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SSRN 2021年

作者： Sengupta, Srona Reed, Madison C. Yu, Jeanna Zhang, Josephine Kim, Aeryon Boronina, Tatiana N. Welsh, Robin A. Yang, Weiming Timmons, Andrew E. Wrabl, James O. Hoh, Rebecca Cole, Robert N. Deeks, Steve Siliciano, Janet D. Siliciano, Robert F. Sadegh-Nasseri, Scheherazade Department of Medicine Johns Hopkins University School of Medicine BaltimoreMD21205 United States Department of Pathology Johns Hopkins University School of Medicine BaltimoreMD21205 United States Department of Inflammation and Oncology Genome Analysis Unit Amgen Research Amgen Inc. South San FranciscoCA94080 United States Mass Spectrometry and Proteomics Facility Department of Biological Chemistry Johns Hopkins University School of Medicine BaltimoreMD21205 United States Department of Biology Johns Hopkins University BaltimoreMD21218 United States Department of Medicine University of California San Francisco San FranciscoCA94143 United States Howard Hughes Medical Institute BaltimoreMD21205 United States The Graduate Program in Immunology Medical Scientist Training Program Johns Hopkins University School of Medicine BaltimoreMD21205 United States

Distinct CD4+T cell epitopes have been associated with spontaneous control of HIV-1 replication, but analysis of antigen-dependent factors that influence epitope selection is lacking. To examine these factors, we used a cell-free antigen processing system that incorporates soluble HLA-DR (DR1), HLA-DM (DM), and cathepsins along with full-length protein antigens for epitope identification by LC-MS/MS. HIV-1 Gag, Pol, Env, Vif, Nef, Tat, and Rev were examined using this system. We identified 35 novel epitopes, including glycopeptides. Epitopes from smaller HIV-1 proteins with crystal structures mapped to regions of low protein stability and higher solvent accessibility. HIV-1 antigens associated with limited CD4+T cell responses were processed efficiently, while some protective epitopes were inefficiently processed. 66% of epitopes obtained from cell-free processing induced memory CD4+T cell responses in HIV-1+ donors, including 10 of 19 novel epitopes. Thus, an in vitro processing system can identify novel HIV-1 epitopes and reveal factors influencing epitope dominance. © 2021, The Authors. All rights reserved.

关键词： Epitopes

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Therapeutic Targeting of Follicular T Cells with Chimeric Antigen Receptor-Expressing Natural Killer Cells (vol 1, pg 100003, 2020)

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CELL REPORTS MEDICINE 2020年第5期1卷 100003-100003页

作者： Reighard, Seth D. Cranert, Stacey A. Rangel, Kelly M. Ali, Ayad Gyurova, Ivayla E. de la Cruz-Lynch, Arthur T. Tuazon, Jasmine A. Khodoun, Marat V. Kottyan, Leah C. Smith, David F. Brunner, Hermine I. Waggoner, Stephen N. Center for Autoimmune Genomics and Etiology Cincinnati Children’s Hospital Medical Center Cincinnati OH 45229 USA Medical Scientist Training Program University of Cincinnati College of Medicine Cincinnati OH 45267 USA Immunology Graduate Training Program University of Cincinnati College of Medicine Cincinnati OH 45267 USA Division of Developmental Biology Cincinnati Children’s Hospital Medical Center Cincinnati OH 45229 USA Pathobiology and Molecular Medicine Graduate Program University of Cincinnati College of Medicine Cincinnati OH 45267 USA Division of Immunology Allergy and Rheumatology Department of Medicine University of Cincinnati Medical Center Cincinnati OH 45267 USA Department of Research Cincinnati Veterans Affairs Medical Center Cincinnati OH 45220 USA Department of Pediatrics University of Cincinnati College of Medicine Cincinnati OH 45267 USA Division of Pediatric Otolaryngology - Head & Neck Surgery Cincinnati Children’s Hospital Medical Center Cincinnati OH 45229 USA Division of Pulmonary and Sleep Medicine Cincinnati Children’s Hospital Medical Center Cincinnati OH 45229 USA Department of Otolaryngology - Head & Neck Surgery University of Cincinnati College of Medicine Cincinnati OH 45267 USA Division of Rheumatology Cincinnati Children’s Hospital Medical Center Cincinnati OH 45229 USA

