., Conway, K., Gregory, J., Andreiuolo, F., Nirschl, J., Abdullaev, Z., Quezado, M., Giannini, C., Snuderl, M., Aldape, K. OXFORD UNIV PRESS INC. 2023

  View details for Web of Science ID 001115245400664

• CLINICOPATHOLOGIC CHARACTERIZATION OF DIFFUSE PEDIATRIC-TYPE HIGH-GRADE GLIOMA, H3-WILDTYPE AND IDH-WILDTYPE: AN AGGRESSIVE AND GENOMICALLY COMPLEX GROUP OF TUMORS AFFECTING CHILDREN AND ADULTS Wu, Z., Turakulov, R., Chung, H., Dazelle, K., Abdullaev, Z., Costa, F., Neto, O., Wadhwani, N., Mao, Q., Robinson, L., Marshall, M., Frosch, M., Cathcart, S., Alexandrescu, S., Fernandes, I., McCord, M., Horbinski, C., Thomas, D., Pytel, P., Conway, K., Gregory, J., Nirschl, J., Vogel, H., Chandra, K., Gokden, M., Lucas, C., Wilson, Y., Han, P., Goodman, A., Dahiya, S., Vortmeyer, A., Quezado, M., Aldape, K., Cimino, P. OXFORD UNIV PRESS INC. 2023

  View details for Web of Science ID 001115245400665

• CDC42BPA::BRAF REPRESENTS A NOVEL FUSION IN DESMOPLASTIC INFANTILE GLIOMA Guinle, M., Nettnin, E. A., Nasajpour, E., Nirschl, J., Garcia, C. A., Vogel, H., Yeom, K., Prolo, L., Petritsch, C. OXFORD UNIV PRESS INC. 2023

  View details for Web of Science ID 001115245400685

• TDP43 pathology in chronic traumatic encephalopathy retinas. Acta neuropathologica communications Phansalkar, R., Goodwill, V. S., Nirschl, J. J., De Lillo, C., Choi, J., Spurlock, E., Coughlin, D. G., Pizzo, D., Sigurdson, C. J., Hiniker, A., Alvarez, V. E., Mckee, A. C., Lin, J. H. 2023; 11 (1): 152

  Abstract

  Chronic traumatic encephalopathy (CTE) is a neurodegenerative disease associated with repetitive head trauma. Brain pathology in CTE is characterized by neuronal loss, gliosis, and a distinctive pattern of neuronal accumulation of hyper-phosphorylated tau (p-tau) and phospho-TDP43 (p-TDP43). Visual anomalies have been reported by patients with CTE, but the ocular pathology underlying these symptoms is unknown. We evaluated retinal pathology in post-mortem eyes collected from 8 contact sport athletes with brain autopsy-confirmed stage IV CTE and compared their findings to retinas from 8 control patients without CTE and with no known history of head injury. Pupil-optic nerve cross sections were prepared and stained with hematoxylin and eosin (H&E), p-tau, p-TDP43, and total TDP43 by immunohistochemistry. No significant retinal degeneration was observed in CTE eyes compared to control eyes by H&E. Strong cytoplasmic p-TDP43 and total TDP43 staining was found in 6/8 CTE eyes in a subset of inner nuclear layer interneurons (INL) of the retina, while only 1/8 control eyes showed similar p-TDP43 pathology. The morphology and location of these inner nuclear layer interneurons were most compatible with retinal horizontal cells, although other retinal cell types present in INL could not be ruled out. No p-tau pathology was observed in CTE or control retinas. These findings identify novel retinal TDP43 pathology in CTE retinas and support further investigation into the role of p-TDP43 in producing visual deficits in patients with CTE.

  View details for DOI 10.1186/s40478-023-01650-6

  View details for PubMedID 37737191

  View details for PubMedCentralID 7914059

• Rapid Deployment of Whole Slide Imaging for Primary Diagnosis in Surgical Pathology at Stanford Medicine Responding to Challenges of the COVID-19 Pandemic ARCHIVES OF PATHOLOGY & LABORATORY MEDICINE Rojansky, R., Jhun, I., Dussaq, A. M., Chirieleison, S. M., Nirschl, J. J., Born, D., Fralick, J., Hetherington, W., Kerr, A. M., Lavezo, J., Lawrence, D. B., Lummus, S., Macasaet, R., Montine, T. J., Ryan, E., Shen, J., Shoemaker, J., Tan, B., Vogel, H., Waraich, P., Yang, E., Young, A., Folkins, A. 2023; 147 (3): 359-367

  View details for DOI 10.5858/arpa.2021-0438-OA)

