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Lanman NA, Meco E, Fitchev P, Kolliegbo AK, Broman MM, Filipovich Y, Kothandaraman H, Cresswell GM, Talaty P, Antoniak M, Brumer S, Glaser AP, Higgins AM, Helfand BT, Franco OE, Crawford SE, Ratliff TL, Hayward SW, Vickman RE. Infiltrating lipid-rich macrophage subpopulations identified as a regulator of increasing prostate size in human benign prostatic hyperplasia. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.07.597992. [PMID: 38915654 PMCID: PMC11195107 DOI: 10.1101/2024.06.07.597992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Macrophages exhibit marked phenotypic heterogeneity within and across disease states, with lipid metabolic reprogramming contributing to macrophage activation and heterogeneity. Chronic inflammation has been observed in human benign prostatic hyperplasia (BPH) tissues, however macrophage activation states and their contributions to this hyperplastic disease have not been defined. We postulated that a shift in macrophage phenotypes with increasing prostate size could involve metabolic alterations resulting in prostatic epithelial or stromal hyperplasia. Single-cell RNA-seq of CD45+ transition zone leukocytes from 10 large (>90 grams) and 10 small (<40 grams) human prostates was conducted. Macrophage subpopulations were defined using marker genes. BPH macrophages do not distinctly categorize into M1 and M2 phenotypes. Instead, macrophages with neither polarization signature preferentially accumulate in large versus small prostates. Specifically, macrophage subpopulations with altered lipid metabolism pathways, demarcated by TREM2 and MARCO expression, significantly accumulate with increased prostate volume. TREM2+ and MARCO+ macrophage abundance positively correlates with patient body mass index and urinary symptom scores. TREM2+ macrophages have significantly higher neutral lipid than TREM2- macrophages from BPH tissues. Lipid-rich macrophages were observed to localize within the stroma in BPH tissues. In vitro studies indicate that lipid-loaded macrophages increase prostate epithelial and stromal cell proliferation compared to control macrophages. These data define two new BPH immune subpopulations, TREM2+ and MARCO+ macrophages, and suggest that lipid-rich macrophages may exacerbate lower urinary tract symptoms in patients with large prostates. Further investigation is needed to evaluate the therapeutic benefit of targeting these cells in BPH.
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Buenaventura T, Bagci H, Patrascan I, Graham JJ, Hipwell KD, Oldenkamp R, King JWD, Urtasun J, Young G, Mouzo D, Gomez-Cabrero D, Rowland BD, Panne D, Fisher AG, Merkenschlager M. Competition shapes the landscape of X-chromosome-linked genetic diversity. Nat Genet 2024; 56:1678-1688. [PMID: 39060501 PMCID: PMC11319201 DOI: 10.1038/s41588-024-01840-5] [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: 09/21/2023] [Accepted: 06/21/2024] [Indexed: 07/28/2024]
Abstract
X chromosome inactivation (XCI) generates clonal heterogeneity within XX individuals. Combined with sequence variation between human X chromosomes, XCI gives rise to intra-individual clonal diversity, whereby two sets of clones express mutually exclusive sequence variants present on one or the other X chromosome. Here we ask whether such clones merely co-exist or potentially interact with each other to modulate the contribution of X-linked diversity to organismal development. Focusing on X-linked coding variation in the human STAG2 gene, we show that Stag2variant clones contribute to most tissues at the expected frequencies but fail to form lymphocytes in Stag2WT Stag2variant mouse models. Unexpectedly, the absence of Stag2variant clones from the lymphoid compartment is due not solely to cell-intrinsic defects but requires continuous competition by Stag2WT clones. These findings show that interactions between epigenetically diverse clones can operate in an XX individual to shape the contribution of X-linked genetic diversity in a cell-type-specific manner.
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Affiliation(s)
- Teresa Buenaventura
- MRC LMS, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
| | - Hakan Bagci
- MRC LMS, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
| | - Ilinca Patrascan
- MRC LMS, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
| | - Joshua J Graham
- Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester, UK
| | - Kelsey D Hipwell
- Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester, UK
| | - Roel Oldenkamp
- Division of Cell Biology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - James W D King
- MRC LMS, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
| | - Jesus Urtasun
- MRC LMS, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
| | - George Young
- MRC LMS, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
| | - Daniel Mouzo
- Translational Bioinformatics Unit, Navarrabiomed, Universidad Pública de Navarra (UPNA), Instituto de Investigación Sanitaria de Navarra (IdiSNA), Pamplona, Spain
| | - David Gomez-Cabrero
- Translational Bioinformatics Unit, Navarrabiomed, Universidad Pública de Navarra (UPNA), Instituto de Investigación Sanitaria de Navarra (IdiSNA), Pamplona, Spain
- Bioscience Program, Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology KAUST, Thuwal, Saudi Arabia
| | - Benjamin D Rowland
- Division of Cell Biology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Daniel Panne
- Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester, UK
| | - Amanda G Fisher
- MRC LMS, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Matthias Merkenschlager
- MRC LMS, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK.