Follicular helper T cells (TFH) are critical for vaccine and infection elicitation of long-lived humoral immunity, but exaggerated TFH responses can promote autoimmunity and other pathologies. It is unfortunate that no clinical interventions exist for the selective depletion of follicular T cells to alleviate these diseases. We engineered a chimeric antigen receptor (CAR) facilitating the specific targeting of cells with high expression levels of human programmed cell death protein 1 (PD-1), a cardinal feature of follicular T cells. CAR-expressing human natural killer (NK) cells robustly and discriminately eliminated PD-1high follicular human T cells in vitro and in a humanized mouse model of lupus-like disease while sparing B cells and other PD-1low T cell subsets, including regulatory T cells. These results establish a strategy for specific targeting of PD-1high T cells that can be advanced as a clinical tool for the selective depletion of pathogenic follicular T cells or other PD-1high target cells in certain disease states.

关键词： systemic lupus erythematosus rheumatoid arthritis Sjögren syndrome allergy cytotherapy cytotoxicity checkpoint PD-L1 NK-92

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Publisher Correction: Multistate and functional protein design using RoseTTAFold sequence space diffusion

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Nature biotechnology 2024年 2024 Oct 7页

作者： Sidney Lyayuga Lisanza Jacob Merle Gershon Samuel W K Tipps Jeremiah Nelson Sims Lucas Arnoldt Samuel J Hendel Miriam K Simma Ge Liu Muna Yase Hongwei Wu Claire D Tharp Xinting Li Alex Kang Evans Brackenbrough Asim K Bera Stacey Gerben Bruce J Wittmann Andrew C McShan David Baker Department of Biochemistry University of Washington Seattle WA USA. Institute for Protein Design University of Washington Seattle WA USA. Graduate Program in Biological Physics Structure and Design University of Washington Seattle WA USA. Department of Molecular Engineering University of Washington Seattle WA USA. Molecular & Cellular Biology Medical Scientist Training Program University of Washington Seattle WA USA. Faculty of Engineering Sciences Heidelberg University Heidelberg Germany. School of Chemistry and Biochemistry Georgia Institute of Technology Atlanta GA USA. Office of the Chief Scientific Officer Microsoft Redmond WA USA. Department of Biochemistry University of Washington Seattle WA USA. dabaker@uw.edu. Institute for Protein Design University of Washington Seattle WA USA. dabaker@uw.edu. Howard Hughes Medical Institute University of Washington Seattle WA USA. dabaker@uw.edu.

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BIOM-25. IDENTIFYING EXTRACELLULAR VESICLES FROM GLIOBLASTOMA OR NON-NEOPLASTIC CELLS VIA IMAGING FLOW CYTOMETRY

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Neuro-Oncology 2020年第SUPPLEMENT_2期22卷 ii7-ii7页

作者： Milbeth Cumba Garcia, Luz Aibaidula, Abudumijiti Kazemi, Nazanin Yeganeh Jung, Miyeon Lucien-Matteoni, Fabrice Markovic, Svetomir Parney, Ian Mayo Clinic Graduate School of Biomedical Sciences Rochester MN USA Mayo Clinic Medical Scientist Training Program Rochester MN USA Mayo Clinic Rochester MN USA

