1
|
Chteinberg E, Kolarova J, Vogt J, Macamo A, Bormann F, Kretzmer H, Speel EJ, van den Oord J, Schneider C, Stilgenbauer S, Becker JC, Winnepenninckx V, Biessen E, Zenke M, Kurz AK, Siebert R, zur Hausen A. The significance of PAX5 in Merkel cell carcinoma. J Pathol 2025; 266:81-94. [PMID: 40034069 PMCID: PMC11985695 DOI: 10.1002/path.6410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 12/16/2024] [Accepted: 01/29/2025] [Indexed: 03/05/2025]
Abstract
Merkel cell carcinoma (MCC) is a highly malignant skin cancer that expresses epithelial-, neuroendocrine-, and lymphoid-associated genes. Here, we focused on B-cell differentiation, which is characterised by the coexpression of PAX5 and TdT. PAX5 is the master regulator of B-cell commitment and is expressed in 65% of MCC cases. Yet little is known about the underlying molecular biology of the frequently reported PAX5 expression in MCC. Multi-omics analyses, including RNA next-generation sequencing, RT-qPCR, immunohistochemistry, and western blotting, were performed to assess PAX5 expression in MCC. Differential DNA methylation analysis at 61,043 PAX5 binding sites in enhancer and promoter elements was performed to detect differences between n = 14 MCC tissues and n = 91 various normal B-cell populations. RNA analysis revealed full-length PAX5 expression in MCC at the transcriptional level using both PAX5 transcription start sites. PAX5 protein expression was found in 40 of 41 MCCs and six out of seven MCC cell lines. DNA methylation array analysis revealed 1,084 hypermethylated loci of enhancer and promoter elements located in PAX5 binding sites in MCC. Of these, 702 loci were associated with 257 genes that are not expressed. The PAX5-associated regulatory elements of these 257 genes were enriched for interferon regulatory factor 4 (IRF4) and SPi-proto-oncogene (SPI1) binding motifs. Neither IRF4 or SPI1 could be detected in MCC on RNA or the protein level. Thus, because of the absence of these transcription factors, we conclude that full-length PAX5 alone cannot induce B-cell differentiation. © 2025 The Author(s). The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
Collapse
Affiliation(s)
- Emil Chteinberg
- Department of Pathology, GROW‐Research Institute for Oncology and ReproductionMaastricht University Medical Centre+MaastrichtThe Netherlands
- Institute for Biomedical Engineering, Department of Cell BiologyRWTH Aachen University HospitalAachenGermany
- Helmholtz Institute for Biomedical EngineeringRWTH Aachen UniversityAachenGermany
- Institute of Human GeneticsUlm University and Ulm University Medical CenterUlmGermany
| | - Julia Kolarova
- Institute of Human GeneticsUlm University and Ulm University Medical CenterUlmGermany
| | - Julia Vogt
- Institute of Human GeneticsUlm University and Ulm University Medical CenterUlmGermany
| | - Amanda Macamo
- Department of Pathology, GROW‐Research Institute for Oncology and ReproductionMaastricht University Medical Centre+MaastrichtThe Netherlands
| | | | - Helene Kretzmer
- Department of Genome RegulationMax Planck Institute for Molecular GeneticsBerlinGermany
| | - Ernst Jan Speel
- Department of Pathology, GROW‐Research Institute for Oncology and ReproductionMaastricht University Medical Centre+MaastrichtThe Netherlands
| | - Joost van den Oord
- Laboratory of Translational Cell and Tissue ResearchUniversity of LeuvenLeuvenBelgium
| | - Christof Schneider
- Department of Internal Medicine III, Division of CLLUniversity Hospital UlmUlmGermany
| | - Stephan Stilgenbauer
- Department of Internal Medicine III, Division of CLLUniversity Hospital UlmUlmGermany
| | - Jürgen C Becker
- Translational Skin Cancer Research (TSCR), German Cancer Consortium (DKTK)University Hospital of EssenEssenGermany
- German Cancer Research Center (DKFZ)HeidelbergGermany
| | - Véronique Winnepenninckx
- Department of Pathology, GROW‐Research Institute for Oncology and ReproductionMaastricht University Medical Centre+MaastrichtThe Netherlands
| | - Erik Biessen
- Experimental Vascular Pathology, Department of Pathology, Cardiovascular Research Institute MaastrichtMaastricht UniversityMaastrichtThe Netherlands
- Institute for Molecular Cardiovascular Research (IMCAR)University Hospital RWTHAachenGermany
| | - Martin Zenke
- Institute for Biomedical Engineering, Department of Cell BiologyRWTH Aachen University HospitalAachenGermany
- Helmholtz Institute for Biomedical EngineeringRWTH Aachen UniversityAachenGermany
- Department of Medicine IV, Hematology, Oncology and Stem Cell Transplantation, Faculty of MedicineRWTH Aachen University HospitalAachenGermany
- Center for Integrated Oncology Aachen Bonn Cologne Düsseldorf (CIO ABCD)AachenGermany
| | | | - Reiner Siebert
- Institute of Human GeneticsUlm University and Ulm University Medical CenterUlmGermany
| | - Axel zur Hausen
- Department of Pathology, GROW‐Research Institute for Oncology and ReproductionMaastricht University Medical Centre+MaastrichtThe Netherlands
| |
Collapse
|
2
|
Klonizakis A, Alcoverro-Bertran M, Massó P, Thomas J, de Andrés-Aguayo L, Wei X, Varamogianni-Mamatsi V, Nikolaou C, Graf T. Synergistic and antagonistic activities of IRF8 and FOS enhancer pairs during an immune-cell fate switch. EMBO J 2025; 44:2025-2055. [PMID: 39972074 PMCID: PMC11961672 DOI: 10.1038/s44318-025-00380-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Revised: 01/10/2025] [Accepted: 01/17/2025] [Indexed: 02/21/2025] Open
Abstract
Cell fate instructive genes tend to be regulated by large clusters of enhancers. Whether and how individual enhancers within such clusters cooperate in regulating gene expression is poorly understood. We have previously developed a computational method, SEGCOND, which identifies hubs that we termed Putative Transcriptional Condensates (PTCs), consisting of enhancer clusters and associated target genes. Here, we use SEGCOND to identify PTCs in a CEBPA-induced B-cell-to-macrophage transdifferentiation system. We find that PTCs are enriched for highly expressed, lineage-restricted genes and associate with BRD4, a component of transcriptional condensates. Further, we performed single and combinatorial deletions of enhancers within two PTCs active during induced transdifferentiation, harboring IRF8 and FOS. Two enhancers within the IRF8 PTC were found to provide a backup mechanism when combined, safeguarding IRF8 expression and efficient transdifferentiation. Unexpectedly, two individual enhancers within the FOS PTC antagonize each other on day 1 of transdifferentiation, delaying the conversion of B-cells into macrophages and reducing FOS expression, while on day 7, they cooperate to increase FOS levels induced cells. Our results reveal complex, differentiation-stage-specific interactions between individual enhancers within enhancer clusters.
Collapse
Affiliation(s)
- Antonios Klonizakis
- Genome Biology Program, Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, 08003, Barcelona, Spain
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra, 08005, Barcelona, Spain
| | - Marc Alcoverro-Bertran
- Genome Biology Program, Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, 08003, Barcelona, Spain
- Josep Carreras Leukaemia Research Institute (IJC), 08916, Badalona, Spain
| | - Pere Massó
- Genome Biology Program, Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, 08003, Barcelona, Spain
| | - Joanna Thomas
- Genome Biology Program, Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, 08003, Barcelona, Spain
- Faculty of Life Sciences and Medicine, King's College, WC2R 2LS, London, UK
| | - Luisa de Andrés-Aguayo
- Genome Biology Program, Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, 08003, Barcelona, Spain
| | - Xiao Wei
- Genome Biology Program, Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, 08003, Barcelona, Spain
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra, 08005, Barcelona, Spain
| | | | - Christoforos Nikolaou
- Institute for Bioinnovation, Biomedical Sciences Research Centre "Alexander Fleming", 16672, Vari, Greece.
| | - Thomas Graf
- Genome Biology Program, Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, 08003, Barcelona, Spain.
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra, 08005, Barcelona, Spain.
| |
Collapse
|
3
|
Lim B, Kamal A, Gomez Ramos B, Adrian Segarra JM, Ibarra IL, Dignas L, Kindinger T, Volz K, Rahbari M, Rahbari N, Poisel E, Kafetzopoulou K, Böse L, Breinig M, Heide D, Gallage S, Barragan Avila JE, Wiethoff H, Berest I, Schnabellehner S, Schneider M, Becker J, Helm D, Grimm D, Mäkinen T, Tschaharganeh DF, Heikenwalder M, Zaugg JB, Mall M. Active repression of cell fate plasticity by PROX1 safeguards hepatocyte identity and prevents liver tumorigenesis. Nat Genet 2025; 57:668-679. [PMID: 39948437 PMCID: PMC11906372 DOI: 10.1038/s41588-025-02081-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Accepted: 01/08/2025] [Indexed: 02/20/2025]
Abstract
Cell fate plasticity enables development, yet unlocked plasticity is a cancer hallmark. While transcription master regulators induce lineage-specific genes to restrict plasticity, it remains unclear whether plasticity is actively suppressed by lineage-specific repressors. Here we computationally predict so-called safeguard repressors for 18 cell types that block phenotypic plasticity lifelong. We validated hepatocyte-specific candidates using reprogramming, revealing that prospero homeobox protein 1 (PROX1) enhanced hepatocyte identity by direct repression of alternative fate master regulators. In mice, Prox1 was required for efficient hepatocyte regeneration after injury and was sufficient to prevent liver tumorigenesis. In line with patient data, Prox1 depletion caused hepatocyte fate loss in vivo and enabled the transition of hepatocellular carcinoma to cholangiocarcinoma. Conversely, overexpression promoted cholangiocarcinoma to hepatocellular carcinoma transdifferentiation. Our findings provide evidence for PROX1 as a hepatocyte-specific safeguard and support a model where cell-type-specific repressors actively suppress plasticity throughout life to safeguard lineage identity and thus prevent disease.
Collapse
Affiliation(s)
- Bryce Lim
- Cell Fate Engineering and Disease Modeling Group, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, Heidelberg, Germany
- HITBR Hector Institute for Translational Brain Research gGmbH, Heidelberg, Germany
- Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Aryan Kamal
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
- European Molecular Biology Laboratory, Molecular Systems Biology Unit, Heidelberg, Germany
- Department of Biomedicine, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Borja Gomez Ramos
- Cell Fate Engineering and Disease Modeling Group, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, Heidelberg, Germany
- HITBR Hector Institute for Translational Brain Research gGmbH, Heidelberg, Germany
- Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Juan M Adrian Segarra
- Cell Fate Engineering and Disease Modeling Group, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, Heidelberg, Germany
- HITBR Hector Institute for Translational Brain Research gGmbH, Heidelberg, Germany
- Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Ignacio L Ibarra
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
- European Molecular Biology Laboratory, Molecular Systems Biology Unit, Heidelberg, Germany
| | - Lennart Dignas
- Cell Fate Engineering and Disease Modeling Group, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, Heidelberg, Germany
- HITBR Hector Institute for Translational Brain Research gGmbH, Heidelberg, Germany
- Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Tim Kindinger
- Cell Fate Engineering and Disease Modeling Group, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, Heidelberg, Germany
- HITBR Hector Institute for Translational Brain Research gGmbH, Heidelberg, Germany
- Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Kai Volz
- Cell Plasticity and Epigenetic Remodeling Helmholtz Group, DKFZ, Heidelberg, Germany
- Institute of Pathology, University Hospital, Heidelberg, Germany
| | - Mohammad Rahbari
- Division of Chronic Inflammation and Cancer, DKFZ, Heidelberg, Germany
- Department of Surgery, University Hospital Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Nuh Rahbari
- Department of Surgery, University Hospital Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- Department of General and Visceral Surgery, University of Ulm, Ulm, Germany
| | - Eric Poisel
- Cell Fate Engineering and Disease Modeling Group, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, Heidelberg, Germany
- HITBR Hector Institute for Translational Brain Research gGmbH, Heidelberg, Germany
- Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Kanela Kafetzopoulou
- Cell Fate Engineering and Disease Modeling Group, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, Heidelberg, Germany
- HITBR Hector Institute for Translational Brain Research gGmbH, Heidelberg, Germany
- Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Lio Böse
- Cell Plasticity and Epigenetic Remodeling Helmholtz Group, DKFZ, Heidelberg, Germany
- Institute of Pathology, University Hospital, Heidelberg, Germany
| | - Marco Breinig
- Cell Plasticity and Epigenetic Remodeling Helmholtz Group, DKFZ, Heidelberg, Germany
- Institute of Pathology, University Hospital, Heidelberg, Germany
| | - Danijela Heide
- Division of Chronic Inflammation and Cancer, DKFZ, Heidelberg, Germany
| | - Suchira Gallage
- Division of Chronic Inflammation and Cancer, DKFZ, Heidelberg, Germany
- Institute for Interdisciplinary Research on Cancer Metabolism and Chronic Inflammation, M3-Research Center for Malignome, Metabolome and Microbiome, Faculty of Medicine, University Tuebingen, Tübingen, Germany
| | | | - Hendrik Wiethoff
- Institute of Pathology, University Hospital, Heidelberg, Germany
| | - Ivan Berest
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
- European Molecular Biology Laboratory, Molecular Systems Biology Unit, Heidelberg, Germany
| | - Sarah Schnabellehner
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | | | - Jonas Becker
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
- Department of Infectious Diseases/Virology, Section Viral Vector Technologies, Medical Faculty and Faculty of Engineering Sciences, Heidelberg University, Center for Integrative Infectious Diseases Research (CIID), BioQuant, Heidelberg, Germany
| | - Dominic Helm
- Proteomics Core Facility, DKFZ, Heidelberg, Germany
| | - Dirk Grimm
- Department of Infectious Diseases/Virology, Section Viral Vector Technologies, Medical Faculty and Faculty of Engineering Sciences, Heidelberg University, Center for Integrative Infectious Diseases Research (CIID), BioQuant, Heidelberg, Germany
- German Center for Infection Research (DZIF), Partner Site Heidelberg, Heidelberg, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Heidelberg, Heidelberg, Germany
| | - Taija Mäkinen
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
- Translational Cancer Medicine Program and Department of Biochemistry and Developmental Biology, University of Helsinki, Helsinki, Finland
- Wihuri Research Institute, Helsinki, Finland
| | - Darjus F Tschaharganeh
- Cell Plasticity and Epigenetic Remodeling Helmholtz Group, DKFZ, Heidelberg, Germany
- Institute of Pathology, University Hospital, Heidelberg, Germany
| | - Mathias Heikenwalder
- Division of Chronic Inflammation and Cancer, DKFZ, Heidelberg, Germany
- Institute for Interdisciplinary Research on Cancer Metabolism and Chronic Inflammation, M3-Research Center for Malignome, Metabolome and Microbiome, Faculty of Medicine, University Tuebingen, Tübingen, Germany
| | - Judith B Zaugg
- European Molecular Biology Laboratory, Molecular Systems Biology Unit, Heidelberg, Germany.
- Department of Biomedicine, University Hospital Basel, University of Basel, Basel, Switzerland.
| | - Moritz Mall
- Cell Fate Engineering and Disease Modeling Group, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, Heidelberg, Germany.
- HITBR Hector Institute for Translational Brain Research gGmbH, Heidelberg, Germany.
- Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany.
| |
Collapse
|
4
|
Kohutek ZA, Caslin HL, Fehrenbach DJ, Heimlich JB, Brown JD, Madhur MS, Ferrell PB, Doran AC. Bone Marrow Niche in Cardiometabolic Disease: Mechanisms and Therapeutic Potential. Circ Res 2025; 136:325-353. [PMID: 39883790 PMCID: PMC11790260 DOI: 10.1161/circresaha.124.323778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/01/2025]
Abstract
Cardiovascular and cardiometabolic diseases are leading causes of morbidity and mortality worldwide, driven in part by chronic inflammation. Emerging research suggests that the bone marrow microenvironment, or marrow niche, plays a critical role in both immune system regulation and disease progression. The bone marrow niche is essential for maintaining hematopoietic stem cells (HSCs) and orchestrating hematopoiesis. Under normal conditions, this niche ensures a return to immune homeostasis after acute stress. However, in the setting of inflammatory conditions such as those seen in cardiometabolic diseases, it becomes dysregulated, leading to enhanced myelopoiesis and immune activation. This review explores the reciprocal relationship between the bone marrow niche and cardiometabolic diseases, highlighting how alterations in the niche contribute to disease development and progression. The niche regulates HSCs through complex interactions with stromal cells, endothelial cells, and signaling molecules. However, in the setting of chronic diseases such as hypertension, atherosclerosis, and diabetes, inflammatory signals disrupt the balance between HSC self-renewal and differentiation, promoting the excessive production of proinflammatory myeloid cells that exacerbate the disease. Key mechanisms discussed include the effects of hyperlipidemia, hyperglycemia, and sympathetic nervous system activation on HSC proliferation and differentiation. Furthermore, the review emphasizes the role of epigenetic modifications and metabolic reprogramming in creating trained immunity, a phenomenon whereby HSCs acquire long-term proinflammatory characteristics that sustain disease states. Finally, we explore therapeutic strategies aimed at targeting the bone marrow niche to mitigate chronic inflammation and its sequelae. Novel interventions that modulate hematopoiesis and restore niche homeostasis hold promise for the treatment of cardiometabolic diseases. By interrupting the vicious cycle of inflammation and marrow dysregulation, such therapies may offer new avenues for reducing cardiovascular risk and improving patient outcomes.