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3
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Ghobashi AH, Lanzloth R, Ladaika CA, Masood A, O’Hagan HM. Single-Cell Profiling Reveals the Impact of Genetic Alterations on the Differentiation of Inflammation-Induced Murine Colon Tumors. Cancers (Basel) 2024; 16:2040. [PMID: 38893159 PMCID: PMC11171101 DOI: 10.3390/cancers16112040] [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: 04/25/2024] [Revised: 05/23/2024] [Accepted: 05/24/2024] [Indexed: 06/21/2024] Open
Abstract
Genetic mutations and chronic inflammation of the colon contribute to the development of colorectal cancer (CRC). Using a murine model of inflammation-induced colon tumorigenesis, we determined how genetic mutations alter colon tumor cell differentiation. Inflammation induced by enterotoxigenic Bacteroides fragilis (ETBF) colonization of multiple intestinal neoplasia (MinApcΔ716/+) mice triggers loss of heterozygosity of Apc causing colon tumor formation. Here, we report that the addition of BRAFV600E mutation (BRAFF-V600ELgr5tm1(Cre/ERT2)CleMinApcΔ716/+, BLM) or knocking out Msh2 (Msh2LoxP/LoxPVil1-creMinApcΔ716/+, MSH2KO) in the Min model altered colon tumor differentiation. Using single-cell RNA sequencing, we uncovered the differences between BLM, Min, and MSH2KO tumors at a single-cell resolution. BLM tumors showed an increase in differentiated tumor epithelial cell lineages and a reduction in the tumor stem cell population. Interestingly, the tumor stem cell population of BLM tumors had revival colon stem cell characteristics with low WNT signaling and an increase in RevCSC marker gene expression. In contrast, MSH2KO tumors were characterized by an increased tumor stem cell population that had higher WNT signaling activity compared to Min tumors. Furthermore, overall BLM tumors had higher expression of transcription factors that drive differentiation, such as Cdx2, than Min tumors. Using RNA velocity, we identified additional potential regulators of BLM tumor differentiation such as NDRG1. The role of CDX2 and NDRG1 as putative regulators for BLM tumor cell differentiation was verified using organoids derived from BLM tumors. Our results demonstrate the critical connections between genetic mutations and cell differentiation in inflammation-induced colon tumorigenesis. Understanding such roles will deepen our understanding of inflammation-associated colon cancer.
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Affiliation(s)
- Ahmed H. Ghobashi
- Genome, Cell, and Developmental Biology Graduate Program, Department of Biology, Indiana University Bloomington, Bloomington, IN 47405, USA
- Medical Sciences Program, Indiana University School of Medicine, Bloomington, IN 47405, USA
- Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indianapolis, IN 46202, USA
| | - Rosie Lanzloth
- Genome, Cell, and Developmental Biology Graduate Program, Department of Biology, Indiana University Bloomington, Bloomington, IN 47405, USA
- Medical Sciences Program, Indiana University School of Medicine, Bloomington, IN 47405, USA
| | - Christopher A. Ladaika
- Genome, Cell, and Developmental Biology Graduate Program, Department of Biology, Indiana University Bloomington, Bloomington, IN 47405, USA
- Medical Sciences Program, Indiana University School of Medicine, Bloomington, IN 47405, USA
- Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indianapolis, IN 46202, USA
| | - Ashiq Masood
- Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indianapolis, IN 46202, USA
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Heather M. O’Hagan
- Medical Sciences Program, Indiana University School of Medicine, Bloomington, IN 47405, USA
- Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indianapolis, IN 46202, USA
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
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4
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Gao L, Lee H, Goodman JH, Ding L. Hematopoietic stem cell niche generation and maintenance are distinguishable by an epitranscriptomic program. Cell 2024; 187:2801-2816.e17. [PMID: 38657601 PMCID: PMC11148849 DOI: 10.1016/j.cell.2024.03.032] [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: 05/10/2023] [Revised: 12/06/2023] [Accepted: 03/22/2024] [Indexed: 04/26/2024]
Abstract
The niche is typically considered as a pre-established structure sustaining stem cells. Therefore, the regulation of its formation remains largely unexplored. Whether distinct molecular mechanisms control the establishment versus maintenance of a stem cell niche is unknown. To address this, we compared perinatal and adult bone marrow mesenchymal stromal cells (MSCs), a key component of the hematopoietic stem cell (HSC) niche. MSCs exhibited enrichment in genes mediating m6A mRNA methylation at the perinatal stage and downregulated the expression of Mettl3, the m6A methyltransferase, shortly after birth. Deletion of Mettl3 from developing MSCs but not osteoblasts led to excessive osteogenic differentiation and a severe HSC niche formation defect, which was significantly rescued by deletion of Klf2, an m6A target. In contrast, deletion of Mettl3 from MSCs postnatally did not affect HSC niche. Stem cell niche generation and maintenance thus depend on divergent molecular mechanisms, which may be exploited for regenerative medicine.