Patients with glioblastoma (GBM) have a median survival of 15 months despite aggressive treatment. Immunosuppressive monocytes are heavily infiltrated in these tumors and in patients’ circulation. Treatment-related pseudo-progression confounds outcome assessment by MRI. Thus, there is a need for additional non-invasive methods to assess treatment response. Extracellular vesicles (EVs) contain tumor-specific microRNA (miRNA) cargo that could serve as a liquid biopsy to distinguish true progression from treatment-related pseudo-progression. We had found significant differences in plasma EVs molecular profile (i.e. miRNA signatures) between GBM patients and healthy donors. Our overall hypothesis is that these differences reflect the EVs cell of origin. Our goal in this project was to develop a fluorescent staining paradigm by flow cytometry to distinguish EVs from different cellsin vitroand determine differences in EV miRNA expression profile between GBM and monocytic cell-derived EVs. Gleolan (5-ALA) is an FDA-approved orally available agent for fluorescence-guided resection of GBM tumors. It is metabolized to protoporphyrin IX (PpIX) in GBM cells but not in non-neoplastic cells and has been reported to aid in the detection of GBM-derived EVs by flow cytometry. However, distinguishing between GBM-derived EVs and EVs from other cells of origin has not been described. We co-cultured human GBM cells (dBT114 or dBT116) and CD14+ monocytes for 72 hours in the presence or absence of 5-ALA. EVs were isolated by ultracentrifugation and stained for CD11b (myeloid cell marker). ImageStream Imaging Flow Cytometry was performed showing clear differentiation between PpIX+ EVs from GBM cells and CD11b+ EVs from monocytes. Interestingly, a small number of double-positive EVs (presumably representing monocyte-derived EVs that had taken up PpIX after phagocytizing GBM cells) were also present. Taken together, we were able to optimize a technique to distinguish EVs originating from GBM

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DIPG-58. Therapeutic HDAC targeting in hypermutant CNS tumors

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Neuro-Oncology 2022年第SUPPLEMENT_1期24卷 i32-i32页

作者： Myers, Carrie Noll, Alyssa Biery, Matthew Meechan, Michael Tahiri, Sophie Foster, Jessica Dun, Matthew Olson, James Vitanza, Nicholas The Ben Towne Center for Childhood Cancer Research Seattle Children’s Research Institute Seattle WA USA Molecular and Cellular Biology Graduate Program and Medical Scientist Training Program University of Washington Seattle Washington USA Division of Oncology The Children's Hospital of Philadelphia Philadelphia PA USA Department of Pediatrics Perelman School of Medicine University of Pennsylvania Philadelphia PA USA Cancer Signaling Research Group School of Biomedical Sciences and Pharmacy College of Health Medicine and Wellbeing University of Newcastle Callaghan NSW Australia Individualised Medicine Program Hunter Medical Research Institute New Lambton Heights NSW Australia Division of Pediatric Hematology Oncology Bone Marrow Transplant and Cellular Therapy Department of Pediatrics Seattle Children’s Hospital University of Washington Seattle WA USA

Diffuse intrinsic pontine glioma (DIPG) is a universally fatal tumor of the pons, most often characterized by mutations in genes encoding histone 3, that led to the classification diffuse midline glioma, H3 K27M-mutant (DMG). However, 15% of DIPG are histone wildtype (H3WT) and can have a hypermutant phenotype, characterized by mutations in DNA mismatch repair that also occur in pediatric high-grade glioma (pHGG). We previously published the preclinical efficacy of quisinostat in DMG. As hypermutant CNS tumors share transcriptional disruption with DMG, we investigated if HDAC inhibition was also therapeutic against hypermutant DIPG and pHGG. We tested PBT-24, a PMS2 mutant, treatment-naïve, patient-derived hypermutant DIPG model, and found similar quisinostat sensitivity compared to other DMG cultures in vitro (IC50 = ~30 nM), as well as significant efficacy in a xenograft flank model (60 day mean tumor size of 1109mm3 [vehicle] vs. 19mm3 [quisinostat-treated]). This in vivo effect was greater than the anti-tumor effect observed in a xenograft flank non-hypermutant DMG model PBT-09 (60 day mean tumor size of 1006mm3 [vehicle] vs. 244mm3 [quisinostat-treated]). To validate the effect of hypermutation on sensitivity to quisinostat, we generated PMS2 knock-out (KO) and MSH2 KO isogenic cell lines using the H3WT model VUMC-DIPG-10. In a xenograft flank model, we observed increased quisinostat sensitivity in the KO models (20 day mean tumor volume of 547mm3 [parental], 396mm3 [PMS2 KO], and 150mm3 [MSH2 KO]). RNA sequencing of quisinostat-treated PBT-24 revealed an increase in acute inflammatory response genes which we are investigating as a mechanism of action for HDACi against hypermutant tumors. Ultimately, we demonstrate the in vivo efficacy of quisinostat against hypermutant DIPG that supports the investigation of HDAC inhibition as a treatment strategy across hypermutant CNS tumors.

