1
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Zhou Z, Li T, Li J, Lin W, Zheng Q. Exosomal transfer of HCC-derived miR-17-5p downregulates NK cell function by targeting RUNX1-NKG2D axis. Int Immunopharmacol 2024; 136:112361. [PMID: 38820961 DOI: 10.1016/j.intimp.2024.112361] [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: 03/11/2024] [Revised: 05/06/2024] [Accepted: 05/26/2024] [Indexed: 06/02/2024]
Abstract
OBJECTIVE Natural killer (NK) cells are an integral part of the staunch defense line against malignant tumors within the tumor microenvironment. Existing research indicates that miRNAs can influence the development of NK cells by negatively modulating gene expression. In this study, we aim to explore how the miR-17-5p in Hepatocellular Carcinoma (HCC) exosomes regulates the killing function of NK cells towards HCC cells through the transcription factor RNX1. METHODS The exosomes were isolated from HCC tissues and cell lines, followed by a second generation sequencing to compare differential miRNAs. Verification was performed using qRT-PCR and Western blot methods. The mutual interactions between miR-17-5p and RUNX1, as well as between RUNX1 and NKG2D, were authenticated using techniques like luciferase reporter gene assays, Western blotting, and Chromatin Immunoprecipitation (ChIP). The cytotoxic activity of NK cells towards HCC cells in vitro was measured using methods such as RTCA and ELISPOT. The zebrafish xenotransplantation was utilized to assess the in vivo killing capacity of NK cells against HCC cells. RESULTS The level of miR-17-5p in exosomes from HCC tissue increased compared to adjacent tissues. We verified that RUNX1 was a target of miR-17-5p and that RUNX1 enhances the transcription of NKG2D. MiR-17-5p was found to downregulate the expression of RUNX1 and NKG2D, subsequently reducing the in vitro and in vivo cytotoxic capabilities of NK cells against HCC cells. CONCLUSIONS The miR-17-5p found within HCC exosomes can target RUNX1, subsequently attenuating the cytotoxic activity of NK cells.
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Affiliation(s)
- Zhifeng Zhou
- Laboratory of Immuno-Oncology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou 350014, China; School of Basic Medical Sciences, Fujian Medical University, Fuzhu, Fujian, China
| | - Tianchuan Li
- Department of Integrated Traditional and Western Medicine, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou 350014, China
| | - Jieyu Li
- Laboratory of Immuno-Oncology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou 350014, China; School of Basic Medical Sciences, Fujian Medical University, Fuzhu, Fujian, China
| | - Wansong Lin
- Laboratory of Immuno-Oncology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou 350014, China; School of Basic Medical Sciences, Fujian Medical University, Fuzhu, Fujian, China.
| | - Qingfeng Zheng
- Department of Thoracic Surgery, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou 350014, China.
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2
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Qin X, Lu J, Wu P, Zhang C, Shi L, Zhu P. Charting epimutation dynamics in human hematopoietic differentiation. BLOOD SCIENCE 2024; 6:e00197. [PMID: 38872911 PMCID: PMC11175913 DOI: 10.1097/bs9.0000000000000197] [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: 03/31/2024] [Accepted: 05/26/2024] [Indexed: 06/15/2024] Open
Abstract
DNA methylation plays a critical role in hematopoietic differentiation. Epimutation is a stochastic variation in DNA methylation that induces epigenetic heterogeneity. However, the effects of epimutations on normal hematopoiesis and hematopoietic diseases remain unclear. In this study, we developed a Julia package called EpiMut that enabled rapid and accurate quantification of epimutations. EpiMut was used to evaluate and provide an epimutation landscape in steady-state hematopoietic differentiation involving 13 types of blood cells ranging from hematopoietic stem/progenitor cells to mature cells. We showed that substantial genomic regions exhibited epigenetic variations rather than significant differences in DNA methylation levels between the myeloid and lymphoid lineages. Stepwise dynamics of epimutations were observed during the differentiation of each lineage. Importantly, we found that epimutation significantly enriched signals associated with lineage differentiation. Furthermore, epimutations in hematopoietic stem cells (HSCs) derived from various sources and acute myeloid leukemia were related to the function of HSCs and malignant cell disorders. Taken together, our study comprehensively documented an epimutation map and uncovered its important roles in human hematopoiesis, thereby offering insights into hematopoietic regulation.
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Affiliation(s)
- Xiaohuan Qin
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Department of Stem Cell and Regenerative Medicine, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Jiayi Lu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Department of Stem Cell and Regenerative Medicine, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Peng Wu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Department of Stem Cell and Regenerative Medicine, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Chunyong Zhang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Department of Stem Cell and Regenerative Medicine, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Lei Shi
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Ping Zhu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Department of Stem Cell and Regenerative Medicine, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
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He M, Li X, Xu B, Lu Y, Lai J, Ling Y, Liu H, An Z, Zhang W, Li F. Reprogramming of 3D genome structure underlying HSPC development in zebrafish. Stem Cell Res Ther 2024; 15:172. [PMID: 38886858 PMCID: PMC11184745 DOI: 10.1186/s13287-024-03798-x] [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: 01/24/2024] [Accepted: 06/10/2024] [Indexed: 06/20/2024] Open
Abstract
BACKGROUND Development of hematopoietic stem and progenitor cells (HSPC) is a multi-staged complex process that conserved between zebrafish and mammals. Understanding the mechanism underlying HSPC development is a holy grail of hematopoietic biology, which is helpful for HSPC clinical application. Chromatin conformation plays important roles in transcriptional regulation and cell fate decision; however, its dynamic and role in HSPC development is poorly investigated. METHODS We performed chromatin structure and multi-omics dissection across different stages of HSPC developmental trajectory in zebrafish for the first time, including Hi-C, RNA-seq, ATAC-seq, H3K4me3 and H3K27ac ChIP-seq. RESULTS The chromatin organization of zebrafish HSPC resemble mammalian cells with similar hierarchical structure. We revealed the multi-scale reorganization of chromatin structure and its influence on transcriptional regulation and transition of cell fate during HSPC development. Nascent HSPC is featured by loose conformation with obscure structure at all layers. Notably, PU.1 was identified as a potential factor mediating formation of promoter-involved loops and regulating gene expression of HSPC. CONCLUSIONS Our results provided a global view of chromatin structure dynamics associated with development of zebrafish HSPC and discovered key transcription factors involved in HSPC chromatin interactions, which will provide new insights into the epigenetic regulatory mechanisms underlying vertebrate HSPC fate decision.
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Affiliation(s)
- Min He
- Division of Cell, Developmental and Integrative Biology, School of Medicine, South China University of Technology, Guangzhou, 510006, China
| | - Xiaoli Li
- Division of Cell, Developmental and Integrative Biology, School of Medicine, South China University of Technology, Guangzhou, 510006, China
- Laboratory of Developmental Biology, Department of Cell Biology and Genetics, School of Basic Medical Sciences, Chongqing Medical University, Chongqing, 400016, China
| | - Bingxiang Xu
- Key Laboratory of Hebei Province for Molecular Biophysics, Institute of Biophysics, School of Health Science & Biomedical Engineering, Hebei University of Technology, Tianjin, 300130, China
| | - Yinbo Lu
- Division of Cell, Developmental and Integrative Biology, School of Medicine, South China University of Technology, Guangzhou, 510006, China
| | - Jingyi Lai
- Division of Cell, Developmental and Integrative Biology, School of Medicine, South China University of Technology, Guangzhou, 510006, China
| | - Yiming Ling
- Division of Cell, Developmental and Integrative Biology, School of Medicine, South China University of Technology, Guangzhou, 510006, China
| | - Huakai Liu
- Vehicle Engineering, School of Mechanical and Automotive Engineering, South China University of Technology, Guangzhou, 510000, China
| | - Ziyang An
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Wenqing Zhang
- Division of Cell, Developmental and Integrative Biology, School of Medicine, South China University of Technology, Guangzhou, 510006, China.
| | - Feifei Li
- Division of Cell, Developmental and Integrative Biology, School of Medicine, South China University of Technology, Guangzhou, 510006, China.
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Garg S, Ni W, Chowdhury B, Weisberg EL, Sattler M, Griffin JD. BRD9 regulates normal human hematopoietic stem cell function and lineage differentiation. Cell Death Differ 2024:10.1038/s41418-024-01306-5. [PMID: 38816579 DOI: 10.1038/s41418-024-01306-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 04/23/2024] [Accepted: 04/25/2024] [Indexed: 06/01/2024] Open
Abstract
Bromodomain containing protein 9 (BRD9), a member of the non-canonical BRG1/BRM-associated factor (ncBAF) chromatin remodeling complex, has been implicated as a synthetic lethal target in AML but its function in normal human hematopoiesis is unknown. In hematopoietic stem and progenitor cells (HSPC) genomic or chemical inhibition of BRD9 led to a proliferative disadvantage and loss of stem cells in vitro. Human HSPCs with reduced BRD9 protein levels produced lower numbers of immature mixed multipotent GEMM colonies in semi-solid media. In lineage-promoting culture conditions, cells with reduced BRD9 levels failed to differentiate into the megakaryocytic lineage and showed delayed differentiation into erythroid cells but enhanced terminal myeloid differentiation. HSPCs with BRD9 knock down (KD) had reduced long-term multilineage engraftment in a xenotransplantation assay. An increased number of downregulated genes in RNAseq analysis after BRD9 KD coupled with a gain in chromatin accessibility at the promoters of several repressive transcription factors (TF) suggest that BRD9 functions in the maintenance of active transcription during HSC differentiation. In particular, the hematopoietic master regulator GATA1 was identified as one of the core TFs regulating the gene networks modulated by BRD9 loss in HSPCs. BRD9 inhibition reduced a GATA1-luciferase reporter signal, further suggesting a role for BRD9 in regulating GATA1 activity. BRD9 is therefore an additional example of epigenetic regulation of human hematopoiesis.
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Affiliation(s)
- Swati Garg
- Dana-Farber Cancer Institute, Dept. of Medical Oncology, Boston, MA, 02215, USA
- Harvard Medical School, Dept. of Medicine, Boston, MA, 02215, USA
| | - Wei Ni
- Dana-Farber Cancer Institute, Dept. of Medical Oncology, Boston, MA, 02215, USA
- Harvard Medical School, Dept. of Medicine, Boston, MA, 02215, USA
| | - Basudev Chowdhury
- Dana-Farber Cancer Institute, Dept. of Medical Oncology, Boston, MA, 02215, USA
- Harvard Medical School, Dept. of Medicine, Boston, MA, 02215, USA
| | - Ellen L Weisberg
- Dana-Farber Cancer Institute, Dept. of Medical Oncology, Boston, MA, 02215, USA
- Harvard Medical School, Dept. of Medicine, Boston, MA, 02215, USA
| | - Martin Sattler
- Dana-Farber Cancer Institute, Dept. of Medical Oncology, Boston, MA, 02215, USA
- Harvard Medical School, Dept. of Medicine, Boston, MA, 02215, USA
| | - James D Griffin
- Dana-Farber Cancer Institute, Dept. of Medical Oncology, Boston, MA, 02215, USA.
- Harvard Medical School, Dept. of Medicine, Boston, MA, 02215, USA.
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5
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Branco A, Rayabaram J, Miranda CC, Fernandes-Platzgummer A, Fernandes TG, Sajja S, da Silva CL, Vemuri MC. Advances in ex vivo expansion of hematopoietic stem and progenitor cells for clinical applications. Front Bioeng Biotechnol 2024; 12:1380950. [PMID: 38846805 PMCID: PMC11153805 DOI: 10.3389/fbioe.2024.1380950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 04/25/2024] [Indexed: 06/09/2024] Open
Abstract
As caretakers of the hematopoietic system, hematopoietic stem cells assure a lifelong supply of differentiated populations that are responsible for critical bodily functions, including oxygen transport, immunological protection and coagulation. Due to the far-reaching influence of the hematopoietic system, hematological disorders typically have a significant impact on the lives of individuals, even becoming fatal. Hematopoietic cell transplantation was the first effective therapeutic avenue to treat such hematological diseases. Since then, key use and manipulation of hematopoietic stem cells for treatments has been aspired to fully take advantage of such an important cell population. Limited knowledge on hematopoietic stem cell behavior has motivated in-depth research into their biology. Efforts were able to uncover their native environment and characteristics during development and adult stages. Several signaling pathways at a cellular level have been mapped, providing insight into their machinery. Important dynamics of hematopoietic stem cell maintenance were begun to be understood with improved comprehension of their metabolism and progressive aging. These advances have provided a solid platform for the development of innovative strategies for the manipulation of hematopoietic stem cells. Specifically, expansion of the hematopoietic stem cell pool has triggered immense interest, gaining momentum. A wide range of approaches have sprouted, leading to a variety of expansion systems, from simpler small molecule-based strategies to complex biomimetic scaffolds. The recent approval of Omisirge, the first expanded hematopoietic stem and progenitor cell product, whose expansion platform is one of the earliest, is predictive of further successes that might arise soon. In order to guarantee the quality of these ex vivo manipulated cells, robust assays that measure cell function or potency need to be developed. Whether targeting hematopoietic engraftment, immunological differentiation potential or malignancy clearance, hematopoietic stem cells and their derivatives need efficient scaling of their therapeutic potency. In this review, we comprehensively view hematopoietic stem cells as therapeutic assets, going from fundamental to translational.
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Affiliation(s)
- André Branco
- Department of Bioengineering and Institute for Bioengineering and Biosciences (iBB), Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Janakiram Rayabaram
- Protein and Cell Analysis, Biosciences Division, Invitrogen Bioservices, Thermo Fisher Scientific, Bangalore, India
| | - Cláudia C. Miranda
- Department of Bioengineering and Institute for Bioengineering and Biosciences (iBB), Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- AccelBio, Collaborative Laboratory to Foster Translation and Drug Discovery, Cantanhede, Portugal
| | - Ana Fernandes-Platzgummer
- Department of Bioengineering and Institute for Bioengineering and Biosciences (iBB), Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Tiago G. Fernandes
- Department of Bioengineering and Institute for Bioengineering and Biosciences (iBB), Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Suchitra Sajja
- Protein and Cell Analysis, Biosciences Division, Invitrogen Bioservices, Thermo Fisher Scientific, Bangalore, India
| | - Cláudia L. da Silva
- Department of Bioengineering and Institute for Bioengineering and Biosciences (iBB), Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
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Brix A, Belleri L, Pezzotta A, Pettinato E, Mazzola M, Zoccolillo M, Marozzi A, Monteiro R, Del Bene F, Mortellaro A, Pistocchi A. ADA2 regulates inflammation and hematopoietic stem cell emergence via the A 2bR pathway in zebrafish. Commun Biol 2024; 7:615. [PMID: 38777862 PMCID: PMC11111730 DOI: 10.1038/s42003-024-06286-3] [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: 09/28/2023] [Accepted: 05/03/2024] [Indexed: 05/25/2024] Open
Abstract
Deficiency of adenosine deaminase 2 (DADA2) is an inborn error of immunity caused by loss-of-function mutations in the adenosine deaminase 2 (ADA2) gene. Clinical manifestations of DADA2 include vasculopathy and immuno-hematological abnormalities, culminating in bone marrow failure. A major gap exists in our knowledge of the regulatory functions of ADA2 during inflammation and hematopoiesis, mainly due to the absence of an ADA2 orthologue in rodents. Exploring these mechanisms is essential for understanding disease pathology and developing new treatments. Zebrafish possess two ADA2 orthologues, cecr1a and cecr1b, with the latter showing functional conservation with human ADA2. We establish a cecr1b-loss-of-function zebrafish model that recapitulates the immuno-hematological and vascular manifestations observed in humans. Loss of Cecr1b disrupts hematopoietic stem cell specification, resulting in defective hematopoiesis. This defect is caused by induced inflammation in the vascular endothelium. Blocking inflammation, pharmacological modulation of the A2r pathway, or the administration of the recombinant human ADA2 corrects these defects, providing insights into the mechanistic link between ADA2 deficiency, inflammation and immuno-hematological abnormalities. Our findings open up potential therapeutic avenues for DADA2 patients.