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Affiliation(s)
- Longfei Gao
- Columbia Stem Cell Initiative, Department of Rehabilitation and Regenerative Medicine, Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Heather Lee
- Columbia Stem Cell Initiative, Department of Rehabilitation and Regenerative Medicine, Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Joshua H Goodman
- Columbia Stem Cell Initiative, Department of Rehabilitation and Regenerative Medicine, Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Lei Ding
- Columbia Stem Cell Initiative, Department of Rehabilitation and Regenerative Medicine, Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA.
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5
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Li F, Xing X, Jin Q, Wang XM, Dai P, Han M, Shi H, Zhang Z, Shao X, Peng Y, Zhu Y, Xu J, Li D, Chen Y, Wu W, Wang Q, Yu C, Chen L, Bai F, Gao D. Sex differences orchestrated by androgens at single-cell resolution. Nature 2024; 629:193-200. [PMID: 38600383 DOI: 10.1038/s41586-024-07291-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 03/11/2024] [Indexed: 04/12/2024]
Abstract
Sex differences in mammalian complex traits are prevalent and are intimately associated with androgens1-7. However, a molecular and cellular profile of sex differences and their modulation by androgens is still lacking. Here we constructed a high-dimensional single-cell transcriptomic atlas comprising over 2.3 million cells from 17 tissues in Mus musculus and explored the effects of sex and androgens on the molecular programs and cellular populations. In particular, we found that sex-biased immune gene expression and immune cell populations, such as group 2 innate lymphoid cells, were modulated by androgens. Integration with the UK Biobank dataset revealed potential cellular targets and risk gene enrichment in antigen presentation for sex-biased diseases. This study lays the groundwork for understanding the sex differences orchestrated by androgens and provides important evidence for targeting the androgen pathway as a broad therapeutic strategy for sex-biased diseases.
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Affiliation(s)
- Fei Li
- Key Laboratory of Multi-Cell Systems, Shanghai Key Laboratory of Molecular Andrology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Xudong Xing
- Biomedical Pioneering Innovation Center (BIOPIC), Peking-Tsinghua Center for Life Sciences, Beijing Advanced Innovation Center for Genomics (ICG), School of Life Sciences, Peking University, Beijing, China
| | - Qiqi Jin
- Key Laboratory of Multi-Cell Systems, Shanghai Key Laboratory of Molecular Andrology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Xiang-Ming Wang
- Biomedical Pioneering Innovation Center (BIOPIC), Peking-Tsinghua Center for Life Sciences, Beijing Advanced Innovation Center for Genomics (ICG), School of Life Sciences, Peking University, Beijing, China
| | - Pengfei Dai
- Key Laboratory of Multi-Cell Systems, Shanghai Key Laboratory of Molecular Andrology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ming Han
- Key Laboratory of Multi-Cell Systems, Shanghai Key Laboratory of Molecular Andrology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Huili Shi
- Key Laboratory of Multi-Cell Systems, Shanghai Key Laboratory of Molecular Andrology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ze Zhang
- Key Laboratory of Systems Health Science of Zhejiang Province, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China
| | - Xianlong Shao
- Key Laboratory of Multi-Cell Systems, Shanghai Key Laboratory of Molecular Andrology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yunyi Peng
- Key Laboratory of Multi-Cell Systems, Shanghai Key Laboratory of Molecular Andrology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yiqin Zhu
- Key Laboratory of Multi-Cell Systems, Shanghai Key Laboratory of Molecular Andrology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Jiayi Xu
- Shanghai Normal University, Shanghai, China
| | - Dan Li
- Human Oncology and Pathogenesis Program, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yu Chen
- Human Oncology and Pathogenesis Program, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Wei Wu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Frontiers Science Center of Pathogenic Microbes and Infection, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Qiao Wang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Frontiers Science Center of Pathogenic Microbes and Infection, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Chen Yu
- Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen, China.
| | - Luonan Chen
- Key Laboratory of Multi-Cell Systems, Shanghai Key Laboratory of Molecular Andrology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China.
