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ASpli: Integrative analysis of splicing landscapes through RNA-Seq assays (Mar, btab141, 2021)

BIOINFORMATICS 2021年第12期37卷 1783-1783页

作者： Mancini, Estefania Rabinovich, Andres Iserte, Javier Yanovsky, Marcelo Chernomoretz, Ariel Gene Regulation Stem Cells and Cancer Program Centre for Genomic Regulation (CRG) The Barcelona Institute of Science and Technology Barcelona Spain Integrative Systems Biology Fundacion Instituto Leloir Buenos Aires Argentina Instituto de Investigaciones Bioquímicas de Buenos Aires Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) Buenos Aires Argentina DStructural Bioinformatics Fundacion Instituto Leloir Buenos Aires Argentina Comparative Genomics of Plant Development Fundacion Instituto Leloir Buenos Aires Argentina

Motivation Genome-wide analysis of alternative splicing has been a very active field of research since the early days of next generation sequencing technologies. Since then, ever-growing data availability and the development of increasingly sophisticated analysis methods have uncovered the complexity of the general splicing repertoire. A large number of splicing analysis methodologies exist, each of them presenting its own strengths and weaknesses. For instance, methods exclusively relying on junction information do not take advantage of the large majority of reads produced in an RNA-seq assay, isoform reconstruction methods might not detect novel intron retention events, some solutions can only handle canonical splicing events, and many existing methods can only perform pairwise *** In this contribution, we present ASpli, a computational suite implemented in R statistical language, that allows the identification of changes in both, annotated and novel alternative-splicing events and can deal with simple, multi-factor or paired experimental designs. Our integrative computational workflow, that considers the same GLM model applied to different sets of reads and junctions, allows computation of complementary splicing signals. Analyzing simulated and real data, we found that the consolidation of these signals resulted in a robust proxy of the occurrence of splicing alterations. While the analysis of junctions allowed us to uncover annotated as well as non-annotated events, read coverage signals notably increased recall capabilities at a very competitive performance when compared against other state-of-the-art splicing analysis *** and implementation ASpli is freely available from the Bioconductor project site https://***/doi:10.18129/*** information Supplementary data are available at Bioinformatics online.

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IHS;An Integrative Method for the Identification of Network Hubs

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SSRN 2020年

作者： Salavaty, Abbas Ramialison, Mirana Currie, Peter D. Australian Regenerative Medicine Institute Monash University ClaytonVIC3800 Australia Development and Stem Cells Program

Biological systems are composed of highly complex networks and decoding the functional significance of individual network components is critical for understanding healthy and diseased states. Several algorithms have been designed to identify the most influential regulatory points, or hub nodes, within a network. However, none of the current methods correct for inherent positional biases which limits their applicability. In addition, none of the currently available hub detection algorithms effectively combine network centrality measures together. To overcome this computational deficit, we undertook a statistical assessment of 200 real-world and simulated networks to decipher associations between centrality measures, and developed an algorithm termed “integrated hubness score” (IHS), which integrates the most important and commonly used network centrality measures, namely degree centrality, betweenness centrality and neighbourhood connectivity, in an unbiased way. When compared against the four most commonly used hub identification methods on four independent validated biological networks, the IHS algorithm outperformed all other assessed methods. Using this universal method, researchers of any discipline can now identify the most influential network nodes. © 2020, The Authors. All rights reserved.

关键词： Complex networks

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Rac GTPases:domain-specific functions in neuronal development

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Neural Regeneration Research 2019年第8期14卷 1367-1368页

作者： Steffen Norgaard Roger Pocock Development and Stem Cells Program Monash Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology Monash University Melbourne Victoria Australia Biotech Research and Innovation Centre University of Copenhagen Copenhagen Denmark

Understanding fundamental mechanisms governing axon outgrowth and guidance can inform the development of therapeutic strategies to restore neuronal function damaged though injury or disease. Axons navigate the extracellular environment by responding to guidance cues that bind to cell surface receptors to relay information intracellularly via Rho GTPase family members, including the Rac GTPases.