Collapse
Affiliation(s)
- Zachary A. Kohutek
- Department of Radiation Oncology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Heather L. Caslin
- Department of Health and Human Performance, University of Houston, Houston, TX 77204, USA
| | - Daniel J. Fehrenbach
- Department of Medicine, Division of Clinical Pharmacology, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - J. Brett Heimlich
- Department of Medicine, Division of Cardiovascular Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Jonathan D. Brown
- Department of Medicine, Division of Cardiovascular Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Meena S. Madhur
- Department of Medicine, Division of Clinical Pharmacology, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - P. Brent Ferrell
- Department of Medicine, Division of Hematology and Oncology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University, Nashville, TN 37212, USA
| | - Amanda C. Doran
- Department of Medicine, Division of Cardiovascular Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University, Nashville, TN 37212, USA
| |
Collapse
|
5
|
Banerjee S, Sanyal S, Hodawadekar S, Naiyer S, Bano N, Banerjee A, Rhoades J, Dong D, Allman D, Atchison ML. YY1 knockout in pro-B cells impairs lineage commitment, enabling unusual hematopoietic lineage plasticity. Genes Dev 2024; 38:887-914. [PMID: 39362773 PMCID: PMC11535188 DOI: 10.1101/gad.351734.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Accepted: 08/29/2024] [Indexed: 10/05/2024]
Abstract
During B-cell development, cells progress through multiple developmental stages, with the pro-B-cell stage defining commitment to the B-cell lineage. YY1 is a ubiquitous transcription factor that is capable of both activation and repression functions. We found here that knockout of YY1 at the pro-B-cell stage eliminates B lineage commitment. YY1 knockout pro-B cells can generate T lineage cells in vitro using the OP9-DL4 feeder system and in vivo after injection into sublethally irradiated Rag1-/- mice. These T lineage-like cells lose their B lineage transcript profile and gain a T-cell lineage profile. Single-cell RNA-seq experiments showed that as YY1 knockout pro-B cells transition into T lineage cells in vitro, various cell clusters adopt transcript profiles representing a multiplicity of hematopoietic lineages, indicating unusual lineage plasticity. In addition, YY1 KO pro-B cells in vivo can give rise to other hematopoietic lineages in vivo. Evaluation of RNA-seq, scRNA-seq, ChIP-seq, and scATAC-seq data indicates that YY1 controls numerous chromatin-modifying proteins leading to increased accessibility of alternative lineage genes in YY1 knockout pro-B cells. Given the ubiquitous nature of YY1 and its dual activation and repression functions, YY1 may regulate commitment in multiple cell lineages.
Collapse
Affiliation(s)
- Sarmistha Banerjee
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Sulagna Sanyal
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Suchita Hodawadekar
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Sarah Naiyer
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Nasreen Bano
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Anupam Banerjee
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Joshua Rhoades
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Dawei Dong
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - David Allman
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Michael L Atchison
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA;
| |
Collapse
|
6
|
Tran NT, Graf R, Acevedo-Ochoa E, Trombke J, Weber T, Sommermann T, Salomon C, Kühn R, Rajewsky K, Chu VT. In vivo CRISPR/Cas9-mediated screen reveals a critical function of TFDP1 and E2F4 transcription factors in hematopoiesis. Leukemia 2024; 38:2003-2015. [PMID: 39043964 PMCID: PMC11347378 DOI: 10.1038/s41375-024-02357-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 07/10/2024] [Accepted: 07/15/2024] [Indexed: 07/25/2024]
Abstract
Hematopoiesis is a continuous process of blood cell production driven by hematopoietic stem and progenitor cells (HSPCs) in the bone marrow. Proliferation and differentiation of HSPCs are regulated by complex transcriptional networks. In order to identify transcription factors with key roles in HSPC-mediated hematopoietic reconstitution, we developed an efficient and robust CRISPR/Cas9-based in vivo genetic screen. Using this experimental system, we identified the TFDP1 transcription factor to be essential for HSPC proliferation and post-transplant hematopoiesis. We further discovered that E2F4, an E2F transcription factor, serves as a binding partner of TFDP1 and is required for HSPC proliferation. Deletion of TFDP1 caused downregulation of genes associated with the cell cycle, with around 50% of these genes being identified as direct targets of TFDP1 and E2F4. Thus, our study expands the transcriptional network governing hematopoietic development through an in vivo CRISPR/Cas9-based genetic screen and identifies TFDP1/E2F4 as positive regulators of cell cycle genes in HSPCs.
Collapse
Affiliation(s)
- Ngoc Tung Tran
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Immune Regulation and Cancer, Berlin, Germany.
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA.
| | - Robin Graf
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Immune Regulation and Cancer, Berlin, Germany
- Charité - Universitätsmedizin Berlin, Berlin, 13125, Germany
- Muscle Research Unit, Experimental and Clinical Research Center, a cooperation between the Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association and the Charité - Universitätsmedizin, Berlin, Germany
| | - Ernesto Acevedo-Ochoa
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Immune Regulation and Cancer, Berlin, Germany
| | - Janine Trombke
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Immune Regulation and Cancer, Berlin, Germany
| | - Timm Weber
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Immune Regulation and Cancer, Berlin, Germany
- Biobank OWL (BOWL), Medical School OWL, Bielefeld University, Bielefeld, Germany
| | - Thomas Sommermann
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Immune Regulation and Cancer, Berlin, Germany
- Dynamic42 GmbH, Jena, Germany
| | - Claudia Salomon
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Immune Regulation and Cancer, Berlin, Germany
| | - Ralf Kühn
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Genome Engineering & Disease Models, Berlin, Germany
| | - Klaus Rajewsky
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Immune Regulation and Cancer, Berlin, Germany.
| | - Van Trung Chu
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Immune Regulation and Cancer, Berlin, Germany.
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Genome Engineering & Disease Models, Berlin, Germany.
| |
Collapse
|
7
|
Salisbury SJ, Daniels RR, Monaghan SJ, Bron JE, Villamayor PR, Gervais O, Fast MD, Sveen L, Houston RD, Robinson N, Robledo D. Keratinocytes drive the epithelial hyperplasia key to sea lice resistance in coho salmon. BMC Biol 2024; 22:160. [PMID: 39075472 PMCID: PMC11287951 DOI: 10.1186/s12915-024-01952-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 06/28/2024] [Indexed: 07/31/2024] Open
Abstract
BACKGROUND Salmonid species have followed markedly divergent evolutionary trajectories in their interactions with sea lice. While sea lice parasitism poses significant economic, environmental, and animal welfare challenges for Atlantic salmon (Salmo salar) aquaculture, coho salmon (Oncorhynchus kisutch) exhibit near-complete resistance to sea lice, achieved through a potent epithelial hyperplasia response leading to rapid louse detachment. The molecular mechanisms underlying these divergent responses to sea lice are unknown. RESULTS We characterized the cellular and molecular responses of Atlantic salmon and coho salmon to sea lice using single-nuclei RNA sequencing. Juvenile fish were exposed to copepodid sea lice (Lepeophtheirus salmonis), and lice-attached pelvic fin and skin samples were collected 12 h, 24 h, 36 h, 48 h, and 60 h after exposure, along with control samples. Comparative analysis of control and treatment samples revealed an immune and wound-healing response that was common to both species, but attenuated in Atlantic salmon, potentially reflecting greater sea louse immunomodulation. Our results revealed unique but complementary roles of three layers of keratinocytes in the epithelial hyperplasia response leading to rapid sea lice rejection in coho salmon. Our results suggest that basal keratinocytes direct the expansion and mobility of intermediate and, especially, superficial keratinocytes, which eventually encapsulate the parasite. CONCLUSIONS Our results highlight the key role of keratinocytes in coho salmon's sea lice resistance and the diverged biological response of the two salmonid host species when interacting with this parasite. This study has identified key pathways and candidate genes that could be manipulated using various biotechnological solutions to improve Atlantic salmon sea lice resistance.
Collapse
Affiliation(s)
- S J Salisbury
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK.
| | - R Ruiz Daniels
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
| | - S J Monaghan
- Institute of Aquaculture, University of Stirling, Stirling, UK
| | - J E Bron
- Institute of Aquaculture, University of Stirling, Stirling, UK
| | - P R Villamayor
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
- Department of Genetics, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - O Gervais
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
| | - M D Fast
- Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, Canada
| | | | - R D Houston
- Benchmark Genetics, 1 Pioneer BuildingMilton Bridge, Edinburgh TechnopolePenicuik, UK
| | - N Robinson
- Nofima AS, Tromsø, Norway.
- Sustainable Aquaculture Laboratory - Temperate and Tropical (SALTT), Deakin University, Melbourne, VIC, 3225, Australia.
| | - D Robledo
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK.
- Department of Genetics, University of Santiago de Compostela, Santiago de Compostela, Spain.
| |
Collapse
|
8
|
Banerjee S, Sanyal S, Hodawadekar S, Naiyer S, Bano N, Banerjee A, Rhoades J, Dong D, Allman D, Atchison ML. Unusual lineage plasticity revealed by YY1 knockout in pro-B cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.22.586298. [PMID: 38586061 PMCID: PMC10996465 DOI: 10.1101/2024.03.22.586298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
During B cell development, cells progress through multiple developmental stages with the pro-B cell stage defining commitment to the B cell lineage. YY1 is a ubiquitous transcription factor that is capable of both activation and repression functions. We find here that knockout of YY1 at the pro-B cell stage eliminates B lineage commitment. YY1 knockout pro-B cells can generate T lineage cells in vitro using the OP9- DL4 feeder system, as well as in vivo after injection into sub-lethally irradiated Rag1 -/- mice. These T lineage-like cells lose their B lineage transcript profile and gain a T cell lineage profile. Single cell-RNA-seq experiments showed that as YY1 knockout pro-B cells transition into T lineage cells, various cell clusters adopt transcript profiles representing a multiplicity of hematopoietic lineages indicating unusual lineage plasticity. Given the ubiquitous nature of YY1 and its dual activation and repression functions, YY1 likely regulates commitment in multiple cell lineages.
Collapse
|
9
|
Shu X, Wang J, Zeng H, Shao L. Progression of Notch signaling regulation of B cells under radiation exposure. Front Immunol 2024; 15:1339977. [PMID: 38524139 PMCID: PMC10957566 DOI: 10.3389/fimmu.2024.1339977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 02/14/2024] [Indexed: 03/26/2024] Open
Abstract
With the continuous development of nuclear technology, the radiation exposure caused by radiation therapy is a serious health hazard. It is of great significance to further develop effective radiation countermeasures. B cells easily succumb to irradiation exposure along with immunosuppressive response. The approach to ameliorate radiation-induced B cell damage is rarely studied, implying that the underlying mechanisms of B cell damage after exposure are eager to be revealed. Recent studies suggest that Notch signaling plays an important role in B cell-mediated immune response. Notch signaling is a critical regulator for B cells to maintain immune function. Although accumulating studies reported that Notch signaling contributes to the functionality of hematopoietic stem cells and T cells, its role in B cells is scarcely appreciated. Presently, we discussed the regulation of Notch signaling on B cells under radiation exposure to provide a scientific basis to prevent radiation-induced B cell damage.
Collapse
Affiliation(s)
- Xin Shu
- Department of Occupational Health and Toxicology, School of Public Health, Jiangxi Medical College, Nanchang University, Nanchang, China
- Jiangxi Provincial Key Laboratory of Preventive Medicine, Jiangxi Medical College, School of Public Health, Nanchang University, Nanchang, China
| | - Jie Wang
- Department of Histology and Embryology, School of Basic Medicine Sciences, Nanchang University, Nanchang, China
| | - Huihong Zeng
- Department of Histology and Embryology, School of Basic Medicine Sciences, Nanchang University, Nanchang, China
| | - Lijian Shao
- Department of Occupational Health and Toxicology, School of Public Health, Jiangxi Medical College, Nanchang University, Nanchang, China
- Jiangxi Provincial Key Laboratory of Preventive Medicine, Jiangxi Medical College, School of Public Health, Nanchang University, Nanchang, China
- Jiangxi Provincial Key Laboratory of Interdisciplinary Science, Nanchang University, Nanchang, China
| |
Collapse
|
10
|
Nechanitzky R, Ramachandran P, Nechanitzky D, Li WY, Wakeham AC, Haight J, Saunders ME, Epelman S, Mak TW. CaSSiDI: novel single-cell "Cluster Similarity Scoring and Distinction Index" reveals critical functions for PirB and context-dependent Cebpb repression. Cell Death Differ 2024; 31:265-279. [PMID: 38383888 PMCID: PMC10923835 DOI: 10.1038/s41418-024-01268-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 01/15/2024] [Accepted: 02/07/2024] [Indexed: 02/23/2024] Open
Abstract
PirB is an inhibitory cell surface receptor particularly prominent on myeloid cells. PirB curtails the phenotypes of activated macrophages during inflammation or tumorigenesis, but its functions in macrophage homeostasis are obscure. To elucidate PirB-related functions in macrophages at steady-state, we generated and compared single-cell RNA-sequencing (scRNAseq) datasets obtained from myeloid cell subsets of wild type (WT) and PirB-deficient knockout (PirB KO) mice. To facilitate this analysis, we developed a novel approach to clustering parameter optimization called "Cluster Similarity Scoring and Distinction Index" (CaSSiDI). We demonstrate that CaSSiDI is an adaptable computational framework that facilitates tandem analysis of two scRNAseq datasets by optimizing clustering parameters. We further show that CaSSiDI offers more advantages than a standard Seurat analysis because it allows direct comparison of two or more independently clustered datasets, thereby alleviating the need for batch-correction while identifying the most similar and different clusters. Using CaSSiDI, we found that PirB is a novel regulator of Cebpb expression that controls the generation of Ly6Clo patrolling monocytes and the expansion properties of peritoneal macrophages. PirB's effect on Cebpb is tissue-specific since it was not observed in splenic red pulp macrophages (RPMs). However, CaSSiDI revealed a segregation of the WT RPM population into a CD68loIrf8+ "neuronal-primed" subset and an CD68hiFtl1+ "iron-loaded" subset. Our results establish the utility of CaSSiDI for single-cell assay analyses and the determination of optimal clustering parameters. Our application of CaSSiDI in this study has revealed previously unknown roles for PirB in myeloid cell populations. In particular, we have discovered homeostatic functions for PirB that are related to Cebpb expression in distinct macrophage subsets.
Collapse
Affiliation(s)
- Robert Nechanitzky
- Princess Margaret Cancer Centre, Ontario Cancer Institute, University Health Network, Toronto, ON, Canada.
- Providence Therapeutics Holdings Inc., Calgary, AB, Canada.
| | - Parameswaran Ramachandran
- Princess Margaret Cancer Centre, Ontario Cancer Institute, University Health Network, Toronto, ON, Canada
| | - Duygu Nechanitzky
- Princess Margaret Cancer Centre, Ontario Cancer Institute, University Health Network, Toronto, ON, Canada
| | - Wanda Y Li
- Centre for Oncology and Immunology, Hong Kong Science Park, Hong Kong SAR, China
| | - Andrew C Wakeham
- Princess Margaret Cancer Centre, Ontario Cancer Institute, University Health Network, Toronto, ON, Canada
| | - Jillian Haight
- Princess Margaret Cancer Centre, Ontario Cancer Institute, University Health Network, Toronto, ON, Canada
| | - Mary E Saunders
- Princess Margaret Cancer Centre, Ontario Cancer Institute, University Health Network, Toronto, ON, Canada
| | - Slava Epelman
- Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada
- Ted Rogers Centre for Heart Research, Translational Biology and Engineering Program, Toronto, ON, Canada
- Peter Munk Cardiac Centre, UHN, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
- Departments of Immunology and Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Tak W Mak
- Princess Margaret Cancer Centre, Ontario Cancer Institute, University Health Network, Toronto, ON, Canada.
- Centre for Oncology and Immunology, Hong Kong Science Park, Hong Kong SAR, China.
- Department of Pathology Department of Pathology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China.
| |
Collapse
|
11
|
Malik S, Biswas J, Sarkar P, Nag S, Gain C, Ghosh Roy S, Bhattacharya B, Ghosh D, Saha A. Differential carbonic anhydrase activities control EBV-induced B-cell transformation and lytic cycle reactivation. PLoS Pathog 2024; 20:e1011998. [PMID: 38530845 PMCID: PMC10997083 DOI: 10.1371/journal.ppat.1011998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 04/05/2024] [Accepted: 03/01/2024] [Indexed: 03/28/2024] Open
Abstract
Epstein-Barr virus (EBV) contributes to ~1% of all human cancers including several B-cell neoplasms. A characteristic feature of EBV life cycle is its ability to transform metabolically quiescent B-lymphocytes into hyperproliferating B-cell blasts with the establishment of viral latency, while intermittent lytic cycle induction is necessary for the production of progeny virus. Our RNA-Seq analyses of both latently infected naïve B-lymphocytes and transformed B-lymphocytes upon lytic cycle replication indicate a contrasting expression pattern of a membrane-associated carbonic anhydrase isoform CA9, an essential component for maintaining cell acid-base homeostasis. We show that while CA9 expression is transcriptionally activated during latent infection model, lytic cycle replication restrains its expression. Pharmacological inhibition of CA-activity using specific inhibitors retards EBV induced B-cell transformation, inhibits B-cells outgrowth and colony formation ability of transformed B-lymphocytes through lowering the intracellular pH, induction of cell apoptosis and facilitating degradation of CA9 transcripts. Reanalyses of ChIP-Seq data along with utilization of EBNA2 knockout virus, ectopic expression of EBNA2 and sh-RNA mediated knockdown of CA9 expression we further demonstrate that EBNA2 mediated CA9 transcriptional activation is essential for EBV latently infected B-cell survival. In contrast, during lytic cycle reactivation CA9 expression is transcriptionally suppressed by the key EBV lytic cycle transactivator, BZLF1 through its transactivation domain. Overall, our study highlights the dynamic alterations of CA9 expression and its activity in regulating pH homeostasis act as one of the major drivers for EBV induced B-cell transformation and subsequent B-cell lymphomagenesis.