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
- Key Laboratory of Systems Health Science of Zhejiang Province, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China.
| | - Fan Bai
- Biomedical Pioneering Innovation Center (BIOPIC), Peking-Tsinghua Center for Life Sciences, Beijing Advanced Innovation Center for Genomics (ICG), School of Life Sciences, Peking University, Beijing, China.
| | - Dong Gao
- Key Laboratory of Multi-Cell Systems, Shanghai Key Laboratory of Molecular Andrology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China.
- Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen, China.
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6
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Zhao N, Lai C, Wang Y, Dai S, Gu H. Understanding the role of DNA methylation in colorectal cancer: Mechanisms, detection, and clinical significance. Biochim Biophys Acta Rev Cancer 2024; 1879:189096. [PMID: 38499079 DOI: 10.1016/j.bbcan.2024.189096] [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: 10/05/2023] [Revised: 02/18/2024] [Accepted: 03/13/2024] [Indexed: 03/20/2024]
Abstract
Colorectal cancer (CRC) is one of the deadliest malignancies worldwide, ranking third in incidence and second in mortality. Remarkably, early stage localized CRC has a 5-year survival rate of over 90%; in stark contrast, the corresponding 5-year survival rate for metastatic CRC (mCRC) is only 14%. Compounding this problem is the staggering lack of effective therapeutic strategies. Beyond genetic mutations, which have been identified as critical instigators of CRC initiation and progression, the importance of epigenetic modifications, particularly DNA methylation (DNAm), cannot be underestimated, given that DNAm can be used for diagnosis, treatment monitoring and prognostic evaluation. This review addresses the intricate mechanisms governing aberrant DNAm in CRC and its profound impact on critical oncogenic pathways. In addition, a comprehensive review of the various techniques used to detect DNAm alterations in CRC is provided, along with an exploration of the clinical utility of cancer-specific DNAm alterations.
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Affiliation(s)
- Ningning Zhao
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China; Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei 230031, China
| | - Chuanxi Lai
- Division of Colorectal Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310016, China
| | - Yunfei Wang
- Zhejiang ShengTing Biotech. Ltd, Hangzhou 310000, China
| | - Sheng Dai
- Division of Colorectal Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310016, China.
| | - Hongcang Gu
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China; Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei 230031, China.
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7
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Ran R, Muñoz Briones J, Jena S, Anderson NL, Olson MR, Green LN, Brubaker DK. Detailed survey of an in vitro intestinal epithelium model by single-cell transcriptomics. iScience 2024; 27:109383. [PMID: 38523788 PMCID: PMC10959667 DOI: 10.1016/j.isci.2024.109383] [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: 07/11/2023] [Revised: 12/01/2023] [Accepted: 02/27/2024] [Indexed: 03/26/2024] Open
Abstract
The co-culture of two adult human colorectal cancer cell lines, Caco-2 and HT29, on Transwell is commonly used as an in vitro gut mimic, yet the translatability of insights from such a system to adult human physiological contexts is not fully characterized. Here, we used single-cell RNA sequencing on the co-culture to obtain a detailed survey of cell type heterogeneity in the system and conducted a holistic comparison with human physiology. We identified the intestinal stem cell-, transit amplifying-, enterocyte-, goblet cell-, and enteroendocrine-like cells in the system. In general, the co-culture was fetal intestine-like, with less variety of gene expression compared to the adult human gut. Transporters for major types of nutrients were found in the majority of the enterocytes-like cells in the system. TLR 4 was not expressed in the sample, indicating that the co-culture model is incapable of mimicking the innate immune aspect of the human epithelium.
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Affiliation(s)
- Ran Ran
- Center for Global Health and Diseases, Department of Pathology, Case Western Reserve University, Cleveland, OH, USA
| | - Javier Muñoz Briones
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA
- Purdue Interdisciplinary Life Science Program, West Lafayette, IN, USA
| | - Smrutiti Jena
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA
| | - Nicole L. Anderson
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Matthew R. Olson
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Leopold N. Green
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA
| | - Douglas K. Brubaker
- Center for Global Health and Diseases, Department of Pathology, Case Western Reserve University, Cleveland, OH, USA
- The Blood, Heart, Lung, and Immunology Research Center, Case Western Reserve University, University Hospitals of Cleveland, Cleveland, OH, USA
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8
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Zhang F, Huang B, Utturkar SM, Luo W, Cresswell G, Herr SA, Zheng S, Napoleon JV, Jiang R, Zhang B, Liu M, Lanman N, Srinivasarao M, Ratliff TL, Low PS. Tumor-specific activation of folate receptor beta enables reprogramming of immune cells in the tumor microenvironment. Front Immunol 2024; 15:1354735. [PMID: 38384467 PMCID: PMC10879311 DOI: 10.3389/fimmu.2024.1354735] [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: 12/12/2023] [Accepted: 01/22/2024] [Indexed: 02/23/2024] Open
Abstract
Folate receptors can perform folate transport, cell adhesion, and/or transcription factor functions. The beta isoform of the folate receptor (FRβ) has attracted considerable attention as a biomarker for immunosuppressive macrophages and myeloid-derived suppressor cells, however, its role in immunosuppression remains uncharacterized. We demonstrate here that FRβ cannot bind folate on healthy tissue macrophages, but does bind folate after macrophage incubation in anti-inflammatory cytokines or cancer cell-conditioned media. We further show that FRβ becomes functionally active following macrophage infiltration into solid tumors, and we exploit this tumor-induced activation to target a toll-like receptor 7 agonist specifically to immunosuppressive myeloid cells in solid tumors without altering myeloid cells in healthy tissues. We then use single-cell RNA-seq to characterize the changes in gene expression induced by the targeted repolarization of tumor-associated macrophages and finally show that their repolarization not only changes their own phenotype, but also induces a proinflammatory shift in all other immune cells of the same tumor mass, leading to potent suppression of tumor growth. Because this selective reprogramming of tumor myeloid cells is accompanied by no systemic toxicity, we propose that it should constitute a safe method to reprogram the tumor microenvironment.
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Affiliation(s)
- Fenghua Zhang
- Department of Chemistry and Institute for Drug Discovery, Purdue University, West Lafayette, IN, United States
| | - Bo Huang
- Department of Chemistry and Institute for Drug Discovery, Purdue University, West Lafayette, IN, United States
| | - Sagar M. Utturkar
- Purdue University Institute for Cancer Research, Purdue University, West Lafayette, IN, United States
| | - Weichuan Luo
- Department of Chemistry and Institute for Drug Discovery, Purdue University, West Lafayette, IN, United States
| | - Gregory Cresswell
- Department of Comparative Pathobiology, Purdue University, West Lafayette, IN, United States
| | - Seth A. Herr
- Department of Chemistry and Institute for Drug Discovery, Purdue University, West Lafayette, IN, United States
| | - Suilan Zheng
- Department of Chemistry and Institute for Drug Discovery, Purdue University, West Lafayette, IN, United States
| | - John V. Napoleon
- Department of Chemistry and Institute for Drug Discovery, Purdue University, West Lafayette, IN, United States
| | - Rina Jiang
- Department of Chemistry and Institute for Drug Discovery, Purdue University, West Lafayette, IN, United States
| | - Boning Zhang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, United States
| | - Muyi Liu
- University of North Texas Health Science Center at Fort Worth, Fort Worth, TX, United States
- Department of Computer Sciences, Purdue University, West Lafayette, IN, United States
| | - Nadia Lanman
- Purdue University Institute for Cancer Research, Purdue University, West Lafayette, IN, United States
- Department of Comparative Pathobiology, Purdue University, West Lafayette, IN, United States
| | - Madduri Srinivasarao
- Department of Chemistry and Institute for Drug Discovery, Purdue University, West Lafayette, IN, United States
| | - Timothy L. Ratliff
- Department of Comparative Pathobiology, Purdue University, West Lafayette, IN, United States
| | - Philip S. Low
- Department of Chemistry and Institute for Drug Discovery, Purdue University, West Lafayette, IN, United States
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9
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Ladaika CA, Ghobashi AH, Boulton WC, Miller SA, O'Hagan HM. Single-cell multi-omics reveals insights into differentiation of rare cell types in mucinous colorectal cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.01.578409. [PMID: 38370733 PMCID: PMC10871185 DOI: 10.1101/2024.02.01.578409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Neuroendocrine cells have been implicated in therapeutic resistance and worse overall survival in many cancer types. Mucinous colorectal cancer (mCRC) is uniquely enriched for enteroendocrine cells (EECs), the neuroendocrine cell of the normal colon epithelium, as compared to non-mucinous CRC. Therefore, targeting EEC differentiation may have clinical value in mCRC. Here, single cell multi-omics was used to uncover epigenetic alterations that accompany EEC differentiation, identify STAT3 as a novel regulator of EEC specification, and discover a rare cancer-specific cell type with enteric neuron-like characteristics. Further experiments demonstrated that lysine-specific demethylase 1 (LSD1) and CoREST2 mediate STAT3 demethylation and regulate STAT3 chromatin binding. Knockdown of CoREST2 in an orthotopic xenograft mouse model resulted in decreased primary tumor growth and lung metastases. In culmination, these results provide rationale for new LSD1 inhibitors that target the interaction between LSD1 with STAT3 or CoREST2, which may improve clinical outcomes for patients with mCRC.
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10
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Clister T, Fey RM, Garrison ZR, Valenzuela CD, Bar A, Leitenberger JJ, Kulkarni RP. Optimization of Tissue Digestion Methods for Characterization of Photoaged Skin by Single Cell RNA Sequencing Reveals Preferential Enrichment of T Cell Subsets. Cells 2024; 13:266. [PMID: 38334658 PMCID: PMC10854603 DOI: 10.3390/cells13030266] [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: 12/29/2023] [Revised: 01/19/2024] [Accepted: 01/27/2024] [Indexed: 02/10/2024] Open
Abstract
Healthy human skin tissue is often used as a control for comparison to diseased skin in patients with skin pathologies, including skin cancers or other inflammatory conditions such as atopic dermatitis or psoriasis. Although non-affected skin from these patients is a more appropriate choice for comparison, there is a paucity of studies examining such tissue. This lack is exacerbated by the difficulty of processing skin tissue for experimental analysis. In addition, choosing a processing protocol for skin tissue which preserves cell viability and identity while sufficiently dissociating cells for single-cell analysis is not a trivial task. Here, we compare three digestion methods for human skin tissue, evaluating the cell yield and viability for each protocol. We find that the use of a sequential dissociation method with multiple enzymatic digestion steps produces the highest cell viability. Using single-cell sequencing, we show this method results in a relative increase in the proportion of non-antigen-presenting mast cells and CD8 T cells as well as a relative decrease in the proportion of antigen-presenting mast cells and KYNU+ CD4 T cells. Overall, our findings support the use of this sequential digestion method on freshly processed human skin samples for optimal cell yield and viability.
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Affiliation(s)
- Terri Clister
- Department of Dermatology, Oregon Health & Science University, Portland, OR 97239, USA; (T.C.); (R.M.F.); (Z.R.G.); (A.B.); (J.J.L.)
| | - Rosalyn M. Fey
- Department of Dermatology, Oregon Health & Science University, Portland, OR 97239, USA; (T.C.); (R.M.F.); (Z.R.G.); (A.B.); (J.J.L.)
| | - Zachary R. Garrison
- Department of Dermatology, Oregon Health & Science University, Portland, OR 97239, USA; (T.C.); (R.M.F.); (Z.R.G.); (A.B.); (J.J.L.)
| | | | - Anna Bar
- Department of Dermatology, Oregon Health & Science University, Portland, OR 97239, USA; (T.C.); (R.M.F.); (Z.R.G.); (A.B.); (J.J.L.)
| | - Justin J. Leitenberger
- Department of Dermatology, Oregon Health & Science University, Portland, OR 97239, USA; (T.C.); (R.M.F.); (Z.R.G.); (A.B.); (J.J.L.)
| | - Rajan P. Kulkarni
- Department of Dermatology, Oregon Health & Science University, Portland, OR 97239, USA; (T.C.); (R.M.F.); (Z.R.G.); (A.B.); (J.J.L.)
- Cancer Early Detection Advanced Research Center (CEDAR), Portland, OR 97239, USA
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
- Operative Care Division, U.S. Department of Veterans Affairs Portland Health Care System, Portland, OR 97239, USA
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11
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Tadros HJ, Turaga D, Zhao Y, Chang-Ru T, Adachi IA, Li X, Martin JF. Activated fibroblasts drive cellular interactions in end-stage pediatric hypertrophic cardiomyopathy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.25.577226. [PMID: 38352607 PMCID: PMC10862753 DOI: 10.1101/2024.01.25.577226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Hypertrophic cardiomyopathy (HCM) is a relatively rare but debilitating diagnosis in the pediatric population and patients with end-stage HCM require heart transplantation. In this study, we performed single-nucleus RNA sequencing on pediatric HCM and control myocardium. We identified distinct underling cellular processes in pediatric, end-stage HCM in cardiomyocytes, fibroblasts, endothelial cells, and myeloid cells, compared to controls. Pediatric HCM was enriched in cardiomyocytes exhibiting "stressed" myocardium gene signatures and underlying pathways associated with cardiac hypertrophy. Cardiac fibroblasts exhibited clear activation signatures and heightened downstream processes associated with fibrosis, more so than adult counterparts. There was notable depletion of tissue-resident macrophages, and increased vascular remodeling in endothelial cells. Our analysis provides the first single nuclei analysis focused on end-stage pediatric HCM.
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Affiliation(s)
- Hanna J Tadros
- Department of Pediatrics, Section of Pediatric Cardiology, Texas Children's Hospital, Baylor College of Medicine, Houston, TX, USA
| | - Diwakar Turaga
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
- Division of Critical Care Medicine, Texas Children's Hospital, Houston TX, USA
| | - Yi Zhao
- The Texas Heart Institute, Houston, TX, USA
| | - Tsai Chang-Ru
- Department of Integrative Physiology, Baylor College of Medicine, Houston, TX, USA
| | - Iki A Adachi
- Department of Surgery, Baylor College of Medicine, Houston, Texas, USA
- Division of Congenital Heart Surgery, Texas Children's Hospital, Houston, TX, USA
| | - Xiao Li
- The Texas Heart Institute, Houston, TX, USA
| | - James F Martin
- The Texas Heart Institute, Houston, TX, USA
- Department of Integrative Physiology, Baylor College of Medicine, Houston, TX, USA
- Center for Organ Repair and Renewal, Baylor College of Medicine, Houston, TX, USA
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12
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Plattner C, Lamberti G, Blattmann P, Kirchmair A, Rieder D, Loncova Z, Sturm G, Scheidl S, Ijsselsteijn M, Fotakis G, Noureen A, Lisandrelli R, Böck N, Nemati N, Krogsdam A, Daum S, Finotello F, Somarakis A, Schäfer A, Wilflingseder D, Gonzalez Acera M, Öfner D, Huber LA, Clevers H, Becker C, Farin HF, Greten FR, Aebersold R, de Miranda NF, Trajanoski Z. Functional and spatial proteomics profiling reveals intra- and intercellular signaling crosstalk in colorectal cancer. iScience 2023; 26:108399. [PMID: 38047086 PMCID: PMC10692669 DOI: 10.1016/j.isci.2023.108399] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 04/21/2023] [Accepted: 11/02/2023] [Indexed: 12/05/2023] Open
Abstract
Precision oncology approaches for patients with colorectal cancer (CRC) continue to lag behind other solid cancers. Functional precision oncology-a strategy that is based on perturbing primary tumor cells from cancer patients-could provide a road forward to personalize treatment. We extend this paradigm to measuring proteome activity landscapes by acquiring quantitative phosphoproteomic data from patient-derived organoids (PDOs). We show that kinase inhibitors induce inhibitor- and patient-specific off-target effects and pathway crosstalk. Reconstruction of the kinase networks revealed that the signaling rewiring is modestly affected by mutations. We show non-genetic heterogeneity of the PDOs and upregulation of stemness and differentiation genes by kinase inhibitors. Using imaging mass-cytometry-based profiling of the primary tumors, we characterize the tumor microenvironment (TME) and determine spatial heterocellular crosstalk and tumor-immune cell interactions. Collectively, we provide a framework for inferring tumor cell intrinsic signaling and external signaling from the TME to inform precision (immuno-) oncology in CRC.
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Affiliation(s)
- Christina Plattner
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Giorgia Lamberti
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Peter Blattmann
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8092 Zurich, Switzerland
| | - Alexander Kirchmair
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Dietmar Rieder
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Zuzana Loncova
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Gregor Sturm
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Stefan Scheidl
- Department of Visceral, Transplant and Thoracic Surgery, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Marieke Ijsselsteijn
- Department of Pathology, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Georgios Fotakis
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Asma Noureen
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Rebecca Lisandrelli
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Nina Böck
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Niloofar Nemati
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Anne Krogsdam
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Sophia Daum
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Francesca Finotello
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Antonios Somarakis
- Department of Radiology, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Alexander Schäfer
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8092 Zurich, Switzerland
| | - Doris Wilflingseder
- Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Miguel Gonzalez Acera
- Department of Medicine 1, Friedrich-Alexander Universität Erlangen-Nürnberg (FAU) and Universitätsklinikum Erlangen, 91054 Erlangen, Germany
| | - Dietmar Öfner
- Department of Visceral, Transplant and Thoracic Surgery, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Lukas A. Huber
- Biocenter, Institute of Cell Biology, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Hans Clevers
- Hubrecht Institute, 3584 CT Utrecht, the Netherlands
| | - Christoph Becker
- Department of Medicine 1, Friedrich-Alexander Universität Erlangen-Nürnberg (FAU) and Universitätsklinikum Erlangen, 91054 Erlangen, Germany
| | - Henner F. Farin
- Institute for Tumor Biology and Experimental Therapy, Georg-Speyer-Haus, 60596 Frankfurt am Main, Germany
- Frankfurt Cancer Institute, Goethe University, 60596 Frankfurt am Main, Germany
- German Cancer Consortium (DKTK), partner site Frankfurt/Mainz, a partnership with DKFZ Heidelberg, Frankfurt/Mainz, Germany
| | - Florian R. Greten
- Institute for Tumor Biology and Experimental Therapy, Georg-Speyer-Haus, 60596 Frankfurt am Main, Germany
- Frankfurt Cancer Institute, Goethe University, 60596 Frankfurt am Main, Germany
- German Cancer Consortium (DKTK), partner site Frankfurt/Mainz, a partnership with DKFZ Heidelberg, Frankfurt/Mainz, Germany
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8092 Zurich, Switzerland
| | - Noel F.C.C. de Miranda
- Department of Pathology, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Zlatko Trajanoski
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, 6020 Innsbruck, Austria
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13
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Song J, Zhang Y, Frieler RA, Andren A, Wood S, Tyrrell DJ, Sajjakulnukit P, Deng JC, Lyssiotis CA, Mortensen RM, Salmon M, Goldstein DR. Itaconate suppresses atherosclerosis by activating a Nrf2-dependent antiinflammatory response in macrophages in mice. J Clin Invest 2023; 134:e173034. [PMID: 38085578 PMCID: PMC10849764 DOI: 10.1172/jci173034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 12/06/2023] [Indexed: 01/22/2024] Open
Abstract
Itaconate has emerged as a critical immunoregulatory metabolite. Here, we examined the therapeutic potential of itaconate in atherosclerosis. We found that both itaconate and the enzyme that synthesizes it, aconitate decarboxylase 1 (Acod1, also known as immune-responsive gene 1 [IRG1]), are upregulated during atherogenesis in mice. Deletion of Acod1 in myeloid cells exacerbated inflammation and atherosclerosis in vivo and resulted in an elevated frequency of a specific subset of M1-polarized proinflammatory macrophages in the atherosclerotic aorta. Importantly, Acod1 levels were inversely correlated with clinical occlusion in atherosclerotic human aorta specimens. Treating mice with the itaconate derivative 4-octyl itaconate attenuated inflammation and atherosclerosis induced by high cholesterol. Mechanistically, we found that the antioxidant transcription factor, nuclear factor erythroid 2-related factor 2 (Nrf2), was required for itaconate to suppress macrophage activation induced by oxidized lipids in vitro and to decrease atherosclerotic lesion areas in vivo. Overall, our work shows that itaconate suppresses atherogenesis by inducing Nrf2-dependent inhibition of proinflammatory responses in macrophages. Activation of the itaconate pathway may represent an important approach to treat atherosclerosis.
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Affiliation(s)
- Jianrui Song
- Department of Internal Medicine, Division of Cardiovascular Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Yanling Zhang
- Department of Biochemistry and Molecular Biology, Soochow University Medical College, Suzhou, Jiangsu, China
| | - Ryan A. Frieler
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, Michigan, USA
| | - Anthony Andren
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, Michigan, USA
| | - Sherri Wood
- Department of Internal Medicine, Division of Cardiovascular Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Daniel J. