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Correction: stem cell transcriptional profiles from mouse subspecies reveal cis-regulatory evolution at translation genes

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Heredity 2024年第5期133卷 370页

作者： Noah M Simon Yujin Kim Joost Gribnau Diana M Bautista James R Dutton Rachel B Brem Biology of Aging Doctoral Program Leonard Davis School of Gerontology University of Southern California Los Angeles CA 90089 USA. Buck Institute for Research on Aging Novato CA 94945 USA. Department of Plant and Microbial Biology University of California Berkeley Berkeley CA 94720 USA. Stem Cell Institute University of Minnesota Minneapolis MN 55455 USA. Department of Genetics Cell Biology and Development University of Minnesota Minneapolis MN 55455 USA. Department of Reproduction and Development Erasmus MC Rotterdam PO Box 2040 CA 3000 Netherlands. Department of Molecular and Cell Biology University of California Berkeley Berkeley CA 94720 USA. Buck Institute for Research on Aging Novato CA 94945 USA. rbrem@berkeley.edu. Department of Plant and Microbial Biology University of California Berkeley Berkeley CA 94720 USA. rbrem@berkeley.edu.

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Cover Image, Volume 236, Number 9, September 2021

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Journal of Cellular Physiology 2021年第9期236卷

作者： Fatemeh Ghaemimanesh Majid Mehravar Saeideh Milani Ensieh M. Poursani Kioomars Saliminejad Monoclonal Antibody Research Center Avicenna Research Institute ACECR Tehran Iran Department of Anatomy and Developmental Biology Development and Stem Cells Program Biomedicine Discovery Institute Monash University Melbourne Australia Blood Transfusion Research Center High Institute for Research and Education in Transfusion Medicine Tehran Iran Hematology Oncology and Stem Cell Transplantation Research Center Tehran University of Medical Sciences Tehran Iran Reproductive Biotechnology Research Center Avicenna Research Institute ACECR Tehran Iran

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Effector Site Immune Dynamics in Refractory Chronic Graft-Versus-Host Disease: A Rockstar Trial Companion Study after Belumosudil Treatment.

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Transplantation and Cellular Therapy 2024年第2期30卷 S269-S270页

作者： Sharma, Rubina, PhD Holtzman, Noa G., MD Pusic, Dr. Iskra, MD, MSCI Cutler, Dr. Corey, MD, MPH, FRCPC Treister, Nathaniel, DMD, DMSc Mehta, Rohtesh S., MD, MPH, MS Alousi, Amin M., MD Vigneswaran, Nadarajah, BDS, DrMedDent, DMD Schueller, Olivier, PhD Macé, Sandrine, PhD Yao, Yu, MD Ji, Ran, PhD Hu, Beifang, PhD Marshall, Kathy Blazar, Bruce R., MD Lee, Stephanie J, MD, MPH Pavletic, Dr. Steven Z., MD, MS Mays, Jacqueline W., DDS, MHSc, PhD National Institute of Dental and Craniofacial Research National Institutes of Health Bethesda MD Immune Deficiency Cellular Therapy Program Center for Cancer Research National Cancer Institute National Institutes of Health Bethesda MD Medicine Division of Oncology Washington University School of Medicine St. Louis MO Division of Transplantation and Cellular Therapy Department of Medical Oncology Dana-Farber Cancer Institute Boston MA Division of Oral Medicine and Dentistry Brigham and Women's Hospital Boston MA Clinical Research Division Fred Hutchinson Cancer Center Seattle WA Department of Stem Cell Transplantation and Cellular Therapy The University of Texas MD Anderson Cancer Center Houston TX University of Texas School of Dentistry at Houston Houston TX Clinical Development Sanofi Cambridge MA Research and Development Sanofi Chilly-Marzarin France Medical Affairs Sanofi Bridgewater NJ Department of Pediatrics Division of Blood & Marrow Transplant & Cellular Therapy University of Minnesota Minneapolis MN Fred Hutchinson Cancer Center Seattle WA