  View details for Web of Science ID 000958483400012

• TDP-43 Proteinopathy in Retina of Chronic Traumatic Encephalopathy Patients Phansalkar, R., Nirschl, J., Goodwill, V., De Lillo, C., Choi, J., Coughlin, D., Pizzo, D., Sigurdson, C., Hiniker, A., Alvarez, V., Mckee, A., Lin, J. ELSEVIER SCIENCE INC. 2023: S1475

  View details for Web of Science ID 000990969803172

• Mitochondrial dysfunction in human hypertrophic cardiomyopathy is linked to cardiomyocyte architecture disruption and corrected by improving NADH-driven mitochondrial respiration. European heart journal Nollet, E. E., Duursma, I., Rozenbaum, A., Eggelbusch, M., Wust, R. C., Schoonvelde, S. A., Michels, M., Jansen, M., van der Wel, N. N., Bedi, K. C., Margulies, K. B., Nirschl, J., Kuster, D. W., van der Velden, J. 2023

  Abstract

  AIMS: Genetic hypertrophic cardiomyopathy (HCM) is caused by mutations in sarcomere protein-encoding genes (i.e. genotype-positive HCM). In an increasing number of patients, HCM occurs in the absence of a mutation (i.e. genotype-negative HCM). Mitochondrial dysfunction is thought to be a key driver of pathological remodelling in HCM. Reports of mitochondrial respiratory function and specific disease-modifying treatment options in patients with HCM are scarce.METHODS AND RESULTS: Respirometry was performed on septal myectomy tissue from patients with HCM (n = 59) to evaluate oxidative phosphorylation and fatty acid oxidation. Mitochondrial dysfunction was most notably reflected by impaired NADH-linked respiration. In genotype-negative patients, but not genotype-positive patients, NADH-linked respiration was markedly depressed in patients with an indexed septal thickness ≥10 compared with <10. Mitochondrial dysfunction was not explained by reduced abundance or fragmentation of mitochondria, as evaluated by transmission electron microscopy. Rather, improper organization of mitochondria relative to myofibrils (expressed as a percentage of disorganized mitochondria) was strongly associated with mitochondrial dysfunction. Pre-incubation with the cardiolipin-stabilizing drug elamipretide and raising mitochondrial NAD+ levels both boosted NADH-linked respiration.CONCLUSION: Mitochondrial dysfunction is explained by cardiomyocyte architecture disruption and is linked to septal hypertrophy in genotype-negative HCM. Despite severe myocardial remodelling mitochondria were responsive to treatments aimed at restoring respiratory function, eliciting the mitochondria as a drug target to prevent and ameliorate cardiac disease in HCM. Mitochondria-targeting therapy may particularly benefit genotype-negative patients with HCM, given the tight link between mitochondrial impairment and septal thickening in this subpopulation.

  View details for DOI 10.1093/eurheartj/ehad028

  View details for PubMedID 36734059

• "Disentangling" mitochondrial dysfunction in hypertrophic cardiomyopathy Nollet, E., Burdzina, A., Wust, R. I., Michels, M., Asselbergs, F. W., van der Wel, N., Bedi, K., Margulies, K., Nirschl, J., Kuster, D., van der Velden, J. ELSEVIER SCI LTD. 2022: S113-S115

  View details for DOI 10.1016/j.yjmcc.2022.08.226

  View details for Web of Science ID 000907054400222

• Expanded analysis of high-grade astrocytoma with piloid features identifies an epigenetically and clinically distinct subtype associated with neurofibromatosis type 1. Acta neuropathologica Cimino, P. J., Ketchum, C., Turakulov, R., Singh, O., Abdullaev, Z., Giannini, C., Pytel, P., Lopez, G. Y., Colman, H., Nasrallah, M. P., Santi, M., Fernandes, I. L., Nirschl, J., Dahiya, S., Neill, S., Solomon, D., Perez, E., Capper, D., Mani, H., Caccamo, D., Ball, M., Badruddoja, M., Chkheidze, R., Camelo-Piragua, S., Fullmer, J., Alexandrescu, S., Yeaney, G., Eberhart, C., Martinez-Lage, M., Chen, J., Zach, L., Kleinschmidt-DeMasters, B. K., Hefti, M., Lopes, M., Nuechterlein, N., Horbinski, C., Rodriguez, F. J., Quezado, M., Pratt, D., Aldape, K. 2022