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Author Correction: A spatial genome aligner for resolving chromatin architectures from multiplexed DNA FISH

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Nature biotechnology 2023年第7期41卷 1027页

作者： Bojing Blair Jia Adam Jussila Colin Kern Quan Zhu Bing Ren Bioinformatics and Systems Biology Graduate Program University of California San Diego La Jolla CA USA. Medical Scientist Training Program University of California San Diego La Jolla CA USA. Department of Cellular and Molecular Medicine Center for Epigenomics University of California San Diego La Jolla CA USA. Department of Cellular and Molecular Medicine Center for Epigenomics University of California San Diego La Jolla CA USA. biren@health.ucsd.edu. Ludwig Institute for Cancer Research La Jolla CA USA. biren@health.ucsd.edu. Institute of Genomic Medicine Moores Cancer Center School of Medicine University of California San Diego La Jolla CA USA. biren@health.ucsd.edu.

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Author Correction: Droplet Hi-C enables scalable, single-cell profiling of chromatin architecture in heterogeneous tissues

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Nature biotechnology 2025年 2025 May 12页

作者： Lei Chang Yang Xie Brett Taylor Zhaoning Wang Jiachen Sun Ethan J Armand Shreya Mishra Jie Xu Melodi Tastemel Audrey Lie Zane A Gibbs Hannah S Indralingam Tuyet M Tan Rafael Bejar Clark C Chen Frank B Furnari Ming Hu Bing Ren Department of Cellular and Molecular Medicine University of California San Diego La Jolla CA USA. Biomedical Sciences Graduate Program University of California San Diego La Jolla CA USA. Medical Scientist Training Program University of California San Diego La Jolla CA USA. Department of Quantitative Health Sciences Lerner Research Institute Cleveland Clinic Foundation Cleveland OH USA. Systems Biology and Bioinformatics PhD Program Case Western Reserve University School of Medicine Cleveland OH USA. Bioinformatics and Systems Biology Program University of California San Diego La Jolla CA USA. Moores Cancer Center UC San Diego La Jolla CA USA. Department of Neurosurgery University of Minnesota Minneapolis MN USA. Department of Medicine University of California San Diego School of Medicine La Jolla CA USA. Department of Cellular and Molecular Medicine University of California San Diego La Jolla CA USA. biren@health.ucsd.edu. Moores Cancer Center UC San Diego La Jolla CA USA. biren@health.ucsd.edu. Center for Epigenomics Institute for Genomic Medicine School of Medicine University of California San Diego La Jolla CA USA. biren@health.ucsd.edu.

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Therapeutic Targeting of Follicular Helper T Cells with Chimeric Antigen Receptor-Expressing Natural Killer Cells

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SSRN 2019年

作者： Reighard, Seth D. Cranert, Stacey A. Rangel, Kelly M. Ali, Ayad Gyurova, Ivayla E. de la Cruz-Lynch, Arthur T. Tuazon, Jasmine A. Kottyan, Leah C. Smith, David F. Brunner, Hermine I. Waggoner, Stephen N. Center for Autoimmune Genomics & Etiology Cincinnati Children’s Hospital Medical Center Medical Scientist Training Program University of Cincinnati College of Medicine Immunology Graduate Training Program University of Cincinnati College of Medicine Division of Developmental Biology Cincinnati Children’s Hospital Medical Center Pathobiology and Molecular Medicine Graduate Program University of Cincinnati College of Medicine Department of Pediatrics University of Cincinnati College of Medicine Division of Pediatric Otolaryngology - Head & Neck Surgery Cincinnati Children’s Hospital Medical Center Division of Pulmonary and Sleep Medicine Cincinnati Children’s Hospital Medical Center Department of Otolaryngology - Head & Neck Surgery University of Cincinnati College of Medicine Division of Rheumatology Cincinnati Children’s Hospital Medical Center