关键词： Rac GTPases domain-specific functions neuronal development

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Changing the public perception of human embryology ( vol 25, pg 1717, 2023)

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NATURE CELL BIOLOGY 2023年第12期25卷 1884-1884页

作者： Rivron, Nicolas C. Martinez-Arias, Alfonso Sermon, Karen Mummery, Christine Scholer, Hans R. Wells, James Nichols, Jenny Hadjantonakis, Anna-Katerina Lancaster, Madeline A. Moris, Naomi Fu, Jianping Sturmey, Roger G. Niakan, Kathy Rossant, Janet Kato, Kazuto Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA) Vienna BioCenter (VBC) Vienna Austria Systems Bioengineering MELIS Universidad Pompeu Fabra and Catalan Institution for Research and Advanced Studies (ICREA) Barcelona Spain Research Group Reproduction and Genetics Vrije Universiteit Brussel Brussels Belgium European Society for Human Reproduction and Embryology (ESHRE) Strombeek-Bever Belgium Leiden University Medical Center Leiden the Netherlands Max Planck Institute for Molecular Biomedicine Münster Germany Center for Stem Cell and Organoid Medicine Cincinnati Children’s Hospital Medical Center Cincinnati OH USA Division of Developmental Biology Cincinnati Children’s Hospital Medical Center Cincinnati OH USA MRC Human Genetics Unit Institute of Genetics and Cancer The University of Edinburgh Crewe Road Edinburgh UK Developmental Biology Program Sloan Kettering Institute Memorial Sloan Kettering Cancer Center New York NY USA MRC Laboratory of Molecular Biology Cambridge UK The Francis Crick Institute London UK Department of Mechanical Engineering University of Michigan Ann Arbor MI USA Department of Biomedical Engineering University of Michigan Ann Arbor MI USA Department of Cell & Developmental Biology University of Michigan Medical School Ann Arbor MI USA Biomedical Institute for Multimorbidity Hull York Medical School University of Hull Hull UK Cambridge Reproduction University of Cambridge Cambridge UK The Centre for Trophoblast Research Department of Physiology Development and Neuroscience University of Cambridge Cambridge UK Human Embryo and Stem Cell Laboratory The Francis Crick Institute London UK Wellcome Trust–Medical Research Council Stem Cell Institute University of Cambridge Jeffrey Cheah Biomedical Centre Cambridge UK Epigenetics Programme Babraham Institute Cambridge UK The Hospital for Sick Children Toronto ON Canada Department of Biomedical Ethics and Public Policy Graduate School of Medicin

Human embryology is flourishing thanks to an impetus provided by embryo models formed from stem cells. These scientific advances require meticulous experimental work and a refined ethical framework, but also sensible ... 详细信息

关键词： Embryology Embryonic stem cells

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Sds-Page Optimization Studies of Residual Proteın Identification and Quantıfıcatıon in Clinically Manufactured Mesenchymal stem Cell Products

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SSRN 2022年

作者： Kilic, Pelin Karabudak, Sema Cosar, Begum Savran, Busra Nigar Yalcin, Merve "Central Research Laboratory" Research and Application Center Ankara Yıldırım Beyazıt University Ankara Turkey Department of Molecular Biology and Genetics Faculty of Arts and Science Başkent University Ankara Turkey HücreCELL® Biotechnology Development and Commerce Inc. Ankara Turkey Department of Biology Middle East Technical University Ankara Turkey School of Pharmacy English Program Ankara University Ankara Turkey Department of Stem Cells and Regenerative Medicine Stem Cell Institute Ankara University Ankara Turkey

In line with the safety, efficacy and quality rules determined by the competent authorities for the clinical use of tissue- and cell-based products, residual substances must be removed from the final products manufactured for clinical purposes. In our study, we carried out residual substance analyses and purity determination studies of trypsin and trypsin inhibitor, which are commonly used for dissociating cells from the bottom of the cell culture dish during the propagation stage of clinically manufactured bone marrow-derived mesenchymal stem cell products, by the use of the sodium dodecyl sulfate-polyacrylamide gel electrophoresis method. Finally, with the interpretation of the outputs of this project, we decided the scale of trypsin and trypsin inhibitor to be removed from the clinically manufactured bone marrow-derived mesenchymal stem cell products. © 2022, The Authors. All rights reserved.

关键词： Cell culture

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Evaluation of the effect of donor weight on adipose stromal/stem cell characteristics by using weight-discordant monozygotic twin pairs

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stem CELL RESEARCH & THERAPY 2021年第1期12卷 1页

作者： Juntunen, Miia Heinonen, Sini Huhtala, Heini Rissanen, Aila Kaprio, Jaakko Kuismanen, Kirsi Pietilainen, Kirsi H. Miettinen, Susanna Patrikoski, Mimmi Tampere Univ Fac Med & Hlth Technol Adult Stem Cell Grp Arvo Ylpon katu 3433014 Tampere Finland Tampere Univ Hosp Development & Innovat Ctr Res Tampere Finland Univ Helsinki Fac Med Res Program Clin & Mol Metabolism Obes Res Unit Helsinki Finland Helsinki Univ Cent Hosp Abdominal Ctr Obes Ctr Helsinki Finland Univ Helsinki Abdominal Ctr Obes Ctr Helsinki Finland Univ Tampere Fac Social Sci Tampere Finland Univ Helsinki HiLIFE Inst Mol Med FIMM Helsinki Finland Tampere Univ Hosp Dept Obstet & Gynecol Tampere Finland