  Abstract

  High-grade astrocytoma with piloid features (HGAP) is a recently recognized glioma type whose classification is dependent on its global epigenetic signature. HGAP is characterized by alterations in the mitogen-activated protein kinase (MAPK) pathway, often co-occurring with CDKN2A/B homozygous deletion and/or ATRX mutation. Experience with HGAP is limited and to better understand this tumor type, we evaluated an expanded cohort of patients (n=144) with these tumors, as defined by DNA methylation array testing, with a subset additionally evaluated by next-generation sequencing (NGS). Among evaluable cases, we confirmed the high prevalence CDKN2A/B homozygous deletion, and/or ATRX mutations/loss in this tumor type, along with a subset showing NF1 alterations. Five of 93 (5.4%) cases sequenced harbored TP53 mutations and RNA fusion analysis identified a single tumor containing an NTRK2 gene fusion, neither of which have been previously reported in HGAP. Clustering analysis revealed the presence of three distinct HGAP subtypes (or groups=g) based on whole-genome DNA methylation patterns, which we provisionally designated as gNF1 (n=18), g1 (n=72), and g2 (n=54) (median ages 43.5years, 47years, and 32years, respectively). Subtype gNF1 is notable for enrichment with patients with Neurofibromatosis Type 1 (33.3%, p=0.0008), confinement to the posterior fossa, hypermethylation in the NF1 enhancer region, a trend towards decreased progression-free survival (p=0.0579), RNA processing pathway dysregulation, and elevated non-neoplastic glia and neuron cell content (p<0.0001 and p<0.0001, respectively). Overall, our expanded cohort broadens the genetic, epigenetic, and clinical phenotype of HGAP and provides evidence for distinct epigenetic subtypes in this tumor type.

  View details for DOI 10.1007/s00401-022-02513-5

  View details for PubMedID 36271929

• A rare neuromyelitis optica mimic: Primary CNS histiocytic sarcoma. Multiple sclerosis (Houndmills, Basingstoke, England) Rogawski, D. S., Nirschl, J. J., McDonald, J., Nie, E., Schwartz, N. U., Vogel, H., Scott, B. J., Gold, C. A., Kipp, L. B. 2022; 28 (10): 1651-1654

  Abstract

  Primary central nervous system (CNS) histiocytic sarcoma is a rare hematolymphoid malignancy with features of mature histiocytes and carries a poor prognosis. We describe a unique case in which a 50-year-old woman presented with recurrent acute brainstem syndrome, area postrema syndrome, and myelitis with corresponding magnetic resonance imaging (MRI) lesions meeting diagnostic criteria for seronegative neuromyelitis optica spectrum disorder (NMOSD). Despite initial improvement with steroids and plasma exchange, she experienced recurrent symptoms over 10months referable to new and persistently enhancing lesions. At autopsy, neuropathology revealed a diffusely infiltrative primary CNS histiocytic sarcoma. This case represents a rare clinicoradiologic mimic of NMOSD, underscoring the importance of evaluation for infiltrative diseases in cases of atypical seronegative NMOSD.

  View details for DOI 10.1177/13524585221097564

  View details for PubMedID 35876468

• Rapid Deployment of Whole Slide Imaging for Primary Diagnosis in Surgical Pathology at Stanford Medicine. Archives of pathology & laboratory medicine Rojansky, R., Jhun, I., Dussaq, A. M., Chirieleison, S. M., Nirschl, J. J., Born, D., Fralick, J., Hetherington, W., Kerr, A. M., Lavezo, J., Lawrence, D. B., Lummus, S., Macasaet, R., Montine, T. J., Ryan, E., Shen, J., Shoemaker, J., Tan, B., Vogel, H., Waraich, P. S., Yang, E., Young, A., Folkins, A. 2022

  Abstract

  Stanford Pathology began stepwise subspecialty implementation of whole slide imaging (WSI) in 2018 soon after the first US Food and Drug Administration approval. In 2020, during the COVID-19 pandemic, the Centers for Medicare & Medicaid Services waived the requirement for pathologists to perform diagnostic tests in Clinical Laboratory Improvement Amendments (CLIA)-licensed facilities. This encouraged rapid implementation of WSI across all surgical pathology subspecialties.To present our experience with validation and implementation of WSI at a large academic medical center encompassing a caseload of more than 50 000 cases per year.Validation was performed independently for 3 subspecialty services with a diagnostic concordance threshold above 95%. Analysis of user experience, staffing, infrastructure, and information technology was performed after department-wide expansion.Diagnostic concordance was achieved in 96% of neuropathology cases, 100% of gynecologic pathology cases, and 98% of immunohistochemistry cases. After full implementation, 8 high-capacity scanners were operational, with whole slide images generated on greater than 2000 slides per weekday, accounting for approximately 80% of histologic slides at Stanford Medicine. Multiple modifications in workflow and information technology were needed to improve performance. Within months of full implementation, most attending pathologists and trainees had adopted WSI for primary diagnosis.WSI across all surgical subspecialities is achievable at scale at an academic medical center; however, adoption required flexibility to adjust workflows and develop tailored solutions. WSI at scale supported the health and safety of medical staff while facilitating high-quality patient care and education during COVID-19 restrictions.