Follicular helper T cells (TFH) are critical for vaccine and infection elicitation of long-lived humoral immunity, but exaggerated TFH responses can promote autoimmunity and other pathologies. Unfortunately, no clinical interventions are currently available for selective depletion of TFH cells to alleviate these disease conditions. We engineered a novel chimeric antigen receptor (CAR) that facilitates specific targeting of cells highly expressing human programmed cell death protein 1 (PD-1), a cardinal feature of TFH cells. CAR-expressing natural killer (NK) cells robustly degranulate in response to PD-1, resulting in discriminatory elimination of human tonsil TFH cells while sparing other T and B-cell subsets. Given that CAR NK cells are emerging as a safe and effective alternative to CAR T cells in cancer immunotherapy, our results suggest a new, clinically-translatable application of CAR NK cells for selective depletion of pathogenic TFH cells in specific disease states. © 2019, The Authors. All rights reserved.

关键词： Diseases

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Author Correction: Investigation of Cas9 antibodies in the human eye

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Nature communications 2022年第1期13卷 2109页

作者： Marcus A Toral Carsten T Charlesworth Benjamin Ng Teja Chemudupati Shota Homma Hiromitsu Nakauchi Alexander G Bassuk Matthew H Porteus Vinit B Mahajan Molecular Surgery Program Department of Ophthalmology Byers Eye Institute Stanford University Palo Alto CA USA. Medical Scientist Training Program and Graduate Program in Molecular Medicine University of Iowa Iowa City IA USA. Department of Pediatrics Stanford University Palo Alto CA USA. Medical Sciences Division University of Oxford Oxford UK. Department of Genetics Stanford University Palo Alto CA USA. Institute for Stem Cell Biology and Regenerative Medicine Stanford University School of Medicine Palo Alto CA USA. Division of Stem Cell Therapy Distinguished Professor Unit Institute of Medical Science University of Tokyo Tokyo Japan. Departments of Pediatrics and Neurology and The Iowa Neuroscience Institute (INI) University of Iowa Iowa City IA USA. Department of Pediatrics Stanford University Palo Alto CA USA. mporteus@stanford.edu. Molecular Surgery Program Department of Ophthalmology Byers Eye Institute Stanford University Palo Alto CA USA. vinit.mahajan@stanford.edu. Veterans Affairs Palo Alto Health Care System Palo Alto CA Palo Alto CA USA. vinit.mahajan@stanford.edu.

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A syndromic neurodevelopmental disorder caused by rare variants in PPFIA3 (vol 111, pg 96, 2024)

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AMERICAN JOURNAL OF HUMAN GENETICS 2024年第4期11卷 805-805页

作者： Paul, Maimuna S. Michener, Sydney L. Pan, Hongling Chan, Hiuling Pfliger, Jessica M. Rosenfeld, Jill A. Lerma, Vanesa C. Tran, Alyssa Longley, Megan A. Lewis, Richard A. Weisz-Hubshman, Monika Bekheirnia, Mir Reza Bekheirnia, Nasim Massingham, Lauren Zech, Michael Wagner, Matias Engels, Hartmut Cremer, Kirsten Mangold, Elisabeth Peters, Sophia Trautmann, Jessica Perne, Claudia Mester, Jessica L. Sacoto, Maria J. Guillen Person, Richard McDonnell, Pamela P. Cohen, Stacey R. Lusk, Laina Cohen, Ana S. A. Le Pichon, Jean-Baptiste Pastinen, Tomi Zhou, Dihong Engleman, Kendra Racine, Caroline Faivre, Laurence Moutton, Sebastien Denomme-Pichon, Anne-Sophie Koh, Hyun Yong Poduri, Annapurna Bolton, Jeffrey Knopp, Cordula Suh, Dong Sun Julia Maier, Andrea Toosi, Mehran Beiraghi Karimiani, Ehsan Ghayoor Maroofian, Reza Schaefer, Gerald Bradley Ramakumaran, Vijayalakshmi Vasudevan, Pradeep Banos-Pinero, Benito Pagnamenta, Alistair T. Prasad, Chitra Osmond, Matthew Schuhmann, Sarah Vasileiou, Georgia Russ-Hall, Sophie Scheffer, Ingrid E. Carvill, Gemma L. Mefford, Heather Bacino, Carlos A. Lee, Brendan H. Chao, Hsiao-Tuan Department of Pediatrics Section of Neurology and Developmental Neuroscience Baylor College of Medicine Houston TX USA Jan and Dan Duncan Neurological Research Institute Texas Children’s Hospital Houston TX USA Cain Pediatric Neurology Research Foundation Laboratories Jan and Dan Duncan Neurological Research Institute Houston TX USA Department of Molecular and Human Genetics Baylor College of Medicine Houston TX USA Augustana College Rock Island IL USA Summer Undergraduate Research Training (SMART) Program Baylor College of Medicine Houston TX USA Graduate Program in Electrical and Computer Engineering Rice University Houston TX USA Department of Psychology University of Houston Houston TX USA Department of Ophthalmology Baylor College of Medicine Houston TX USA Renal Genetics Clinic Baylor College of Medicine Houston TX USA Rhode Island Hospital and Hasbro Children’s Hospital Providence RI USA Institute of Neurogenomics Helmholtz Zentrum München Munich Germany Institute of Human Genetics School of Medicine Technical University Munich Germany Institute for Advanced Study Technical University of Munich Garching Germany Division of Pediatric Neurology Developmental Neurology and Social Pediatrics Dr. von Hauner Children’s Hospital Munich Germany Institute of Human Genetics School of Medicine University Hospital Bonn University of Bonn Bonn Germany GeneDx Gaithersburg MD USA Epilepsy NeuroGenetics Initiative (ENGIN) Division of Neurology Children’s Hospital of Philadelphia Philadelphia PA USA Department of Neurology Perelman School of Medicine University of Pennsylvania Philadelphia PA USA Children’s Mercy Kansas City Genomic Medicine Center The University of Missouri-Kansas City (UMKC) School of Medicine Kansas City MO USA Department of Pediatrics Children’s Mercy Kansas City Kansas City MO USA Children’s Mercy Research Institute Kansas City MO USA Children’s Mercy Hospital Kansas City MO USA University Hospital Dijon Franc

PPFIA3 encodes the protein-tyrosine phosphatase, receptor-type, F-polypeptide-interacting-protein-alpha-3 (PPFIA3), which is a member of the LAR-protein-tyrosine phosphatase-interacting-protein (liprin) family involved in synapse formation and function, synaptic vesicle transport, and presynaptic active zone assembly. The protein structure and function are evolutionarily well conserved, but human diseases related to PPFIA3 dysfunction are not yet reported in OMIM. Here, we report 20 individuals with rare PPFIA3 variants (19 heterozygous and 1 compound heterozygous) presenting with developmental delay, intellectual disability, hypotonia, dysmorphisms, microcephaly or macrocephaly, autistic features, and epilepsy with reduced penetrance. Seventeen unique PPFIA3 variants were detected in 18 families. To determine the pathogenicity of PPFIA3 variants in vivo, we generated transgenic fruit flies producing either human wild-type (WT) PPFIA3 or five missense variants using GAL4-UAS targeted gene expression systems. In the fly overexpression assays, we found that the PPFIA3 variants in the region encoding the N-terminal coiled-coil domain exhibited stronger phenotypes compared to those affecting the C-terminal region. In the loss-of-function fly assay, we show that the homozygous loss of fly Liprin-α leads to embryonic lethality. This lethality is partially rescued by the expression of human PPFIA3 WT, suggesting human PPFIA3 function is partially conserved in the fly. However, two of the tested variants failed to rescue the lethality at the larval stage and one variant failed to rescue lethality at the adult stage. Altogether, the human and fruit fly data reveal that the rare PPFIA3 variants are dominant-negative loss-of-function alleles that perturb multiple developmental processes and synapse formation.

关键词： neurodevelopmental disorder synaptic protein active zone protein Mendelian phenotypes fruit flies

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