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Affiliation(s)
- Alessia Brix
- Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, L.I.T.A., via Fratelli Cervi 93, Segrate, 20054, Milan, Italy
| | - Laura Belleri
- Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, L.I.T.A., via Fratelli Cervi 93, Segrate, 20054, Milan, Italy
- Department of Development, Institut de la Vision, 17 Rue Moreau, 75012, Paris, France
| | - Alex Pezzotta
- Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, L.I.T.A., via Fratelli Cervi 93, Segrate, 20054, Milan, Italy
| | - Emanuela Pettinato
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, via Olgettina 60, 20132, Milan, Italy
| | - Mara Mazzola
- Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, L.I.T.A., via Fratelli Cervi 93, Segrate, 20054, Milan, Italy
| | - Matteo Zoccolillo
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, via Olgettina 60, 20132, Milan, Italy
| | - Anna Marozzi
- Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, L.I.T.A., via Fratelli Cervi 93, Segrate, 20054, Milan, Italy
| | - Rui Monteiro
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, Edgbaston, B15 2TTB, UK
| | - Filippo Del Bene
- Department of Development, Institut de la Vision, 17 Rue Moreau, 75012, Paris, France
| | - Alessandra Mortellaro
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, via Olgettina 60, 20132, Milan, Italy.
| | - Anna Pistocchi
- Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, L.I.T.A., via Fratelli Cervi 93, Segrate, 20054, Milan, Italy.
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Miyake K, Ito J, Karasuyama H. Novel insights into the ontogeny of basophils. FRONTIERS IN ALLERGY 2024; 5:1402841. [PMID: 38803659 PMCID: PMC11128600 DOI: 10.3389/falgy.2024.1402841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Accepted: 05/01/2024] [Indexed: 05/29/2024] Open
Abstract
Basophils are the least common granulocytes, accounting for <1% of peripheral blood leukocytes. In the last 20 years, analytical tools for mouse basophils have been developed, and we now recognize that basophils play critical roles in various immune reactions, including the development of allergic inflammation and protective immunity against parasites. Moreover, the combined use of flow cytometric analyses and knockout mice has uncovered several progenitor cells committed to basophils in mice. Recently, advancements in single-cell RNA sequencing (scRNA-seq) technologies have challenged the classical view of the differentiation of various hematopoietic cell lineages. This is also true for basophil differentiation, and studies using scRNA-seq analysis have provided novel insights into basophil differentiation, including the association of basophil differentiation with that of erythrocyte/megakaryocyte and the discovery of novel basophil progenitor cells in the mouse bone marrow. In this review, we summarize the recent findings of basophil ontogeny in both mice and humans, mainly focusing on studies using scRNA-seq analyses.
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Affiliation(s)
- Kensuke Miyake
- Institute of Research, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
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8
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Zhang Y, Kang Z, Liu M, Wang L, Liu F. Single-cell omics identifies inflammatory signaling as a trans-differentiation trigger in mouse embryos. Dev Cell 2024; 59:961-978.e7. [PMID: 38508181 DOI: 10.1016/j.devcel.2024.02.010] [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: 05/16/2023] [Revised: 01/08/2024] [Accepted: 02/28/2024] [Indexed: 03/22/2024]
Abstract
Trans-differentiation represents a direct lineage conversion; however, insufficient characterization of this process hinders its potential applications. Here, to explore a potential universal principal for trans-differentiation, we performed single-cell transcriptomic analysis of endothelial-to-hematopoietic transition (EHT), endothelial-to-mesenchymal transition, and epithelial-to-mesenchymal transition in mouse embryos. We applied three scoring indexes of entropies, cell-type signature transcription factor expression, and critical transition signals to show common features underpinning the fate plasticity of transition states. Cross-model comparison identified inflammatory-featured transition states and a common trigger role of interleukin-33 in promoting fate conversions. Multimodal profiling (integrative transcriptomic and chromatin accessibility analysis) demonstrated the inflammatory regulation of hematopoietic specification. Furthermore, multimodal omics and fate-mapping analyses showed that endothelium-specific Spi1, as an inflammatory effector, governs appropriate chromatin accessibility and transcriptional programs to safeguard EHT. Overall, our study employs single-cell omics to identify critical transition states/signals and the common trigger role of inflammatory signaling in developmental-stress-induced fate conversions.
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Affiliation(s)
- Yifan Zhang
- Shandong Provincial Key Laboratory of Animal Cell and Developmental Biology, School of Life Sciences, Shandong University, Qingdao, China
| | - Zhixin Kang
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Membrane Biology, Institute for Stem Cell and Regeneration, Institute of Zoology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
| | - Mengyao Liu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Lu Wang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Feng Liu
- Shandong Provincial Key Laboratory of Animal Cell and Developmental Biology, School of Life Sciences, Shandong University, Qingdao, China; Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Membrane Biology, Institute for Stem Cell and Regeneration, Institute of Zoology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China.
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9
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Toriseva M, Björkgren I, Junnila A, Mehmood A, Mattsson J, Raimoranta I, Kim B, Laiho A, Nees M, Elo L, Poutanen M, Breton S, Sipilä P. RUNX transcription factors are essential in maintaining epididymal epithelial differentiation. Cell Mol Life Sci 2024; 81:183. [PMID: 38630262 PMCID: PMC11023966 DOI: 10.1007/s00018-024-05211-5] [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: 09/04/2023] [Revised: 01/06/2024] [Accepted: 03/18/2024] [Indexed: 04/19/2024]
Abstract
Apart from the androgen receptor, transcription factors (TFs) that are required for the development and formation of the different segments of the epididymis have remained unknown. We identified TF families expressed in the developing epididymides, of which many showed segment specificity. From these TFs, down-regulation of runt related transcription factors (RUNXs) 1 and 2 expression coincides with epithelial regression in Dicer1 cKO mice. Concomitant deletion of both Runx1 and Runx2 in a mouse epididymal epithelial cell line affected cell morphology, adhesion and mobility in vitro. Furthermore, lack of functional RUNXs severely disturbed the formation of 3D epididymal organoid-like structures. Transcriptomic analysis of the epididymal cell organoid-like structures indicated that RUNX1 and RUNX2 are involved in the regulation of MAPK signaling, NOTCH pathway activity, and EMT-related gene expression. This suggests that RUNXs are master regulators of several essential signaling pathways, and necessary for the maintenance of proper differentiation of the epididymal epithelium.
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Affiliation(s)
- Mervi Toriseva
- Institute of Biomedicine, Cancer Research Unit and FICAN West Cancer Centre Laboratory, University of Turku and Turku University Hospital, Turku, Finland
| | - Ida Björkgren
- Institute of Biomedicine, Research Centre for Integrative Physiology and Pharmacology, Turku Center for Disease Modeling, University of Turku, Turku, Finland
| | - Arttu Junnila
- Institute of Biomedicine, Research Centre for Integrative Physiology and Pharmacology, Turku Center for Disease Modeling, University of Turku, Turku, Finland
| | - Arfa Mehmood
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Jesse Mattsson
- Institute of Biomedicine, Cancer Research Unit and FICAN West Cancer Centre Laboratory, University of Turku and Turku University Hospital, Turku, Finland
| | - Inka Raimoranta
- Institute of Biomedicine, Research Centre for Integrative Physiology and Pharmacology, Turku Center for Disease Modeling, University of Turku, Turku, Finland
| | - Bongki Kim
- Program in Membrane Biology/Division of Nephrology, Massachusetts General Hospital, Simches Research Center, Boston, MA, 02114, USA
- Department of Animal Resources Science, Kongju National University, Chungcheongnam-do, Yesan, 32439, Republic of Korea
| | - Asta Laiho
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Matthias Nees
- Institute of Biomedicine, Cancer Research Unit and FICAN West Cancer Centre Laboratory, University of Turku and Turku University Hospital, Turku, Finland
| | - Laura Elo
- Institute of Biomedicine, Research Centre for Integrative Physiology and Pharmacology, Turku Center for Disease Modeling, University of Turku, Turku, Finland
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Matti Poutanen
- Institute of Biomedicine, Research Centre for Integrative Physiology and Pharmacology, Turku Center for Disease Modeling, University of Turku, Turku, Finland
- Institute of Medicine, The Sahlgrenska Academy, Gothenburg University, Göteborg, Sweden
| | - Sylvie Breton
- Program in Membrane Biology/Division of Nephrology, Massachusetts General Hospital, Simches Research Center, Boston, MA, 02114, USA
- Department of Obstetrics, Gynecology and Reproduction, Faculty of Medicine, Research Center-CHU de Québec, Université Laval, Québec, QC, Canada
| | - Petra Sipilä
- Institute of Biomedicine, Research Centre for Integrative Physiology and Pharmacology, Turku Center for Disease Modeling, University of Turku, Turku, Finland.
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10
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Del Carpio-Cano F, Mao G, Goldfinger LE, Wurtzel J, Guan L, Alam MA, Lee K, Poncz M, Rao AK. Altered platelet-megakaryocyte endocytosis and trafficking of albumin and fibrinogen in RUNX1 haplodeficiency. Blood Adv 2024; 8:1699-1714. [PMID: 38330198 PMCID: PMC10997914 DOI: 10.1182/bloodadvances.2023011098] [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: 06/30/2023] [Revised: 01/11/2024] [Accepted: 01/29/2024] [Indexed: 02/10/2024] Open
Abstract
ABSTRACT Platelet α-granules have numerous proteins, some synthesized by megakaryocytes (MK) and others not synthesized but incorporated by endocytosis, an incompletely understood process in platelets/MK. Germ line RUNX1 haplodeficiency, referred to as familial platelet defect with predisposition to myeloid malignancies (FPDMMs), is associated with thrombocytopenia, platelet dysfunction, and granule deficiencies. In previous studies, we found that platelet albumin, fibrinogen, and immunoglobulin G (IgG) were decreased in a patient with FPDMM. We now show that platelet endocytosis of fluorescent-labeled albumin, fibrinogen, and IgG is decreased in the patient and his daughter with FPDMM. In megakaryocytic human erythroleukemia (HEL) cells, small interfering RNA RUNX1 knockdown (KD) increased uptake of these proteins over 24 hours compared with control cells, with increases in caveolin-1 and flotillin-1 (2 independent regulators of clathrin-independent endocytosis), LAMP2 (a lysosomal marker), RAB11 (a marker of recycling endosomes), and IFITM3. Caveolin-1 downregulation in RUNX1-deficient HEL cells abrogated the increased uptake of albumin, but not fibrinogen. Albumin, but not fibrinogen, partially colocalized with caveolin-1. RUNX1 KD resulted in increased colocalization of albumin with flotillin and fibrinogen with RAB11, suggesting altered trafficking of both proteins. The increased uptake of albumin and fibrinogen, as well as levels of caveolin-1, flotillin-1, LAMP2, and IFITM3, were recapitulated by short hairpin RNA RUNX1 KD in CD34+-derived MK. To our knowledge, these studies provide first evidence that platelet endocytosis of albumin and fibrinogen is impaired in some patients with RUNX1-haplodeficiency and suggest that megakaryocytes have enhanced endocytosis with defective trafficking, leading to loss of these proteins by distinct mechanisms. This study provides new insights into mechanisms governing endocytosis and α-granule deficiencies in RUNX1-haplodeficiency.
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Affiliation(s)
- Fabiola Del Carpio-Cano
- Sol Sherry Thrombosis Research Center, Lewis Katz School of Medicine at Temple University, Philadelphia, PA
| | - Guangfen Mao
- Sol Sherry Thrombosis Research Center, Lewis Katz School of Medicine at Temple University, Philadelphia, PA
| | - Lawrence E. Goldfinger
- Division of Hematology, Department of Medicine, Cardeza Foundation for Hematologic Research, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA
| | - Jeremy Wurtzel
- Division of Hematology, Department of Medicine, Cardeza Foundation for Hematologic Research, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA
| | - Liying Guan
- Sol Sherry Thrombosis Research Center, Lewis Katz School of Medicine at Temple University, Philadelphia, PA
| | - Mohammad Afaque Alam
- Sol Sherry Thrombosis Research Center, Lewis Katz School of Medicine at Temple University, Philadelphia, PA
| | - Kiwon Lee
- Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, PA
- Department of Bioscience and Biotechnology, Hankuk University of Foreign Studies, Seoul, Korea
| | - Mortimer Poncz
- Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, PA
| | - A. Koneti Rao
- Sol Sherry Thrombosis Research Center, Lewis Katz School of Medicine at Temple University, Philadelphia, PA
- Department of Medicine, Lewis Katz School of Medicine at Temple University, Philadelphia, PA
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11
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Gonzalez Galofre ZN, Kilpatrick AM, Marques M, Sá da Bandeira D, Ventura T, Gomez Salazar M, Bouilleau L, Marc Y, Barbosa AB, Rossi F, Beltran M, van de Werken HJG, van IJcken WFJ, Henderson NC, Forbes SJ, Crisan M. Runx1+ vascular smooth muscle cells are essential for hematopoietic stem and progenitor cell development in vivo. Nat Commun 2024; 15:1653. [PMID: 38395882 PMCID: PMC10891074 DOI: 10.1038/s41467-024-44913-z] [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: 02/25/2020] [Accepted: 01/09/2024] [Indexed: 02/25/2024] Open
Abstract
Hematopoietic stem cells (HSCs) produce all essential cellular components of the blood. Stromal cell lines supporting HSCs follow a vascular smooth muscle cell (vSMC) differentiation pathway, suggesting that some hematopoiesis-supporting cells originate from vSMC precursors. These pericyte-like precursors were recently identified in the aorta-gonad-mesonephros (AGM) region; however, their role in the hematopoietic development in vivo remains unknown. Here, we identify a subpopulation of NG2+Runx1+ perivascular cells that display a sclerotome-derived vSMC transcriptomic profile. We show that deleting Runx1 in NG2+ cells impairs the hematopoietic development in vivo and causes transcriptional changes in pericytes/vSMCs, endothelial cells and hematopoietic cells in the murine AGM. Importantly, this deletion leads also to a significant reduction of HSC reconstitution potential in the bone marrow in vivo. This defect is developmental, as NG2+Runx1+ cells were not detected in the adult bone marrow, demonstrating the existence of a specialised pericyte population in the HSC-generating niche, unique to the embryo.
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Affiliation(s)
- Zaniah N Gonzalez Galofre
- Centre for Cardiovascular Science, The University of Edinburgh, Edinburgh, UK
- Centre for Regenerative Medicine/Institute for Regeneration and Repair, The University of Edinburgh, Edinburgh, UK
| | - Alastair M Kilpatrick
- Centre for Regenerative Medicine/Institute for Regeneration and Repair, The University of Edinburgh, Edinburgh, UK
| | - Madalena Marques
- Centre for Regenerative Medicine/Institute for Regeneration and Repair, The University of Edinburgh, Edinburgh, UK
| | - Diana Sá da Bandeira
- Centre for Cardiovascular Science, The University of Edinburgh, Edinburgh, UK
- Centre for Regenerative Medicine/Institute for Regeneration and Repair, The University of Edinburgh, Edinburgh, UK
| | - Telma Ventura
- Centre for Regenerative Medicine/Institute for Regeneration and Repair, The University of Edinburgh, Edinburgh, UK
| | - Mario Gomez Salazar
- Centre for Regenerative Medicine/Institute for Regeneration and Repair, The University of Edinburgh, Edinburgh, UK
| | - Léa Bouilleau
- Centre for Regenerative Medicine/Institute for Regeneration and Repair, The University of Edinburgh, Edinburgh, UK
| | - Yvan Marc
- Centre for Regenerative Medicine/Institute for Regeneration and Repair, The University of Edinburgh, Edinburgh, UK
| | - Ana B Barbosa
- Centre for Regenerative Medicine/Institute for Regeneration and Repair, The University of Edinburgh, Edinburgh, UK
| | - Fiona Rossi
- Centre for Regenerative Medicine/Institute for Regeneration and Repair, The University of Edinburgh, Edinburgh, UK
| | - Mariana Beltran
- Centre for Inflammation Research/Institute for Regeneration and Repair, The University of Edinburgh, Edinburgh, UK
| | - Harmen J G van de Werken
- Cancer Computational Biology Center, Erasmus MC Cancer Institute, University Medical Center, 3000 CA, Rotterdam, The Netherlands
- Department of Urology, Erasmus MC Cancer Institute, University Medical Center, 3000 CA, Rotterdam, The Netherlands
- Department of Immunology, Erasmus MC Cancer Institute, University Medical Center, 3000 CA, Rotterdam, The Netherlands
| | - Wilfred F J van IJcken
- Center for Biomics, Department of Cell Biology, Erasmus MC University Medical Centre, 3015 GE, Rotterdam, The Netherlands
| | - Neil C Henderson
- Centre for Inflammation Research/Institute for Regeneration and Repair, The University of Edinburgh, Edinburgh, UK
- MRC Human Genetics Unit, Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK
| | - Stuart J Forbes
- Centre for Regenerative Medicine/Institute for Regeneration and Repair, The University of Edinburgh, Edinburgh, UK
| | - Mihaela Crisan
- Centre for Cardiovascular Science, The University of Edinburgh, Edinburgh, UK.