  View details for DOI 10.5858/arpa.2021-0438-OA

  View details for PubMedID 35802938

• Primary central nervous system histiocytic sarcoma presenting as neuromyelitis optica Nirschl, J., Rogawski, D., McDonald, J., Nie, E., Schwartz, N., Scott, B., Gratzinger, D., Gold, C., Kipp, L., Vogel, H. OXFORD UNIV PRESS INC. 2022: 491

  View details for Web of Science ID 000798368400189

• Biological data annotation via a human-augmenting AI-based labeling system. NPJ digital medicine van der Wal, D., Jhun, I., Laklouk, I., Nirschl, J., Richer, L., Rojansky, R., Theparee, T., Wheeler, J., Sander, J., Feng, F., Mohamad, O., Savarese, S., Socher, R., Esteva, A. 2021; 4 (1): 145

  Abstract

  Biology has become a prime area for the deployment of deep learning and artificial intelligence (AI), enabled largely by the massive data sets that the field can generate. Key to most AI tasks is the availability of a sufficiently large, labeled data set with which to train AI models. In the context of microscopy, it is easy to generate image data sets containing millions of cells and structures. However, it is challenging to obtain large-scale high-quality annotations for AI models. Here, we present HALS (Human-Augmenting Labeling System), a human-in-the-loop data labeling AI, which begins uninitialized and learns annotations from a human, in real-time. Using a multi-part AI composed of three deep learning models, HALS learns from just a few examples and immediately decreases the workload of the annotator, while increasing the quality of their annotations. Using a highly repetitive use-case-annotating cell types-and running experiments with seven pathologists-experts at the microscopic analysis of biological specimens-we demonstrate a manual work reduction of 90.60%, and an average data-quality boost of 4.34%, measured across four use-cases and two tissue stain types.

  View details for DOI 10.1038/s41746-021-00520-6

  View details for PubMedID 34620993

• Black and Blue: Eyes and Dyes Sobel, R., Nirschl, J., Hammer, P., Sanchez, R., Pershing, S., Louie, C., Lin, J. OXFORD UNIV PRESS INC. 2021: 579

  View details for Web of Science ID 000671021700089

• Creatine transport and pathological changes in creatine transporter deficient mice. Journal of inherited metabolic disease Wawro, A. M., Gajera, C. R., Baker, S. A., Nirschl, J. J., Vogel, H. n., Montine, T. J. 2021

  Abstract

  The severe impact on brain function and lack of effective therapy for patients with creatine (Cr) transporter deficiency motivated the generation of three ubiquitous Slc6a8 deficient mice (-/y). While each mouse knock-out line has similar behavioral effects at 2 to 3 months of age, other features critical to the efficient use of these mice in drug discovery are unclear or lacking: the concentration of Cr in brain and heart differ widely between mouse lines, there are limited data on histopathologic changes, and no data on Cr uptake. Here, we determined survival, measured endogenous Cr and uptake of its deuterium-labeled analogue Cr-d3 using a liquid chromatography coupled with tandem mass spectrometry assay, and performed comprehensive histopathologic examination on the Slc6a8-/y mouse developed by Skelton et. al. Our results show that Slc6a8-/y mice have widely varying organ-specific uptake of Cr-d3, significantly diminished growth with the exception of brain, progressive vacuolar myopathy, and markedly shortened lifespan. This article is protected by copyright. All rights reserved.

  View details for DOI 10.1002/jimd.12358

  View details for PubMedID 33389772

• Actin cables and comet tails organize mitochondrial networks in mitosis. Nature Moore, A. S., Coscia, S. M., Simpson, C. L., Ortega, F. E., Wait, E. C., Heddleston, J. M., Nirschl, J. J., Obara, C. J., Guedes-Dias, P. n., Boecker, C. A., Chew, T. L., Theriot, J. A., Lippincott-Schwartz, J. n., Holzbaur, E. L. 2021

  Abstract

  Symmetric cell division requires the even partitioning of genetic information and cytoplasmic contents between daughter cells. Whereas the mechanisms coordinating the segregation of the genome are well known, the processes that ensure organelle segregation between daughter cells remain less well understood1. Here we identify multiple actin assemblies with distinct but complementary roles in mitochondrial organization and inheritance in mitosis. First, we find a dense meshwork of subcortical actin cables assembled throughout the mitotic cytoplasm. This network scaffolds the endoplasmic reticulum and organizes three-dimensional mitochondrial positioning to ensure the equal segregation of mitochondrial mass at cytokinesis. Second, we identify a dynamic wave of actin filaments reversibly assembling on the surface of mitochondria during mitosis. Mitochondria sampled by this wave are enveloped within actin clouds that can spontaneously break symmetry to form elongated comet tails. Mitochondrial comet tails promote randomly directed bursts of movement that shuffle mitochondrial position within the mother cell to randomize inheritance of healthy and damaged mitochondria between daughter cells. Thus, parallel mechanisms mediated by the actin cytoskeleton ensure both equal and random inheritance of mitochondria in symmetrically dividing cells.

  View details for DOI 10.1038/s41586-021-03309-5

  View details for PubMedID 33658713

• In vitro amplification of pathogenic tau conserves disease-specific bioactive characteristics. Acta neuropathologica Xu, H., O'Reilly, M., Gibbons, G. S., Changolkar, L., McBride, J. D., Riddle, D. M., Zhang, B., Stieber, A., Nirschl, J., Kim, S., Hoxha, K., Brunden, K. R., Schellenberg, G. D., Trojanowski, J. Q., Lee, V. M. 2021

  Abstract

  The microtubule-associated protein tau (tau) forms hyperphosphorylated aggregates in the brains of tauopathy patients that can be pathologically and biochemically defined as distinct tau strains. Recent studies show that these tau strains exhibit strain-specific biological activities, also referred to as pathogenicities, in the tau spreading models. Currently, the specific pathogenicity of human-derived tau strains cannot be fully recapitulated by synthetic tau preformed fibrils (pffs), which are generated from recombinant tau protein. Reproducing disease-relevant tau pathology in cell and animal models necessitates the use of human brain-derived tau seeds. However, the availability of human-derived tau is extremely limited. Generation of tau variants that can mimic the pathogenicity of human-derived tau seeds would significantly extend the scale of experimental design within the field of tauopathy research. Previous studies have demonstrated that in vitro seeding reactions can amplify the beta-sheet structure of tau protein from a minute quantity of human-derived tau. However, whether the strain-specific pathogenicities of the original, human-derived tau seeds are conserved in the amplified tau strains has yet to be experimentally validated. Here, we used biochemically enriched brain-derived tau seeds from Alzheimer's disease (AD), corticobasal degeneration (CBD) and progressive supranuclear palsy (PSP) patient brains with a modified seeding protocol to template the recruitment of recombinant 2N4R (T40) tauin vitro. We quantitatively interrogated efficacy of the amplification reactions and the pathogenic fidelity of the amplified material to the original tau seeds using recently developed sporadic tau spreading models. Our data suggest that different tau strains can be faithfully amplified in vitro from tau isolated from different tauopathy brains and that the amplified tau variants retain their strain-dependent pathogenic characteristics.

  View details for DOI 10.1007/s00401-020-02253-4

  View details for PubMedID 33385254

• The development and convergence of co-pathologies in Alzheimer's disease. Brain : a journal of neurology Robinson, J. L., Richardson, H. n., Xie, S. X., Suh, E. n., Van Deerlin, V. M., Alfaro, B. n., Loh, N. n., Porras-Paniagua, M. n., Nirschl, J. J., Wolk, D. n., Lee, V. M., Lee, E. B., Trojanowski, J. Q. 2020

  Abstract

  Cerebral amyloid angiopathy (CAA), limbic-predominant age-related TDP-43 encephalopathy neuropathological change (LATE-NC) and Lewy bodies occur in the absence of clinical and neuropathological Alzheimer's disease, but their prevalence and severity dramatically increase in Alzheimer's disease. To investigate how plaques, tangles, age and apolipoprotein E ε4 (APOE ε4) interact with co-pathologies in Alzheimer's disease, we analysed 522 participants ≥50 years of age with and without dementia from the Center for Neurodegenerative Disease Research (CNDR) autopsy program and 1340 participants in the National Alzheimer's Coordinating Center (NACC) database. Consensus criteria were applied for Alzheimer's disease using amyloid phase and Braak stage. Co-pathology was staged for CAA (neocortical, allocortical, and subcortical), LATE-NC (amygdala, hippocampal, and cortical), and Lewy bodies (brainstem, limbic, neocortical, and amygdala predominant). APOE genotype was determined for all CNDR participants. Ordinal logistic regression was performed to quantify the effect of independent variables on the odds of having a higher stage after checking the proportional odds assumption. We found that without dementia, increasing age associated with all pathologies including CAA (odds ratio 1.63, 95% confidence interval 1.38-1.94, P < 0.01), LATE-NC (1.48, 1.16-1.88, P < 0.01), and Lewy bodies (1.45, 1.15-1.83, P < 0.01), but APOE ε4 only associated with CAA (4.80, 2.16-10.68, P < 0.01). With dementia, increasing age associated with LATE-NC (1.30, 1.15-1.46, P < 0.01), while Lewy bodies associated with younger ages (0.90, 0.81-1.00, P = 0.04), and APOE ε4 only associated with CAA (2.36, 1.52-3.65, P < 0.01). A longer disease course only associated with LATE-NC (1.06, 1.01-1.11, P = 0.01). Dementia in the NACC cohort associated with the second and third stages of CAA (2.23, 1.50-3.30, P < 0.01), LATE-NC (5.24, 3.11-8.83, P < 0.01), and Lewy bodies (2.41, 1.51-3.84, P < 0.01). Pathologically, increased Braak stage associated with CAA (5.07, 2.77-9.28, P < 0.01), LATE-NC (5.54, 2.33-13.15, P < 0.01), and Lewy bodies (4.76, 2.07-10.95, P < 0.01). Increased amyloid phase associated with CAA (2.27, 1.07-4.80, P = 0.03) and Lewy bodies (6.09, 1.66-22.33, P = 0.01). In summary, we describe widespread distributions of CAA, LATE-NC and Lewy bodies that progressively accumulate alongside plaques and tangles in Alzheimer's disease dementia. CAA interacted with plaques and tangles especially in APOE ε4 positive individuals; LATE-NC associated with tangles later in the disease course; most Lewy bodies associated with moderate to severe plaques and tangles.