Background Adipose stromal/stem cells (ASCs) are promising candidates for future clinical applications. ASCs have regenerative capacity, low immunogenicity, and immunomodulatory ability. The success of future cell-based therapies depends on the appropriate selection of donors. Several factors, including age, sex, and body mass index (BMI), may influence ASC characteristics. Our aim was to investigate the effect of acquired weight on ASC characteristics under the same genetic background using ASCs derived from monozygotic (MZ) twin pairs. Methods ASCs were isolated from subcutaneous adipose tissue from five weight-discordant (WD, within-pair difference in BMI > 3 kg/m(2)) MZ twin pairs, with measured BMI and metabolic status. The ASC immunophenotype, proliferation and osteogenic and adipogenic differentiation capacity were studied. ASC immunogenicity, immunosuppression capacity and the expression of inflammation markers were investigated. ASC angiogenic potential was assessed in cocultures with endothelial cells. Results ASCs showed low immunogenicity, proliferation, and osteogenic differentiation capacity independent of weight among all donors. ASCs showed a mesenchymal stem cell-like immunophenotype;however, the expression of CD146 was significantly higher in leaner WD twins than in heavier cotwins. ASCs from heavier twins from WD pairs showed significantly greater adipogenic differentiation capacity and higher expression of TNF and lower angiogenic potential compared with their leaner cotwins. ASCs showed immunosuppressive capacity in direct cocultures;however, heavier WD twins showed stronger immunosuppressive capacity than leaner cotwins. Conclusions Our genetically matched data suggest that a higher weight of the donor may have some effect on ASC characteristics, especially on angiogenic and adipogenic potential, which should be considered when ASCs are used clinically.

关键词： Adipose stem cells Cell surface markers Differentiation Immunogenicity Immunosuppression Proliferation

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Bone Morphogenic Protein 9(BMP9)/Growth Differentiation Factor 2(GDF2)modulates mouse adult hippocampal neurogenesis by regulating the survival of early neural progenitors

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Genes & Diseases 2023年第4期10卷 1175-1179页

作者： Mary Rose Rogers Wei Zeng Xian Zhang Ruidong Li Qiang Wei Yuhan Kong Piao Zhao Guozhi Zhao Yonghui Wang Jiamin Zhong Yi Zhu Rex C.Haydon Hue H.Luu Russell R.Reid Daniel A.Peterson Michael J.Lee Tong-Chuan He Molecular Oncology Laboratory Department of Orthopaedic Surgery and Rehabilitation MedicineThe University of Chicago Medical CenterChicagoIL 60637USA Graduate Program Committee on Genetics Genomics and System BiologyThe University of ChicagoChicagoIL 60637USA Department of Interventional Neurology The First Dongguan Affiliated HospitalGuangdong Medical UniversityDongguanGuangdong 523475China Department of Neurology The Second Affiliated Hospital of Jianghan UniversityWuhanHubei 430000China Department of Orthopaedic Surgery The Second Affiliated Hospital of Chongqing Medical UniversityChongqing 400010China Department of Clinical Laboratory Medicine Rehabilitation MedicineOrthopaedic Surgery and UrologyThe First Affiliated Hospital of Chongqing Medical UniversityChongqing 400016China Department of Endocrinology Shanghai Jiao-Tong University School of MedicineShanghai 200000China Ministry of Education Key Laboratory of Diagnostic Medicine and Department of Clinical BiochemistryThe School of Laboratory MedicineChongqing Medical UniversityChongqing 400016China Department of Orthopaedic Surgery Beijing HospitalChinese Academy of Medical Sciences&Peking Union Medical CollegeBeijing 100730China Laboratory of Craniofacial Suture Biology and Development Department of Surgery Section of Plastic SurgeryThe University of Chicago Medical CenterChicagoIL 60637USA Center for Stem Cell and Regenerative Medicine Rosalind Franklin University of Medicine and ScienceNorth ChicagoIL 60064USA

Adult neurogenesis occurs in two specialized regions of the mammalian brain,the subventricular zone(SVZ)and the subgranular zone(SGZ)of the dentate gyrus(DG).^(1)Adult hippocampal neural stem cells(NSCs),referred to as Type 1 cells represented by radial glia-like cells(RGLs),generate Type 2 cells that are divided into Type 2a and Type 2 b subpopulations,the latter of which give rise to Type 3 cells(neuroblasts).