- Centre for Regenerative Medicine/Institute for Regeneration and Repair, The University of Edinburgh, Edinburgh, UK.
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12
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Al-Amoodi AS, Kai J, Li Y, Malki JS, Alghamdi A, Al-Ghuneim A, Saera-Vila A, Habuchi S, Merzaban JS. α1,3-fucosylation treatment improves cord blood CD34 negative hematopoietic stem cell navigation. iScience 2024; 27:108882. [PMID: 38322982 PMCID: PMC10845921 DOI: 10.1016/j.isci.2024.108882] [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: 08/24/2023] [Revised: 11/24/2023] [Accepted: 01/08/2024] [Indexed: 02/08/2024] Open
Abstract
For almost two decades, clinicians have overlooked the diagnostic potential of CD34neg hematopoietic stem cells because of their limited homing capacity relative to CD34posHSCs when injected intravenously. This has contributed to the lack of appeal of using umbilical cord blood in HSC transplantation because its stem cell count is lower than bone marrow. The present study reveals that the homing and engraftment of CD34negHSCs can be improved by adding the Sialyl Lewis X molecule via α1,3-fucosylation. This unlocks the potential for using this more primitive stem cell to treat blood disorders because our findings show CD34negHSCs have the capacity to regenerate cells in the bone marrow of mice for several months. Furthermore, our RNA sequencing analysis revealed that CD34negHSCs have unique adhesion pathways, downregulated in CD34posHSCs, that facilitate interaction with the bone marrow niche. Our findings suggest that CD34neg cells will best thrive when the HSC resides in its microenvironment.
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Affiliation(s)
- Asma S. Al-Amoodi
- Bioscience Program, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Jing Kai
- Bioscience Program, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Yanyan Li
- Bioscience Program, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Jana S. Malki
- Bioscience Program, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Abdullah Alghamdi
- Bioscience Program, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Arwa Al-Ghuneim
- Bioscience Program, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia
| | | | - Satoshi Habuchi
- Bioscience Program, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Jasmeen S. Merzaban
- Bioscience Program, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia
- KAUST Smart-Health Initiative, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
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13
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Imaz-Rosshandler I, Rode C, Guibentif C, Harland LTG, Ton MLN, Dhapola P, Keitley D, Argelaguet R, Calero-Nieto FJ, Nichols J, Marioni JC, de Bruijn MFTR, Göttgens B. Tracking early mammalian organogenesis - prediction and validation of differentiation trajectories at whole organism scale. Development 2024; 151:dev201867. [PMID: 37982461 PMCID: PMC10906099 DOI: 10.1242/dev.201867] [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: 04/12/2023] [Accepted: 10/30/2023] [Indexed: 11/21/2023]
Abstract
Early organogenesis represents a key step in animal development, during which pluripotent cells diversify to initiate organ formation. Here, we sampled 300,000 single-cell transcriptomes from mouse embryos between E8.5 and E9.5 in 6-h intervals and combined this new dataset with our previous atlas (E6.5-E8.5) to produce a densely sampled timecourse of >400,000 cells from early gastrulation to organogenesis. Computational lineage reconstruction identified complex waves of blood and endothelial development, including a new programme for somite-derived endothelium. We also dissected the E7.5 primitive streak into four adjacent regions, performed scRNA-seq and predicted cell fates computationally. Finally, we defined developmental state/fate relationships by combining orthotopic grafting, microscopic analysis and scRNA-seq to transcriptionally determine cell fates of grafted primitive streak regions after 24 h of in vitro embryo culture. Experimentally determined fate outcomes were in good agreement with computationally predicted fates, demonstrating how classical grafting experiments can be revisited to establish high-resolution cell state/fate relationships. Such interdisciplinary approaches will benefit future studies in developmental biology and guide the in vitro production of cells for organ regeneration and repair.
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Affiliation(s)
- Ivan Imaz-Rosshandler
- Department of Haematology, University of Cambridge, Cambridge CB2 0RE, UK
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Christina Rode
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Carolina Guibentif
- Department of Microbiology and Immunology, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Luke T. G. Harland
- Department of Haematology, University of Cambridge, Cambridge CB2 0RE, UK
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
| | - Mai-Linh N. Ton
- Department of Haematology, University of Cambridge, Cambridge CB2 0RE, UK
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
| | - Parashar Dhapola
- Division of Molecular Hematology, Lund Stem Cell Center, Lund University, 221 00 Lund, Sweden
| | - Daniel Keitley
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | - Ricard Argelaguet
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK
- Altos Labs Cambridge Institute, Granta Park, Cambridge CB21 6GP, UK
| | - Fernando J. Calero-Nieto
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
| | - Jennifer Nichols
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
| | - John C. Marioni
- Wellcome Sanger Institute, Wellcome Genome Campus, Saffron Walden CB10 1SA, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Saffron Walden CB10 1SA, UK
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK
| | - Marella F. T. R. de Bruijn
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Berthold Göttgens
- Department of Haematology, University of Cambridge, Cambridge CB2 0RE, UK
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
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14
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Martinez TC, McNerney ME. Haploinsufficient Transcription Factors in Myeloid Neoplasms. ANNUAL REVIEW OF PATHOLOGY 2024; 19:571-598. [PMID: 37906947 DOI: 10.1146/annurev-pathmechdis-051222-013421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Many transcription factors (TFs) function as tumor suppressor genes with heterozygous phenotypes, yet haploinsufficiency generally has an underappreciated role in neoplasia. This is no less true in myeloid cells, which are normally regulated by a delicately balanced and interconnected transcriptional network. Detailed understanding of TF dose in this circuitry sheds light on the leukemic transcriptome. In this review, we discuss the emerging features of haploinsufficient transcription factors (HITFs). We posit that: (a) monoallelic and biallelic losses can have distinct cellular outcomes; (b) the activity of a TF exists in a greater range than the traditional Mendelian genetic doses; and (c) how a TF is deleted or mutated impacts the cellular phenotype. The net effect of a HITF is a myeloid differentiation block and increased intercellular heterogeneity in the course of myeloid neoplasia.
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Affiliation(s)
- Tanner C Martinez
- Department of Pathology, Department of Pediatrics, Section of Hematology/Oncology, The University of Chicago Medicine Comprehensive Cancer Center, The University of Chicago, Chicago, Illinois, USA;
- Medical Scientist Training Program, The University of Chicago, Chicago, Illinois, USA
| | - Megan E McNerney
- Department of Pathology, Department of Pediatrics, Section of Hematology/Oncology, The University of Chicago Medicine Comprehensive Cancer Center, The University of Chicago, Chicago, Illinois, USA;
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15
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Yu K, Deuitch N, Merguerian M, Cunningham L, Davis J, Bresciani E, Diemer J, Andrews E, Young A, Donovan F, Sood R, Craft K, Chong S, Chandrasekharappa S, Mullikin J, Liu PP. Genomic landscape of patients with germline RUNX1 variants and familial platelet disorder with myeloid malignancy. Blood Adv 2024; 8:497-511. [PMID: 38019014 PMCID: PMC10837196 DOI: 10.1182/bloodadvances.2023011165] [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: 07/10/2023] [Revised: 11/07/2023] [Accepted: 11/07/2023] [Indexed: 11/30/2023] Open
Abstract
ABSTRACT Familial platelet disorder with associated myeloid malignancies (FPDMM) is caused by germline RUNX1 mutations and characterized by thrombocytopenia and increased risk of hematologic malignancies. We recently launched a longitudinal natural history study for patients with FPDMM. Among 27 families with research genomic data by the end of 2021, 26 different germline RUNX1 variants were detected. Besides missense mutations enriched in Runt homology domain and loss-of-function mutations distributed throughout the gene, splice-region mutations and large deletions were detected in 6 and 7 families, respectively. In 25 of 51 (49%) patients without hematologic malignancy, somatic mutations were detected in at least 1 of the clonal hematopoiesis of indeterminate potential (CHIP) genes or acute myeloid leukemia (AML) driver genes. BCOR was the most frequently mutated gene (in 9 patients), and multiple BCOR mutations were identified in 4 patients. Mutations in 6 other CHIP- or AML-driver genes (TET2, DNMT3A, KRAS, LRP1B, IDH1, and KMT2C) were also found in ≥2 patients without hematologic malignancy. Moreover, 3 unrelated patients (1 with myeloid malignancy) carried somatic mutations in NFE2, which regulates erythroid and megakaryocytic differentiation. Sequential sequencing data from 19 patients demonstrated dynamic changes of somatic mutations over time, and stable clones were more frequently found in older adult patients. In summary, there are diverse types of germline RUNX1 mutations and high frequency of somatic mutations related to clonal hematopoiesis in patients with FPDMM. Monitoring changes in somatic mutations and clinical manifestations prospectively may reveal mechanisms for malignant progression and inform clinical management. This trial was registered at www.clinicaltrials.gov as #NCT03854318.
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Affiliation(s)
- Kai Yu
- Oncogenesis and Development Section, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
| | - Natalie Deuitch
- Oncogenesis and Development Section, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
| | - Matthew Merguerian
- Oncogenesis and Development Section, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
- Department of Pediatrics, Johns Hopkins University School of Medicine, Balltimore, MD
| | - Lea Cunningham
- Oncogenesis and Development Section, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
- Immune Deficiency Cellular Therapy Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Joie Davis
- Oncogenesis and Development Section, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
| | - Erica Bresciani
- Oncogenesis and Development Section, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
| | - Jamie Diemer
- Oncogenesis and Development Section, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
| | - Elizabeth Andrews
- Immune Deficiency Cellular Therapy Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Alice Young
- NIH Intramural Sequencing Center, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
| | - Frank Donovan
- Genomics Core, Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
| | - Raman Sood
- Oncogenesis and Development Section, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
| | - Kathleen Craft
- Oncogenesis and Development Section, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
| | - Shawn Chong
- Oncogenesis and Development Section, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
| | - Settara Chandrasekharappa
- Genomics Core, Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
| | - Jim Mullikin
- NIH Intramural Sequencing Center, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
| | - Paul P. Liu
- Oncogenesis and Development Section, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
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16
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Zhou S, Zhao T, Chen X, Zhang W, Zou X, Yang Y, Wang Q, Zhang P, Zhou T, Feng T. Runx1 Deficiency Promotes M2 Macrophage Polarization Through Enhancing STAT6 Phosphorylation. Inflammation 2023; 46:2241-2253. [PMID: 37530929 DOI: 10.1007/s10753-023-01874-7] [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: 05/09/2023] [Revised: 07/03/2023] [Accepted: 07/06/2023] [Indexed: 08/03/2023]
Abstract
Our previous study had demonstrated that Runx1 promoted LPS-induced macrophage inflammatory response, however, the role of Runx1 in M2 macrophage polarization still remains largely unknown. This study was conducted to investigate the role of Runx1 in IL-4/IL-13-induced M2 macrophage polarization and its potential regulatory mechanism. We found that exposure of macrophages to IL-4/IL-13 induced a remarkable increasement in Runx1 expression level. Specifically, we established genetically modified mice lacking Runx1 in myeloid cells, including macrophages. RNA-Seq was performed to identify differentially expressed genes (DEGs) between Runx1 knockout and WT control bone marrow-derived macrophages (BMDMs). We identified 686 DEGs, including many genes which were highly expressed in M2 macrophage. In addition, bioinformatics analysis indicated that these DEGs were significantly enriched in extracellular matrix-related processes. Moreover, RT-qPCR analysis showed that there was an obvious upregulation in the relative expression levels of M2 marker genes, including Arg1, Ym1, Fizz1, CD71, Mmp9, and Tgm2, in Runx1 knockout macrophages, as compared to WT controls. Consistently, similar results were obtained in the protein and enzymatic activity levels of Arg1. Finally, we found that the STAT6 phosphorylation level was significantly enhanced in Runx1 knockout macrophages, and the STAT6 inhibitor AS1517499 partly reduced the upregulated effect of Runx1 deficiency on the M2 macrophage polarization. Taken together, Runx1 deficiency facilitates IL-4/IL-13-induced M2 macrophage polarization through enhancing STAT6 phosphorylation.
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Affiliation(s)
- Siyuan Zhou
- Department of Clinical Laboratory, The Affiliated Changzhou Second People's Hospital of Nanjing Medical University, Changzhou, 213000, Jiangsu, China
| | - Ting Zhao
- Department of Clinical Laboratory, The Affiliated Changzhou Second People's Hospital of Nanjing Medical University, Changzhou, 213000, Jiangsu, China
| | - Xuqiong Chen
- Department of Clinical Laboratory, The Affiliated Changzhou Second People's Hospital of Nanjing Medical University, Changzhou, 213000, Jiangsu, China
| | - Wuwen Zhang
- Department of Clinical Laboratory, The Affiliated Changzhou Second People's Hospital of Nanjing Medical University, Changzhou, 213000, Jiangsu, China
| | - Xiaoyi Zou
- Department of Clinical Laboratory, The Affiliated Changzhou Second People's Hospital of Nanjing Medical University, Changzhou, 213000, Jiangsu, China
| | - Yi Yang
- Department of Clinical Laboratory, The Affiliated Changzhou Second People's Hospital of Nanjing Medical University, Changzhou, 213000, Jiangsu, China
| | - Qinshi Wang
- Department of Clinical Laboratory, The Affiliated Changzhou Second People's Hospital of Nanjing Medical University, Changzhou, 213000, Jiangsu, China
| | - Ping Zhang
- Department of Clinical Laboratory, The Affiliated Changzhou Second People's Hospital of Nanjing Medical University, Changzhou, 213000, Jiangsu, China
| | - Tong Zhou
- Department of Pediatrics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Tongbao Feng
- Department of Clinical Laboratory, The Affiliated Changzhou Second People's Hospital of Nanjing Medical University, Changzhou, 213000, Jiangsu, China.
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17
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Boussaty EC, Tedeschi N, Novotny M, Ninoyu Y, Du E, Draf C, Zhang Y, Manor U, Scheuermann RH, Friedman R. Cochlear transcriptome analysis of an outbred mouse population (CFW). Front Cell Neurosci 2023; 17:1256619. [PMID: 38094513 PMCID: PMC10716316 DOI: 10.3389/fncel.2023.1256619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 10/11/2023] [Indexed: 12/20/2023] Open
Abstract
Age-related hearing loss (ARHL) is the most common cause of hearing loss and one of the most prevalent conditions affecting the elderly worldwide. Despite evidence from our lab and others about its polygenic nature, little is known about the specific genes, cell types, and pathways involved in ARHL, impeding the development of therapeutic interventions. In this manuscript, we describe, for the first time, the complete cell-type specific transcriptome of the aging mouse cochlea using snRNA-seq in an outbred mouse model in relation to auditory threshold variation. Cochlear cell types were identified using unsupervised clustering and annotated via a three-tiered approach-first by linking to expression of known marker genes, then using the NSForest algorithm to select minimum cluster-specific marker genes and reduce dimensional feature space for statistical comparison of our clusters with existing publicly-available data sets on the gEAR website, and finally, by validating and refining the annotations using Multiplexed Error Robust Fluorescence In Situ Hybridization (MERFISH) and the cluster-specific marker genes as probes. We report on 60 unique cell-types expanding the number of defined cochlear cell types by more than two times. Importantly, we show significant specific cell type increases and decreases associated with loss of hearing acuity implicating specific subsets of hair cell subtypes, ganglion cell subtypes, and cell subtypes within the stria vascularis in this model of ARHL. These results provide a view into the cellular and molecular mechanisms responsible for age-related hearing loss and pathways for therapeutic targeting.
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Affiliation(s)
- Ely Cheikh Boussaty
- Department of Otolaryngology, University of California, San Diego, La Jolla, CA, United States
| | - Neil Tedeschi
- J. Craig Venter Institute, La Jolla, CA, United States
| | - Mark Novotny
- J. Craig Venter Institute, La Jolla, CA, United States
| | - Yuzuru Ninoyu
- Department of Otolaryngology, University of California, San Diego, La Jolla, CA, United States
| | - Eric Du
- Department of Otolaryngology, University of California, San Diego, La Jolla, CA, United States
| | - Clara Draf
- Department of Otolaryngology, University of California, San Diego, La Jolla, CA, United States
| | - Yun Zhang
- J. Craig Venter Institute, La Jolla, CA, United States
| | - Uri Manor
- Department of Cell and Developmental Biology, University of California San Diego, Salk Institute for Biological Studies, Waitt Advanced Biophotonics Center, La Jolla, CA, United States
| | - Richard H. Scheuermann
- J. Craig Venter Institute, La Jolla, CA, United States
- Department of Pathology, University of California, San Diego, La Jolla, CA, United States
| | - Rick Friedman
- Department of Otolaryngology, University of California, San Diego, La Jolla, CA, United States
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18
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Carpio-Cano FD, Mao G, Goldfinger LE, Wurtzel J, Guan L, Alam AM, Lee K, Poncz ME, Rao AK. Altered Platelet-Megakaryocyte Endocytosis and Trafficking of Albumin and Fibrinogen in RUNX1 Haplodeficiency. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.10.23.23297335. [PMID: 37961544 PMCID: PMC10635164 DOI: 10.1101/2023.10.23.23297335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Platelet α-granules have numerous proteins, some synthesized by megakaryocytes (MK) and others not synthesized but incorporated by endocytosis, an incompletely understood process in platelets/MK. Germline RUNX1 haplodeficiency, referred to as familial platelet defect with predisposition to myeloid malignancies (FPDMM), is associated with thrombocytopenia, platelet dysfunction and granule deficiencies. In previous studies, we found that platelet albumin, fibrinogen and IgG levels were decreased in a FPDMM patient. We now show that platelet endocytosis of fluorescent-labeled albumin, fibrinogen and IgG is decreased in the patient and his daughter with FPDMM. In megakaryocytic human erythroleukemia (HEL) cells, siRNA RUNX1 knockdown (KD) increased uptake of these proteins over 24 hours compared to control cells, with increases in caveolin-1 and flotillin-1 (two independent regulators of clathrin-independent endocytosis), LAMP2 (a lysosomal marker), RAB11 (a marker of recycling endosomes) and IFITM3. Caveolin-1 downregulation in RUNX1-deficient HEL cells abrogated the increased uptake of albumin, but not fibrinogen. Albumin, but not fibrinogen, partially colocalized with caveolin-1. RUNX1 knockdown increased colocalization of albumin with flotillin and of fibrinogen with RAB11 suggesting altered trafficking of both. The increased albumin and fibrinogen uptake and levels of caveolin-1, flotillin-1, LAMP2 and IFITM3 were recapitulated by shRNA RUNX1 knockdown in CD34 + -derived MK. These studies provide the first evidence that in RUNX1- haplodeficiency platelet endocytosis of albumin and fibrinogen is impaired and that megakaryocytes have enhanced endocytosis with defective trafficking leading to loss of these proteins by distinct mechanisms. They provide new insights into mechanisms governing endocytosis and α-granule deficiencies in RUNX1- haplodeficiency. Key points Platelet content and endocytosis of α-granule proteins, albumin, fibrinogen and IgG, are decreased in germline RUNX1 haplodeficiency. In RUNX1 -deficient HEL cells and primary MK endocytosis is enhanced with defective trafficking leading to decreased protein levels.
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Ji N, Huang W, Dang H, Xiao H, Shi Y, Guo J, Chen K, Wang J, Zou J. CBFβ is induced by spring viremia of carp virus and promotes virus replication in zebrafish. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2023; 147:104751. [PMID: 37268261 DOI: 10.1016/j.dci.2023.104751] [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: 02/08/2023] [Revised: 05/30/2023] [Accepted: 05/30/2023] [Indexed: 06/04/2023]
Abstract
The core binding factor subunit beta (CBFβ) is a transcription factor that forms a complex with virial proteins to promote viral infection. In this study, we identified a CBFβ homolog from zebrafish (zfCBFβ) and characterized the biological activity. The deduced zfCBFβ protein was highly similar to orthologs from other species. The zfcbfβ gene was constitutively expressed in tissues and was induced in immune tissues after infection with spring viremia carp virus (SVCV) and stimulation with poly(I:C). Interestingly, zfcbfβ is not induced by type I interferons. Overexpression of zfcbfβ induced tnfα expression but inhibited isg15 expression. Also, overexpression of zfcbfβ significantly increased SVCV titer in the EPC cells. Co-immunoprecipitation assay revealed that zfCBFβ interacts with SVCV phosphoprotein (SVCVP) and host p53, resulting in the increased stability of zfCBFβ. Our results provide evidence that CBFβ is targeted by virus to suppress host antiviral response.
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Affiliation(s)
- Ning Ji
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306, China; International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, 201306, China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, China
| | - Wenji Huang
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306, China; International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, 201306, China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, China
| | - Huifeng Dang
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306, China; International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, 201306, China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, China
| | - Hehe Xiao
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306, China; International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, 201306, China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, China
| | - Yanjie Shi
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306, China; International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, 201306, China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, China
| | - Jiahong Guo
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306, China; International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, 201306, China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, China
| | - Kangyong Chen
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306, China; International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, 201306, China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, China
| | - Junya Wang
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306, China; International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, 201306, China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, China
| | - Jun Zou
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306, China; International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, 201306, China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266200, China.
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20
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Eriksson A, Engvall M, Mathot L, Österroos A, Rippin M, Cavelier L, Ladenvall C, Baliakas P. Somatic Exonic Deletions in RUNX1 Constitutes a Novel Recurrent Genomic Abnormality in Acute Myeloid Leukemia. Clin Cancer Res 2023; 29:2826-2834. [PMID: 37022349 DOI: 10.1158/1078-0432.ccr-23-0122] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 03/08/2023] [Accepted: 04/04/2023] [Indexed: 04/07/2023]
Abstract
PURPOSE In acute myeloid leukemia (AML), somatic mutations (commonly missense, nonsense, and frameshift indels) in RUNX1 are associated with a dismal clinical outcome. Inherited RUNX1 mutations cause familial platelet disorder. As approximately 5%-10% of germline RUNX1 mutations are large exonic deletions, we hypothesized that such exonic RUNX1 aberrations may also be acquired during the development of AML. EXPERIMENTAL DESIGN Sixty patients with well-characterized AML were analyzed with multiplex ligation-dependent probe amplification (n = 60), microarray (n = 11), and/or whole-genome sequencing (n = 8). RESULTS In total, 25 (42% of the cohort) RUNX1-aberrant patients (defined by the presence of classical mutations and/or exonic deletions) were identified. Sixteen patients (27%) carried only exonic deletions, 5 (8%) carried classical mutations, and 4 (7%) carried both exonic deletions and mutations. No significant difference was observed between patients with classical RUNX1 mutations and RUNX1 exonic deletions in median overall survival (OS, 53.1 vs. 38.8 months, respectively, P = 0.63). When applying the European Leukemia Net (ELN) classification including the RUNX1-aberrant group, 20% of the patients initially stratified as intermediate-risk (5% of the whole cohort) were reassigned to the high-risk group, which improved the performance of ELN classification regarding OS between intermediate- and high-risk groups (18.9 vs. 9.6 months, P = 0.09). CONCLUSIONS Somatic RUNX1 exonic deletions constitute a novel recurrent aberration in AML. Our findings have important clinical implications regarding AML classification, risk stratification, and treatment decision. Moreover, they argue in favor of further investigating such genomic aberrations not only in RUNX1 but also in other genes implicated in cancer biology and management. See related commentary by Chakraborty and Stengel, p. 2742.
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Affiliation(s)
- Anna Eriksson
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Marie Engvall
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Lucy Mathot
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- Department of Clinical Genetics, Uppsala University Hospital, Uppsala, Sweden
| | - Albin Österroos
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Martin Rippin
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Lucia Cavelier
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Clinical Genetics, Karolinska University Hospital, Solna, Sweden
| | - Claes Ladenvall
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Panagiotis Baliakas
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- Department of Clinical Genetics, Uppsala University Hospital, Uppsala, Sweden
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21
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Zerella JR, Homan CC, Arts P, Brown AL, Scott HS, Hahn CN. Transcription factor genetics and biology in predisposition to bone marrow failure and hematological malignancy. Front Oncol 2023; 13:1183318. [PMID: 37377909 PMCID: PMC10291195 DOI: 10.3389/fonc.2023.1183318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 05/26/2023] [Indexed: 06/29/2023] Open
Abstract
Transcription factors (TFs) play a critical role as key mediators of a multitude of developmental pathways, with highly regulated and tightly organized networks crucial for determining both the timing and pattern of tissue development. TFs can act as master regulators of both primitive and definitive hematopoiesis, tightly controlling the behavior of hematopoietic stem and progenitor cells (HSPCs). These networks control the functional regulation of HSPCs including self-renewal, proliferation, and differentiation dynamics, which are essential to normal hematopoiesis. Defining the key players and dynamics of these hematopoietic transcriptional networks is essential to understanding both normal hematopoiesis and how genetic aberrations in TFs and their networks can predispose to hematopoietic disease including bone marrow failure (BMF) and hematological malignancy (HM). Despite their multifaceted and complex involvement in hematological development, advances in genetic screening along with elegant multi-omics and model system studies are shedding light on how hematopoietic TFs interact and network to achieve normal cell fates and their role in disease etiology. This review focuses on TFs which predispose to BMF and HM, identifies potential novel candidate predisposing TF genes, and examines putative biological mechanisms leading to these phenotypes. A better understanding of the genetics and molecular biology of hematopoietic TFs, as well as identifying novel genes and genetic variants predisposing to BMF and HM, will accelerate the development of preventative strategies, improve clinical management and counseling, and help define targeted treatments for these diseases.
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Affiliation(s)
- Jiarna R. Zerella
- Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA, Australia
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, Australia
| | - Claire C. Homan
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, Australia
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, SA, Australia
| | - Peer Arts
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, Australia
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, SA, Australia
| | - Anna L. Brown
- Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA, Australia
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, Australia
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, SA, Australia
| | - Hamish S. Scott
- Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA, Australia
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, Australia
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, SA, Australia
| | - Christopher N. Hahn
- Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA, Australia
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, Australia
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, SA, Australia
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22
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Boussaty EC, Tedeschi N, Novotny M, Ninoyu Y, Du E, Draf C, Zhang Y, Manor U, Scheuermann RH, Friedman R. Cochlear transcriptome analysis of an outbred mouse population (CFW). BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.15.528661. [PMID: 36824745 PMCID: PMC9948975 DOI: 10.1101/2023.02.15.528661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
Age-related hearing loss (ARHL) is the most common cause of hearing loss and one of the most prevalent conditions affecting the elderly worldwide. Despite evidence from our lab and others about its polygenic nature, little is known about the specific genes, cell types and pathways involved in ARHL, impeding the development of therapeutic interventions. In this manuscript, we describe, for the first time, the complete cell-type specific transcriptome of the aging mouse cochlea using snRNA-seq in an outbred mouse model in relation to auditory threshold variation. Cochlear cell types were identified using unsupervised clustering and annotated via a three-tiered approach - first by linking to expression of known marker genes, then using the NS-Forest algorithm to select minimum cluster-specific marker genes and reduce dimensional feature space for statistical comparison of our clusters with existing publicly-available data sets on the gEAR website (https://umgear.org/), and finally, by validating and refining the annotations using Multiplexed Error Robust Fluorescence In Situ Hybridization (MERFISH) and the cluster-specific marker genes as probes. We report on 60 unique cell-types expanding the number of defined cochlear cell types by more than two times. Importantly, we show significant specific cell type increases and decreases associated with loss of hearing acuity implicating specific subsets of hair cell subtypes, ganglion cell subtypes, and cell subtypes withing the stria vascularis in this model of ARHL. These results provide a view into the cellular and molecular mechanisms responsible for age-related hearing loss and pathways for therapeutic targeting.
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Affiliation(s)
| | | | | | - Yuzuru Ninoyu
- Department of Otolaryngology, University of California, San Diego, CA
| | - Eric Du
- Department of Otolaryngology, University of California, San Diego, CA
| | - Clara Draf
- Department of Otolaryngology, University of California, San Diego, CA
| | - Yun Zhang
- J. Craig Venter Institute, La Jolla, CA
| | - Uri Manor
- Salk Institute for Biological Studies, Waitt Advanced Biophotonics Center, La Jolla, CA, United States
| | - Richard H. Scheuermann
- J. Craig Venter Institute, La Jolla, CA
- Department of Pathology, University of California, San Diego, CA
| | - Rick Friedman
- Department of Otolaryngology, University of California, San Diego, CA
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23
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Cheng CK, Yung YL, Chan HY, Leung KT, Chan KYY, Leung AWK, Cheng FWT, Li CK, Wan TSK, Luo X, Pitts HA, Cheung JS, Chan NPH, Ng MHL. Deep genomic characterization highlights complexities and prognostic markers of pediatric acute myeloid leukemia. Commun Biol 2023; 6:356. [PMID: 37002311 PMCID: PMC10066286 DOI: 10.1038/s42003-023-04732-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 03/20/2023] [Indexed: 04/03/2023] Open
Abstract
Pediatric acute myeloid leukemia (AML) is an uncommon but aggressive hematological malignancy. The poor outcome is attributed to inadequate prognostic classification and limited treatment options. A thorough understanding on the genetic basis of pediatric AML is important for the development of effective approaches to improve outcomes. Here, by comprehensively profiling fusion genes as well as mutations and copy number changes of 141 myeloid-related genes in 147 pediatric AML patients with subsequent variant functional characterization, we unveil complex mutational patterns of biological relevance and disease mechanisms including MYC deregulation. Also, our findings highlight TP53 alterations as strong adverse prognostic markers in pediatric AML and suggest the core spindle checkpoint kinase BUB1B as a selective dependency in this aggressive subgroup. Collectively, our present study provides detailed genomic characterization revealing not only complexities and mechanistic insights into pediatric AML but also significant risk stratification and therapeutic strategies to tackle the disease.
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Affiliation(s)
- Chi-Keung Cheng
- Blood Cancer Cytogenetics and Genomics Laboratory, Department of Anatomical and Cellular Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
| | - Yuk-Lin Yung
- Blood Cancer Cytogenetics and Genomics Laboratory, Department of Anatomical and Cellular Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
| | - Hoi-Yun Chan
- Blood Cancer Cytogenetics and Genomics Laboratory, Department of Anatomical and Cellular Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
| | - Kam-Tong Leung
- Department of Paediatrics, The Chinese University of Hong Kong, Hong Kong, China
| | - Kathy Y Y Chan
- Department of Paediatrics, The Chinese University of Hong Kong, Hong Kong, China
| | - Alex W K Leung
- Department of Paediatrics, The Chinese University of Hong Kong, Hong Kong, China
| | - Frankie W T Cheng
- Department of Paediatrics, The Chinese University of Hong Kong, Hong Kong, China
| | - Chi-Kong Li
- Department of Paediatrics, The Chinese University of Hong Kong, Hong Kong, China
| | - Thomas S K Wan
- Blood Cancer Cytogenetics and Genomics Laboratory, Department of Anatomical and Cellular Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
| | - Xi Luo
- Blood Cancer Cytogenetics and Genomics Laboratory, Department of Anatomical and Cellular Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
| | - Herbert-Augustus Pitts
- Blood Cancer Cytogenetics and Genomics Laboratory, Department of Anatomical and Cellular Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
| | - Joyce S Cheung
- Blood Cancer Cytogenetics and Genomics Laboratory, Department of Anatomical and Cellular Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
| | - Natalie P H Chan
- Blood Cancer Cytogenetics and Genomics Laboratory, Department of Anatomical and Cellular Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
| | - Margaret H L Ng
- Blood Cancer Cytogenetics and Genomics Laboratory, Department of Anatomical and Cellular Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China.
- State Key Laboratory of Translational Oncology, The Chinese University of Hong Kong, Hong Kong, China.
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24
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Hey J, Halperin C, Hartmann M, Mayer S, Schönung M, Lipka DB, Scherz-Shouval R, Plass C. DNA methylation landscape of tumor-associated macrophages reveals pathways, transcription factors and prognostic value relevant to triple-negative breast cancer patients. Int J Cancer 2023; 152:1226-1242. [PMID: 36408934 DOI: 10.1002/ijc.34364] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 10/17/2022] [Accepted: 11/03/2022] [Indexed: 11/23/2022]
Abstract
The accumulation of myeloid cells, particularly tumor-associated macrophages (TAMs), characterizes the tumor microenvironment (TME) of many solid cancers, including breast cancer. Compared to healthy tissue-resident macrophages, TAMs acquire distinct transcriptomes and tumor-promoting functions by largely unknown mechanisms. Here, we hypothesize the involvement of TME signaling and subsequent epigenetic reprogramming of TAMs. Using the 4T1 mouse model of triple-negative breast cancer, we demonstrate that the presence of cancer cells significantly alters the DNA methylation landscape of macrophages and, to a lesser extent, bone marrow-derived monocytes (BMDMs). TAM methylomes, dissected into BMDM-originating and TAM-specific epigenetic programs, implicated transcription factors (TFs) and signaling pathways involved in TAM reprogramming, correlated with cancer-specific gene expression patterns. Utilizing published single-cell gene expression data, we linked microenvironmentally-derived signals to the cancer-specific DNA methylation landscape of TAMs. These integrative analyses highlighted the role of altered cytokine production in the TME (eg, TGF-β, IFN-γ and CSF1) on the induction of specific TFs (eg, FOSL2, STAT1 and RUNX3) responsible for the epigenetic reprogramming of TAMs. DNA methylation deconvolution identified a TAM-specific signature associated with the identified signaling pathways and TFs, corresponding with severe tumor grade and poor prognosis of breast cancer patients. Similarly, immunosuppressive TAM functions were identified, such as induction of the immune inhibitory receptor-ligand PD-L1 by DNA hypomethylation of Cd274. Collectively, these results provide strong evidence that the epigenetic landscapes of macrophages and monocytes are perturbed by the presence of breast cancer, pointing to molecular mechanisms of TAM reprogramming, impacting patient outcomes.
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Affiliation(s)
- Joschka Hey
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Faculty of Biosciences, Ruprecht Karl University of Heidelberg, Heidelberg, Germany
| | - Coral Halperin
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Mark Hartmann
- Translational Cancer Epigenomics, Division Translational Medical Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Shimrit Mayer
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Maximilian Schönung
- Faculty of Biosciences, Ruprecht Karl University of Heidelberg, Heidelberg, Germany.,Translational Cancer Epigenomics, Division Translational Medical Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Daniel B Lipka
- Translational Cancer Epigenomics, Division Translational Medical Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Ruth Scherz-Shouval
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Christoph Plass
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
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25
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Jeong HC, Shukla S, Fok WC, Huynh TN, Batista LFZ, Parker R. USB1 is a miRNA deadenylase that regulates hematopoietic development. Science 2023; 379:901-907. [PMID: 36862787 PMCID: PMC10827040 DOI: 10.1126/science.abj8379] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 02/03/2023] [Indexed: 03/04/2023]
Abstract
Mutations in the 3' to 5' RNA exonuclease USB1 cause hematopoietic failure in poikiloderma with neutropenia (PN). Although USB1 is known to regulate U6 small nuclear RNA maturation, the molecular mechanism underlying PN remains undetermined, as pre-mRNA splicing is unaffected in patients. We generated human embryonic stem cells harboring the PN-associated mutation c.531_delA in USB1 and show that this mutation impairs human hematopoiesis. Dysregulated microRNA (miRNA) levels in USB1 mutants during blood development contribute to hematopoietic failure, because of a failure to remove 3'-end adenylated tails added by PAPD5/7. Modulation of miRNA 3'-end adenylation through genetic or chemical inhibition of PAPD5/7 rescues hematopoiesis in USB1 mutants. This work shows that USB1 acts as a miRNA deadenylase and suggests PAPD5/7 inhibition as a potential therapy for PN.
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Affiliation(s)
- Ho-Chang Jeong
- Division of Hematology, Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA
- Center for Genome Integrity, Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Siddharth Shukla
- Department of Biochemistry, University of Colorado, Boulder, CO 80303, USA
- Howard Hughes Medical Institute, Chevy Chase MD 20815, USA
| | - Wilson Chun Fok
- Division of Hematology, Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA
- Center for Genome Integrity, Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Thao Ngoc Huynh
- Department of Biochemistry, University of Colorado, Boulder, CO 80303, USA
- Howard Hughes Medical Institute, Chevy Chase MD 20815, USA
| | - Luis Francisco Zirnberger Batista
- Division of Hematology, Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA
- Center for Genome Integrity, Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Roy Parker
- Department of Biochemistry, University of Colorado, Boulder, CO 80303, USA
- Howard Hughes Medical Institute, Chevy Chase MD 20815, USA
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26
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Khan AS, Campbell KJ, Cameron ER, Blyth K. The RUNX/CBFβ Complex in Breast Cancer: A Conundrum of Context. Cells 2023; 12:641. [PMID: 36831308 PMCID: PMC9953914 DOI: 10.3390/cells12040641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 02/07/2023] [Accepted: 02/10/2023] [Indexed: 02/19/2023] Open
Abstract
Dissecting and identifying the major actors and pathways in the genesis, progression and aggressive advancement of breast cancer is challenging, in part because neoplasms arising in this tissue represent distinct diseases and in part because the tumors themselves evolve. This review attempts to illustrate the complexity of this mutational landscape as it pertains to the RUNX genes and their transcription co-factor CBFβ. Large-scale genomic studies that characterize genetic alterations across a disease subtype are a useful starting point and as such have identified recurring alterations in CBFB and in the RUNX genes (particularly RUNX1). Intriguingly, the functional output of these mutations is often context dependent with regards to the estrogen receptor (ER) status of the breast cancer. Therefore, such studies need to be integrated with an in-depth understanding of both the normal and corrupted function in mammary cells to begin to tease out how loss or gain of function can alter the cell phenotype and contribute to disease progression. We review how alterations to RUNX/CBFβ function contextually ascribe to breast cancer subtypes and discuss how the in vitro analyses and mouse model systems have contributed to our current understanding of these proteins in the pathogenesis of this complex set of diseases.
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Affiliation(s)
- Adiba S. Khan
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Rd, Glasgow G61 1BD, UK; (A.S.K.); (K.J.C.)
- School of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G61 1QH, UK
| | - Kirsteen J. Campbell
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Rd, Glasgow G61 1BD, UK; (A.S.K.); (K.J.C.)
| | - Ewan R. Cameron
- School of Biodiversity One Health & Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G61 1QH, UK;
| | - Karen Blyth
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Rd, Glasgow G61 1BD, UK; (A.S.K.); (K.J.C.)
- School of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G61 1QH, UK
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Control of focal adhesion kinase activation by RUNX1-regulated miRNAs in high-risk AML. Leukemia 2023; 37:776-787. [PMID: 36788336 DOI: 10.1038/s41375-023-01841-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 01/29/2023] [Accepted: 02/03/2023] [Indexed: 02/16/2023]
Abstract
We recently described a 16-gene expression signature for improved risk stratification of acute myeloid leukemia (AML) patients called the AML Prognostic Score (APS). A subset of APS-high-risk AML patients showed increased levels of focal adhesion kinase (FAK), encoded by the Protein Tyrosine Kinase 2 (PTK2) gene, which was correlated with RUNX1 mutations. RUNX1 mutant cells are more sensitive to PTK2 inhibitors. As we were not able to detect RUNX1-binding sites in the PTK2 promoter, we hypothesized that RUNX1 might regulate micro(mi)RNAs that repress PTK2, such that loss-of-function RUNX1 mutations would result in reduced miRNA expression and derepression of PTK2. Examination of paired RNA-seq and miRNA-seq data from 301 AML cases revealed two miRNAs that positively correlated with RUNX1 expression, contained RUNX1-binding sites in their promoters and were predicted to target PTK2. We show that the hsa-let7a-2-3p and hsa-miR-135a-5p promoters are regulated by RUNX1, and that PTK2 is a direct target of both miRNAs. Even in the absence of RUNX1 mutations, hsa-let7a-2-3p and hsa-miR-135a-5p regulate PTK2 expression, and reduced expression of these two miRNAs sensitizes AML cells to PTK2 inhibition. These data explain how RUNX1 regulates PTK2, and identify potential miRNA biomarkers for targeting AML with PTK2 inhibitors.
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Geckin B, Zoodsma M, Kilic G, Debisarun PA, Rakshit S, Adiga V, Ahmed A, Parthiban C, Kumar NC, D’Souza G, Baltissen MP, Martens JHA, Domínguez-Andrés J, Li Y, Vyakarnam A, Netea MG. Differences in Immune Responses in Individuals of Indian and European Origin: Relevance for the COVID-19 Pandemic. Microbiol Spectr 2023; 11:e0023123. [PMID: 36779734 PMCID: PMC10100912 DOI: 10.1128/spectrum.00231-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 01/26/2023] [Indexed: 02/14/2023] Open
Abstract
During the coronavirus disease 2019 (COVID-19) pandemic, large differences in susceptibility and mortality due to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection have been reported between populations in Europe and South Asia. While both host and environmental factors (including Mycobacterium bovis BCG vaccination) have been proposed to explain this, the potential biological substrate of these differences is unknown. We purified peripheral blood mononuclear cells from individuals living in India and the Netherlands at baseline and 10 to 12 weeks after BCG vaccination. We compared chromatin accessibility between the two populations at baseline, as well as gene transcription profiles and cytokine production capacities upon stimulation. The chromatin accessibility of genes important for adaptive immunity was higher in the Indians than in the Europeans, while the latter had more accessible chromatin regions in genes of the innate immune system. At the transcriptional level, we observed that the Indian volunteers displayed a more tolerant immune response to stimulation, in contrast to a more exaggerated response in the Europeans. BCG vaccination strengthened the tolerance program in the Indians but not in the Europeans. These differences may partly explain the different impact of COVID-19 on the two populations. IMPORTANCE In this study, we assessed the differences in immune responses in individuals from India and Europe. This aspect is of great relevance, because of the described differences in morbidity and mortality between India and Europe during the pandemic. We found a significant difference in chromatin accessibility in immune cells from the two populations, followed by a more balanced and effective response in individuals from India. These exciting findings represent a very important piece of the puzzle for understanding the COVID-19 pandemic at a global level.
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Affiliation(s)
- Büsra Geckin
- Department of Internal Medicine, Radboud Center for Infectious Diseases, Radboud University Medical Centre, Nijmegen, The Netherlands
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Martijn Zoodsma
- Centre for Individualised Infection Medicine (CiiM), a joint venture between the Helmholtz Centre for Infection Research (HZI) and Hannover Medical School (MHH), Hannover, Germany
- TWINCORE Centre for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre for Infection Research (HZI) and the Hannover Medical School (MHH), Hannover, Germany
| | - Gizem Kilic
- Department of Internal Medicine, Radboud Center for Infectious Diseases, Radboud University Medical Centre, Nijmegen, The Netherlands
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Priya A. Debisarun
- Department of Internal Medicine, Radboud Center for Infectious Diseases, Radboud University Medical Centre, Nijmegen, The Netherlands
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Srabanti Rakshit
- Laboratory of Immunology of HIV-TB Co-infection, Centre for Infectious Disease Research, Indian Institute of Science, Bangalore, India
| | - Vasista Adiga
- Laboratory of Immunology of HIV-TB Co-infection, Centre for Infectious Disease Research, Indian Institute of Science, Bangalore, India
| | - Asma Ahmed
- Laboratory of Immunology of HIV-TB Co-infection, Centre for Infectious Disease Research, Indian Institute of Science, Bangalore, India
| | - Chaitra Parthiban
- Laboratory of Immunology of HIV-TB Co-infection, Centre for Infectious Disease Research, Indian Institute of Science, Bangalore, India
| | - Nirutha Chetan Kumar
- Laboratory of Immunology of HIV-TB Co-infection, Centre for Infectious Disease Research, Indian Institute of Science, Bangalore, India
| | - George D’Souza
- Laboratory of Immunology of HIV-TB Co-infection, Centre for Infectious Disease Research, Indian Institute of Science, Bangalore, India
| | - Marijke P. Baltissen
- Department of Molecular Biology, Radboud University, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Joost H. A. Martens
- Department of Molecular Biology, Radboud University, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Jorge Domínguez-Andrés
- Department of Internal Medicine, Radboud Center for Infectious Diseases, Radboud University Medical Centre, Nijmegen, The Netherlands
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Yang Li
- Department of Internal Medicine, Radboud Center for Infectious Diseases, Radboud University Medical Centre, Nijmegen, The Netherlands
- Centre for Individualised Infection Medicine (CiiM), a joint venture between the Helmholtz Centre for Infection Research (HZI) and Hannover Medical School (MHH), Hannover, Germany
- TWINCORE Centre for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre for Infection Research (HZI) and the Hannover Medical School (MHH), Hannover, Germany
| | - Annapurna Vyakarnam
- Laboratory of Immunology of HIV-TB Co-infection, Centre for Infectious Disease Research, Indian Institute of Science, Bangalore, India
- Peter Gorer Department of Immunobiology, School of Immunology and Microbial Sciences, Faculty of Life Sciences & Medicine, Guy’s Hospital, King’s College London, London, United Kingdom
| | - Mihai G. Netea
- Department of Internal Medicine, Radboud Center for Infectious Diseases, Radboud University Medical Centre, Nijmegen, The Netherlands
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Immunology and Metabolism, Life & Medical Sciences Institute, University of Bonn, Bonn, Germany
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Valdivia AO, He Y, Ren X, Wen D, Dong L, Nazari H, Li X. Probable Treatment Targets for Diabetic Retinopathy Based on an Integrated Proteomic and Genomic Analysis. Transl Vis Sci Technol 2023; 12:8. [PMID: 36745438 PMCID: PMC9910385 DOI: 10.1167/tvst.12.2.8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Purpose Using previously approved medications for new indications can expedite the lengthy and expensive drug development process. We describe a bioinformatics pipeline that integrates genomics and proteomics platforms to identify already-approved drugs that might be useful to treat diabetic retinopathy (DR). Methods Proteomics analysis of vitreous humor samples from 12 patients undergoing pars plana vitrectomy for DR and a whole genome dataset (UKBiobank TOPMed-imputed) from 1330 individuals with DR and 395,155 controls were analyzed independently to identify biological pathways associated with DR. Common biological pathways shared between both datasets were further analyzed (STRING and REACTOME analyses) to identify target proteins for probable drug modulation. Curated target proteins were subsequently analyzed by the BindingDB database to identify chemical compounds they interact with. Identified chemical compounds were further curated through the Expasy SwissSimilarity database for already-approved drugs that interact with target proteins. Results The pathways in each dataset (proteomics and genomics) converged in the upregulation of a previously unknown pathway involved in DR (RUNX2 signaling; constituents MMP-13 and LGALS3), with an emphasis on its role in angiogenesis and blood-retina barrier. Bioinformatics analysis identified U.S. Food and Drug Administration (FDA)-approved medications (raltitrexed, pemetrexed, glyburide, probenecid, clindamycin hydrochloride, and ticagrelor) that, in theory, may modulate this pathway. Conclusions The bioinformatics pipeline described here identifies FDA-approved drugs that can be used for new alternative indications. These theoretical candidate drugs should be validated with experimental studies. Translational Relevance Our study suggests possible drugs for DR treatment based on an integrated proteomics and genomics pipeline. This approach can potentially expedite the drug discovery process by identifying already-approved drugs that might be used for new indications.
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Affiliation(s)
- Anddre Osmar Valdivia
- Department of Ophthalmology and Visual Neuroscience, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Ye He
- Tianjin Key Laboratory of Retinal Functions and Diseases, Tianjin Branch of National Clinical Research Center for Ocular Disease, Eye Institute and School of Optometry, Tianjin Medical University Eye Hospital, Tianjin, China
| | - Xinjun Ren
- Tianjin Key Laboratory of Retinal Functions and Diseases, Tianjin Branch of National Clinical Research Center for Ocular Disease, Eye Institute and School of Optometry, Tianjin Medical University Eye Hospital, Tianjin, China
| | - Dejia Wen
- Tianjin Key Laboratory of Retinal Functions and Diseases, Tianjin Branch of National Clinical Research Center for Ocular Disease, Eye Institute and School of Optometry, Tianjin Medical University Eye Hospital, Tianjin, China
| | - Lijie Dong
- Tianjin Key Laboratory of Retinal Functions and Diseases, Tianjin Branch of National Clinical Research Center for Ocular Disease, Eye Institute and School of Optometry, Tianjin Medical University Eye Hospital, Tianjin, China
| | - Hossein Nazari
- Department of Ophthalmology and Visual Neuroscience, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Xiaorong Li
- Tianjin Key Laboratory of Retinal Functions and Diseases, Tianjin Branch of National Clinical Research Center for Ocular Disease, Eye Institute and School of Optometry, Tianjin Medical University Eye Hospital, Tianjin, China
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Yu K, Deuitch N, Merguerian M, Cunningham L, Davis J, Bresciani E, Diemer J, Andrews E, Young A, Donovan F, Sood R, Craft K, Chong S, Chandrasekharappa S, Mullikin J, Liu PP. Genomic Landscape of Patients with Germline RUNX1 Variants and Familial Platelet Disorder with Myeloid Malignancy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.17.524290. [PMID: 36789433 PMCID: PMC9928034 DOI: 10.1101/2023.01.17.524290] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Germline RUNX1 mutations lead to familial platelet disorder with associated myeloid malignancies (FPDMM), which is characterized by thrombocytopenia and a life-long risk (35-45%) of hematological malignancies. We recently launched a longitudinal natural history study for patients with FPDMM at the NIH Clinical Center. Among 29 families with research genomic data, 28 different germline RUNX1 variants were detected. Besides missense mutations enriched in Runt homology domain and loss-of-function mutations distributed throughout the gene, splice-region mutations and large deletions were detected in 6 and 7 families, respectively. In 24 of 54 (44.4%) non-malignant patients, somatic mutations were detected in at least one of the clonal hematopoiesis of indeterminate potential (CHIP) genes or acute myeloid leukemia (AML) driver genes. BCOR was the most frequently mutated gene (in 9 patients), and multiple BCOR mutations were identified in 4 patients. Mutations in 7 other CHIP or AML driver genes ( DNMT3A, TET2, NRAS, SETBP1, SF3B1, KMT2C , and LRP1B ) were also found in more than one non-malignant patient. Moreover, three unrelated patients (one with myeloid malignancy) carried somatic mutations in NFE2 , which regulates erythroid and megakaryocytic differentiation. Sequential sequencing data from 19 patients demonstrated dynamic changes of somatic mutations over time, and stable clones were more frequently found in elderly patients. In summary, there are diverse types of germline RUNX1 mutations and high frequency of somatic mutations related to clonal hematopoiesis in patients with FPDMM. Monitoring dynamic changes of somatic mutations prospectively will benefit patients’ clinical management and reveal mechanisms for progression to myeloid malignancies. Key Points Comprehensive genomic profile of patients with FPDMM with germline RUNX1 mutations. Rising clonal hematopoiesis related secondary mutations that may lead to myeloid malignancies.
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Windisch R, Kreissig S, Wichmann C. Defined Human Leukemic CD34+ Liquid Cultures to Study HDAC/Transcriptional Repressor Complexes. Methods Mol Biol 2023; 2589:27-49. [PMID: 36255616 DOI: 10.1007/978-1-0716-2788-4_3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Defined human primary cell model systems with growth dependence on oncogenes are highly requested to investigate tumor pathogenesis and to validate pharmacological inhibitors that specifically target oncoproteins and their executing protein complex partners. In acute myeloid leukemia (AML), transcription factors such as RUNX1 and MLL1, which are important for normal blood cell development, frequently harbor mutations including chromosomal translocations with other coding genes, resulting in tumor-promoting gain-of-function fusion proteins. These oncoproteins completely modify transcriptional programs, thereby inducing malignant cell phenotypes. A common theme of the chimeric gene products is their physical interaction with a variety of chromatin-modifying effector molecules, including histone acetyltransferases (HATs) and histone deacetylases (HDACs). These aberrant multiprotein machineries disturb gene expression and promote malignant cell growth. In this chapter, we briefly summarize the current understanding regarding AML-associated oncogene-driven human CD34+ blood progenitor cell expansion in ex vivo liquid cultures. We provide a step-by-step protocol to establish oncogene-induced human CD34+ blood progenitor cell cultures suitable to analyze the impact of transcriptional repressor/HDAC activity in these human AML cell models.
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Affiliation(s)
- Roland Windisch
- Department of Transfusion Medicine, Cell Therapeutics and Hemostaseology, University Hospital, LMU Munich, Munich, Germany
| | - Sophie Kreissig
- Department of Transfusion Medicine, Cell Therapeutics and Hemostaseology, University Hospital, LMU Munich, Munich, Germany
| | - Christian Wichmann
- Department of Transfusion Medicine, Cell Therapeutics and Hemostaseology, University Hospital, LMU Munich, Munich, Germany.
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Hou S, Liu C, Yao Y, Bai Z, Gong Y, Wang C, He J, You G, Zhang G, Liu B, Lan Y. Hematopoietic Stem Cell Development in Mammalian Embryos. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1442:1-16. [PMID: 38228955 DOI: 10.1007/978-981-99-7471-9_1] [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: 01/18/2024]
Abstract
Hematopoietic stem cells (HSCs) are situated at the top of the adult hematopoietic hierarchy in mammals and give rise to the majority of blood cells throughout life. Recently, with the advance of multiple single-cell technologies, researchers have unprecedentedly deciphered the cellular and molecular evolution, the lineage relationships, and the regulatory mechanisms underlying HSC emergence in mammals. In this review, we describe the precise vascular origin of HSCs in mouse and human embryos, emphasizing the conservation in the unambiguous arterial characteristics of the HSC-primed hemogenic endothelial cells (HECs). Serving as the immediate progeny of some HECs, functional pre-HSCs of mouse embryos can now be isolated at single-cell level using defined surface marker combinations. Heterogeneity regrading cell cycle status or lineage differentiation bias within HECs, pre-HSCs, or emerging HSCs in mouse embryos has been figured out. Several epigenetic regulatory mechanisms of HSC generation, including long noncoding RNA, DNA methylation modification, RNA splicing, and layered epigenetic modifications, have also been recently uncovered. In addition to that of HSCs, the cellular and molecular events underlying the development of multiple hematopoietic progenitors in human embryos/fetus have been unraveled with the use of series of single-cell technologies. Specifically, yolk sac-derived myeloid-biased progenitors have been identified as the earliest multipotent hematopoietic progenitors in human embryo, serving as an important origin of fetal liver monocyte-derived macrophages. Moreover, the development of multiple hematopoietic lineages in human embryos such as T and B lymphocytes, innate lymphoid cells, as well as myeloid cells like monocytes, macrophages, erythrocytes, and megakaryocytes has also been depicted and reviewed here.
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Affiliation(s)
- Siyuan Hou
- Key Laboratory for Regenerative Medicine of Ministry of Education, Institute of Hematology, School of Medicine, Jinan University, Guangzhou, Guangdong, China
- State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Institute of Hematology, Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Chen Liu
- State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Institute of Hematology, Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Yingpeng Yao
- Key Laboratory for Regenerative Medicine of Ministry of Education, Institute of Hematology, School of Medicine, Jinan University, Guangzhou, Guangdong, China
| | - Zhijie Bai
- State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Institute of Hematology, Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Yandong Gong
- State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Institute of Hematology, Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Chaojie Wang
- Key Laboratory for Regenerative Medicine of Ministry of Education, Institute of Hematology, School of Medicine, Jinan University, Guangzhou, Guangdong, China
| | - Jian He
- State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Institute of Hematology, Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Guoju You
- State Key Laboratory of Primate Biomedical Research, State Key Laboratory of Experimental Hematology, School of Medicine, Tsinghua University, Beijing, China
| | - Guangyu Zhang
- State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Institute of Hematology, Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Bing Liu
- Key Laboratory for Regenerative Medicine of Ministry of Education, Institute of Hematology, School of Medicine, Jinan University, Guangzhou, Guangdong, China
- State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Institute of Hematology, Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Yu Lan
- Key Laboratory for Regenerative Medicine of Ministry of Education, Institute of Hematology, School of Medicine, Jinan University, Guangzhou, Guangdong, China
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Wang X, Liu S, Yu J. Multi-lineage Differentiation from Hematopoietic Stem Cells. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1442:159-175. [PMID: 38228964 DOI: 10.1007/978-981-99-7471-9_10] [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: 01/18/2024]
Abstract
The hematopoietic stem cells (HSCs) have the ability to differentiate and give rise to all mature blood cells. Commitment to differentiation progressively limits the self-renewal potential of the original HSCs by regulating the level of lineage-specific gene expression. In this review, we will summarize the current understanding of the molecular mechanisms underlying HSC differentiation toward erythroid, myeloid, and lymphocyte lineages. Moreover, we will decipher how the single-cell technologies advance the lineage-biased HSC subpopulations and their differentiation potential.
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Affiliation(s)
- Xiaoshuang Wang
- The State Key Laboratory for Complex, Severe, and Rare Diseases, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences / Peking Union Medical College, Beijing, China.
- The Institute of Blood Transfusion, Chinese Academy of Medical Sciences / Peking Union Medical College, Chengdu, China.
| | - Siqi Liu
- State Key Laboratory of Common Mechanism Research for Major Diseases, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences / Peking Union Medical College, Beijing, China
| | - Jia Yu
- State Key Laboratory of Common Mechanism Research for Major Diseases, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences / Peking Union Medical College, Beijing, China.
- The Institute of Blood Transfusion, Chinese Academy of Medical Sciences / Peking Union Medical College, Chengdu, China.
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Xie S, Chen M, Fang W, Liu S, Wu Q, Liu C, Xing Y, Shi W, Xu M, Zhang M, Chen S, Zeng X, Wang S, Deng W, Tang Q. Diminished arachidonate 5-lipoxygenase perturbs phase separation and transcriptional response of Runx2 to reverse pathological ventricular remodeling. EBioMedicine 2022; 86:104359. [PMID: 36395739 PMCID: PMC9672960 DOI: 10.1016/j.ebiom.2022.104359] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 10/26/2022] [Accepted: 10/26/2022] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Arachidonate 5-lipoxygenase (Alox5) belongs to a class of nonheme iron-containing dioxygenases involved in the catalysis of leukotriene biosynthesis. However, the effects of Alox5 itself on pathological cardiac remodeling and heart failure remain elusive. METHODS The role of Alox5 in pathological cardiac remodeling was investigated by Alox5 genetic depletion, AAV9-mediated overexpression in cardiomyocytes, and a bone marrow (BM) transplantation approach. Neonatal rat cardiomyocytes were used to explore the effects of Alox5 in vitro. Molecular and signaling pathways were revealed by CUT &Tag, IP-MS, RNA sequencing and bioinformatic analyses. FINDINGS Untargeted metabolomics showed that serum 5-HETE (a primary product of Alox5) levels were little changed in patients with cardiac hypertrophy, while Alox5 expression was significantly upregulated in murine hypertensive cardiac samples and human cardiac samples of hypertrophy, which prompted us to test whether high Alox5 levels under hypertensive stimuli were directly associated with pathologic myocardium in an enzymatic activity-independent manner. Herein, we revealed that Alox5 deficiency significantly ameliorated transverse aortic constriction (TAC)-induced hypertrophy. Cardiomyocyte-specific Alox5 depletion attenuated hypertensive ventricular remodeling. Conversely, cardiac-specifical Alox5 overexpression showed a pro-hypertrophic cardiac phenotype. Ablation of Alox5 in bone marrow-derived cells did not affect pathological cardiac remodeling and heart failure. Mechanically, Runx2 was identified as a target of Alox5. In this regard, Alox5 PEST domain could directly bind to Runx2 PTS domain, promoting nuclear localization of Runx2 in an enzymatic activity-independent manner, simultaneously contributed to liquid-liquid phase separation (LLPS) of Runx2 at specific domain in the nucleus and increased transcription of EGFR in cardiomyocytes. Runx2 depletion alleviated hypertrophy in Ang II-pretreated Alox5-overexpressing cardiomyocytes. INTERPRETATION Overall, our study demonstrated that targeting Alox5 exerted a protective effect against cardiac remodeling and heart failure under hypertensive stimuli by disturbing LLPS of Runx2 and substantial reduction of EGFR transcription activation in cardiomyocytes. Our findings suggest that negative modulation of Alox5-Runx2 may provide a therapeutic approach against pathological cardiac remodeling and heart failure. FUNDING National Natural Science Foundation of China.
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Affiliation(s)
- Saiyang Xie
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan, China,Hubei Key Laboratory of Metabolic and Chronic Diseases, Wuhan, China
| | - Mengya Chen
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan, China,Hubei Key Laboratory of Metabolic and Chronic Diseases, Wuhan, China
| | - Wenxi Fang
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan, China,Hubei Key Laboratory of Metabolic and Chronic Diseases, Wuhan, China
| | - Shiqiang Liu
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan, China,Hubei Key Laboratory of Metabolic and Chronic Diseases, Wuhan, China
| | - Qingqing Wu
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan, China,Hubei Key Laboratory of Metabolic and Chronic Diseases, Wuhan, China
| | - Chen Liu
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan, China,Hubei Key Laboratory of Metabolic and Chronic Diseases, Wuhan, China
| | - Yun Xing
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan, China,Hubei Key Laboratory of Metabolic and Chronic Diseases, Wuhan, China
| | - Wenke Shi
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan, China,Hubei Key Laboratory of Metabolic and Chronic Diseases, Wuhan, China
| | - Man Xu
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan, China,Hubei Key Laboratory of Metabolic and Chronic Diseases, Wuhan, China
| | - Min Zhang
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan, China,Hubei Key Laboratory of Metabolic and Chronic Diseases, Wuhan, China
| | - Si Chen
- Cardiovascular Research Institute of Wuhan University, Wuhan 430060, China
| | - Xiaofeng Zeng
- Cardiovascular Research Institute of Wuhan University, Wuhan 430060, China
| | - Shasha Wang
- Cardiovascular Research Institute of Wuhan University, Wuhan 430060, China
| | - Wei Deng
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan, China,Hubei Key Laboratory of Metabolic and Chronic Diseases, Wuhan, China,Department of Cardiology, The Fifth Affiliated Hospital of Xinjiang Medical University, Ürümqi, China,Corresponding author. Department of Cardiology, Renmin Hospital of Wuhan University, Jiefang Road 238, Wuhan 430060, China.
| | - Qizhu Tang
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan, China,Hubei Key Laboratory of Metabolic and Chronic Diseases, Wuhan, China,Corresponding author. Department of Cardiology, Renmin Hospital of Wuhan University, Jiefang Road 238, Wuhan 430060, China.
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Chakraborty A, Wang JG, Ay F. dcHiC detects differential compartments across multiple Hi-C datasets. Nat Commun 2022; 13:6827. [PMID: 36369226 PMCID: PMC9652325 DOI: 10.1038/s41467-022-34626-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 11/01/2022] [Indexed: 11/13/2022] Open
Abstract
The compartmental organization of mammalian genomes and its changes play important roles in distinct biological processes. Here, we introduce dcHiC, which utilizes a multivariate distance measure to identify significant changes in compartmentalization among multiple contact maps. Evaluating dcHiC on four collections of bulk and single-cell contact maps from in vitro mouse neural differentiation (n = 3), mouse hematopoiesis (n = 10), human LCLs (n = 20) and post-natal mouse brain development (n = 3 stages), we show its effectiveness and sensitivity in detecting biologically relevant changes, including those orthogonally validated. dcHiC reported regions with dynamically regulated genes associated with cell identity, along with correlated changes in chromatin states, subcompartments, replication timing and lamin association. With its efficient implementation, dcHiC enables high-resolution compartment analysis as well as standalone browser visualization, differential interaction identification and time-series clustering. dcHiC is an essential addition to the Hi-C analysis toolbox for the ever-growing number of bulk and single-cell contact maps. Available at: https://github.com/ay-lab/dcHiC .
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Affiliation(s)
- Abhijit Chakraborty
- Centers for Autoimmunity, Inflammation and Cancer Immunotherapy, La Jolla Institute for Immunology, La Jolla, CA, 92037, USA.
| | - Jeffrey G Wang
- Centers for Autoimmunity, Inflammation and Cancer Immunotherapy, La Jolla Institute for Immunology, La Jolla, CA, 92037, USA
- The Bishop's School, La Jolla, CA, 92037, USA
- Harvard College, Cambridge, MA, 02138, USA
| | - Ferhat Ay
- Centers for Autoimmunity, Inflammation and Cancer Immunotherapy, La Jolla Institute for Immunology, La Jolla, CA, 92037, USA.
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, 92093, USA.
- Department of Pediatrics, University of California San Diego, La Jolla, CA, 92093, USA.
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Zheng Z, He H, Tang XT, Zhang H, Gou F, Yang H, Cao J, Shi S, Yang Z, Sun G, Xie X, Zeng Y, Wen A, Lan Y, Zhou J, Liu B, Zhou BO, Cheng T, Cheng H. Uncovering the emergence of HSCs in the human fetal bone marrow by single-cell RNA-seq analysis. Cell Stem Cell 2022; 29:1562-1579.e7. [DOI: 10.1016/j.stem.2022.10.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 02/24/2022] [Accepted: 10/12/2022] [Indexed: 11/06/2022]
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Michaels YS, Edgar JM, Major MC, Castle EL, Zimmerman C, Yin T, Hagner A, Lau C, Hsu HH, Ibañez-Rios MI, Durland LJ, Knapp DJHF, Zandstra PW. DLL4 and VCAM1 enhance the emergence of T cell-competent hematopoietic progenitors from human pluripotent stem cells. SCIENCE ADVANCES 2022; 8:eabn5522. [PMID: 36001668 PMCID: PMC9401626 DOI: 10.1126/sciadv.abn5522] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 07/12/2022] [Indexed: 05/13/2023]
Abstract
T cells show tremendous efficacy as cellular therapeutics. However, obtaining primary T cells from human donors is expensive and variable. Pluripotent stem cells (PSCs) have the potential to provide a renewable source of T cells, but differentiating PSCs into hematopoietic progenitors with T cell potential remains an important challenge. Here, we report an efficient serum- and feeder-free system for differentiating human PSCs into hematopoietic progenitors and T cells. This fully defined approach allowed us to study the impact of individual proteins on blood emergence and differentiation. Providing DLL4 and VCAM1 during the endothelial-to-hematopoietic transition enhanced downstream progenitor T cell output by ~80-fold. These two proteins synergized to activate notch signaling in nascent hematopoietic stem and progenitor cells, and VCAM1 additionally promoted an inflammatory transcriptional program. We also established optimized medium formulations that enabled efficient and chemically defined maturation of functional CD8αβ+, CD4-, CD3+, TCRαβ+ T cells with a diverse TCR repertoire.
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Affiliation(s)
- Yale S. Michaels
- School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - John M. Edgar
- School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Matthew C. Major
- School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Elizabeth L. Castle
- School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Carla Zimmerman
- School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Ting Yin
- Institute of Biomedical Engineering, University of Toronto, Toronto, Ontario M5S 3G9, Canada
| | - Andrew Hagner
- School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Charles Lau
- School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Han Hsuan Hsu
- School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - M. Iliana Ibañez-Rios
- Institut de recherche en immunologie et en cancérologie and Département de pathologie et biologie cellulaire, Université de Montréal, Montreal, QC H3T 1J4, Canada
| | - Lauren J. Durland
- School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - David J. H. F. Knapp
- Institut de recherche en immunologie et en cancérologie and Département de pathologie et biologie cellulaire, Université de Montréal, Montreal, QC H3T 1J4, Canada
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Peter W. Zandstra
- School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
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Molecular Pathways in Clonal Hematopoiesis: From the Acquisition of Somatic Mutations to Transformation into Hematologic Neoplasm. LIFE (BASEL, SWITZERLAND) 2022; 12:life12081135. [PMID: 36013314 PMCID: PMC9410004 DOI: 10.3390/life12081135] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Revised: 07/23/2022] [Accepted: 07/26/2022] [Indexed: 11/16/2022]
Abstract
Hematopoietic stem cell aging, through the acquisition of somatic mutations, gives rise to clonal hematopoiesis (CH). While a high prevalence of CH has been described in otherwise healthy older adults, CH confers an increased risk of both hematologic and non-hematologic diseases. Classification of CH into clonal hematopoiesis of indeterminate potential (CHIP) and clonal cytopenia of undetermined significance (CCUS) further describes this neoplastic myeloid precursor state and stratifies individuals at risk of developing clinically significant complications. The sequential acquisition of driver mutations, such as DNMT3A, TET2, and ASXL1, provide a selective advantage and lead to clonal expansion. Inflammation, microbiome signatures, and external selective pressures also contribute to clonal evolution. Despite significant progress in recent years, the precise molecular mechanisms driving CH transformation to hematologic neoplasms are not well defined. Further understanding of these complex mechanisms may improve risk stratification and introduce therapeutic interventions in CH. Here we discuss the genetic drivers underpinning CH, mechanisms for clonal evolution, and transformation to hematologic neoplasm.
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Pan-cancer landscape of the RUNX protein family reveals their potential as carcinogenic biomarkers and the mechanisms underlying their action. J Transl Int Med 2022; 10:156-174. [PMID: 35959452 PMCID: PMC9328034 DOI: 10.2478/jtim-2022-0013] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Abstract
Background
The RUNX family of transcription factors plays an important regulatory role in tumor development. Although the importance of RUNX in certain cancer types is well known, the pan-cancer landscape remains unclear.
Materials and Methods
Data from The Cancer Genome Atlas (TCGA) provides a pan-cancer overview of the RUNX genes. Hence, herein, we performed a pan-cancer analysis of abnormal RUNX expression and deciphered the potential regulatory mechanism. Specifically, we used TCGA multi-omics data combined with multiple online tools to analyze transcripts, genetic alterations, DNA methylation, clinical prognoses, miRNA networks, and potential target genes.
Results
RUNX genes are consistently overexpressed in esophageal, gastric, pancreatic, and pan-renal cancers. The total protein expression of RUNX1 in lung adenocarcinoma, kidney renal clear cell carcinoma (KIRC), and uterine corpus endometrial carcinoma (UCEC) is consistent with the mRNA expression results. Moreover, increased phosphorylation on the T14 and T18 residues of RUNX1 may represent potential pathogenic factors. The RUNX genes are significantly associated with survival in pan-renal cancer, brain lower-grade glioma, and uveal melanoma. Meanwhile, various mutations and posttranscriptional changes, including the RUNX1 D96 mutation in invasive breast carcinoma, the co-occurrence of RUNX gene mutations in UCEC, and methylation changes in the RUNX2 promoter in KIRC, may be associated with cancer development. Finally, analysis of epigenetic regulator co-expression, miRNA networks, and target genes revealed the carcinogenicity, abnormal expression, and direct regulation of RUNX genes.
Conclusions
We successfully analyzed the pan-cancer abnormal expression and prognostic value of RUNX genes, thereby providing potential biomarkers for various cancers. Further, mutations revealed via genetic alteration analysis may serve as a basis for personalized patient therapies.
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40
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Embryonic Origins of the Hematopoietic System: Hierarchies and Heterogeneity. Hemasphere 2022; 6:e737. [PMID: 35647488 PMCID: PMC9132533 DOI: 10.1097/hs9.0000000000000737] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 04/28/2022] [Indexed: 11/26/2022] Open
Abstract
The hierarchical framework of the adult blood system as we know it from current medical and hematology textbooks, displays a linear branching network of dividing and differentiated cells essential for the growth and maintenance of the healthy organism. This view of the hierarchy has evolved over the last 75 years. An amazing increase in cellular complexity has been realized; however, innovative single-cell technologies continue to uncover essential cell types and functions in animal models and the human blood system. The most potent cell of the hematopoietic hierarchy is the hematopoietic stem cell. Stem cells for adult tissues are the long-lived self-renewing cellular component, which ensure that differentiated tissue-specific cells are maintained and replaced through the entire adult lifespan. Although much blood research is focused on hematopoietic tissue homeostasis, replacement and regeneration during adult life, embryological studies have widened and enriched our understanding of additional developmental hierarchies and interacting cells of this life-sustaining tissue. Here, we review the current state of knowledge of the hierarchical organization and the vast heterogeneity of the hematopoietic system from embryonic to adult stages.
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RUNX1 inhibition using lipid nanoparticle-mediated siRNA delivery as an effective treatment for acute leukemias. Exp Hematol 2022; 112-113:1-8. [DOI: 10.1016/j.exphem.2022.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 05/16/2022] [Accepted: 05/17/2022] [Indexed: 11/19/2022]
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42
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Lemma RB, Fleischer T, Martinsen E, Ledsaak M, Kristensen V, Eskeland R, Gabrielsen OS, Mathelier A. Pioneer transcription factors are associated with the modulation of DNA methylation patterns across cancers. Epigenetics Chromatin 2022; 15:13. [PMID: 35440061 PMCID: PMC9016969 DOI: 10.1186/s13072-022-00444-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 03/14/2022] [Indexed: 12/15/2022] Open
Abstract
Methylation of cytosines on DNA is a prominent modification associated with gene expression regulation. Aberrant DNA methylation patterns have recurrently been linked to dysregulation of the regulatory program in cancer cells. To shed light on the underlying molecular mechanism driving this process, we hypothesised that aberrant methylation patterns could be controlled by the binding of specific transcription factors (TFs) across cancer types. By combining DNA methylation arrays and gene expression data with TF binding sites (TFBSs), we explored the interplay between TF binding and DNA methylation in 19 cancer types. We performed emQTL (expression–methylation quantitative trait loci) analyses independently in each cancer type and identified 13 TFs whose expression levels are correlated with local DNA methylation patterns around their binding sites in at least 2 cancer types. The 13 TFs are mainly associated with local demethylation and are enriched for pioneer function, suggesting a specific role for these TFs in modulating chromatin structure and transcription in cancer patients. Furthermore, we confirmed that de novo methylation is precluded across cancers at CpGs lying in genomic regions enriched for TF binding signatures associated with SP1, CTCF, NRF1, GABPA, KLF9, and/or YY1. The modulation of DNA methylation associated with TF binding was observed at cis-regulatory regions controlling immune- and cancer-associated pathways, corroborating that the emQTL signals were derived from both cancer and tumor-infiltrating cells. As a case example, we experimentally confirmed that FOXA1 knock-down is associated with higher methylation in regions bound by FOXA1 in breast cancer MCF-7 cells. Finally, we reported physical interactions between FOXA1 with TET1 and TET2 both in an in vitro setup and in vivo at physiological levels in MCF-7 cells, adding further support for FOXA1 attracting TET1 and TET2 to induce local demethylation in cancer cells.
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Affiliation(s)
- Roza Berhanu Lemma
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, Oslo, Norway
| | - Thomas Fleischer
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Emily Martinsen
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, Oslo, Norway.,Institute of Basic Medical Sciences, Department of Molecular Medicine, and Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Marit Ledsaak
- Institute of Basic Medical Sciences, Department of Molecular Medicine, and Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Vessela Kristensen
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway.,Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Ragnhild Eskeland
- Institute of Basic Medical Sciences, Department of Molecular Medicine, and Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | | | - Anthony Mathelier
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, Oslo, Norway. .,Department of Medical Genetics, Oslo University Hospital, Oslo, Norway.
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43
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Li X, Xu R, Ye JX, Yuan FL. Suppression of bone remodeling associated with long-term bisphosphonate treatment is mediated by microRNA-30a-5p. Bioengineered 2022; 13:9741-9753. [PMID: 35412438 PMCID: PMC9161941 DOI: 10.1080/21655979.2022.2060584] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Oral bisphosphonates (BPs) are a first-line treatment for osteoporosis. It is becoming a hot topic to identify new indicators for the early prediction of therapeutic effects and adverse reactions during the long-term use of BPs. To determine whether microRNA (miRNA) expression is modulated by long-term BPs treatment, we performed miRNA expression profiling analysis in patients receiving long-term BP treatment for postmenopausal OP. To assess the effect of BPs on miRNA expression, we used an Affymetrix Genechip miRNA array to analyze serum samples obtained from postmenopausal OP patients on long-term BP treatment and healthy controls. MiRNAs affected by BPs and their predicted targets were examined. We also investigated the effects of miRNA on osteoblast differentiation in vitro and on ovariectomy-induced bone loss in vivo. We observed that the level of miR-30a-5p was significantly increased in patients receiving long-term BP treatment for postmenopausal OP. Furthermore, miR-30a-5p was negatively correlated with bone formation. Consistent with this, in vitro osteoblast activity and matrix mineralization were increased by an antagomir of miR-30a-5p and decreased by an agomir of miR-30a-5p. We also found that miR-30a-5p directly targeted RUNX1 to inhibit osteoblastic differentiation. Consistent with the in vitro results, miR-30a-5p antagomir administration promoted bone formation in ovariectomized mice. Our findings identified miR-30a-5p as a novel mediator of long-term BP treatment that regulates bone formation in postmenopausal OP patients.
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Affiliation(s)
- Xia Li
- Institute of Integrated Chinese and Western Medicine, The Hospital Affiliated to Jiangnan University, Wuxi, Jiangsu, China
| | - Ruisheng Xu
- Institute of Integrated Chinese and Western Medicine, The Hospital Affiliated to Jiangnan University, Wuxi, Jiangsu, China
| | - Jun-Xing Ye
- Institute of Integrated Chinese and Western Medicine, The Hospital Affiliated to Jiangnan University, Wuxi, Jiangsu, China.,Department of Orthopaedics and Central Laboratory, The Third Hospital Affiliated to Nantong University, Wuxi, Jiangsu, China
| | - Feng-Lai Yuan
- Institute of Integrated Chinese and Western Medicine, The Hospital Affiliated to Jiangnan University, Wuxi, Jiangsu, China.,Department of Orthopaedics, The Hospital Affiliated to Jiangnan University, Wuxi, Jiangsu, China
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44
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Crlz-1 Homozygous Null Knockout Mouse Embryos Are Lethally Stopped in Their Early Development. Genes (Basel) 2022; 13:genes13030511. [PMID: 35328065 PMCID: PMC8951461 DOI: 10.3390/genes13030511] [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: 02/24/2022] [Accepted: 03/10/2022] [Indexed: 02/04/2023] Open
Abstract
Although the conditional gene knockout (KO) is a better choice for observing its phenotype in a specific cell, tissue, and/or organ, the simple null gene KO could nevertheless be attempted initially to scan its overall phenotypes at the level of the whole-body system, especially for a new gene such as Crlz-1. Therefore, with a hope to glean phenotypic clues for Crlz-1 at the whole-body system, we attempted to generate its null KO mice. Contrary to our original desire, Crlz-1 homozygous null KO mice were not born. However, in the chasing of their homozygous KO embryos, they were found to be lethally impaired from early development, remaining in a state of small globular mass without ever leading to a body shape, indicating the critical role of Crlz-1 as a Wnt target gene for the proliferation and/or differentiation of cells during early mouse embryonic development.
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45
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Tibbs E, Cao X. Emerging Canonical and Non-Canonical Roles of Granzyme B in Health and Disease. Cancers (Basel) 2022; 14:1436. [PMID: 35326588 PMCID: PMC8946077 DOI: 10.3390/cancers14061436] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 03/05/2022] [Accepted: 03/08/2022] [Indexed: 12/23/2022] Open
Abstract
The Granzyme (Gzm) family has classically been recognized as a cytotoxic tool utilized by cytotoxic T lymphocytes (CTL) and natural killer (NK) cells to illicit cell death to infected and cancerous cells. Their importance is established based on evidence showing that deficiencies in these cell death executors result in defective immune responses. Recent findings have shown the importance of Granzyme B (GzmB) in regulatory immune cells, which may contribute to tumor growth and immune evasion during cancer development. Other studies have shown that members of the Gzm family are important for biological processes such as extracellular matrix remodeling, angiogenesis and organized vascular degradation. With this growing body of evidence, it is becoming more important to understand the broader function of Gzm's rather than a specific executor of cell death, and we should be aware of the many alternative roles that Gzm's play in physiological and pathological conditions. Therefore, we review the classical as well as novel non-canonical functions of GzmB and discuss approaches to utilize these new findings to address current gaps in our understanding of the immune system and tissue development.
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Affiliation(s)
- Ellis Tibbs
- Department of Microbiology and Immunology, School of Medicine, University of Maryland Baltimore, Baltimore, MD 21201, USA;
| | - Xuefang Cao
- Department of Microbiology and Immunology, School of Medicine, University of Maryland Baltimore, Baltimore, MD 21201, USA;
- Marlene and Stewart Greenebaum Comprehensive Cancer Center, University of Maryland Baltimore, Baltimore, MD 21201, USA
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46
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Hu Y, Pan Q, Zhou K, Ling Y, Wang H, Li Y. RUNX1 inhibits the antiviral immune response against influenza A virus through attenuating type I interferon signaling. Virol J 2022; 19:39. [PMID: 35248104 PMCID: PMC8897766 DOI: 10.1186/s12985-022-01764-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 02/14/2022] [Indexed: 11/10/2022] Open
Abstract
Background Influenza A viruses (IAVs) are zoonotic, segmented negative-stranded RNA viruses. The rapid mutation of IAVs results in host immune response escape and antiviral drug and vaccine resistance. RUNX1 is a transcription factor that not only plays essential roles in hematopoiesis, but also functions as a regulator in inflammation. However, its role in the innate immunity to IAV infection has not been well studied. Methods To investigate the effects of RUNX1 on IAV infection and explore the mechanisms that RUNX1 uses during IAV infection. We infected the human alveolar epithelial cell line (A549) with influenza virus A/Puerto Rico/8/34 (H1N1) (PR8) and examined RUNX1 expression by Western blot and qRT-PCR. We also knocked down or overexpressed RUNX1 in A549 cells, then evaluated viral replication by Western blot, qRT-PCR, and viral titration. Results We found RUNX1 expression is induced by IAV H1N1 PR8 infection, but not by poly(I:C) treatment, in the human alveolar epithelial cell line A549. Knockdown of RUNX1 significantly inhibited IAV infection. Conversely, overexpression of RUNX1 efficiently promoted production of progeny viruses. Additionally, RUNX1 knockdown increased IFN-β and ISGs production while RUNX1 overexpression compromised IFN-β and ISGs production upon PR8 infection in A549 cells. We further showed that RUNX1 may attenuate the interferon signaling transduction by hampering the expression of IRF3 and STAT1 during IAV infection. Conclusions Taken together, we found RUNX1 attenuates type I interferon signaling to facilitate IAV infection in A549 cells.
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47
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Heazlewood SY, Ahmad T, Mohenska M, Guo BB, Gangatirkar P, Josefsson EC, Ellis SL, Ratnadiwakara M, Cao H, Cao B, Heazlewood CK, Williams B, Fulton M, White JF, Ramialison M, Nilsson SK, Änkö ML. The RNA-binding protein SRSF3 has an essential role in megakaryocyte maturation and platelet production. Blood 2022; 139:1359-1373. [PMID: 34852174 PMCID: PMC8900270 DOI: 10.1182/blood.2021013826] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 11/06/2021] [Indexed: 11/20/2022] Open
Abstract
RNA processing is increasingly recognized as a critical control point in the regulation of different hematopoietic lineages including megakaryocytes responsible for the production of platelets. Platelets are anucleate cytoplasts that contain a rich repertoire of RNAs encoding proteins with essential platelet functions derived from the parent megakaryocyte. It is largely unknown how RNA binding proteins contribute to the development and functions of megakaryocytes and platelets. We show that serine-arginine-rich splicing factor 3 (SRSF3) is essential for megakaryocyte maturation and generation of functional platelets. Megakaryocyte-specific deletion of Srsf3 in mice led to macrothrombocytopenia characterized by megakaryocyte maturation arrest, dramatically reduced platelet counts, and abnormally large functionally compromised platelets. SRSF3 deficient megakaryocytes failed to reprogram their transcriptome during maturation and to load platelets with RNAs required for normal platelet function. SRSF3 depletion led to nuclear accumulation of megakaryocyte mRNAs, demonstrating that SRSF3 deploys similar RNA regulatory mechanisms in megakaryocytes as in other cell types. Our study further suggests that SRSF3 plays a role in sorting cytoplasmic megakaryocyte RNAs into platelets and demonstrates how SRSF3-mediated RNA processing forms a central part of megakaryocyte gene regulation. Understanding SRSF3 functions in megakaryocytes and platelets provides key insights into normal thrombopoiesis and platelet pathologies as SRSF3 RNA targets in megakaryocytes are associated with platelet diseases.
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Affiliation(s)
- Shen Y Heazlewood
- Biomedical Manufacturing CSIRO, VIC, Australia
- Australian Regenerative Medicine Institute, Monash University, VIC, Australia
| | - Tanveer Ahmad
- Biomedical Manufacturing CSIRO, VIC, Australia
- Australian Regenerative Medicine Institute, Monash University, VIC, Australia
| | - Monika Mohenska
- Australian Regenerative Medicine Institute, Monash University, VIC, Australia
| | - Belinda B Guo
- School of Biomedical Sciences, Pathology and Laboratory Science, University of Western Australia, WA, Australia
| | | | - Emma C Josefsson
- Walter and Eliza Hall Institute of Medical Research, VIC, Australia
- Department of Medical Biology, The University of Melbourne, VIC, Australia
| | - Sarah L Ellis
- Peter MacCallum Cancer Centre, and Sir Peter MacCallum Department of Oncology, University of Melbourne, VIC, Australia
- Olivia Newton-John Cancer Research Institute, Microscopy Facility and School of Cancer Medicine, La Trobe University, VIC, Australia
| | - Madara Ratnadiwakara
- Australian Regenerative Medicine Institute, Monash University, VIC, Australia
- Hudson Institute of Medical Research, VIC, Australia; and
- Department of Molecular and Translational Sciences, Monash University, VIC, Australia
| | - Huimin Cao
- Biomedical Manufacturing CSIRO, VIC, Australia
- Australian Regenerative Medicine Institute, Monash University, VIC, Australia
| | - Benjamin Cao
- Biomedical Manufacturing CSIRO, VIC, Australia
- Australian Regenerative Medicine Institute, Monash University, VIC, Australia
| | - Chad K Heazlewood
- Biomedical Manufacturing CSIRO, VIC, Australia
- Australian Regenerative Medicine Institute, Monash University, VIC, Australia
| | - Brenda Williams
- Biomedical Manufacturing CSIRO, VIC, Australia
- Australian Regenerative Medicine Institute, Monash University, VIC, Australia
| | - Madeline Fulton
- Biomedical Manufacturing CSIRO, VIC, Australia
- Australian Regenerative Medicine Institute, Monash University, VIC, Australia
| | | | - Mirana Ramialison
- Australian Regenerative Medicine Institute, Monash University, VIC, Australia
| | - Susan K Nilsson
- Biomedical Manufacturing CSIRO, VIC, Australia
- Australian Regenerative Medicine Institute, Monash University, VIC, Australia
| | - Minna-Liisa Änkö
- Australian Regenerative Medicine Institute, Monash University, VIC, Australia
- Hudson Institute of Medical Research, VIC, Australia; and
- Department of Molecular and Translational Sciences, Monash University, VIC, Australia
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48
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Umemoto T, Johansson A, Ahmad SAI, Hashimoto M, Kubota S, Kikuchi K, Odaka H, Era T, Kurotaki D, Sashida G, Suda T. ATP citrate lyase controls hematopoietic stem cell fate and supports bone marrow regeneration. EMBO J 2022; 41:e109463. [PMID: 35229328 PMCID: PMC9016348 DOI: 10.15252/embj.2021109463] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 01/21/2022] [Accepted: 01/25/2022] [Indexed: 01/08/2023] Open
Abstract
In order to support bone marrow regeneration after myeloablation, hematopoietic stem cells (HSCs) actively divide to provide both stem and progenitor cells. However, the mechanisms regulating HSC function and cell fate choice during hematopoietic recovery remain unclear. We herein provide novel insights into HSC regulation during regeneration by focusing on mitochondrial metabolism and ATP citrate lyase (ACLY). After 5-fluorouracil-induced myeloablation, HSCs highly expressing endothelial protein C receptor (EPCRhigh ) were enriched within the stem cell fraction at the expense of more proliferative EPCRLow HSCs. These EPCRHigh HSCs were initially more primitive than EPCRLow HSCs and enabled stem cell expansion by enhancing histone acetylation, due to increased activity of ACLY in the early phase of hematopoietic regeneration. In the late phase of recovery, HSCs enhanced differentiation potential by increasing the accessibility of cis-regulatory elements in progenitor cell-related genes, such as CD48. In conditions of reduced mitochondrial metabolism and ACLY activity, these HSCs maintained stem cell phenotypes, while ACLY-dependent histone acetylation promoted differentiation into CD48+ progenitor cells. Collectively, these results indicate that the dynamic control of ACLY-dependent metabolism and epigenetic alterations is essential for HSC regulation during hematopoietic regeneration.
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Affiliation(s)
- Terumasa Umemoto
- Laboratory of Hematopoietic Stem Cell EngineeringInternational Research Center for Medical SciencesKumamoto UniversityKumamotoJapan
| | - Alban Johansson
- Laboratory of Hematopoietic Stem Cell EngineeringInternational Research Center for Medical SciencesKumamoto UniversityKumamotoJapan
| | - Shah Adil Ishtiyaq Ahmad
- Laboratory of Hematopoietic Stem Cell EngineeringInternational Research Center for Medical SciencesKumamoto UniversityKumamotoJapan
| | - Michihiro Hashimoto
- Laboratory of Stem Cell RegulationInternational Research Center for Medical SciencesKumamoto UniversityKumamotoJapan
| | - Sho Kubota
- Laboratory of Transcriptional Regulation in LeukemogenesisInternational Research Center for Medical SciencesKumamoto UniversityKumamotoJapan
| | - Kenta Kikuchi
- Laboratory of Chromatin Organization in Immune Cell DevelopmentInternational Research Center for Medical SciencesKumamoto UniversityKumamotoJapan
| | - Haruki Odaka
- Department of Cell ModulationInstitute of Molecular Embryology and GeneticsKumamoto UniversityKumamotoJapan
| | - Takumi Era
- Department of Cell ModulationInstitute of Molecular Embryology and GeneticsKumamoto UniversityKumamotoJapan
| | - Daisuke Kurotaki
- Laboratory of Chromatin Organization in Immune Cell DevelopmentInternational Research Center for Medical SciencesKumamoto UniversityKumamotoJapan
| | - Goro Sashida
- Laboratory of Transcriptional Regulation in LeukemogenesisInternational Research Center for Medical SciencesKumamoto UniversityKumamotoJapan
| | - Toshio Suda
- Laboratory of Stem Cell RegulationInternational Research Center for Medical SciencesKumamoto UniversityKumamotoJapan,Cancer Science Institute of SingaporeNational University of SingaporeSingapore CitySingapore
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49
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Effective therapy for AML with RUNX1 mutation by cotreatment with inhibitors of protein translation and BCL2. Blood 2022; 139:907-921. [PMID: 34601571 PMCID: PMC8832475 DOI: 10.1182/blood.2021013156] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 09/19/2021] [Indexed: 11/20/2022] Open
Abstract
The majority of RUNX1 mutations in acute myeloid leukemia (AML) are missense or deletion-truncation and behave as loss-of-function mutations. Following standard therapy, AML patients expressing mtRUNX1 exhibit inferior clinical outcome than those without mutant RUNX1. Studies presented here demonstrate that as compared with AML cells lacking mtRUNX1, their isogenic counterparts harboring mtRUNX1 display impaired ribosomal biogenesis and differentiation, as well as exhibit reduced levels of wild-type RUNX1, PU.1, and c-Myc. Compared with AML cells with only wild-type RUNX1, AML cells expressing mtRUNX1 were also more sensitive to the protein translation inhibitor homoharringtonine (omacetaxine) and BCL2 inhibitor venetoclax. Homoharringtonine treatment repressed enhancers and their BRD4 occupancy and was associated with reduced levels of c-Myc, c-Myb, MCL1, and Bcl-xL. Consistent with this, cotreatment with omacetaxine and venetoclax or BET inhibitor induced synergistic in vitro lethality in AML expressing mtRUNX1. Compared with each agent alone, cotreatment with omacetaxine and venetoclax or BET inhibitor also displayed improved in vivo anti-AML efficacy, associated with improved survival of immune-depleted mice engrafted with AML cells harboring mtRUNX1. These findings highlight superior efficacy of omacetaxine-based combination therapies for AML harboring mtRUNX1.
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Miyajima Y, Noguchi S, Tanaka Y, Li JR, Nishimura H, Kishima M, Lim J, Furuhata E, Suzuki T, Kasukawa T, Suzuki H. Prediction of transcription factors associated with DNA demethylation during human cellular development. Chromosome Res 2022; 30:109-121. [PMID: 35142952 PMCID: PMC8942926 DOI: 10.1007/s10577-022-09685-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 01/18/2022] [Accepted: 01/24/2022] [Indexed: 12/19/2022]
Abstract
DNA methylation of CpG dinucleotides is an important epigenetic modification involved in the regulation of mammalian gene expression, with each type of cell developing a specific methylation profile during its differentiation. Recently, it has been shown that a small subgroup of transcription factors (TFs) might promote DNA demethylation at their binding sites. We developed a bioinformatics pipeline to predict from genome-wide DNA methylation data TFs that promote DNA demethylation at their binding site. We applied the pipeline to International Human Epigenome Consortium methylome data and selected 393 candidate transcription factor binding motifs and associated 383 TFs that are likely associated with DNA demethylation. Validation of a subset of the candidate TFs using an in vitro assay suggested that 28 of 49 TFs from various TF families had DNA-demethylation-promoting activity; TF families, such as bHLH and ETS, contained both TFs with and without the activity. The identified TFs showed large demethylated/methylated CpG ratios and their demethylated CpGs showed significant bias toward hypermethylation in original cells. Furthermore, the identified TFs promoted demethylation of distinct sets of CpGs, with slight overlap of the targeted CpGs among TF family members, which was consistent with the results of a gene ontology (GO) term analysis of the identified TFs. Gene expression analysis of the identified TFs revealed that multiple TFs from various families are specifically expressed in human cells and tissues. Together, our results suggest that a large number of TFs from various TF families are associated with cell-type-specific DNA demethylation during human cellular development.
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Affiliation(s)
- Yurina Miyajima
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
| | - Shuhei Noguchi
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
| | - Yuki Tanaka
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Kanagawa, 230-0045, Japan
| | - Jing-Ru Li
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
| | - Hajime Nishimura
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
| | - Mami Kishima
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
| | - Joanne Lim
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
| | - Erina Furuhata
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
| | - Takahiro Suzuki
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Kanagawa, 230-0045, Japan
| | - Takeya Kasukawa
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
| | - Harukazu Suzuki
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan.
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