  View details for DOI 10.1093/brain/awaa438

  View details for PubMedID 33449993

• Computational Histomorphometric Approach for Heart Transplant Rejection Atta-Fosu, T., Janowczyk, A., Nirschl, J., Lal, P., Feldman, M., Peyster, E., Margulies, K., Madabhushi, A. NATURE PUBLISHING GROUP. 2019

  View details for Web of Science ID 000478081100302

• Kinesin-3 Responds to Local Microtubule Dynamics to Target Synaptic Cargo Delivery to the Presynapse. Current biology : CB Guedes-Dias, P. n., Nirschl, J. J., Abreu, N. n., Tokito, M. K., Janke, C. n., Magiera, M. M., Holzbaur, E. L. 2019; 29 (2): 268–82.e8

  Abstract

  Neurons in the CNS establish thousands of en passant synapses along their axons. Robust neurotransmission depends on the replenishment of synaptic components in a spatially precise manner. Using live-cell microscopy and single-molecule reconstitution assays, we find that the delivery of synaptic vesicle precursors (SVPs) to en passant synapses in hippocampal neurons is specified by an interplay between the kinesin-3 KIF1A motor and presynaptic microtubules. Presynaptic sites are hotspots of dynamic microtubules rich in GTP-tubulin. KIF1A binds more weakly to GTP-tubulin than GDP-tubulin and competes with end-binding (EB) proteins for binding to the microtubule plus end. A disease-causing mutation within KIF1A that reduces preferential binding to GDP- versus GTP-rich microtubules disrupts SVP delivery and reduces presynaptic release upon neuronal stimulation. Thus, the localized enrichment of dynamic microtubules along the axon specifies a localized unloading zone that ensures the accurate delivery of SVPs, controlling presynaptic strength in hippocampal neurons.

  View details for DOI 10.1016/j.cub.2018.11.065

  View details for PubMedID 30612907

  View details for PubMedCentralID PMC6342647

• A deep-learning classifier identifies patients with clinical heart failure using whole-slide images of H&E tissue. PloS one Nirschl, J. J., Janowczyk, A. n., Peyster, E. G., Frank, R. n., Margulies, K. B., Feldman, M. D., Madabhushi, A. n. 2018; 13 (4): e0192726

  Abstract

  Over 26 million people worldwide suffer from heart failure annually. When the cause of heart failure cannot be identified, endomyocardial biopsy (EMB) represents the gold-standard for the evaluation of disease. However, manual EMB interpretation has high inter-rater variability. Deep convolutional neural networks (CNNs) have been successfully applied to detect cancer, diabetic retinopathy, and dermatologic lesions from images. In this study, we develop a CNN classifier to detect clinical heart failure from H&E stained whole-slide images from a total of 209 patients, 104 patients were used for training and the remaining 105 patients for independent testing. The CNN was able to identify patients with heart failure or severe pathology with a 99% sensitivity and 94% specificity on the test set, outperforming conventional feature-engineering approaches. Importantly, the CNN outperformed two expert pathologists by nearly 20%. Our results suggest that deep learning analytics of EMB can be used to predict cardiac outcome.

  View details for DOI 10.1371/journal.pone.0192726

  View details for PubMedID 29614076

  View details for PubMedCentralID PMC5882098

• Amyotrophic lateral sclerosis-linked mutations increase the viscosity of liquid-like TDP-43 RNP granules in neurons. Proceedings of the National Academy of Sciences of the United States of America Gopal, P. P., Nirschl, J. J., Klinman, E. n., Holzbaur, E. L. 2017; 114 (12): E2466–E2475

  Abstract

  Ribonucleoprotein (RNP) granules are enriched in specific RNAs and RNA-binding proteins (RBPs) and mediate critical cellular processes. Purified RBPs form liquid droplets in vitro through liquid-liquid phase separation and liquid-like non-membrane-bound structures in cells. Mutations in the human RBPs TAR-DNA binding protein 43 (TDP-43) and RNA-binding protein FUS cause amyotrophic lateral sclerosis (ALS), but the biophysical properties of these proteins have not yet been studied in neurons. Here, we show that TDP-43 RNP granules in axons of rodent primary cortical neurons display liquid-like properties, including fusion with rapid relaxation to circular shape, shear stress-induced deformation, and rapid fluorescence recovery after photobleaching. RNP granules formed from wild-type TDP-43 show distinct biophysical properties depending on axonal location, suggesting maturation to a more stabilized structure is dependent on subcellular context, including local density and aging. Superresolution microscopy demonstrates that the stabilized population of TDP-43 RNP granules in the proximal axon is less circular and shows spiculated edges, whereas more distal granules are both more spherical and more dynamic. RNP granules formed by ALS-linked mutant TDP-43 are more viscous and exhibit disrupted transport dynamics. We propose these altered properties may confer toxic gain of function and reflect differential propensity for pathological transformation.

  View details for DOI 10.1073/pnas.1614462114

  View details for PubMedID 28265061

  View details for PubMedCentralID PMC5373408

• Deep Learning Tissue Segmentation in Cardiac Histopathology Images DEEP LEARNING FOR MEDICAL IMAGE ANALYSIS Nirschl, J. J., Janowczyk, A., Peyster, E. G., Frank, R., Margulies, K. B., Feldman, M. D., Madabhushi, A., Zhou, S. K., Greenspan, H., Shen, D. 2017: 179–95

  View details for DOI 10.1016/B978-0-12-810408-8.00011-0

  View details for Web of Science ID 000416611100009

• The impact of cytoskeletal organization on the local regulation of neuronal transport. Nature reviews. Neuroscience Nirschl, J. J., Ghiretti, A. E., Holzbaur, E. L. 2017; 18 (10): 585–97

  Abstract

  Neurons are akin to modern cities in that both are dependent on robust transport mechanisms. Like the best mass transit systems, trafficking in neurons must be tailored to respond to local requirements. Neurons depend on both high-speed, long-distance transport and localized dynamics to correctly deliver cargoes and to tune synaptic responses. Here, we focus on the mechanisms that provide localized regulation of the transport machinery, including the cytoskeleton and molecular motors, to yield compartment-specific trafficking in the axon initial segment, axon terminal, dendrites and spines. The synthesis of these mechanisms provides a sophisticated and responsive transit system for the cell.

  View details for DOI 10.1038/nrn.2017.100

  View details for PubMedID 28855741

  View details for PubMedCentralID PMC6400490

• α-Tubulin Tyrosination and CLIP-170 Phosphorylation Regulate the Initiation of Dynein-Driven Transport in Neurons. Cell reports Nirschl, J. J., Magiera, M. M., Lazarus, J. E., Janke, C. n., Holzbaur, E. L. 2016; 14 (11): 2637–52

  Abstract

  Motor-cargo recruitment to microtubules is often the rate-limiting step of intracellular transport, and defects in this recruitment can cause neurodegenerative disease. Here, we use in vitro reconstitution assays with single-molecule resolution, live-cell transport assays in primary neurons, computational image analysis, and computer simulations to investigate the factors regulating retrograde transport initiation in the distal axon. We find that phosphorylation of the cytoskeletal-organelle linker protein CLIP-170 and post-translational modifications of the microtubule track combine to precisely control the initiation of retrograde transport. Computer simulations of organelle dynamics in the distal axon indicate that while CLIP-170 primarily regulates the time to microtubule encounter, the tyrosination state of the microtubule lattice regulates the likelihood of binding. These mechanisms interact to control transport initiation in the axon in a manner sensitive to the specialized cytoskeletal architecture of the neuron.

  View details for DOI 10.1016/j.celrep.2016.02.046

  View details for PubMedID 26972003

  View details for PubMedCentralID PMC4819336

• Live-cell imaging of retrograde transport initiation in primary neurons. Methods in cell biology Nirschl, J. J., Holzbaur, E. L. 2016; 131: 269–76

  Abstract

  Axonal transport is an essential function in neurons, as mutations in either motor proteins or their adaptors cause neurodegeneration. While some mutations cause a complete block in axonal transport, other mutations affect transport more subtly. This is especially true of mutations identified in human patients, many of which impair but do not block motor function in the cell. Dissecting the pathogenic mechanisms of these more subtle mutations requires assays that can tease apart the distinct phases of axonal transport, including transport initiation, sustained/regulated motility, and cargo-specific sorting or delivery. Here, we describe a live-cell photobleaching assay to assess retrograde flux from the distal axon tip, a measure for distal transport initiation. We have previously used this method to show that the CAP-Gly domain of DCTN1 is required for efficient retrograde transport initiation in the distal axon, but it is not required to maintain retrograde flux along the mid-axon (Moughamian & Holzbaur, 2012). This approach has allowed us to examine the effects of disease-causing mutations in the axonal transport machinery, and in combination with other assays, will be useful in determining the mechanisms and regulation of axonal transport in normal and diseased conditions.

  View details for DOI 10.1016/bs.mcb.2015.06.002

  View details for PubMedID 26794519

• Lipid Rafts Assemble Dynein Ensembles. Trends in biochemical sciences Nirschl, J. J., Ghiretti, A. E., Holzbaur, E. L. 2016; 41 (5): 393–94

  Abstract

  New work by Rai et al. identifies a novel mechanism regulating phagosome transport in cells: the clustering of dynein motors into lipid microdomains, leading to enhanced unidirectional motility. Clustering may be especially important for dynein, a motor that works most efficiently in teams.

  View details for DOI 10.1016/j.tibs.2016.03.005

  View details for PubMedID 27061495

  View details for PubMedCentralID PMC4851571

• LC3 Binding to the Scaffolding Protein JIP1 Regulates Processive Dynein-Driven Transport of Autophagosomes DEVELOPMENTAL CELL Fu, M., Nirschl, J. J., Holzbaur, E. L. 2014; 29 (5): 577-590

  Abstract

  Autophagy is essential for maintaining cellular homeostasis in neurons, where autophagosomes undergo robust unidirectional retrograde transport along axons. We find that the motor scaffolding protein JIP1 binds directly to the autophagosome adaptor LC3 via a conserved LIR motif. This interaction is required for the initial exit of autophagosomes from the distal axon, for sustained retrograde transport along the midaxon, and for autophagosomal maturation in the proximal axon. JIP1 binds directly to the dynein activator dynactin but also binds to and activates kinesin-1 in a phosphorylation-dependent manner. Following JIP1 depletion, phosphodeficient JIP1-S421A rescues retrograde transport, while phosphomimetic JIP1-S421D aberrantly activates anterograde transport. During normal autophagosome transport, residue S421 of JIP1 may be maintained in a dephosphorylated state by autophagosome-associated MKP1 phosphatase. Moreover, binding of LC3 to JIP1 competitively disrupts JIP1-mediated activation of kinesin. Thus, dual mechanisms prevent aberrant activation of kinesin to ensure robust retrograde transport of autophagosomes along the axon.

  View details for DOI 10.1016/j.devcel.2014.04.015

  View details for Web of Science ID 000337644700010

  View details for PubMedID 24914561

  View details for PubMedCentralID PMC4109720

• Automated quantification of locomotion, social interaction, and mate preference in Drosophila mutants. Journal of neurogenetics Iyengar, A., Imoehl, J., Ueda, A., Nirschl, J., Wu, C. F. 2012; 26 (3-4): 306-16

  Abstract

  Automated tracking methods facilitate screening for and characterization of abnormal locomotion or more complex behaviors in Drosophila. We developed the Iowa Fly Locomotion and Interaction Tracker (IowaFLI Tracker), a MATLAB-based video analysis system, to identify and track multiple flies in a small arena. We report altered motor activity in the K(+) and Na(+) channel mutants, Hk(1) and para(ts1), which had previously been shown to display abnormal larval locomotion. Environmental factors influencing individual behavior, such as available "social space," were studied by using IowaFLI Tracker to simultaneously track multiple flies in the same arena. We found that crowding levels affect individual fly activity, with the total movement of individual flies attenuated around a particular density. This observation may have important implications in the design of activity chambers for studying particular kinds of social interactions. IowaFLI Tracker also directly quantifies social interactions by tracking the amount of time individuals are in proximity to one another-visualized as an "interactogram." This feature enables the development of a "target-preference" assay to study male courtship behavior where males are presented with a choice between two immobilized, decapitated females, and their locomotion and interactions quantified. We used this assay to study the chemosensory mutants olf D (para(olfD), sbl(2)) and Gr32a and their preferences towards virgin or mated females. Male olf D flies showed reduced courtship levels, with no clear preference towards either, whereas Gr32a males preferentially courted with virgin females over mated females in this assay. These initial results demonstrate that IowaFLI Tracker can be employed to explore motor coordination and social interaction phenomena in behavioral mutants of Drosophila.

  View details for DOI 10.3109/01677063.2012.729626

  View details for PubMedID 23106154

  View details for PubMedCentralID PMC3613147