Collapse
Affiliation(s)
- Samaresh Malik
- Institute of Health Sciences, Presidency University, Kolkata, West Bengal, India
| | - Joyanta Biswas
- Institute of Health Sciences, Presidency University, Kolkata, West Bengal, India
| | - Purandar Sarkar
- Institute of Health Sciences, Presidency University, Kolkata, West Bengal, India
| | - Subhadeep Nag
- Institute of Health Sciences, Presidency University, Kolkata, West Bengal, India
| | - Chandrima Gain
- Institute of Health Sciences, Presidency University, Kolkata, West Bengal, India
| | - Shatadru Ghosh Roy
- Institute of Health Sciences, Presidency University, Kolkata, West Bengal, India
| | - Bireswar Bhattacharya
- National Institute of Pharmaceutical Education and Research, Kolkata, West Bengal, India
| | - Dipanjan Ghosh
- National Institute of Pharmaceutical Education and Research, Kolkata, West Bengal, India
| | - Abhik Saha
- Institute of Health Sciences, Presidency University, Kolkata, West Bengal, India
| |
Collapse
|
12
|
Kagoshima H, Ohnishi H, Yamamoto R, Yasumoto A, Tona Y, Nakagawa T, Omori K, Yamamoto N. EBF1 Limits the Numbers of Cochlear Hair and Supporting Cells and Forms the Scala Tympani and Spiral Limbus during Inner Ear Development. J Neurosci 2024; 44:e1060232023. [PMID: 38176908 PMCID: PMC10869149 DOI: 10.1523/jneurosci.1060-23.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 11/12/2023] [Accepted: 12/13/2023] [Indexed: 01/06/2024] Open
Abstract
Early B-cell factor 1 (EBF1) is a basic helix-loop-helix transcription factor essential for the differentiation of various tissues. Our single-cell RNA sequencing data suggest that Ebf1 is expressed in the sensory epithelium of the mouse inner ear. Here, we found that the murine Ebf1 gene and its protein are expressed in the prosensory domain of the inner ear, medial region of the cochlear duct floor, otic mesenchyme, and cochleovestibular ganglion. Ebf1 deletion in mice results in incomplete formation of the spiral limbus and scala tympani, increased number of cells in the organ of Corti and Kölliker's organ, and aberrant course of the spiral ganglion axons. Ebf1 deletion in the mouse cochlear epithelia caused the proliferation of SOX2-positive cochlear cells at E13.5, indicating that EBF1 suppresses the proliferation of the prosensory domain and cells of Kölliker's organ to facilitate the development of appropriate numbers of hair and supporting cells. Furthermore, mice with deletion of cochlear epithelium-specific Ebf1 showed poor postnatal hearing function. Our results suggest that Ebf1 is essential for normal auditory function in mammals.
Collapse
Affiliation(s)
- Hiroki Kagoshima
- Department of Otolaryngology, Head and Neck Surgery, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
| | - Hiroe Ohnishi
- Department of Otolaryngology, Head and Neck Surgery, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
| | - Ryosuke Yamamoto
- Biological Sciences, Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Toronto, Ontario M4N 3M5, Canada
| | - Akiyoshi Yasumoto
- Department of Otolaryngology, Head and Neck Surgery, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
| | - Yosuke Tona
- Department of Otolaryngology, Head and Neck Surgery, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
| | - Takayuki Nakagawa
- Department of Otolaryngology, Head and Neck Surgery, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
| | - Koichi Omori
- Department of Otolaryngology, Head and Neck Surgery, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
| | - Norio Yamamoto
- Department of Otolaryngology, Head and Neck Surgery, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
- Department of Otolaryngology, Kobe City Medical Center General Hospital, Hyogo 650-0047, Japan
| |
Collapse
|
13
|
Sigvardsson M. Early B-Cell Factor 1: An Archetype for a Lineage-Restricted Transcription Factor Linking Development to Disease. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1459:143-156. [PMID: 39017843 DOI: 10.1007/978-3-031-62731-6_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/18/2024]
Abstract
The development of highly specialized blood cells from hematopoietic stem cells (HSCs) in the bone marrow (BM) is dependent upon a stringently orchestrated network of stage- and lineage-restricted transcription factors (TFs). Thus, the same stem cell can give rise to various types of differentiated blood cells. One of the key regulators of B-lymphocyte development is early B-cell factor 1 (EBF1). This TF belongs to a small, but evolutionary conserved, family of proteins that harbor a Zn-coordinating motif and an IPT/TIG (immunoglobulin-like, plexins, transcription factors/transcription factor immunoglobulin) domain, creating a unique DNA-binding domain (DBD). EBF proteins play critical roles in diverse developmental processes, including body segmentation in the Drosophila melanogaster embryo, and retina formation in mice. While several EBF family members are expressed in neuronal cells, adipocytes, and BM stroma cells, only B-lymphoid cells express EBF1. In the absence of EBF1, hematopoietic progenitor cells (HPCs) fail to activate the B-lineage program. This has been attributed to the ability of EBF1 to act as a pioneering factor with the ability to remodel chromatin, thereby creating a B-lymphoid-specific epigenetic landscape. Conditional inactivation of the Ebf1 gene in B-lineage cells has revealed additional functions of this protein in relation to the control of proliferation and apoptosis. This may explain why EBF1 is frequently targeted by mutations in human leukemia cases. This chapter provides an overview of the biochemical and functional properties of the EBF family proteins, with a focus on the roles of EBF1 in normal and malignant B-lymphocyte development.
Collapse
Affiliation(s)
- Mikael Sigvardsson
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden.
- Division of Molecular Hematology, Lund University, Lund, Sweden.
| |
Collapse
|
14
|
Jiao A, Zhang C, Wang X, Sun L, Liu H, Su Y, Lei L, Li W, Ding R, Ding C, Dou M, Tian P, Sun C, Yang X, Zhang L, Zhang B. Single-cell sequencing reveals the evolution of immune molecules across multiple vertebrate species. J Adv Res 2024; 55:73-87. [PMID: 36871615 PMCID: PMC10770119 DOI: 10.1016/j.jare.2023.02.017] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 02/11/2023] [Accepted: 02/26/2023] [Indexed: 03/06/2023] Open
Abstract
INTRODUCTION Both innate and adaptive immune system undergo evolution from low to high vertebrates. Due to the limitation of conventional approaches in identifying broader spectrum of immune cells and molecules from various vertebrates, it remains unclear how immune molecules evolve among vertebrates. OBJECTIVES Here, we utilized carry out comparative transcriptome analysis in various immune cells across seven vertebrate species. METHODS Single-cell RNA sequencing (scRNA-seq). RESULTS We uncovered both conserved and species-specific profiling of gene expression in innate and adaptive immunity. Macrophages exhibited highly-diversified genes and developed sophisticated molecular signaling networks along with evolution, indicating effective and versatile functions in higher species. In contrast, B cells conservatively evolved with less differentially-expressed genes in analyzed species. Interestingly, T cells represented a dominant immune cell populations in all species and unique T cell populations were identified in zebrafish and pig. We also revealed compensatory TCR cascade components utilized by different species. Inter-species comparison of core gene programs demonstrated mouse species has the highest similarity in immune transcriptomes to human. CONCLUSIONS Therefore, our comparative study reveals gene transcription characteristics across multiple vertebrate species during the evolution of immune system, providing insights for species-specific immunity as well as the translation of animal studies to human physiology and disease.
Collapse
Affiliation(s)
- Anjun Jiao
- Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, China; Institute of Infection and Immunity, Translational Medicine Institute, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi 710061, China
| | - Cangang Zhang
- Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, China; Institute of Infection and Immunity, Translational Medicine Institute, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi 710061, China
| | - Xin Wang
- Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, China; Institute of Infection and Immunity, Translational Medicine Institute, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi 710061, China
| | - Lina Sun
- Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, China; Institute of Infection and Immunity, Translational Medicine Institute, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi 710061, China
| | - Haiyan Liu
- Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, China; Institute of Infection and Immunity, Translational Medicine Institute, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi 710061, China
| | - Yanhong Su
- Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, China; Institute of Infection and Immunity, Translational Medicine Institute, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi 710061, China
| | - Lei Lei
- Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, China; Institute of Infection and Immunity, Translational Medicine Institute, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi 710061, China; Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University), Ministry of Education, Xi'an, Shaanxi 710061, China; Xi'an Key Laboratory of Immune Related Diseases, Xi'an, Shaanxi 710061, China
| | - Wenhua Li
- Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, China; Institute of Infection and Immunity, Translational Medicine Institute, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi 710061, China
| | - Renyi Ding
- Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, China; Institute of Infection and Immunity, Translational Medicine Institute, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi 710061, China
| | - Chenguang Ding
- The First Affiliated Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, China
| | - Meng Dou
- The First Affiliated Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, China
| | - Puxun Tian
- The First Affiliated Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, China
| | - Chenming Sun
- Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, China; Institute of Infection and Immunity, Translational Medicine Institute, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi 710061, China; Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University), Ministry of Education, Xi'an, Shaanxi 710061, China; Xi'an Key Laboratory of Immune Related Diseases, Xi'an, Shaanxi 710061, China
| | - Xiaofeng Yang
- Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, China; Institute of Infection and Immunity, Translational Medicine Institute, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi 710061, China; Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University), Ministry of Education, Xi'an, Shaanxi 710061, China; Xi'an Key Laboratory of Immune Related Diseases, Xi'an, Shaanxi 710061, China.
| | - Lianjun Zhang
- Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, China; Suzhou Institute of Systems Medicine, Suzhou 215123, China.
| | - Baojun Zhang
- Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, China; Institute of Infection and Immunity, Translational Medicine Institute, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi 710061, China; Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University), Ministry of Education, Xi'an, Shaanxi 710061, China; Xi'an Key Laboratory of Immune Related Diseases, Xi'an, Shaanxi 710061, China.
| |
Collapse
|
15
|
Kim EE, Shekhar A, Ramachandran J, Khodadadi-Jamayran A, Liu FY, Zhang J, Fishman GI. The transcription factor EBF1 non-cell-autonomously regulates cardiac growth and differentiation. Development 2023; 150:dev202054. [PMID: 37787076 PMCID: PMC10652039 DOI: 10.1242/dev.202054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 09/18/2023] [Indexed: 10/04/2023]
Abstract
Reciprocal interactions between non-myocytes and cardiomyocytes regulate cardiac growth and differentiation. Here, we report that the transcription factor Ebf1 is highly expressed in non-myocytes and potently regulates heart development. Ebf1-deficient hearts display myocardial hypercellularity and reduced cardiomyocyte size, ventricular conduction system hypoplasia, and conduction system disease. Growth abnormalities in Ebf1 knockout hearts are observed as early as embryonic day 13.5. Transcriptional profiling of Ebf1-deficient embryonic cardiac non-myocytes demonstrates dysregulation of Polycomb repressive complex 2 targets, and ATAC-Seq reveals altered chromatin accessibility near many of these same genes. Gene set enrichment analysis of differentially expressed genes in cardiomyocytes isolated from E13.5 hearts of wild-type and mutant mice reveals significant enrichment of MYC targets and, consistent with this finding, we observe increased abundance of MYC in mutant hearts. EBF1-deficient non-myocytes, but not wild-type non-myocytes, are sufficient to induce excessive accumulation of MYC in co-cultured wild-type cardiomyocytes. Finally, we demonstrate that BMP signaling induces Ebf1 expression in embryonic heart cultures and controls a gene program enriched in EBF1 targets. These data reveal a previously unreported non-cell-autonomous pathway controlling cardiac growth and differentiation.
Collapse
Affiliation(s)
- Eugene E. Kim
- Leon H. Charney Division of Cardiology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Akshay Shekhar
- Leon H. Charney Division of Cardiology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Jayalakshmi Ramachandran
- Leon H. Charney Division of Cardiology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | | | - Fang-Yu Liu
- Leon H. Charney Division of Cardiology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Jie Zhang
- Leon H. Charney Division of Cardiology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Glenn I. Fishman
- Leon H. Charney Division of Cardiology, NYU Grossman School of Medicine, New York, NY 10016, USA
| |
Collapse
|
16
|
Carraro C, Bonaguro L, Srinivasa R, van Uelft M, Isakzai V, Schulte-Schrepping J, Gambhir P, Elmzzahi T, Montgomery JV, Hayer H, Li Y, Theis H, Kraut M, Mahbubani KT, Aschenbrenner AC, König I, Fava E, Fried HU, De Domenico E, Beyer M, Saglam A, Schultze JL. Chromatin accessibility profiling of targeted cell populations with laser capture microdissection coupled to ATAC-seq. CELL REPORTS METHODS 2023; 3:100598. [PMID: 37776856 PMCID: PMC10626193 DOI: 10.1016/j.crmeth.2023.100598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 08/04/2023] [Accepted: 09/05/2023] [Indexed: 10/02/2023]
Abstract
Spatially resolved omics technologies reveal context-dependent cellular regulatory networks in tissues of interest. Beyond transcriptome analysis, information on epigenetic traits and chromatin accessibility can provide further insights on gene regulation in health and disease. Nevertheless, compared to the enormous advancements in spatial transcriptomics technologies, the field of spatial epigenomics is much younger and still underexplored. In this study, we report laser capture microdissection coupled to ATAC-seq (LCM-ATAC-seq) applied to fresh frozen samples for the spatial characterization of chromatin accessibility. We first demonstrate the efficient use of LCM coupled to in situ tagmentation and evaluate its performance as a function of cell number, microdissected areas, and tissue type. Further, we demonstrate its use for the targeted chromatin accessibility analysis of discrete contiguous or scattered cell populations in tissues via single-nuclei capture based on immunostaining for specific cellular markers.
Collapse
Affiliation(s)
- Caterina Carraro
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V., Bonn, Germany; Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany.
| | - Lorenzo Bonaguro
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V., Bonn, Germany; Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany; PRECISE Platform for Genomics and Epigenomics, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V. and University of Bonn, Bonn, Germany
| | - Rachana Srinivasa
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V., Bonn, Germany; Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Martina van Uelft
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V., Bonn, Germany; Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Victoria Isakzai
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V., Bonn, Germany; Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Jonas Schulte-Schrepping
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V., Bonn, Germany; Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany; PRECISE Platform for Genomics and Epigenomics, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V. and University of Bonn, Bonn, Germany
| | - Prerna Gambhir
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V., Bonn, Germany; Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Tarek Elmzzahi
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V., Bonn, Germany; Immunogenomics & Neurodegeneration, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V., Bonn, Germany
| | - Jessica V Montgomery
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V., Bonn, Germany
| | - Hannah Hayer
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V., Bonn, Germany; Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Yuanfang Li
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V., Bonn, Germany; Immunogenomics & Neurodegeneration, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V., Bonn, Germany
| | - Heidi Theis
- PRECISE Platform for Genomics and Epigenomics, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V. and University of Bonn, Bonn, Germany
| | - Michael Kraut
- PRECISE Platform for Genomics and Epigenomics, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V. and University of Bonn, Bonn, Germany
| | - Krishnaa T Mahbubani
- Department of Surgery, University of Cambridge, and Cambridge NIHR Biomedical Research Centre, Cambridge, UK
| | - Anna C Aschenbrenner
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V., Bonn, Germany
| | - Ireen König
- Core Research Facilities and Services, Light Microscope Facility (LMF), Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V., Bonn, Germany
| | - Eugenio Fava
- Core Research Facilities and Services, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V., Bonn, Germany
| | - Hans-Ulrich Fried
- Core Research Facilities and Services, Light Microscope Facility (LMF), Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V., Bonn, Germany
| | - Elena De Domenico
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V., Bonn, Germany; Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany; PRECISE Platform for Genomics and Epigenomics, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V. and University of Bonn, Bonn, Germany
| | - Marc Beyer
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V., Bonn, Germany; PRECISE Platform for Genomics and Epigenomics, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V. and University of Bonn, Bonn, Germany; Immunogenomics & Neurodegeneration, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V., Bonn, Germany
| | - Adem Saglam
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V., Bonn, Germany; PRECISE Platform for Genomics and Epigenomics, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V. and University of Bonn, Bonn, Germany.
| | - Joachim L Schultze
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V., Bonn, Germany; Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany; PRECISE Platform for Genomics and Epigenomics, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V. and University of Bonn, Bonn, Germany
| |
Collapse
|
17
|
Wright M, Smed MK, Nelson JL, Olsen J, Hetland ML, Jewell NP, Zoffmann V, Jawaheer D. Pre-pregnancy gene expression signatures are associated with subsequent improvement/worsening of rheumatoid arthritis during pregnancy. Arthritis Res Ther 2023; 25:191. [PMID: 37794420 PMCID: PMC10548620 DOI: 10.1186/s13075-023-03169-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 09/12/2023] [Indexed: 10/06/2023] Open
Abstract
BACKGROUND While many women with rheumatoid arthritis (RA) improve during pregnancy and others worsen, there are no biomarkers to predict this improvement or worsening. In our unique RA pregnancy cohort that includes a pre-pregnancy baseline, we have examined pre-pregnancy gene co-expression networks to identify differences between women with RA who subsequently improve during pregnancy and those who worsen. METHODS Blood samples were collected before pregnancy (T0) from 19 women with RA and 13 healthy women enrolled in our prospective pregnancy cohort. RA improvement/worsening between T0 and 3rd trimester was assessed by changes in the Clinical Disease Activity Index (CDAI). Pre-pregnancy expression profiles were examined by RNA sequencing and differential gene expression analysis. Weighted gene co-expression network analysis (WGCNA) was used to identify co-expression modules correlated with the improvement/worsening of RA during pregnancy and to assess their functional relevance. RESULTS Of the 19 women with RA, 14 improved during pregnancy (RAimproved) while 5 worsened (RAworsened). At the T0 baseline, however, the mean CDAI was similar between the two groups. WGCNA identified one co-expression module related to B cell function that was significantly correlated with the worsening of RA during pregnancy and was significantly enriched in genes differentially expressed between the RAimproved and RAworsened groups. A neutrophil-related expression signature was also identified in the RAimproved group at the T0 baseline. CONCLUSION The pre-pregnancy gene expression signatures identified represent potential biomarkers to predict the subsequent improvement/worsening of RA during pregnancy, which has important implications for the personalized treatment of RA during pregnancy.