IntroductionBelumosudil (KD025) is an oral selective rho-associated coiled-coil kinase 2 (ROCK2) inhibitor approved for 3 rd line therapy of chronic graft-versus-host disease (cGVHD). Prior studies demonstrated reduced peripheral blood IL-17 activity and regulatory T cell recovery after ROCK2 inhibition but did not examine responses directly in cGVHD affected tissues. Here, we report tissue-level cGVHD immune dynamics after 6-months of belumosudil treatment in oral mucosa, salivary glands, and skin. MethodsThis companion study is an extension of the pivotal ROCKstar study and evaluated belumosudil 200 mg QD or BID in a total of twenty participants with oral cGVHD (aged 21-77 years) who received 2 to 5 prior lines of systemic therapy. The primary goal of this study was to characterize changes in the local immune cellular profile and IL-17 signaling before and after 6 months of treatment with belumosudil. Enrolled subjects with oral cGVHD consented to additional collection of saliva, peripheral blood and biopsy of the skin, oral mucosa and labial salivary glands at baseline and six months after initiating belumosudil or upon discontinuation of belumosudil if earlier. Matched biospecimens were blinded and analyzed for immune cells and analytes. Comparisons used paired tests at alpha 0.05. ResultsSignificant changes were identified in cGVHD affected tissues after belumosudil treatment. Responders to belumosudil based on overall (N=12) or oral-specific (N=10) NIH response criteria after treatment demonstrated a decrease in oral mucosal collagen type III and I, respectively. In parallel, multiplex immunohistochemistry identified immune cells including CD3 + and CD4 + that significantly decreased in frequency in oral mucosa after treatment in all subjects (Table 1). A decrease in IL-17 + cells was noted in both oral mucosa (N=14 evaluable pairs) and salivary glands (N=11 evaluable pairs) from all subjects. Fewer trends were noted in skin (N=14 evaluable pairs), though lowe

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Indirect Mechanisms of Transcription Factor-Mediated Gene Regulation during Cell Fate Changes

Advanced genetics (Hoboken, N.J.)

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Advanced genetics (Hoboken, N.J.) 2022年第4期3卷 2200015页

作者： Michael R Larcombe Sheng Hsu Jose M Polo Anja S Knaupp Department of Anatomy and Developmental Biology Monash University Clayton Victoria 3168 Australia. Development and Stem Cells Program Monash Biomedicine Discovery Institute Clayton Victoria 3168 Australia. Australian Regenerative Medicine Institute Monash University Clayton Victoria 3168 Australia. South Australian Immunogenomics Cancer Institute Faculty of Health and Medical Sciences University of Adelaide Adelaide South Australia 5005 Australia. Adelaide Centre for Epigenetics Faculty of Health and Medical Sciences University of Adelaide Adelaide South Australia 5005 Australia.

Transcription factors (TFs) are the master regulators of cellular identity, capable of driving cell fate transitions including differentiations, reprogramming, and transdifferentiations. Pioneer TFs recognize partial motifs exposed on nucleosomal DNA, allowing for TF-mediated activation of repressed chromatin. Moreover, there is evidence suggesting that certain TFs can repress actively expressed genes either directly through interactions with accessible regulatory elements or indirectly through mechanisms that impact the expression, activity, or localization of other regulatory factors. Recent evidence suggests that during reprogramming, the reprogramming TFs initiate opening of chromatin regions rich in somatic TF motifs that are inaccessible in the initial and final cellular states. It is postulated that analogous to a sponge, these transiently accessible regions "soak up" somatic TFs, hence lowering the initial barriers to cell fate changes. This indirect TF-mediated gene regulation event, which is aptly named the "sponge effect," may play an essential role in the silencing of the somatic transcriptional network during different cellular conversions.

关键词： cellular reprogramming decoy DNA iPSCs pluripotency sponge effect transcription factor transcription factor sequestration transiently accessible chromatin regions

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Cell culture-derived extracellular vesicles: Considerations for reporting cell culturing parameters

Journal of Extracellular Biology

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Journal of Extracellular Biology 2023年第10期2卷 e115页

作者： Shekari, Faezeh Alibhai, Faisal J. Baharvand, Hossein Börger, Verena Bruno, Stefania Davies, Owen Giebel, Bernd Gimona, Mario Salekdeh, Ghasem Hosseini Martin-Jaular, Lorena Mathivanan, Suresh Nelissen, Inge Nolte-’t Hoen, Esther Perut, Francesca Pluchino, Stefano Pocsfalvi, Gabriella Salomon, Carlos Soekmadji, Carolina Staubach, Simon Torrecilhas, Ana Claudia Shelke, Ganesh Vilas Tertel, Tobias Zhu, Dandan Théry, Clotilde Witwer, Kenneth Nieuwland, Rienk Department of Stem Cells and Developmental Biology Cell Science Research Center Royan Institute for Stem Cell Biology and Technology ACECR Tehran Iran Advanced Therapy Medicinal Product Technology Development Center (ATMP-TDC) Cell Science Research Center Royan Institute for Stem Cell Biology and Technology ACECR Tehran Iran University Health Network Toronto Canada Department of Developmental Biology School of Basic Sciences and Advanced Technologies in Biology University of Science and Culture Tehran Iran Institute for Transfusion Medicine University Hospital Essen University of Duisburg-Essen Essen Germany Department of Medical Sciences and Molecular Biotechnology Center University of Torino Turin Italy School of Sport Exercise and Health Sciences Loughborough University Loughborough United Kingdom GMP Unit Spinal Cord Injury & Tissue Regeneration Centre Salzburg (SCI-TReCS) and Research Program “Nanovesicular Therapies” Paracelsus Medical University Salzburg Austria Faculty of Natural Sciences Macquarie University North Ryde NSW Australia Institut Curie INSERM U932 and Curie CoreTech Extracellular Vesicles PSL Research University Paris France Department of Biochemistry and Genetics La Trobe Institute for Molecular Science La Trobe University Melbourne VIC Australia VITO (Flemish Institute for Technological Research) Health department Boeretang Belgium Department of Biomolecular Health Sciences Faculty of Veterinary Medicine Utrecht University Utrecht Netherlands School of Pharmacy and Pharmaceutical Sciences & Trinity Biomedical Sciences Institute Trinity College Dublin Dublin Ireland Biomedical Science and Technologies and Nanobiotechnology Lab IRCCS Istituto Ortopedico Rizzoli Bologna Italy Department of Clinical Neurosciences University of Cambridge Cambridge United Kingdom Institute of Biosciences and BioResources National Research Council Naples Italy Translational Extracellular Vesicles in Obstetrics and Gynae-Oncology Group UQ Centre for Cli

Cell culture-conditioned medium (CCM) is a valuable source of extracellular vesicles (EVs) for basic scientific, therapeutic and diagnostic applications. Cell culturing parameters affect the biochemical composition, release and possibly the function of CCM-derived EVs (CCM-EV). The CCM-EV task force of the Rigor and Standardization Subcommittee of the International Society for Extracellular Vesicles aims to identify relevant cell culturing parameters, describe their effects based on current knowledge, recommend reporting parameters and identify outstanding questions. While some recommendations are valid for all cell types, cell-specific recommendations may need to be established for non-mammalian sources, such as bacteria, yeast and plant cells. Current progress towards these goals is summarized in this perspective paper, along with a checklist to facilitate transparent reporting of cell culturing parameters to improve the reproducibility of CCM-EV research. © 2023 The Authors. Journal of Extracellular Biology published by Wiley Periodicals LLC on behalf of International Society for Extracellular Vesicles.

关键词： cell culture-conditioned medium cellular therapy ectosomes exosomes extracellular vesicles in vitro reproducibility rigor standardization

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Plain language summary of the outcomes from the first Rare Bone Disease Summit: current challenges and priority actions

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Future Rare Diseases 2025年第1期5卷

作者： Inês Alves Manju Chandran Emma Albee Michelle Davis Edward C. Hsiao Anna Petryk Oliver Semler Marwan Sleiman ANDO Portugal Évora PortugalSchool of Health and Human Development CHRC University of Évora Évora Portugal Osteoporosis and Bone Metabolism Unit Department of Endocrinology Singapore General Hospital DUKE NUS Medical School Singapore Singapore Patient Author Seal Cove USAInternational Fibrodysplasia Ossificans Progressiva Association (IFOPA) North Kansas City USA International Fibrodysplasia Ossificans Progressiva Association (IFOPA) North Kansas City USA Division of Endocrinology and Metabolism the Institute for Human Genetics the Eli and Edythe Broad Institute for Regeneration Medicine and Stem Cell Research the Program in Craniofacial Biology and the Department of Medicine University of California San Francisco USA Global Medical Affairs Alexion Pharmaceuticals Inc AstraZeneca Rare Disease Boston USA Department of Pediatrics Faculty of Medicine and University Hospital Cologne University of Cologne Cologne GermanyCenter for Rare Diseases Faculty of Medicine and University Hospital Cologne University of Cologne Cologne Germany Global Medical Affairs Ipsen Boulogne-Billancourt France

Plain Language SummaryWhat is this summary about?Rare bone diseasesare uncommon medical conditions that primarily affect the bones, cartilage, and muscles of themusculoskeletal system. People living with these rare conditions face challenges such as delays in diagnosis, limited accessibility to rare bone disease medical experts, difficulty communicating withhealthcare professionals, and limited treatment options. The Rare Bone DiseaseSummitbrought together people with a personal and/or professional interest in rare bone diseases to discuss and propose actions to address the current biggest problems faced by people living with these *** Rare Bone Disease Summit was held online over two days in December 2021 with 65 attendees from across the world. These people representedpatient advocacy groups,medical and scientific organizations,medical education providers, healthcare professionals, and scientific experts from thepharmaceutical *** to say(download PDF and double click sound icon to play sound)…Musculoskeletal system:MUS-kuh-low-SKEH-luh-tuhl SIS-tuhmFibrodysplasia ossificans progressiva:FYE-broh-dis-PLAY-zhuh OSS-if-ih-kans pro-GRESS-ih-vuhHypophosphatasia:HY-poh-FOSS-fuh-TAY-zhuhOsteogenesis imperfecta:OSS-tee-oh-JEN-uh-sis im-purr-FECK-tuhAchondroplasia:AY-kon-druh-PLAY-zhuhFibrous dysplasia:FYE-bruhs dis-PLAY-zhuhWhat are the key takeaways?Discussions during the Rare Bone Disease Summit identified key bottlenecks that arise when trying to treat people with rare bone diseases, such asIt can take a long time to diagnose rare bone diseases correctly and get a patient connected to the right medical *** are relatively few rare bone disease medical experts worldwide compared with the number of dedicated healthcare professionals in other *** people with rare bone diseases grow older, there is not enough support available to help with the changes that come with the transition frompediatricto adult and/or adult *** d

关键词： Rare bone diseases multistakeholder meeting lay summary plain language summary patient-centered care pathway patient experience

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CHEK2 GERMLINE VARIANTS AND ALLOGENEIC HEMATOPOIETIC stem CELL TRANSPLANT OUTCOMES

EJC Paediatric Oncology

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EJC Paediatric Oncology 2023年 2卷 100058-100058页

作者： Lahtinen, Atte K Koski, Jessica Ritari, Jarmo Hyvärinen, Kati Koskela, Satu Partanen, Jukka Vettenranta, Kim Koskenvuo, Minna Niittyvuopio, Riitta Salmenniemi, Urpu Itälä-Remes, Maija Jahnukainen, Kirsi Kilpivaara, Outi Wartiovaara- Kautto, Ulla Karu, Maarja Applied Tumor Genomics Research Program Faculty of Medicine University of Helsinki Helsinki Finland Department of Medical and Clinical Genetics Medicum Faculty of Medicine University of Helsinki Helsinki Finland Research and Development Finnish Red Cross Blood Service Helsinki Finland New Children's Hospital Pediatric Research Center University of Helsinki and Helsinki University Hospital Helsinki Finland Helsinki University Hospital Comprehensive Cancer Center Department of Hematology and University of Helsinki Helsinki Finland Turku University Hospital Department of Clinical Hematology and Stem Cell Transplant Unit and University of Turku Turku Finland Helsinki University Hospital Comprehensive Cancer Center Department of Hematology and University of Helsinki Helsinki Finland. ulla.wartiovaara New Children's Hospital University of Helsinki and Helsinki University Hospital Helsinki Finland Department of Hematology and Oncology Tallinn Children's Hospital Tallinn Estonia

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H2A.Z is essential for oocyte maturation and fertility in female mouse

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Nature structural & molecular biology 2025年 2025 Jun 13页

作者： Qianhua Xu Chunyi Huang Jia Ming Xukun Lu Ling Liu Zhenhai Du Zhen Chen Jie Na Guohong Li Yunlong Xiang Yu Zhang Wei Xie Center for Stem Cell Biology and Regenerative Medicine MOE Key Laboratory of Bioinformatics New Cornerstone Science Laboratory School of Life Sciences Tsinghua University Beijing China. Tsinghua-Peking Center for Life Sciences Beijing China. Peking University-Tsinghua University-National Institute of Biological Sciences Joint Graduate Program School of Life Sciences Tsinghua University Beijing China. Center for Stem Cell Biology and Regenerative Medicine School of Medicine Tsinghua University Beijing China. State Key Laboratory of Reproductive Medicine and Offspring Health Center for Reproductive Medicine Institute of Women Children and Reproductive Health Shandong University Shandong China. New Cornerstone Science Laboratory Frontier Science Center for Immunology and Metabolism Hubei Key Laboratory of Cell Homeostasis College of Life Sciences Taikang Center for Life and Medical Sciences Wuhan University Wuhan China. National Laboratory of Biomacromolecules and Key Laboratory of Epigenetic Regulation and Intervention Institute of Biophysics Chinese Academy of Sciences Beijing China. School of Life Sciences University of Chinese Academy of Sciences Beijing China. Center for Medical Epigenetics School of Basic Medical Sciences Chongqing Medical University Chongqing China. xiangyl@***. Center for Medical Epigenetics Children's Hospital of Chongqing Medical University Chongqing China. xiangyl@***. Obstetrics and Gynecology Hospital Institute of Reproduction and Development Fudan University Shanghai China. zhang_yu_sfy@***. Research Units of Embryo Original Diseases Chinese Academy of Medical Sciences Shanghai China. zhang_yu_sfy@***. Center for Stem Cell Biology and Regenerative Medicine MOE Key Laboratory of Bioinformatics New Cornerstone Science Laboratory School of Life Sciences Tsinghua University Beijing China. xiewei121@***. Tsinghua-Peking Center for Life Sciences Beijing China. xiewei121@tsinghua.edu.cn.

Oocyte maturation is essential for both gametogenesis and early development, when large amounts of transcripts are produced without DNA replication. Histone variants, which can be incorporated at cis-regulatory elements in a replication-independent manner, are naturally suited for such regulation. However, their roles during mammalian oocyte maturation remain elusive. Here we show that oocyte-specific depletion of H2A.Z, an evolutionarily conserved histone variant, in female mice results in profound epigenetic and transcriptional alterations, impedes resumption of oocyte meiosis II and causes infertility. Mechanistically, H2A.Z in mouse oocytes is incorporated into chromatin at active promoters and putative enhancers. Interestingly, H2A.Z is depleted from CG-rich silenced promoters, including poised Polycomb target genes, in fully grown oocytes (FGOs), unlike what occurs in growing oocytes, early embryos and mouse embryonic stem cells. In FGOs, the presence of H2A.Z correlates with histone acetylation, except in regions marked by DNA methylation and H3K36me3. Depletion of H2A.Z leads to impaired activities of a subset of promoters and enhancers, correlated with defective gene expression. Consistent with a role in gene activation, H2A.Z in FGOs is widely acetylated at the promoters and enhancers. Together, our findings uncover an essential role of H2A.Z in mammalian oocyte maturation and female fertility.

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Author Correction: Multiplexed inhibition of immunosuppressive genes with Cas13d for combinatorial cancer immunotherapy

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Nature biotechnology 2025年 2025 Feb 3页

作者： Feifei Zhang Ryan D Chow Emily He Chuanpeng Dong Shan Xin Daniyal Mirza Yanzhi Feng Xiaolong Tian Nipun Verma Medha Majety Yueqi Zhang Guangchuan Wang Sidi Chen Department of Genetics Yale University School of Medicine New Haven CT USA. System Biology Institute Yale University West Haven CT USA. Center for Cancer Systems Biology Yale University West Haven CT USA. M.D.-Ph.D. Program Yale University West Haven CT USA. Molecular Cell Biology Genetics and Development Program Yale University New Haven CT USA. Yale College New Haven CT USA. Immunobiology Program Yale University New Haven CT USA. Department of Therapeutic Radiology Yale University School of Medicine New Haven CT USA. Department of Genetics Yale University School of Medicine New Haven CT USA. guangchuan.wang@***. System Biology Institute Yale University West Haven CT USA. guangchuan.wang@***. Center for Cancer Systems Biology Yale University West Haven CT USA. guangchuan.wang@***. Key Laboratory of Multi-Cell Systems Shanghai Institute of Biochemistry and Cell Biology Center for Excellence in Molecular Cell Science Chinese Academy of Sciences Shanghai China. guangchuan.wang@***. Department of Genetics Yale University School of Medicine New Haven CT USA. sidi.chen@yale.edu. System Biology Institute Yale University West Haven CT USA. sidi.chen@yale.edu. Center for Cancer Systems Biology Yale University West Haven CT USA. sidi.chen@yale.edu. M.D.-Ph.D. Program Yale University West Haven CT USA. sidi.chen@yale.edu. Molecular Cell Biology Genetics and Development Program Yale University New Haven CT USA. sidi.chen@yale.edu. Yale College New Haven CT USA. sidi.chen@yale.edu. Immunobiology Program Yale University New Haven CT USA. sidi.chen@yale.edu. Department of Neurosurgery Yale University School of Medicine New Haven CT USA. sidi.chen@yale.edu. Yale Comprehensive Cancer Center Yale University School of Medicine New Haven CT USA. sidi.chen@yale.edu. Yale Stem Cell Center Yale University School of Medicine New Haven CT USA. sidi.chen@yale.edu. Yale Center for Biomedical Data Science Yale University School of Medicine New Have

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Author Correction: A placental model of SARS-CoV-2 infection reveals ACE2-dependent susceptibility and differentiation impairment in syncytiotrophoblasts

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Nature cell biology 2024年第2期26卷 305页

作者： J Chen J A Neil J P Tan R Rudraraju M Mohenska Y B Y Sun E Walters N G Bediaga G Sun Y Zhou Y Li D Drew P Pymm W H Tham Y Wang F J Rossello G Nie X Liu K Subbarao J M Polo Department of Anatomy and Developmental Biology Monash University Clayton Victoria Australia. Development and Stem Cells Program Monash Biomedicine Discovery Institute Clayton Victoria Australia. Australian Regenerative Medicine Institute Monash University Clayton Victoria Australia. Department of Microbiology and Immunology The University of Melbourne at the Peter Doherty Institute for Infection and Immunity Melbourne Victoria Australia. Adelaide Centre for Epigenetics Faculty of Health and Medical Sciences The University of Adelaide Adelaide South Australia Australia. South Australian Immunogenomics Cancer Institute Faculty of Health and Medical Sciences The University of Adelaide Adelaide South Australia Australia. Implantation and Pregnancy Research Laboratory School of Health and Biomedical Sciences RMIT University Melbourne Victoria Australia. Infectious Diseases and Immune Defences Division The Walter and Eliza Hall Institute of Medical Research Parkville Victoria Australia. Department of Medical Biology University of Melbourne Melbourne Victoria Australia. University of Melbourne Centre for Cancer Research The University of Melbourne Melbourne Victoria Australia. School of Life Sciences Westlake University Hangzhou China. Research Center for Industries of the Future Westlake University Hangzhou China. Westlake Laboratory of Life Sciences and Biomedicine Hangzhou China. Westlake Institute for Advanced Study Hangzhou China. Department of Microbiology and Immunology The University of Melbourne at the Peter Doherty Institute for Infection and Immunity Melbourne Victoria Australia. kanta.subbarao@***. WHO Collaborating Centre for Reference and Research on Influenza Melbourne Victoria Australia. kanta.subbarao@***. Department of Anatomy and Developmental Biology Monash University Clayton Victoria Australia. jose.polo@monash.edu. Development and Stem Cells Program Monash Biomedicine Discovery Institute Clayton Victoria Australia. jose.polo@monas

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