关键词： neural progenitor ventricular

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development of novel technology for the visualization and quantitation of angiogenesis and the alveolar-capillary network in a mouse model of fibrosis

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American Journal of Physiology - Lung Cellular and Molecular Physiology 2025年第6期328卷 L866-L876页

作者： Thorndyke, Hannah F. Lundberg, Evan P. Gaxon, Edwin Ortiz Dawson, Maggie M. Mason, Emma C. Hollaway, Julia M. Vladar, Eszter K. Escobar, David Coronado Majka, Susan M. Division of Pulmonary Critical Care & Sleep Medicine Department of Medicine National Jewish Health Denver CO United States Cell Stem Cell and Development Graduate Program University of Colorado Anschutz Medical Campus Aurora CO United States Department of Medicine University of Colorado Anschutz Medical Campus Aurora CO United States Onimagin Technologies SCA Cordoba Spain Gates Center for Regenerative Medicine and Stem Cell Biology University of Colorado Aurora CO United States

Adaptive angiogenesis can drive repair or underlie the pathogenesis of tissue remodeling. Pulmonary vascular dysfunction is a major manifestation of chronic lung disease (CLD), but the role of angiogenesis in the development of CLD is not well defined. Microvascular capillaries in the alveolar-capillary network are the vessels most affected by pruning and remodeling in the lung, resulting in reduced capillary length and diameter with subsequent loss of gas exchange surfaces. Our lab has previously demonstrated that microvascular endothelial progenitor cells (mvEPCs) drive reparative angiogenesis. We hypothesize that visualization of the alveolar-capillary microvasculature in three-dimensions is essential to define the mechanisms governing repair versus progression to the pathogenesis of CLD. To address this gap in knowledge, we have developed a simple and reliable fluorescent perfusion technique that will allow the quantitation of microvessel structure in the alveolar-capillary network using mouse models of lung injury. This approach may be used in various organ systems to visualize microvasculature structure and its role in disease. Copyright © 2025 The Authors.

关键词： alveolar-capillary network ATP binding cassette subfamily G member 2 (ABCG2) fibrosis microvascular endothelial progenitor cell (mvEPC) reparative angiogenesis

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Experimental and real-world evidence supporting the computational repurposing of bumetanide for APOE4-related Alzheimer's disease ( Oct, 10.1038/s43587-021-00122-7, 2021)

NATURE AGING

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NATURE AGING 2021年第12期1卷 1202-1202页

作者： Taubes, Alice Nova, Phil Zalocusky, Kelly A. Kosti, Idit Bicak, Mesude Zilberter, Misha Y. Hao, Yanxia Yoon, Seo Yeon Oskotsky, Tomiko Pineda, Silvia Chen, Bin Jones, Emily Aery A. Choudhary, Krishna Grone, Brian Balestra, Maureen E. Chaudhry, Fayzan Paranjpe, Ishan De Freitas, Jessica Koutsodendris, Nicole Chen, Nuo Wang, Celine Chang, William An, Alice Glicksberg, Benjamin S. Sirota, Marina Huang, Yadong Gladstone Institute of Neurological Disease Gladstone Institutes San Francisco CA USA Biomedical Sciences Graduate Program University of California San Francisco CA USA Gladstone Center for Translational Advancement Gladstone Institutes San Francisco CA USA Department of Neurology University of California San Francisco CA USA Bakar Computational Health Sciences Institute University of California San Francisco CA USA Department of Pediatrics University of California San Francisco CA USA Hasso Plattner Institute for Digital Health at Mount Sinai Icahn School of Medicine at Mount Sinai New York NY USA Department of Genetics and Genomic Sciences Icahn School of Medicine at Mount Sinai New York NY USA Department of Surgery University of California San Francisco CA USA Gladstone Institute of Data Science and Biotechnology Gladstone Institutes San Francisco CA USA Development and Stem Cell Biology Graduate Program University of California San Francisco CA USA Department of Pathology University of California San Francisco CA USA

The evident genetic, pathological and clinical heterogeneity of Alzheimer’s disease (AD) poses challenges for traditional drug development. We conducted a computational drug-repurposing screen for drugs to treat apolipoprotein E4 (APOE4)-related AD. We first established APOE genotype-dependent transcriptomic signatures of AD by analyzing publicly available human brain databases. We then queried these signatures against the Connectivity Map database, which contains transcriptomic perturbations of more than 1,300 drugs, to identify those that best reverse APOE genotype-specific AD signatures. Bumetanide was identified as a top drug for APOE4-related AD. Treatment of APOE4-knock-in mice without or with amyloid β (Aβ) accumulation using bumetanide rescued electrophysiological, pathological or cognitive deficits. Single-nucleus RNA sequencing revealed transcriptomic reversal of AD signatures in specific cell types in these mice, a finding confirmed in APOE4 induced pluripotent stem cell (iPSC)-derived neurons. In humans, bumetanide exposure was associated with a significantly lower AD prevalence in individuals over the age of 65 years in two electronic health record databases, suggesting the effectiveness of bumetanide in preventing AD.