Collapse
Affiliation(s)
- Matthew Wright
- Children's Hospital Oakland Research Institute, Oakland, CA, USA
- Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | | | - J Lee Nelson
- Fred Hutchinson Cancer Center, Seattle, WA, USA
- University of Washington, Seattle, WA, USA
| | - Jørn Olsen
- University of California Los Angeles, Los Angeles, CA, USA
- Aarhus University Hospital, Aarhus, Denmark
| | - Merete Lund Hetland
- DANBIO Registry and Copenhagen Centre for Arthritis Research, Centre for Rheumatology and Spine Diseases, Rigshospitalet, Glostrup, Denmark
- University of Copenhagen, Copenhagen, Denmark
| | | | - Vibeke Zoffmann
- Juliane Marie Centeret, Rigshospitalet, Copenhagen, Denmark
- University of Copenhagen, Copenhagen, Denmark
| | - Damini Jawaheer
- Children's Hospital Oakland Research Institute, Oakland, CA, USA.
- Division of Rheumatology, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA.
| |
Collapse
|
18
|
Christou-Kent M, Cuartero S, Garcia-Cabau C, Ruehle J, Naderi J, Erber J, Neguembor MV, Plana-Carmona M, Alcoverro-Bertran M, De Andres-Aguayo L, Klonizakis A, Julià-Vilella E, Lynch C, Serrano M, Hnisz D, Salvatella X, Graf T, Stik G. CEBPA phase separation links transcriptional activity and 3D chromatin hubs. Cell Rep 2023; 42:112897. [PMID: 37516962 DOI: 10.1016/j.celrep.2023.112897] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 06/02/2023] [Accepted: 07/14/2023] [Indexed: 08/01/2023] Open
Abstract
Cell identity is orchestrated through an interplay between transcription factor (TF) action and genome architecture. The mechanisms used by TFs to shape three-dimensional (3D) genome organization remain incompletely understood. Here we present evidence that the lineage-instructive TF CEBPA drives extensive chromatin compartment switching and promotes the formation of long-range chromatin hubs during induced B cell-to-macrophage transdifferentiation. Mechanistically, we find that the intrinsically disordered region (IDR) of CEBPA undergoes in vitro phase separation (PS) dependent on aromatic residues. Both overexpressing B cells and native CEBPA-expressing cell types such as primary granulocyte-macrophage progenitors, liver cells, and trophectoderm cells reveal nuclear CEBPA foci and long-range 3D chromatin hubs at CEBPA-bound regions. In short, we show that CEBPA can undergo PS through its IDR, which may underlie in vivo foci formation and suggest a potential role of PS in regulating CEBPA function.
Collapse
Affiliation(s)
- Marie Christou-Kent
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Sergi Cuartero
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Spain; Germans Trias I Pujol Research Institute (IGTP), Badalona, Spain
| | - Carla Garcia-Cabau
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Julia Ruehle
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Julian Naderi
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany
| | - Julia Erber
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Maria Victoria Neguembor
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Marcos Plana-Carmona
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
| | | | - Luisa De Andres-Aguayo
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Antonios Klonizakis
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
| | | | - Cian Lynch
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain; Altos Labs, Cambridge Institute of Science, Cambridge CB21 6GP, UK
| | - Manuel Serrano
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain; Altos Labs, Cambridge Institute of Science, Cambridge CB21 6GP, UK
| | - Denes Hnisz
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany
| | - Xavier Salvatella
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain; ICREA, Passeig Lluís Companys 23, 08010 Barcelona, Spain
| | - Thomas Graf
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain.
| | - Grégoire Stik
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Spain.
| |
Collapse
|
19
|
Sigvardsson M. Transcription factor networks link B-lymphocyte development and malignant transformation in leukemia. Genes Dev 2023; 37:703-723. [PMID: 37673459 PMCID: PMC10546977 DOI: 10.1101/gad.349879.122] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/08/2023]
Abstract
Rapid advances in genomics have opened unprecedented possibilities to explore the mutational landscapes in malignant diseases, such as B-cell acute lymphoblastic leukemia (B-ALL). This disease is manifested as a severe defect in the production of normal blood cells due to the uncontrolled expansion of transformed B-lymphocyte progenitors in the bone marrow. Even though classical genetics identified translocations of transcription factor-coding genes in B-ALL, the extent of the targeting of regulatory networks in malignant transformation was not evident until the emergence of large-scale genomic analyses. There is now evidence that many B-ALL cases present with mutations in genes that encode transcription factors with critical roles in normal B-lymphocyte development. These include PAX5, IKZF1, EBF1, and TCF3, all of which are targeted by translocations or, more commonly, partial inactivation in cases of B-ALL. Even though there is support for the notion that germline polymorphisms in the PAX5 and IKZF1 genes predispose for B-ALL, the majority of leukemias present with somatic mutations in transcription factor-encoding genes. These genetic aberrations are often found in combination with mutations in genes that encode components of the pre-B-cell receptor or the IL-7/TSLP signaling pathways, all of which are important for early B-cell development. This review provides an overview of our current understanding of the molecular interplay that occurs between transcription factors and signaling events during normal and malignant B-lymphocyte development.
Collapse
Affiliation(s)
- Mikael Sigvardsson
- Department of Biomedical and Clinical Sciences, Linköping University, 58185 Linköping, Sweden; Division of Molecular Hematology, Lund University, 22184 Lund, Sweden
| |
Collapse
|
20
|
Novakovsky G, Fornes O, Saraswat M, Mostafavi S, Wasserman WW. ExplaiNN: interpretable and transparent neural networks for genomics. Genome Biol 2023; 24:154. [PMID: 37370113 DOI: 10.1186/s13059-023-02985-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Accepted: 06/12/2023] [Indexed: 06/29/2023] Open
Abstract
Deep learning models such as convolutional neural networks (CNNs) excel in genomic tasks but lack interpretability. We introduce ExplaiNN, which combines the expressiveness of CNNs with the interpretability of linear models. ExplaiNN can predict TF binding, chromatin accessibility, and de novo motifs, achieving performance comparable to state-of-the-art methods. Its predictions are transparent, providing global (cell state level) as well as local (individual sequence level) biological insights into the data. ExplaiNN can serve as a plug-and-play platform for pretrained models and annotated position weight matrices. ExplaiNN aims to accelerate the adoption of deep learning in genomic sequence analysis by domain experts.
Collapse
Affiliation(s)
- Gherman Novakovsky
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - Oriol Fornes
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - Manu Saraswat
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada
- Division of Computational Genomics and Systems Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Sara Mostafavi
- Paul G. Allen School of Computer Science and Engineering, University of Washington (UW), Seattle, USA
| | - Wyeth W Wasserman
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada.
| |
Collapse
|
21
|
Qiu C, Martin BK, Welsh IC, Daza RM, Le TM, Huang X, Nichols EK, Taylor ML, Fulton O, O’Day DR, Gomes AR, Ilcisin S, Srivatsan S, Deng X, Disteche CM, Noble WS, Hamazaki N, Moens CB, Kimelman D, Cao J, Schier AF, Spielmann M, Murray SA, Trapnell C, Shendure J. A single-cell transcriptional timelapse of mouse embryonic development, from gastrula to pup. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.05.535726. [PMID: 37066300 PMCID: PMC10104014 DOI: 10.1101/2023.04.05.535726] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
The house mouse, Mus musculus, is an exceptional model system, combining genetic tractability with close homology to human biology. Gestation in mouse development lasts just under three weeks, a period during which its genome orchestrates the astonishing transformation of a single cell zygote into a free-living pup composed of >500 million cells. Towards a global framework for exploring mammalian development, we applied single cell combinatorial indexing (sci-*) to profile the transcriptional states of 12.4 million nuclei from 83 precisely staged embryos spanning late gastrulation (embryonic day 8 or E8) to birth (postnatal day 0 or P0), with 2-hr temporal resolution during somitogenesis, 6-hr resolution through to birth, and 20-min resolution during the immediate postpartum period. From these data (E8 to P0), we annotate dozens of trajectories and hundreds of cell types and perform deeper analyses of the unfolding of the posterior embryo during somitogenesis as well as the ontogenesis of the kidney, mesenchyme, retina, and early neurons. Finally, we leverage the depth and temporal resolution of these whole embryo snapshots, together with other published data, to construct and curate a rooted tree of cell type relationships that spans mouse development from zygote to pup. Throughout this tree, we systematically nominate sets of transcription factors (TFs) and other genes as candidate drivers of the in vivo differentiation of hundreds of mammalian cell types. Remarkably, the most dramatic shifts in transcriptional state are observed in a restricted set of cell types in the hours immediately following birth, and presumably underlie the massive changes in physiology that must accompany the successful transition of a placental mammal to extrauterine life.
Collapse
Affiliation(s)
- Chengxiang Qiu
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Beth K. Martin
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | | | - Riza M. Daza
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Truc-Mai Le
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Xingfan Huang
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, WA, USA
| | - Eva K. Nichols
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Megan L. Taylor
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Olivia Fulton
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Diana R. O’Day
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | | | - Saskia Ilcisin
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Sanjay Srivatsan
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Medical Scientist Training Program, University of Washington, Seattle, WA, USA
| | - Xinxian Deng
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Christine M. Disteche
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - William Stafford Noble
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, WA, USA
| | - Nobuhiko Hamazaki
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Howard Hughes Medical Institute, Seattle, WA, USA
| | - Cecilia B. Moens
- Division of Basic Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - David Kimelman
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Junyue Cao
- Laboratory of Single-cell genomics and Population dynamics, The Rockefeller University, New York, NY, USA
| | - Alexander F. Schier
- Biozentrum, University of Basel, Basel, Switzerland
- Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA
| | - Malte Spielmann
- Max Planck Institute for Molecular Genetics, Berlin, Germany
- Institute of Human Genetics, University Hospitals Schleswig-Holstein, University of Lübeck and Kiel University, Lübeck, Kiel, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Hamburg, Lübeck, Kiel, Lübeck, Germany
| | | | - Cole Trapnell
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA
- Howard Hughes Medical Institute, Seattle, WA, USA
| |
Collapse
|
22
|
Shevyrev D, Tereshchenko V, Berezina TN, Rybtsov S. Hematopoietic Stem Cells and the Immune System in Development and Aging. Int J Mol Sci 2023; 24:ijms24065862. [PMID: 36982935 PMCID: PMC10056303 DOI: 10.3390/ijms24065862] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 03/13/2023] [Accepted: 03/16/2023] [Indexed: 03/30/2023] Open
Abstract
Hematopoietic stem cells (HSCs) support haematopoiesis throughout life and give rise to the whole variety of cells of the immune system. Developing in the early embryo, passing through the precursor stage, and maturing into the first HSCs, they undergo a fairly large number of divisions while maintaining a high regenerative potential due to high repair activity. This potential is greatly reduced in adult HSCs. They go into a state of dormancy and anaerobic metabolism to maintain their stemness throughout life. However, with age, changes occur in the pool of HSCs that negatively affect haematopoiesis and the effectiveness of immunity. Niche aging and accumulation of mutations with age reduces the ability of HSCs to self-renew and changes their differentiation potential. This is accompanied by a decrease in clonal diversity and a disturbance of lymphopoiesis (decrease in the formation of naive T- and B-cells) and the predominance of myeloid haematopoiesis. Aging also affects mature cells, regardless of HSC, therefore, phagocytic activity and the intensity of the oxidative burst decrease, and the efficiency of processing and presentation of antigens by myeloid cells is impaired. Aging cells of innate and adaptive immunity produce factors that form a chronic inflammatory background. All these processes have a serious negative impact on the protective properties of the immune system, increasing inflammation, the risk of developing autoimmune, oncological, and cardiovascular diseases with age. Understanding the mechanisms of reducing the regenerative potential in a comparative analysis of embryonic and aging HSCs, the features of inflammatory aging will allow us to get closer to deciphering the programs for the development, aging, regeneration and rejuvenation of HSCs and the immune system.
Collapse
Affiliation(s)
- Daniil Shevyrev
- Centre for Cell Technology and Immunology, Sirius University of Science and Technology, Sirius, 354340 Sochi, Russia
| | - Valeriy Tereshchenko
- Centre for Cell Technology and Immunology, Sirius University of Science and Technology, Sirius, 354340 Sochi, Russia
| | - Tatiana N Berezina
- Department of Scientific Basis of Extreme Psychology, Moscow State University of Psychology and Education, 127051 Moscow, Russia
| | - Stanislav Rybtsov
- Centre for Cell Technology and Immunology, Sirius University of Science and Technology, Sirius, 354340 Sochi, Russia
- Centre for Regenerative Medicine, University of Edinburgh, Edinburgh EH8 9YL, UK
| |
Collapse
|
23
|
Doghish AS, Abulsoud AI, Elshaer SS, Abdelmaksoud NM, Zaki MB, El-Mahdy HA, Ismail A, Fathi D, Elsakka EGE. miRNAs as cornerstones in chronic lymphocytic leukemia pathogenesis and therapeutic resistance- An emphasis on the interaction of signaling pathways. Pathol Res Pract 2023; 243:154363. [PMID: 36764011 DOI: 10.1016/j.prp.2023.154363] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 02/01/2023] [Accepted: 02/04/2023] [Indexed: 02/10/2023]
Abstract
Chronic lymphocytic leukemia (CLL) accounts for the vast majority of cases of leukemia. Patients of advanced age are more likely to develop the condition, which has a highly varied clinical course. Consideration of illness features and preceding treatment sequence, as well as patient preferences and comorbidities, is necessary for selecting the appropriate treatment for the appropriate patient. Therefore, there is an urgent need for novel biomarkers with high sensitivity and specificity to detect CLL early, monitor CLL patients, select the treatment responders, and reduce ineffective treatment, unwanted side effects, and unnecessary expenses. In both homeostasis and illness, microRNAs (miRNAs/miRs) play a vital role as master regulators of gene expression and, by extension, protein expression. MiRNAs typically reduce the stability of mRNAs, including those encoding genes involved in tumorigenesis processes as cell cycle regulation, inflammation, stress response, angiogenesis, differentiation, apoptosis, and invasion. Due to their unique properties, miRNAs are rapidly being exploited as accurate biomarkers for illness detection, and medicines based on miRNA targets are finding widespread application in clinical practice. Accordingly, the current review serves as a quick primer on CLL and the biogenesis of miRNAs. In addition to providing a brief overview of the miRNAs whose function in the progression of CLL has been established by recent in vitro or in vivo research through articulating the influence of these miRNAs on a wide variety of cellular functions, including increased proliferative potential; support for angiogenesis; cell cycle aberration; evasion of apoptosis; promotion of metastasis; and reduced sensitivity to specific treatments.
Collapse
Affiliation(s)
- Ahmed S Doghish
- Department of Biochemistry, Faculty of Pharmacy, Badr University in Cairo (BUC), Badr City, Cairo 11829, Egypt; Biochemistry and Molecular Biology Department, Faculty of Pharmacy (Boys), Al-Azhar University, Nasr City, 11231, Cairo, Egypt.
| | - Ahmed I Abulsoud
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy (Boys), Al-Azhar University, Nasr City, 11231, Cairo, Egypt; Department of Biochemistry and Biotechnology, Faculty of Pharmacy, Heliopolis University, Cairo 11785, Egypt
| | - Shereen Saeid Elshaer
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy (Boys), Al-Azhar University, Nasr City, 11231, Cairo, Egypt; Department of Biochemistry and Biotechnology, Faculty of Pharmacy, Heliopolis University, Cairo 11785, Egypt
| | - Nourhan M Abdelmaksoud
- Department of Biochemistry and Biotechnology, Faculty of Pharmacy, Heliopolis University, Cairo 11785, Egypt; Department of Biochemistry, Faculty of Pharmacy (Girls), Al-Azhar University, Nasr City, Cairo 11823, Egypt
| | - Mohamed Bakr Zaki
- Department of Biochemistry, Faculty of Pharmacy, University of Sadat City, Menoufia 32897, Egypt
| | - Hesham A El-Mahdy
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy (Boys), Al-Azhar University, Nasr City, 11231, Cairo, Egypt.
| | - Ahmed Ismail
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy (Boys), Al-Azhar University, Nasr City, 11231, Cairo, Egypt
| | - Doaa Fathi
- Department of Biochemistry and Biotechnology, Faculty of Pharmacy, Heliopolis University, Cairo 11785, Egypt
| | - Elsayed G E Elsakka
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy (Boys), Al-Azhar University, Nasr City, 11231, Cairo, Egypt
| |
Collapse
|
24
|
Leca J, Lemonnier F, Meydan C, Foox J, El Ghamrasni S, Mboumba DL, Duncan GS, Fortin J, Sakamoto T, Tobin C, Hodgson K, Haight J, Smith LK, Elia AJ, Butler D, Berger T, de Leval L, Mason CE, Melnick A, Gaulard P, Mak TW. IDH2 and TET2 mutations synergize to modulate T Follicular Helper cell functional interaction with the AITL microenvironment. Cancer Cell 2023; 41:323-339.e10. [PMID: 36736318 DOI: 10.1016/j.ccell.2023.01.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 04/11/2022] [Accepted: 01/11/2023] [Indexed: 02/05/2023]
Abstract
Angioimmunoblastic T cell lymphoma (AITL) is a peripheral T cell lymphoma that originates from T follicular helper (Tfh) cells and exhibits a prominent tumor microenvironment (TME). IDH2 and TET2 mutations co-occur frequently in AITL, but their contribution to tumorigenesis is poorly understood. We developed an AITL mouse model that is driven by Idh2 and Tet2 mutations. Malignant Tfh cells display aberrant transcriptomic and epigenetic programs that impair TCR signaling. Neoplastic Tfh cells bearing combined Idh2 and Tet2 mutations show altered cross-talk with germinal center B cells that promotes B cell clonal expansion while decreasing Fas-FasL interaction and reducing B cell apoptosis. The plasma cell count and angiogenesis are also increased in the Idh2-mutated tumors, implying a major relationship between Idh2 mutation and the characteristic AITL TME. Our mouse model recapitulates several features of human IDH2-mutated AITL and provides a rationale for exploring therapeutic targeting of Tfh-TME cross-talk for AITL patients.
Collapse
Affiliation(s)
- Julie Leca
- University Health Network, Princess Margaret Cancer Centre, Toronto, ON M5G 1L7, Canada.
| | - Franҫois Lemonnier
- University Paris-Est Créteil, INSERM U955, Institut Mondor de Recherche Biomédicale, 94010 Créteil, France; AP-HP, Lymphoid Malignancies Unit, Henri Mondor Hospital, 94010 Créteil, France
| | - Cem Meydan
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10021, USA; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Jonathan Foox
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10021, USA; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Samah El Ghamrasni
- University Health Network, Princess Margaret Cancer Centre, Toronto, ON M5G 1L7, Canada
| | - Diana-Laure Mboumba
- University Paris-Est Créteil, INSERM U955, Institut Mondor de Recherche Biomédicale, 94010 Créteil, France
| | - Gordon S Duncan
- University Health Network, Princess Margaret Cancer Centre, Toronto, ON M5G 1L7, Canada
| | - Jerome Fortin
- University Health Network, Princess Margaret Cancer Centre, Toronto, ON M5G 1L7, Canada
| | - Takashi Sakamoto
- University Health Network, Princess Margaret Cancer Centre, Toronto, ON M5G 1L7, Canada; Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Chantal Tobin
- University Health Network, Princess Margaret Cancer Centre, Toronto, ON M5G 1L7, Canada
| | - Kelsey Hodgson
- University Health Network, Princess Margaret Cancer Centre, Toronto, ON M5G 1L7, Canada
| | - Jillian Haight
- University Health Network, Princess Margaret Cancer Centre, Toronto, ON M5G 1L7, Canada
| | - Logan K Smith
- University Health Network, Princess Margaret Cancer Centre, Toronto, ON M5G 1L7, Canada
| | - Andrew J Elia
- University Health Network, Princess Margaret Cancer Centre, Toronto, ON M5G 1L7, Canada
| | - Daniel Butler
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10021, USA
| | - Thorsten Berger
- University Health Network, Princess Margaret Cancer Centre, Toronto, ON M5G 1L7, Canada
| | - Laurence de Leval
- Institute of Pathology, Department of Laboratory Medicine and Pathology, Lausanne University Hospital, Lausanne 1011, Switzerland; Lausanne University, Lausanne 1011, Switzerland
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10021, USA; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10065, USA; WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY 10021, USA
| | - Ari Melnick
- Department of Medicine, Division of Hematology and Medical Oncology, Weill Cornell Medicine, New York, NY 10065, USA
| | - Philippe Gaulard
- University Paris-Est Créteil, INSERM U955, Institut Mondor de Recherche Biomédicale, 94010 Créteil, France; AP-HP, Pathology Department, Henri Mondor Hosital, 94010 Créteil, France
| | - Tak W Mak
- University Health Network, Princess Margaret Cancer Centre, Toronto, ON M5G 1L7, Canada; Departments of Medical Biophysics and Immunology, University of Toronto, Toronto, ON M5G 1L7, Canada; Department of Pathology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China; Centre for Oncology and Immunology, Hong Kong Science Park, Hong Kong SAR, China.
| |
Collapse
|
25
|
Castiello MC, Brandas C, Capo V, Villa A. HyperIgE in hypomorphic recombination-activating gene defects. Curr Opin Immunol 2023; 80:102279. [PMID: 36529093 DOI: 10.1016/j.coi.2022.102279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 11/28/2022] [Indexed: 12/23/2022]
Abstract
Increased immunogloblulin-E (IgE) levels associated with eosinophilia represent a common finding observed in Omenn syndrome, a severe immunodeficiency caused by decreased V(D)J recombination, leading to restricted T- and B-cell receptor repertoire. V(D)J recombination is initiated by the lymphoid-restricted recombination-activating gene (RAG) recombinases. The lack of RAG proteins causes a block in lymphocyte differentiation, resulting in T-B- severe combined immunodeficiency. Conversely, hypomorphic mutations allow the generation of few T and B cells, leading to a spectrum of immunological phenotypes, in which immunodeficiency associates to inflammation, immune dysregulation, and autoimmunity. Elevated IgE levels are frequently observed in hypomorphic RAG patients. Here, we describe the role of RAG genes in lymphocyte differentiation and maintenance of immune tolerance.
Collapse
Affiliation(s)
- Maria Carmina Castiello
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy; Institute of Genetic and Biomedical Research, Milan Unit, National Research Council, Milan, Italy
| | - Chiara Brandas
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy; Translational and Molecular Medicine (DIMET), University of Milano-Bicocca, Monza, Italy
| | - Valentina Capo
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy; Institute of Genetic and Biomedical Research, Milan Unit, National Research Council, Milan, Italy
| | - Anna Villa
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy; Institute of Genetic and Biomedical Research, Milan Unit, National Research Council, Milan, Italy.
| |
Collapse
|
26
|
Nechanitzky R, Nechanitzky D, Ramachandran P, Duncan GS, Zheng C, Göbl C, Gill KT, Haight J, Wakeham AC, Snow BE, Bradaschia-Correa V, Ganguly M, Lu Z, Saunders ME, Flavell RA, Mak TW. Cholinergic control of Th17 cell pathogenicity in experimental autoimmune encephalomyelitis. Cell Death Differ 2023; 30:407-416. [PMID: 36528755 PMCID: PMC9950465 DOI: 10.1038/s41418-022-01092-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 11/03/2022] [Accepted: 11/11/2022] [Indexed: 12/23/2022] Open
Abstract
Experimental autoimmune encephalomyelitis (EAE) is a mouse model of multiple sclerosis (MS) in which Th17 cells have a crucial but unclear function. Here we show that choline acetyltransferase (ChAT), which synthesizes acetylcholine (ACh), is a critical driver of pathogenicity in EAE. Mice with ChAT-deficient Th17 cells resist disease progression and show reduced brain-infiltrating immune cells. ChAT expression in Th17 cells is linked to strong TCR signaling, expression of the transcription factor Bhlhe40, and increased Il2, Il17, Il22, and Il23r mRNA levels. ChAT expression in Th17 cells is independent of IL21r signaling but dampened by TGFβ, implicating ChAT in controlling the dichotomous nature of Th17 cells. Our study establishes a cholinergic program in which ACh signaling primes chronic activation of Th17 cells, and thereby constitutes a pathogenic determinant of EAE. Our work may point to novel targets for therapeutic immunomodulation in MS.
Collapse
Affiliation(s)
- Robert Nechanitzky
- Princess Margaret Cancer Centre, Ontario Cancer Institute, University Health Network, Toronto, ON, Canada
| | - Duygu Nechanitzky
- Princess Margaret Cancer Centre, Ontario Cancer Institute, University Health Network, Toronto, ON, Canada
| | - Parameswaran Ramachandran
- Princess Margaret Cancer Centre, Ontario Cancer Institute, University Health Network, Toronto, ON, Canada
| | - Gordon S Duncan
- Princess Margaret Cancer Centre, Ontario Cancer Institute, University Health Network, Toronto, ON, Canada
| | - Chunxing Zheng
- Princess Margaret Cancer Centre, Ontario Cancer Institute, University Health Network, Toronto, ON, Canada
| | - Christoph Göbl
- Department of Pathology and Biomedical Science, University of Otago Christchurch, Christchurch, New Zealand
| | - Kyle T Gill
- Princess Margaret Cancer Centre, Ontario Cancer Institute, University Health Network, Toronto, ON, Canada
| | - Jillian Haight
- Princess Margaret Cancer Centre, Ontario Cancer Institute, University Health Network, Toronto, ON, Canada
| | - Andrew C Wakeham
- Princess Margaret Cancer Centre, Ontario Cancer Institute, University Health Network, Toronto, ON, Canada
| | - Bryan E Snow
- Princess Margaret Cancer Centre, Ontario Cancer Institute, University Health Network, Toronto, ON, Canada
| | | | - Milan Ganguly
- Histology Core, The Centre for Phenogenomics, Toronto, ON, Canada
| | - Zhibin Lu
- UHN Bioinformatics and HPC Core, Toronto, ON, Canada
| | - Mary E Saunders
- Princess Margaret Cancer Centre, Ontario Cancer Institute, University Health Network, Toronto, ON, Canada
| | - Richard A Flavell
- Department of Immunobiology, School of Medicine, Yale University, New Haven, CT, 06520, USA
- Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Tak W Mak
- Princess Margaret Cancer Centre, Ontario Cancer Institute, University Health Network, Toronto, ON, Canada.
- Departments of Immunology and Medical Biophysics, University of Toronto, Toronto, ON, Canada.
- Department of Pathology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China.
- Centre for Oncology and Immunology, Hong Kong Science Park, Hong Kong SAR, China.
| |
Collapse
|
27
|
Larcombe MR, Hsu S, Polo JM, Knaupp AS. Indirect Mechanisms of Transcription Factor-Mediated Gene Regulation during Cell Fate Changes. ADVANCED GENETICS (HOBOKEN, N.J.) 2022; 3:2200015. [PMID: 36911290 PMCID: PMC9993476 DOI: 10.1002/ggn2.202200015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Indexed: 06/18/2023]
Abstract
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.
Collapse
Affiliation(s)
- Michael R. Larcombe
- Department of Anatomy and Developmental BiologyMonash UniversityClaytonVictoria3168Australia
- Development and Stem Cells ProgramMonash Biomedicine Discovery InstituteClaytonVictoria3168Australia
- Australian Regenerative Medicine InstituteMonash UniversityClaytonVictoria3168Australia
| | - Sheng Hsu
- Department of Anatomy and Developmental BiologyMonash UniversityClaytonVictoria3168Australia
- Development and Stem Cells ProgramMonash Biomedicine Discovery InstituteClaytonVictoria3168Australia
- Australian Regenerative Medicine InstituteMonash UniversityClaytonVictoria3168Australia
| | - Jose M. Polo
- Department of Anatomy and Developmental BiologyMonash UniversityClaytonVictoria3168Australia
- Development and Stem Cells ProgramMonash Biomedicine Discovery InstituteClaytonVictoria3168Australia
- Australian Regenerative Medicine InstituteMonash UniversityClaytonVictoria3168Australia
- South Australian Immunogenomics Cancer Institute, Faculty of Health and Medical SciencesUniversity of AdelaideAdelaideSouth Australia5005Australia
- Adelaide Centre for Epigenetics, Faculty of Health and Medical SciencesUniversity of AdelaideAdelaideSouth Australia5005Australia
| | - Anja S. Knaupp
- Department of Anatomy and Developmental BiologyMonash UniversityClaytonVictoria3168Australia
- Development and Stem Cells ProgramMonash Biomedicine Discovery InstituteClaytonVictoria3168Australia
- Australian Regenerative Medicine InstituteMonash UniversityClaytonVictoria3168Australia
| |
Collapse
|
28
|
Belcheva KT, Chaudhuri J. Maintenance of Lineage Identity: Lessons from a B Cell. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2022; 209:2073-2081. [PMID: 36426973 DOI: 10.4049/jimmunol.2200497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 08/17/2022] [Indexed: 01/04/2023]
Abstract
The maintenance of B cell identity requires active transcriptional control that enforces a B cell-specific program and suppresses alternative lineage genes. Accordingly, disrupting the B cell identity regulatory network compromises B cell function and induces cell fate plasticity by allowing derepression of alternative lineage-specific transcriptional programs. Although the B lineage is incredibly resistant to most differentiating factors, loss of just a single B lineage-specific transcription factor or the forced expression of individual non-B cell lineage transcription factors can radically disrupt B cell maintenance and allow dedifferentiation or transdifferentiation into entirely distinct lineages. B lymphocytes thereby offer an insightful and useful case study of how a specific cell lineage can maintain a stable identity throughout life and how perturbations of a single master regulator can induce cellular plasticity. In this article, we review the regulatory mechanisms that safeguard B cell identity, and we discuss how dysregulation of the B cell maintenance program can drive malignant transformation and enable therapeutic resistance.
Collapse
Affiliation(s)
- Kalina T Belcheva
- Biochemistry, Cellular and Molecular Biology Allied Program, Weill Cornell Graduate School of Medical Sciences, New York, NY; and
| | - Jayanta Chaudhuri
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY
| |
Collapse
|
29
|
Lenaerts A, Kucinski I, Deboutte W, Derecka M, Cauchy P, Manke T, Göttgens B, Grosschedl R. EBF1 primes B-lymphoid enhancers and limits the myeloid bias in murine multipotent progenitors. J Exp Med 2022; 219:e20212437. [PMID: 36048017 PMCID: PMC9437269 DOI: 10.1084/jem.20212437] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 06/23/2022] [Accepted: 08/03/2022] [Indexed: 11/04/2022] Open
Abstract
Hematopoietic stem cells (HSCs) and multipotent progenitors (MPPs) generate all cells of the blood system. Despite their multipotency, MPPs display poorly understood lineage bias. Here, we examine whether lineage-specifying transcription factors, such as the B-lineage determinant EBF1, regulate lineage preference in early progenitors. We detect low-level EBF1 expression in myeloid-biased MPP3 and lymphoid-biased MPP4 cells, coinciding with expression of the myeloid determinant C/EBPα. Hematopoietic deletion of Ebf1 results in enhanced myelopoiesis and reduced HSC repopulation capacity. Ebf1-deficient MPP3 and MPP4 cells exhibit an augmented myeloid differentiation potential and a transcriptome with an enriched C/EBPα signature. Correspondingly, EBF1 binds the Cebpa enhancer, and the deficiency and overexpression of Ebf1 in MPP3 and MPP4 cells lead to an up- and downregulation of Cebpa expression, respectively. In addition, EBF1 primes the chromatin of B-lymphoid enhancers specifically in MPP3 cells. Thus, our study implicates EBF1 in regulating myeloid/lymphoid fate bias in MPPs by constraining C/EBPα-driven myelopoiesis and priming the B-lymphoid fate.
Collapse
Affiliation(s)
- Aurelie Lenaerts
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- International Max Planck Research School for Molecular and Cellular Biology, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Iwo Kucinski
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Haematology, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
| | - Ward Deboutte
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Marta Derecka
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Pierre Cauchy
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Thomas Manke
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Berthold Göttgens
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Haematology, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
| | - Rudolf Grosschedl
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| |
Collapse
|
30
|
Kogut S, Paculova H, Rodriguez P, Boyd J, Richman A, Palaria A, Schjerven H, Frietze S. Ikaros Regulates microRNA Networks in Acute Lymphoblastic Leukemia. EPIGENOMES 2022; 6:37. [PMID: 36278683 PMCID: PMC9624360 DOI: 10.3390/epigenomes6040037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 10/13/2022] [Accepted: 10/14/2022] [Indexed: 11/24/2022] Open
Abstract
The hematopoietic transcription factor Ikaros (IKZF1) regulates normal B cell development and functions as a tumor suppressor in precursor B cell acute lymphoblastic leukemia (B-ALL). MicroRNAs (miRNAs) are small regulatory RNAs that through post-transcriptional gene regulation play critical roles in intracellular processes including cell growth in cancer. However, the role of Ikaros in the regulation of miRNA expression in developing B cells is unknown. In this study, we examined the Ikaros-regulated miRNA targets using human IKZF1-mutated Ph+ B-ALL cell lines. Inducible expression of wild-type Ikaros (the Ik1 isoform) caused B-ALL growth arrest and exit from the cell cycle. Global miRNA expression analysis revealed a total of 31 miRNAs regulated by IK1, and ChIP-seq analysis showed that Ikaros bound to several Ik1-responsive miRNA genes. Examination of the prognostic significance of miRNA expression in B-ALL indicate that the IK1-regulated miRNAs hsa-miR-26b, hsa-miR-130b and hsa-miR-4649 are significantly associated with outcome in B-ALL. Our findings establish a potential regulatory circuit between the tumor-suppressor Ikaros and the oncogenic miRNA networks in IKZF1-mutated B-ALL. These results indicate that Ikaros regulates the expression of a subset of miRNAs, of which several may contribute to B-ALL growth.
Collapse
Affiliation(s)
- Sophie Kogut
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, VT 05405, USA
| | - Hana Paculova
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, VT 05405, USA
| | - Princess Rodriguez
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT 05405, USA
| | - Joseph Boyd
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, VT 05405, USA
| | - Alyssa Richman
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, VT 05405, USA
- Cellular Molecular Biomedical Sciences Program, University of Vermont, Burlington, VT 05405, USA
| | - Amrita Palaria
- Department of Laboratory Medicine, University of California, San Francisco, CA 94143, USA
| | - Hilde Schjerven
- Department of Laboratory Medicine, University of California, San Francisco, CA 94143, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94143, USA
| | - Seth Frietze
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, VT 05405, USA
- The University of Vermont Cancer Center, Burlington, VT 05405, USA
| |
Collapse
|
31
|
Liu C, Omilusik K, Toma C, Kurd NS, Chang JT, Goldrath AW, Wang W. Systems-level identification of key transcription factors in immune cell specification. PLoS Comput Biol 2022; 18:e1010116. [PMID: 36156073 PMCID: PMC9536753 DOI: 10.1371/journal.pcbi.1010116] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 10/06/2022] [Accepted: 08/10/2022] [Indexed: 01/30/2023] Open
Abstract
Transcription factors (TFs) are crucial for regulating cell differentiation during the development of the immune system. However, the key TFs for orchestrating the specification of distinct immune cells are not fully understood. Here, we integrated the transcriptomic and epigenomic measurements in 73 mouse and 61 human primary cell types, respectively, that span the immune cell differentiation pathways. We constructed the cell-type-specific transcriptional regulatory network and assessed the global importance of TFs based on the Taiji framework, which is a method we have previously developed that can infer the global impact of TFs using integrated transcriptomic and epigenetic data. Integrative analysis across cell types revealed putative driver TFs in cell lineage-specific differentiation in both mouse and human systems. We have also identified TF combinations that play important roles in specific developmental stages. Furthermore, we validated the functions of predicted novel TFs in murine CD8+ T cell differentiation and showed the importance of Elf1 and Prdm9 in the effector versus memory T cell fate specification and Kdm2b and Tet3 in promoting differentiation of CD8+ tissue resident memory (Trm) cells, validating the approach. Thus, we have developed a bioinformatic approach that provides a global picture of the regulatory mechanisms that govern cellular differentiation in the immune system and aids the discovery of novel mechanisms in cell fate decisions.
Collapse
Affiliation(s)
- Cong Liu
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, United States of America
| | - Kyla Omilusik
- Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Clara Toma
- Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Nadia S. Kurd
- Department of Medicine, University of California San Diego, La Jolla, California, United States of America
| | - John T. Chang
- Department of Medicine, University of California San Diego, La Jolla, California, United States of America
| | - Ananda W. Goldrath
- Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Wei Wang
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, United States of America
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California, United States of America
| |
Collapse
|
32
|
Corbett RJ, Luttman AM, Herrera-Uribe J, Liu H, Raney NE, Grabowski JM, Loving CL, Tuggle CK, Ernst CW. Assessment of DNA methylation in porcine immune cells reveals novel regulatory elements associated with cell-specific gene expression and immune capacity traits. BMC Genomics 2022; 23:575. [PMID: 35953767 PMCID: PMC9367135 DOI: 10.1186/s12864-022-08773-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 07/18/2022] [Indexed: 11/15/2022] Open
Abstract
Background Genetics studies in the porcine immune system have enhanced selection practices for disease resistance phenotypes and increased the efficacy of porcine models in biomedical research; however limited functional annotation of the porcine immunome has hindered progress on both fronts. Among epigenetic mechanisms that regulate gene expression, DNA methylation is the most ubiquitous modification made to the DNA molecule and influences transcription factor binding as well as gene and phenotype expression. Human and mouse DNA methylation studies have improved mapping of regulatory elements in these species, but comparable studies in the pig have been limited in scope. Results We performed whole-genome bisulfite sequencing to assess DNA methylation patterns in nine pig immune cell populations: CD21+ and CD21− B cells, four T cell fractions (CD4+, CD8+, CD8+CD4+, and SWC6γδ+), natural killer and myeloid cells, and neutrophils. We identified 54,391 cell differentially methylated regions (cDMRs), and clustering by cDMR methylation rate grouped samples by cell lineage. 32,737 cDMRs were classified as cell lowly methylated regions (cLMRs) in at least one cell type, and cLMRs were broadly enriched in genes and regions of intermediate CpG density. We observed strong correlations between differential methylation and expression across immune cell populations, with cell-specific low methylation disproportionately impacting genes exhibiting enriched gene expression in the same cell type. Motif analysis of cLMRs revealed cell type-specific enrichment of transcription factor binding motifs, indicating that cell-specific methylation patterns may influence accessibility by trans-acting factors. Lastly, cDMRs were enriched for immune capacity GWAS SNPs, and many such overlaps occurred within genes known to influence immune cell development and function (CD8B, NDRG1). Conclusion Our DNA methylation data improve functional annotation of the porcine genome through characterization of epigenomic regulatory patterns that contribute to immune cell identity and function, and increase the potential for identifying mechanistic links between genotype and phenotype. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08773-5.
Collapse
Affiliation(s)
- Ryan J Corbett
- Genetics & Genome Sciences Graduate Program, Michigan State University, East Lansing, MI, USA
| | - Andrea M Luttman
- Genetics & Genome Sciences Graduate Program, Michigan State University, East Lansing, MI, USA
| | | | - Haibo Liu
- Department of Animal Science, Iowa State University, Ames, IA, USA
| | - Nancy E Raney
- Department of Animal Science, Michigan State University, East Lansing, MI, USA
| | - Jenna M Grabowski
- Department of Animal Science, Michigan State University, East Lansing, MI, USA
| | | | | | - Catherine W Ernst
- Department of Animal Science, Michigan State University, East Lansing, MI, USA.
| |
Collapse
|
33
|
Bayer M, Boller S, Ramamoothy S, Zolotarev N, Cauchy P, Iwanami N, Mittler G, Boehm T, Grosschedl R. Tnpo3 enables EBF1 function in conditions of antagonistic Notch signaling. Genes Dev 2022; 36:901-915. [PMID: 36167471 PMCID: PMC9575695 DOI: 10.1101/gad.349696.122] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 09/02/2022] [Indexed: 02/03/2023]
Abstract
Transcription factor EBF1 (early B cell factor 1) acts as a key regulator of B cell specification. The transcriptional network in which EBF1 operates has been extensively studied; however, the regulation of EBF1 function remains poorly defined. By mass spectrometric analysis of proteins associated with endogenous EBF1 in pro-B cells, we identified the nuclear import receptor Transportin-3 (Tnpo3) and found that it interacts with the immunoglobulin-like fold domain of EBF1. We delineated glutamic acid 271 of EBF1 as a critical residue for the association with Tnpo3. EBF1E271A showed normal nuclear localization; however, it had an impaired B cell programming ability in conditions of Notch signaling, as determined by retroviral transduction of Ebf1 -/- progenitors. By RNA-seq analysis of EBF1E271A-expressing progenitors, we found an up-regulation of T lineage determinants and down-regulation of early B genes, although similar chromatin binding of EBF1E271A and EBF1wt was detected in pro-B cells expressing activated Notch1. B lineage-specific inactivation of Tnpo3 in mice resulted in a block of early B cell differentiation, accompanied by a down-regulation of B lineage genes and up-regulation of T and NK lineage genes. Taken together, our observations suggest that Tnpo3 ensures B cell programming by EBF1 in nonpermissive conditions.
Collapse
Affiliation(s)
- Marc Bayer
- Laboratory of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Sören Boller
- Laboratory of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Senthilkumar Ramamoothy
- Laboratory of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Nikolay Zolotarev
- Laboratory of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Pierre Cauchy
- Laboratory of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Norimasa Iwanami
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Gerhard Mittler
- Laboratory of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Thomas Boehm
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
- Faculty of Medicine, University of Freiburg, 79108 Freiburg, Germany
| | - Rudolf Grosschedl
- Laboratory of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| |
Collapse
|
34
|
Hernandez-Davies JE, Dollinger EP, Pone EJ, Felgner J, Liang L, Strohmeier S, Jan S, Albin TJ, Jain A, Nakajima R, Jasinskas A, Krammer F, Esser-Kahn A, Felgner PL, Nie Q, Davies DH. Magnitude and breadth of antibody cross-reactivity induced by recombinant influenza hemagglutinin trimer vaccine is enhanced by combination adjuvants. Sci Rep 2022; 12:9198. [PMID: 35654904 PMCID: PMC9163070 DOI: 10.1038/s41598-022-12727-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 04/26/2022] [Indexed: 12/15/2022] Open
Abstract
The effects of adjuvants for increasing the immunogenicity of influenza vaccines are well known. However, the effect of adjuvants on increasing the breadth of cross-reactivity is less well understood. In this study we have performed a systematic screen of different toll-like receptor (TLR) agonists, with and without a squalene-in-water emulsion on the immunogenicity of a recombinant trimerized hemagglutinin (HA) vaccine in mice after single-dose administration. Antibody (Ab) cross-reactivity for other variants within and outside the immunizing subtype (homosubtypic and heterosubtypic cross-reactivity, respectively) was assessed using a protein microarray approach. Most adjuvants induced broad IgG profiles, although the response to a combination of CpG, MPLA and AddaVax (termed 'IVAX-1') appeared more quickly and reached a greater magnitude than the other formulations tested. Antigen-specific plasma cell labeling experiments show the components of IVAX-1 are synergistic. This adjuvant preferentially stimulates CD4 T cells to produce Th1>Th2 type (IgG2c>IgG1) antibodies and cytokine responses. Moreover, IVAX-1 induces identical homo- and heterosubtypic IgG and IgA cross-reactivity profiles when administered intranasally. Consistent with these observations, a single-cell transcriptomics analysis demonstrated significant increases in expression of IgG1, IgG2b and IgG2c genes of B cells in H5/IVAX-1 immunized mice relative to naïve mice, as well as significant increases in expression of the IFNγ gene of both CD4 and CD8 T cells. These data support the use of adjuvants for enhancing the breath and durability of antibody responses of influenza virus vaccines.
Collapse
Affiliation(s)
- Jenny E Hernandez-Davies
- Vaccine Research and Development Center, Department of Physiology and Biophysics, School of Medicine, University of California, Irvine, CA, 92697, USA
| | | | - Egest J Pone
- Vaccine Research and Development Center, Department of Physiology and Biophysics, School of Medicine, University of California, Irvine, CA, 92697, USA
| | - Jiin Felgner
- Vaccine Research and Development Center, Department of Physiology and Biophysics, School of Medicine, University of California, Irvine, CA, 92697, USA
| | - Li Liang
- Vaccine Research and Development Center, Department of Physiology and Biophysics, School of Medicine, University of California, Irvine, CA, 92697, USA
| | - Shirin Strohmeier
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Sharon Jan
- Vaccine Research and Development Center, Department of Physiology and Biophysics, School of Medicine, University of California, Irvine, CA, 92697, USA
| | - Tyler J Albin
- Department of Chemistry, University of California, Irvine, CA, 92697, USA
- Avidity Biosciences, San Diego, CA, 92121, USA
| | - Aarti Jain
- Vaccine Research and Development Center, Department of Physiology and Biophysics, School of Medicine, University of California, Irvine, CA, 92697, USA
| | - Rie Nakajima
- Vaccine Research and Development Center, Department of Physiology and Biophysics, School of Medicine, University of California, Irvine, CA, 92697, USA
| | - Algimantas Jasinskas
- Vaccine Research and Development Center, Department of Physiology and Biophysics, School of Medicine, University of California, Irvine, CA, 92697, USA
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Aaron Esser-Kahn
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, 60637, USA
| | - Philip L Felgner
- Vaccine Research and Development Center, Department of Physiology and Biophysics, School of Medicine, University of California, Irvine, CA, 92697, USA
| | - Qing Nie
- Department of Mathematics, University of California, Irvine, CA, 92697, USA
| | - D Huw Davies
- Vaccine Research and Development Center, Department of Physiology and Biophysics, School of Medicine, University of California, Irvine, CA, 92697, USA.
| |
Collapse
|
35
|
Peña-Pérez L, Kharazi S, Frengen N, Krstic A, Bouderlique T, Hauenstein J, He M, Somuncular E, Li Wang X, Dahlberg C, Gustafsson C, Johansson AS, Walfridsson J, Kadri N, Woll P, Kierczak M, Qian H, Westerberg L, Luc S, Månsson R. FOXO Dictates Initiation of B Cell Development and Myeloid Restriction in Common Lymphoid Progenitors. Front Immunol 2022; 13:880668. [PMID: 35603175 PMCID: PMC9116193 DOI: 10.3389/fimmu.2022.880668] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 03/23/2022] [Indexed: 12/23/2022] Open
Abstract
The development of B cells relies on an intricate network of transcription factors critical for developmental progression and lineage commitment. In the B cell developmental trajectory, a temporal switch from predominant Foxo3 to Foxo1 expression occurs at the CLP stage. Utilizing VAV-iCre mediated conditional deletion, we found that the loss of FOXO3 impaired B cell development from LMPP down to B cell precursors, while the loss of FOXO1 impaired B cell commitment and resulted in a complete developmental block at the CD25 negative proB cell stage. Strikingly, the combined loss of FOXO1 and FOXO3 resulted in the failure to restrict the myeloid potential of CLPs and the complete loss of the B cell lineage. This is underpinned by the failure to enforce the early B-lineage gene regulatory circuitry upon a predominantly pre-established open chromatin landscape. Altogether, this demonstrates that FOXO3 and FOXO1 cooperatively govern early lineage restriction and initiation of B-lineage commitment in CLPs.
Collapse
Affiliation(s)
- Lucía Peña-Pérez
- Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Shabnam Kharazi
- Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Nicolai Frengen
- Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Aleksandra Krstic
- Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Thibault Bouderlique
- Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Julia Hauenstein
- Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Minghui He
- Department of Microbiology Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Ece Somuncular
- Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Medicine, Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Xiaoze Li Wang
- Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Carin Dahlberg
- Department of Microbiology Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Charlotte Gustafsson
- Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Ann-Sofie Johansson
- Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Medicine, Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Julian Walfridsson
- Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Medicine, Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Nadir Kadri
- Department of Medicine, Solna, Karolinska Institutet, Stockholm, Sweden
| | - Petter Woll
- Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Medicine, Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Marcin Kierczak
- Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Hong Qian
- Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Medicine, Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Lisa Westerberg
- Department of Microbiology Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Sidinh Luc
- Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Medicine, Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Robert Månsson
- Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden.,Hematology Center, Karolinska University Hospital, Stockholm, Sweden
| |
Collapse
|
36
|
Reilly A, Philip Creamer J, Stewart S, Stolla MC, Wang Y, Du J, Wellington R, Busch S, Estey EH, Becker PS, Fang M, Keel SB, Abkowitz JL, Soma LA, Ma J, Duan Z, Doulatov S. Lamin B1 deletion in myeloid neoplasms causes nuclear anomaly and altered hematopoietic stem cell function. Cell Stem Cell 2022; 29:577-592.e8. [PMID: 35278369 PMCID: PMC9018112 DOI: 10.1016/j.stem.2022.02.010] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 01/05/2022] [Accepted: 02/15/2022] [Indexed: 11/19/2022]
Abstract
Abnormal nuclear morphology is a hallmark of malignant cells widely used in cancer diagnosis. Pelger-Huët anomaly (PHA) is a common abnormality of neutrophil nuclear morphology of unknown molecular etiology in myeloid neoplasms (MNs). We show that loss of nuclear lamin B1 (LMNB1) encoded on chromosome 5q, which is frequently deleted in MNs, induces defects in nuclear morphology and human hematopoietic stem cell (HSC) function associated with malignancy. LMNB1 deficiency alters genome organization inducing in vitro and in vivo expansion of HSCs, myeloid-biased differentiation with impaired lymphoid commitment, and genome instability due to defective DNA damage repair. Nuclear dysmorphology of neutrophils in patients with MNs is associated with 5q deletions spanning the LMNB1 locus, and lamin B1 loss is both necessary and sufficient to cause PHA in normal and 5q-deleted neutrophils. LMNB1 loss thus causes acquired PHA and links abnormal nuclear morphology with HSCs and progenitor cell fate determination via genome organization.
Collapse
Affiliation(s)
- Andreea Reilly
- Division of Hematology, Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - J Philip Creamer
- Division of Hematology, Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Sintra Stewart
- Division of Hematology, Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Massiel C Stolla
- Division of Hematology, Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Yuchuan Wang
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Jing Du
- Division of Laboratory Medicine, University of Washington, Seattle, WA 98195, USA
| | - Rachel Wellington
- Division of Hematology, Department of Medicine, University of Washington, Seattle, WA 98195, USA; Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA
| | - Stephanie Busch
- Division of Hematology, Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Elihu H Estey
- Division of Hematology, Department of Medicine, University of Washington, Seattle, WA 98195, USA; Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Pamela S Becker
- Division of Hematology, Department of Medicine, University of Washington, Seattle, WA 98195, USA; Division of Hematology/Oncology, Chao Family Comprehensive Cancer Center, University of California Irvine, Irvine, CA 92617, USA; Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Min Fang
- Department of Clinical Transplant Research, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Siobán B Keel
- Division of Hematology, Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Janis L Abkowitz
- Division of Hematology, Department of Medicine, University of Washington, Seattle, WA 98195, USA; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Lorinda A Soma
- Division of Laboratory Medicine, University of Washington, Seattle, WA 98195, USA
| | - Jian Ma
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Zhijun Duan
- Division of Hematology, Department of Medicine, University of Washington, Seattle, WA 98195, USA; Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98195, USA
| | - Sergei Doulatov
- Division of Hematology, Department of Medicine, University of Washington, Seattle, WA 98195, USA; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98195, USA.
| |
Collapse
|
37
|
Baskar R, Chen AF, Favaro P, Reynolds W, Mueller F, Borges L, Jiang S, Park HS, Kool ET, Greenleaf WJ, Bendall SC. Integrating transcription-factor abundance with chromatin accessibility in human erythroid lineage commitment. CELL REPORTS METHODS 2022; 2:100188. [PMID: 35463156 PMCID: PMC9017139 DOI: 10.1016/j.crmeth.2022.100188] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 01/20/2022] [Accepted: 03/01/2022] [Indexed: 01/01/2023]
Abstract
Master transcription factors (TFs) directly regulate present and future cell states by binding DNA regulatory elements and driving gene-expression programs. Their abundance influences epigenetic priming to different cell fates at the chromatin level, especially in the context of differentiation. In order to link TF protein abundance to changes in TF motif accessibility and open chromatin, we developed InTAC-seq, a method for simultaneous quantification of genome-wide chromatin accessibility and intracellular protein abundance in fixed cells. Our method produces high-quality data and is a cost-effective alternative to single-cell techniques. We showcase our method by purifying bone marrow (BM) progenitor cells based on GATA-1 protein levels and establish high GATA-1-expressing BM cells as both epigenetically and functionally similar to erythroid-committed progenitors.
Collapse
Affiliation(s)
- Reema Baskar
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
- Cancer Biology Program, Stanford University, Stanford, CA 94305, USA
| | - Amy F. Chen
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Patricia Favaro
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Warren Reynolds
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Fabian Mueller
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Luciene Borges
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Sizun Jiang
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Hyun Shin Park
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Eric T. Kool
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
- ChEM-H Institute, Stanford University, Stanford, CA 94305, USA
| | - William J. Greenleaf
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
- Department of Applied Physics, Stanford University, Stanford, CA 94305, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Sean C. Bendall
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| |
Collapse
|
38
|
Zhou Y, Petrovic J, Zhao J, Zhang W, Bigdeli A, Zhang Z, Berger SL, Pear WS, Faryabi RB. EBF1 nuclear repositioning instructs chromatin refolding to promote therapy resistance in T leukemic cells. Mol Cell 2022; 82:1003-1020.e15. [PMID: 35182476 PMCID: PMC8897266 DOI: 10.1016/j.molcel.2022.01.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 11/05/2021] [Accepted: 01/19/2022] [Indexed: 12/12/2022]
Abstract
Chromatin misfolding has been implicated in cancer pathogenesis; yet, its role in therapy resistance remains unclear. Here, we systematically integrated sequencing and imaging data to examine the spatial and linear chromatin structures in targeted therapy-sensitive and -resistant human T cell acute lymphoblastic leukemia (T-ALL). We found widespread alterations in successive layers of chromatin organization including spatial compartments, contact domain boundaries, and enhancer positioning upon the emergence of targeted therapy resistance. The reorganization of genome folding structures closely coincides with the restructuring of chromatin activity and redistribution of architectural proteins. Mechanistically, the derepression and repositioning of the B-lineage-determining transcription factor EBF1 from the heterochromatic nuclear envelope to the euchromatic interior instructs widespread genome refolding and promotes therapy resistance in leukemic T cells. Together, our findings suggest that lineage-determining transcription factors can instruct changes in genome topology as a driving force for epigenetic adaptations in targeted therapy resistance.
Collapse
Affiliation(s)
- Yeqiao Zhou
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Penn Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Jelena Petrovic
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Penn Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Jingru Zhao
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Penn Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Wu Zhang
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Ashkan Bigdeli
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Penn Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Zhen Zhang
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Penn Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Shelley L Berger
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Penn Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Warren S Pear
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Robert B Faryabi
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Penn Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA.
| |
Collapse
|
39
|
Merkerova MD, Klema J, Kundrat D, Szikszai K, Krejcik Z, Hrustincova A, Trsova I, LE AV, Cermak J, Jonasova A, Belickova M. Noncoding RNAs and Their Response Predictive Value in Azacitidine-treated Patients With Myelodysplastic Syndrome and Acute Myeloid Leukemia With Myelodysplasia-related Changes. Cancer Genomics Proteomics 2022; 19:205-228. [PMID: 35181589 DOI: 10.21873/cgp.20315] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 01/07/2022] [Accepted: 01/14/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND/AIM Prediction of response to azacitidine (AZA) treatment is an important challenge in hematooncology. In addition to protein coding genes (PCGs), AZA efficiency is influenced by various noncoding RNAs (ncRNAs), including long ncRNAs (lncRNAs), circular RNAs (circRNAs), and transposable elements (TEs). MATERIALS AND METHODS RNA sequencing was performed in patients with myelodysplastic syndromes or acute myeloid leukemia before AZA treatment to assess contribution of ncRNAs to AZA mechanisms and propose novel disease prediction biomarkers. RESULTS Our analyses showed that lncRNAs had the strongest predictive potential. The combined set of the best predictors included 14 lncRNAs, and only four PCGs, one circRNA, and no TEs. Epigenetic regulation and recombinational repair were suggested as crucial for AZA response, and network modeling defined three deregulated lncRNAs (CTC-482H14.5, RP11-419K12.2, and RP11-736I24.4) associated with these processes. CONCLUSION The expression of various ncRNAs can influence the effect of AZA and new ncRNA-based predictive biomarkers can be defined.
Collapse
Affiliation(s)
| | - Jiri Klema
- Department of Computer Sciences, Czech Technical University, Prague, Czech Republic
| | - David Kundrat
- Department of Genomics, Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Katarina Szikszai
- Department of Genomics, Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Zdenek Krejcik
- Department of Genomics, Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Andrea Hrustincova
- Department of Genomics, Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Iva Trsova
- Department of Genomics, Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Anh Vu LE
- Department of Computer Sciences, Czech Technical University, Prague, Czech Republic
| | - Jaroslav Cermak
- Laboratory of Anemias, Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Anna Jonasova
- First Department of Medicine, General University Hospital, Prague, Czech Republic
| | - Monika Belickova
- Department of Genomics, Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| |
Collapse
|
40
|
Hait TA, Elkon R, Shamir R. CT-FOCS: a novel method for inferring cell type-specific enhancer–promoter maps. Nucleic Acids Res 2022; 50:e55. [PMID: 35100425 PMCID: PMC9178001 DOI: 10.1093/nar/gkac048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 01/09/2022] [Accepted: 01/15/2022] [Indexed: 11/13/2022] Open
Abstract
Spatiotemporal gene expression patterns are governed to a large extent by the activity of enhancer elements, which engage in physical contacts with their target genes. Identification of enhancer–promoter (EP) links that are functional only in a specific subset of cell types is a key challenge in understanding gene regulation. We introduce CT-FOCS (cell type FOCS), a statistical inference method that uses linear mixed effect models to infer EP links that show marked activity only in a single or a small subset of cell types out of a large panel of probed cell types. Analyzing 808 samples from FANTOM5, covering 472 cell lines, primary cells and tissues, CT-FOCS inferred such EP links more accurately than recent state-of-the-art methods. Furthermore, we show that strictly cell type-specific EP links are very uncommon in the human genome.
Collapse
Affiliation(s)
- Tom Aharon Hait
- The Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv 69978, Israel
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Ran Elkon
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
- Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 69978, Israel
| | - Ron Shamir
- The Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv 69978, Israel
| |
Collapse
|
41
|
Hagman JR, Arends T, Laborda C, Knapp JR, Harmacek L, O'Connor BP. Chromodomain helicase DNA-binding 4 (CHD4) regulates early B cell identity and V(D)J recombination. Immunol Rev 2021; 305:29-42. [PMID: 34927255 DOI: 10.1111/imr.13054] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 11/22/2021] [Accepted: 12/02/2021] [Indexed: 12/20/2022]
Abstract
B lymphocytes develop from uncommitted precursors into immunoglobulin (antibody)-producing B cells, a major arm of adaptive immunity. Progression of early progenitors to antibody-expressing cells in the bone marrow is orchestrated by the temporal regulation of different gene programs at discrete developmental stages. A major question concerns how B cells control the accessibility of these genes to transcription factors. Research has implicated nucleosome remodeling ATPases as mediators of chromatin accessibility. Here, we describe studies of chromodomain helicase DNA-binding 4 (CHD4; also known as Mi-2β) in early B cell development. CHD4 comprises multiple domains that function in nucleosome mobilization and histone binding. CHD4 is a key component of Nucleosome Remodeling and Deacetylase, or NuRD (Mi-2) complexes, which assemble with other proteins that mediate transcriptional repression. We review data demonstrating that CHD4 is necessary for B lineage identity: early B lineage progression, proliferation in response to interleukin-7, responses to DNA damage, and cell survival in vivo. CHD4-NuRD is also required for the Ig heavy-chain repertoire by promoting utilization of distal variable (VH ) gene segments in V(D)J recombination. In conclusion, the regulation of chromatin accessibility by CHD4 is essential for production of antibodies by B cells, which in turn mediate humoral immune responses to pathogens and disease.
Collapse
Affiliation(s)
- James R Hagman
- Department of Immunology and Genomic Medicine, National Jewish Health, Denver, Colorado, USA.,Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA.,Program in Molecular Biology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Tessa Arends
- Program in Molecular Biology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Curtis Laborda
- Center for Genes, Environment, and Health, National Jewish Health, Denver, Colorado, USA
| | - Jennifer R Knapp
- Center for Genes, Environment, and Health, National Jewish Health, Denver, Colorado, USA
| | - Laura Harmacek
- Center for Genes, Environment, and Health, National Jewish Health, Denver, Colorado, USA
| | - Brian P O'Connor
- Department of Immunology and Genomic Medicine, National Jewish Health, Denver, Colorado, USA.,Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA.,Center for Genes, Environment, and Health, National Jewish Health, Denver, Colorado, USA
| |
Collapse
|
42
|
A regulatory network of microRNAs confers lineage commitment during early developmental trajectories of B and T lymphocytes. Proc Natl Acad Sci U S A 2021; 118:2104297118. [PMID: 34750254 DOI: 10.1073/pnas.2104297118] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/10/2021] [Indexed: 11/18/2022] Open
Abstract
The commitment of hematopoietic multipotent progenitors (MPPs) toward a particular lineage involves activation of cell type-specific genes and silencing of genes that promote alternate cell fates. Although the gene expression programs of early-B and early-T lymphocyte development are mutually exclusive, we show that these cell types exhibit significantly correlated microRNA (miRNA) profiles. However, their corresponding miRNA targetomes are distinct and predominated by transcripts associated with natural killer, dendritic cell, and myeloid lineages, suggesting that miRNAs function in a cell-autonomous manner. The combinatorial expression of miRNAs miR-186-5p, miR-128-3p, and miR-330-5p in MPPs significantly attenuates their myeloid differentiation potential due to repression of myeloid-associated transcripts. Depletion of these miRNAs caused a pronounced de-repression of myeloid lineage targets in differentiating early-B and early-T cells, resulting in a mixed-lineage gene expression pattern. De novo motif analysis combined with an assay of promoter activities indicates that B as well as T lineage determinants drive the expression of these miRNAs in lymphoid lineages. Collectively, we present a paradigm that miRNAs are conserved between developing B and T lymphocytes, yet they target distinct sets of promiscuously expressed lineage-inappropriate genes to suppress the alternate cell-fate options. Thus, our studies provide a comprehensive compendium of miRNAs with functional implications for B and T lymphocyte development.
Collapse
|
43
|
George TB, Strawn NK, Leviyang S. Tree-Based Co-Clustering Identifies Chromatin Accessibility Patterns Associated With Hematopoietic Lineage Structure. Front Genet 2021; 12:707117. [PMID: 34659332 PMCID: PMC8517275 DOI: 10.3389/fgene.2021.707117] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Accepted: 09/14/2021] [Indexed: 01/21/2023] Open
Abstract
Chromatin accessibility, as measured by ATACseq, varies between hematopoietic cell types in different lineages of the hematopoietic differentiation tree, e.g. T cells vs. B cells, but methods that associate variation in chromatin accessibility to the lineage structure of the differentiation tree are lacking. Using an ATACseq dataset recently published by the ImmGen consortium, we construct associations between chromatin accessibility and hematopoietic cell types using a novel co-clustering approach that accounts for the structure of the hematopoietic, differentiation tree. Under a model in which all loci and cell types within a co-cluster have a shared accessibility state, we show that roughly 80% of cell type associated accessibility variation can be captured through 12 cell type clusters and 20 genomic locus clusters, with the cell type clusters reflecting coherent components of the differentiation tree. Using publicly available ChIPseq datasets, we show that our clustering reflects transcription factor binding patterns with implications for regulation across cell types. We show that traditional methods such as hierarchical and kmeans clusterings lead to cell type clusters that are more dispersed on the tree than our tree-based algorithm. We provide a python package, chromcocluster, that implements the algorithms presented.
Collapse
Affiliation(s)
| | | | - Sivan Leviyang
- Department of Mathematics and Statistics, Georgetown University, Washington, DC, United States
| |
Collapse
|
44
|
Charton C, Youm DJ, Ko BJ, Seol D, Kim B, Chai HH, Lim D, Kim H. The transcriptomic blueprint of molt in rooster using various tissues from Ginkkoridak (Korean long-tailed chicken). BMC Genomics 2021; 22:594. [PMID: 34348642 PMCID: PMC8340483 DOI: 10.1186/s12864-021-07903-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 07/13/2021] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Annual molt is a critical stage in the life cycle of birds. Although the most extensively documented aspects of molt are the renewing of plumage and the remodeling of the reproductive tract in laying hens, in chicken, molt deeply affects various tissues and physiological functions. However, with exception of the reproductive tract, the effect of molt on gene expression across the tissues known to be affected by molt has to date never been investigated. The present study aimed to decipher the transcriptomic effects of molt in Ginkkoridak, a Korean long-tailed chicken. Messenger RNA data available across 24 types of tissue samples (9 males) and a combination of mRNA and miRNA data on 10 males and 10 females blood were used. RESULTS The impact of molt on gene expression and gene transcript usage appeared to vary substantially across tissues types in terms of histological entities or physiological functions particularly related to nervous system. Blood was the tissue most affected by molt in terms of differentially expressed genes in both sexes, closely followed by meninges, bone marrow and heart. The effect of molt in blood appeared to differ between males and females, with a more than fivefold difference in the number of down-regulated genes between both sexes. The blueprint of molt in roosters appeared to be specific to tissues or group of tissues, with relatively few genes replicating extensively across tissues, excepted for the spliceosome genes (U1, U4) and the ribosomal proteins (RPL21, RPL23). By integrating miRNA and mRNA data, when chickens molt, potential roles of miRNA were discovered such as regulation of neurogenesis, regulation of immunity and development of various organs. Furthermore, reliable candidate biomarkers of molt were found, which are related to cell dynamics, nervous system or immunity, processes or functions that have been shown to be extensively modulated in response to molt. CONCLUSIONS Our results provide a comprehensive description at the scale of the whole organism deciphering the effects of molt on the transcriptome in chicken. Also, the conclusion of this study can be used as a valuable resource in transcriptome analyses of chicken in the future and provide new insights related to molt.
Collapse
Affiliation(s)
- Clémentine Charton
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Dong-Jae Youm
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Byung June Ko
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Donghyeok Seol
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
- eGnome, Inc, Seoul, Republic of Korea
| | - Bongsang Kim
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
- eGnome, Inc, Seoul, Republic of Korea
| | - Han-Ha Chai
- Animal Genomics & Bioinformatics Division, National Institute of Animal Science, RDA, 1500, Wanju, Republic of Korea
| | - Dajeong Lim
- Animal Genomics & Bioinformatics Division, National Institute of Animal Science, RDA, 1500, Wanju, Republic of Korea
| | - Heebal Kim
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea.
- eGnome, Inc, Seoul, Republic of Korea.
| |
Collapse
|
45
|
Crickx E, Chappert P, Sokal A, Weller S, Azzaoui I, Vandenberghe A, Bonnard G, Rossi G, Fadeev T, Storck S, Fadlallah J, Meignin V, Rivière E, Audia S, Godeau B, Michel M, Weill JC, Reynaud CA, Mahévas M. Rituximab-resistant splenic memory B cells and newly engaged naive B cells fuel relapses in patients with immune thrombocytopenia. Sci Transl Med 2021; 13:13/589/eabc3961. [PMID: 33853929 DOI: 10.1126/scitranslmed.abc3961] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 10/29/2020] [Accepted: 03/22/2021] [Indexed: 01/19/2023]
Abstract
Rituximab (RTX), an antibody targeting CD20, is widely used as a first-line therapeutic strategy in B cell-mediated autoimmune diseases. However, a large proportion of patients either do not respond to the treatment or relapse during B cell reconstitution. Here, we characterize the cellular basis responsible for disease relapse in secondary lymphoid organs in humans, taking advantage of the opportunity offered by therapeutic splenectomy in patients with relapsing immune thrombocytopenia. By analyzing the B and plasma cell immunoglobulin gene repertoire at bulk and antigen-specific single-cell level, we demonstrate that relapses are associated with two responses coexisting in germinal centers and involving preexisting mutated memory B cells that survived RTX treatment and naive B cells generated upon reconstitution of the B cell compartment. To identify distinctive characteristics of the memory B cells that escaped RTX-mediated depletion, we analyzed RTX refractory patients who did not respond to treatment at the time of B cell depletion. We identified, by single-cell RNA sequencing (scRNA-seq) analysis, a population of quiescent splenic memory B cells that present a unique, yet reversible, RTX-shaped phenotype characterized by down-modulation of B cell-specific factors and expression of prosurvival genes. Our results clearly demonstrate that these RTX-resistant autoreactive memory B cells reactivate as RTX is cleared and give rise to plasma cells and further germinal center reactions. Their continued surface expression of CD19 makes them efficient targets for current anti-CD19 therapies. This study thus identifies a pathogenic contributor to autoimmune diseases that can be targeted by available therapeutic agents.
Collapse
Affiliation(s)
- Etienne Crickx
- Institut Necker-Enfants Malades, INSERM U1151/CNRS UMS8253, Université Paris Descartes, Sorbonne Paris Cité, 75993 Paris Cedex 14, France.,Service de Médecine Interne, Centre national de référence des cytopénies auto-immunes de l'adulte, Hôpital Henri Mondor, Assistance Publique Hôpitaux de Paris (AP-HP), Université Paris Est Créteil, 94000 Créteil, France
| | - Pascal Chappert
- Institut Necker-Enfants Malades, INSERM U1151/CNRS UMS8253, Université Paris Descartes, Sorbonne Paris Cité, 75993 Paris Cedex 14, France.,Inovarion, 75005 Paris, France
| | - Aurélien Sokal
- Institut Necker-Enfants Malades, INSERM U1151/CNRS UMS8253, Université Paris Descartes, Sorbonne Paris Cité, 75993 Paris Cedex 14, France
| | - Sandra Weller
- Institut Necker-Enfants Malades, INSERM U1151/CNRS UMS8253, Université Paris Descartes, Sorbonne Paris Cité, 75993 Paris Cedex 14, France
| | - Imane Azzaoui
- Service de Médecine Interne, Centre national de référence des cytopénies auto-immunes de l'adulte, Hôpital Henri Mondor, Assistance Publique Hôpitaux de Paris (AP-HP), Université Paris Est Créteil, 94000 Créteil, France.,INSERM U955, Université Paris Est Créteil (UPEC), 94000 Créteil, France
| | - Alexis Vandenberghe
- Service de Médecine Interne, Centre national de référence des cytopénies auto-immunes de l'adulte, Hôpital Henri Mondor, Assistance Publique Hôpitaux de Paris (AP-HP), Université Paris Est Créteil, 94000 Créteil, France.,INSERM U955, Université Paris Est Créteil (UPEC), 94000 Créteil, France
| | - Guillaume Bonnard
- INSERM U955, Université Paris Est Créteil (UPEC), 94000 Créteil, France
| | - Geoffrey Rossi
- Institut Necker-Enfants Malades, INSERM U1151/CNRS UMS8253, Université Paris Descartes, Sorbonne Paris Cité, 75993 Paris Cedex 14, France
| | - Tatiana Fadeev
- Institut Necker-Enfants Malades, INSERM U1151/CNRS UMS8253, Université Paris Descartes, Sorbonne Paris Cité, 75993 Paris Cedex 14, France
| | - Sébastien Storck
- Institut Necker-Enfants Malades, INSERM U1151/CNRS UMS8253, Université Paris Descartes, Sorbonne Paris Cité, 75993 Paris Cedex 14, France
| | - Jehane Fadlallah
- Service d'immunologie clinique, Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris, Université Paris Diderot, Sorbonne Paris Cité, 75010 Paris, France
| | - Véronique Meignin
- Service d'anatomopathologie, Hôpital Saint-Louis (AP-HP), 75010 Paris, France
| | - Etienne Rivière
- Service de médecine interne, Hôpital Haut-Lévêque, 33604 Pessac, France
| | - Sylvain Audia
- Service de médecine interne, Hôpital du Bocage, 21000 Dijon, France
| | - Bertrand Godeau
- Service de Médecine Interne, Centre national de référence des cytopénies auto-immunes de l'adulte, Hôpital Henri Mondor, Assistance Publique Hôpitaux de Paris (AP-HP), Université Paris Est Créteil, 94000 Créteil, France
| | - Marc Michel
- Service de Médecine Interne, Centre national de référence des cytopénies auto-immunes de l'adulte, Hôpital Henri Mondor, Assistance Publique Hôpitaux de Paris (AP-HP), Université Paris Est Créteil, 94000 Créteil, France
| | - Jean-Claude Weill
- Institut Necker-Enfants Malades, INSERM U1151/CNRS UMS8253, Université Paris Descartes, Sorbonne Paris Cité, 75993 Paris Cedex 14, France
| | - Claude-Agnès Reynaud
- Institut Necker-Enfants Malades, INSERM U1151/CNRS UMS8253, Université Paris Descartes, Sorbonne Paris Cité, 75993 Paris Cedex 14, France
| | - Matthieu Mahévas
- Institut Necker-Enfants Malades, INSERM U1151/CNRS UMS8253, Université Paris Descartes, Sorbonne Paris Cité, 75993 Paris Cedex 14, France. .,Service de Médecine Interne, Centre national de référence des cytopénies auto-immunes de l'adulte, Hôpital Henri Mondor, Assistance Publique Hôpitaux de Paris (AP-HP), Université Paris Est Créteil, 94000 Créteil, France.,INSERM U955, Université Paris Est Créteil (UPEC), 94000 Créteil, France
| |
Collapse
|
46
|
Rawle DJ, Le TT, Dumenil T, Yan K, Tang B, Nguyen W, Watterson D, Modhiran N, Hobson-Peters J, Bishop C, Suhrbier A. ACE2-lentiviral transduction enables mouse SARS-CoV-2 infection and mapping of receptor interactions. PLoS Pathog 2021; 17:e1009723. [PMID: 34214142 PMCID: PMC8282004 DOI: 10.1371/journal.ppat.1009723] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 07/15/2021] [Accepted: 06/17/2021] [Indexed: 02/07/2023] Open
Abstract
SARS-CoV-2 uses the human ACE2 (hACE2) receptor for cell attachment and entry, with mouse ACE2 (mACE2) unable to support infection. Herein we describe an ACE2-lentivirus system and illustrate its utility for in vitro and in vivo SARS-CoV-2 infection models. Transduction of non-permissive cell lines with hACE2 imparted replication competence, and transduction with mACE2 containing N30D, N31K, F83Y and H353K substitutions, to match hACE2, rescued SARS-CoV-2 replication. Intrapulmonary hACE2-lentivirus transduction of C57BL/6J mice permitted significant virus replication in lung epithelium. RNA-Seq and histological analyses illustrated that this model involved an acute inflammatory disease followed by resolution and tissue repair, with a transcriptomic profile similar to that seen in COVID-19 patients. hACE2-lentivirus transduction of IFNAR-/- and IL-28RA-/- mouse lungs was used to illustrate that loss of type I or III interferon responses have no significant effect on virus replication. However, their importance in driving inflammatory responses was illustrated by RNA-Seq analyses. We also demonstrate the utility of the hACE2-lentivirus transduction system for vaccine evaluation in C57BL/6J mice. The ACE2-lentivirus system thus has broad application in SARS-CoV-2 research, providing a tool for both mutagenesis studies and mouse model development.
Collapse
Affiliation(s)
- Daniel J. Rawle
- Immunology Department, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Thuy T. Le
- Immunology Department, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Troy Dumenil
- Immunology Department, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Kexin Yan
- Immunology Department, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Bing Tang
- Immunology Department, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Wilson Nguyen
- Immunology Department, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Daniel Watterson
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, Queensland, Australia
- Australian Infectious Disease Research Centre, GVN Center of Excellence, Brisbane, Queensland, Australia
| | - Naphak Modhiran
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, Queensland, Australia
| | - Jody Hobson-Peters
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, Queensland, Australia
- Australian Infectious Disease Research Centre, GVN Center of Excellence, Brisbane, Queensland, Australia
| | - Cameron Bishop
- Immunology Department, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Andreas Suhrbier
- Immunology Department, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
- Australian Infectious Disease Research Centre, GVN Center of Excellence, Brisbane, Queensland, Australia
| |
Collapse
|
47
|
EBF1 and PAX5 control pro-B cell expansion via opposing regulation of the Myc gene. Blood 2021; 137:3037-3049. [PMID: 33619557 DOI: 10.1182/blood.2020009564] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 02/06/2021] [Indexed: 12/12/2022] Open
Abstract
Genes encoding B lineage-restricted transcription factors are frequently mutated in B-lymphoid leukemias, suggesting a close link between normal and malignant B-cell development. One of these transcription factors is early B-cell factor 1 (EBF1), a protein of critical importance for lineage specification and survival of B-lymphoid progenitors. Here, we report that impaired EBF1 function in mouse B-cell progenitors results in reduced expression of Myc. Ectopic expression of MYC partially rescued B-cell expansion in the absence of EBF1 both in vivo and in vitro. Using chromosome conformation analysis in combination with ATAC-sequencing, chromatin immunoprecipitation-sequencing, and reporter gene assays, six EBF1-responsive enhancer elements were identified within the Myc locus. CRISPR-Cas9-mediated targeting of EBF1-binding sites identified one element of key importance for Myc expression and pro-B cell expansion. These data provide evidence that Myc is a direct target of EBF1. Furthermore, chromatin immunoprecipitation-sequencing analysis revealed that several regulatory elements in the Myc locus are targets of PAX5. However, ectopic expression of PAX5 in EBF1-deficient cells inhibits the cell cycle and reduces Myc expression, suggesting that EBF1 and PAX5 act in an opposing manner to regulate Myc levels. This hypothesis is further substantiated by the finding that Pax5 inactivation reduces requirements for EBF1 in pro-B-cell expansion. The binding of EBF1 and PAX5 to regulatory elements in the human MYC gene in a B-cell acute lymphoblastic leukemia cell line indicates that the EBF1:PAX5:MYC regulatory loop is conserved and may control both normal and malignant B-cell development.
Collapse
|
48
|
Yoshikawa G, Miyazaki K, Ogata H, Miyazaki M. The Evolution of Rag Gene Enhancers and Transcription Factor E and Id Proteins in the Adaptive Immune System. Int J Mol Sci 2021; 22:ijms22115888. [PMID: 34072618 PMCID: PMC8199221 DOI: 10.3390/ijms22115888] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 05/23/2021] [Accepted: 05/24/2021] [Indexed: 11/17/2022] Open
Abstract
Adaptive immunity relies on the V(D)J DNA recombination of immunoglobulin (Ig) and T cell receptor (TCR) genes, which enables the recognition of highly diverse antigens and the elicitation of antigen-specific immune responses. This process is mediated by recombination-activating gene (Rag) 1 and Rag2 (Rag1/2), whose expression is strictly controlled in a cell type-specific manner; the expression of Rag1/2 genes represents a hallmark of lymphoid lineage commitment. Although Rag genes are known to be evolutionally conserved among jawed vertebrates, how Rag genes are regulated by lineage-specific transcription factors (TFs) and how their regulatory system evolved among vertebrates have not been fully elucidated. Here, we reviewed the current body of knowledge concerning the cis-regulatory elements (CREs) of Rag genes and the evolution of the basic helix-loop-helix TF E protein regulating Rag gene CREs, as well as the evolution of the antagonist of this protein, the Id protein. This may help to understand how the adaptive immune system develops along with the evolution of responsible TFs and enhancers.
Collapse
Affiliation(s)
- Genki Yoshikawa
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji 611-0011, Japan;
| | - Kazuko Miyazaki
- Laboratory of Immunology, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto 606-8507, Japan;
| | - Hiroyuki Ogata
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji 611-0011, Japan;
- Correspondence: (H.O.); (M.M.)
| | - Masaki Miyazaki
- Laboratory of Immunology, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto 606-8507, Japan;
- Correspondence: (H.O.); (M.M.)
| |
Collapse
|
49
|
Strid T, Okuyama K, Tingvall-Gustafsson J, Kuruvilla J, Jensen CT, Lang S, Prasad M, Somasundaram R, Åhsberg J, Cristobal S, Soneji S, Ungerbäck J, Sigvardsson M. B Lymphocyte Specification Is Preceded by Extensive Epigenetic Priming in Multipotent Progenitors. THE JOURNAL OF IMMUNOLOGY 2021; 206:2700-2713. [PMID: 34021049 DOI: 10.4049/jimmunol.2100048] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 03/27/2021] [Indexed: 11/19/2022]
Abstract
B lymphocyte development is dependent on the interplay between the chromatin landscape and lineage-specific transcription factors. It has been suggested that B lineage commitment is associated with major changes in the nuclear chromatin environment, proposing a critical role for lineage-specific transcription factors in the formation of the epigenetic landscape. In this report, we have used chromosome conformation capture in combination with assay for transposase-accessible chromatin sequencing analysis to enable highly efficient annotation of both proximal and distal transcriptional control elements to genes activated in B lineage specification in mice. A large majority of these genes were annotated to at least one regulatory element with an accessible chromatin configuration in multipotent progenitors. Furthermore, the majority of binding sites for the key regulators of B lineage specification, EBF1 and PAX5, occurred in already accessible regions. EBF1 did, however, cause a dynamic change in assay for transposase-accessible chromatin accessibility and was critical for an increase in distal promoter-enhancer interactions. Our data unravel an extensive epigenetic priming at regulatory elements annotated to lineage-restricted genes and provide insight into the interplay between the epigenetic landscape and transcription factors in cell specification.
Collapse
Affiliation(s)
- Tobias Strid
- Department of Biological and Clinical Sciences, Linköping University, Linköping, Sweden.,Division of Molecular Hematology, Lund University, Lund, Sweden; and.,Department of Clinical Pathology, Biological and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Kazuki Okuyama
- Department of Biological and Clinical Sciences, Linköping University, Linköping, Sweden
| | | | - Jacob Kuruvilla
- Division of Molecular Hematology, Lund University, Lund, Sweden; and
| | | | - Stefan Lang
- Division of Molecular Hematology, Lund University, Lund, Sweden; and
| | - Mahadesh Prasad
- Department of Biological and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Rajesh Somasundaram
- Department of Biological and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Josefine Åhsberg
- Department of Biological and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Susana Cristobal
- Department of Biological and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Shamit Soneji
- Division of Molecular Hematology, Lund University, Lund, Sweden; and
| | - Jonas Ungerbäck
- Division of Molecular Hematology, Lund University, Lund, Sweden; and
| | - Mikael Sigvardsson
- Department of Biological and Clinical Sciences, Linköping University, Linköping, Sweden; .,Division of Molecular Hematology, Lund University, Lund, Sweden; and
| |
Collapse
|
50
|
The Multifaceted Role and Utility of MicroRNAs in Indolent B-Cell Non-Hodgkin Lymphomas. Biomedicines 2021; 9:biomedicines9040333. [PMID: 33806113 PMCID: PMC8064455 DOI: 10.3390/biomedicines9040333] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 03/14/2021] [Accepted: 03/18/2021] [Indexed: 02/07/2023] Open
Abstract
Normal B-cell development is a tightly regulated complex procedure, the deregulation of which can lead to lymphomagenesis. One common group of blood cancers is the B-cell non-Hodgkin lymphomas (NHLs), which can be categorized according to the proliferation and spread rate of cancer cells into indolent and aggressive ones. The most frequent indolent B-cell NHLs are follicular lymphoma and marginal zone lymphoma. MicroRNAs (miRNAs) are small non-coding RNAs that can greatly influence protein expression. Based on the multiple interactions among miRNAs and their targets, complex networks of gene expression regulation emerge, which normally are essential for proper B-cell development. Multiple miRNAs have been associated with B-cell lymphomas, as the deregulation of these complex networks can lead to such pathological states. The aim of the present review is to summarize the existing information regarding the multifaceted role of miRNAs in indolent B-cell NHLs, affecting the main B-cell subpopulations. We attempt to provide insight into their biological function, the complex miRNA-mRNA interactions, and their biomarker utility in these malignancies. Lastly, we address the limitations that hinder the investigation of the role of miRNAs in these lymphomas and discuss ways that these problems could be overcome in the future.
Collapse
|