关键词： Ageing Alzheimer's disease Computational neuroscience Life Sciences general

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FLT3 is genetically essential for ITD-mutated leukemic stem cells but dispensable for human hematopoietic stem cells

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Blood 2025年第20期145卷 2361-2373页

作者： Araújo, Joana L. Wagenblast, Elvin Voisin, Veronique McLeod, Jessica Gan, Olga I. Bansal, Suraj Jin, Liqing Mitchell, Amanda Gratton, Blaise Cutting, Sarah Arruda, Andrea Doedens, Monica Travas, Anthea Kim, Dennis Capo-Chichi, Jose-Mario Abelson, Sagi Minden, Mark D. Wang, Jean C. Y. Sobrinho-Simões, Manuel A. Pinto-do-Ó, Perpétua Lechman, Eric Dick, John E. Princess Margaret Cancer Centre University Health Network Toronto ON Canada Department of Hematology Centro Hospitalar Universitário de São João Porto Portugal Faculty of Medicine University of Porto Porto Portugal Instituto de Investigação e Inovação em Saúde University of Porto Porto Portugal Instituto Nacional de Investigação Biomédica University of Porto Porto Portugal Ipatimup-Instituto de Patologia e Imunologia Molecular da Universidade do Porto Porto Portugal Department of Oncological Sciences Icahn School of Medicine at Mount Sinai New York NY United States Division of Pediatric Hematology-Oncology Department of Pediatrics Icahn School of Medicine at Mount Sinai New York NY United States Tisch Cancer Institute Black Family Stem Cell Institute The Mindich Child Health and Development Institute Center for Advancement of Blood Cancer Therapies Icahn School of Medicine at Mount Sinai New York NY United States Department of Medical Oncology and Hematology Princess Margaret Cancer Centre University Health Network Toronto ON Canada Department of Hematology University of Toronto Toronto ON Canada Laboratory Medicine Program University Health Network Toronto ON Canada Department of Laboratory Medicine and Pathobiology Faculty of Medicine University of Toronto Toronto ON Canada Ontario Institute for Cancer Research Toronto ON Canada Department of Molecular Genetics University of Toronto Toronto ON Canada Department of Medicine University of Toronto Toronto ON Canada Instituto de Ciências Biomédicas Abel Salazar University of Porto Porto Portugal Division of Hematology and Oncology University of Pittsburgh School of Medicine Pittsburgh PA United States Cancer Therapeutics Program University of Pittsburgh Medical Center Hillman Cancer Center Pittsburgh PA United States

Leukemic stem cells (LSCs) fuel acute myeloid leukemia (AML) growth and relapse, but therapies tailored toward eradicating LSCs without harming normal hematopoietic stem cells (HSCs) are lacking. FMS-like tyrosine kinase 3 (FLT3) is considered an important therapeutic target due to frequent mutation in AML and association with relapse. However, there has been limited clinical success with FLT3 drug targeting, suggesting either that FLT3 is not a vulnerability in LSC or that more potent inhibition is required, a scenario where HSC toxicity could become limiting. We tested these possibilities by ablating FLT3 using CRISPR/Cas9-mediated FLT3 knockout (FLT3-KO) in human LSCs and HSCs followed by functional xenograft assays. FLT3-KO in LSCs from FLT3–internal tandem duplication (ITD)-mutated but not FLT3–wild-type AMLs resulted in short-term leukemic grafts of FLT3-KO edited cells that disappeared by 12 weeks. By contrast, FLT3-KO in HSCs from the fetal liver, cord blood, and adult bone marrow did not impair multilineage hematopoiesis in primary and secondary xenografts. Our study establishes FLT3 as an ideal therapeutic target where ITD-positive LSCs are eradicated upon FLT3 deletion whereas HSCs are spared. These findings support the development of more potent FLT3-targeting drugs or gene-editing approaches for LSC eradication to improve clinical outcomes. © 2025 American Society of Hematology

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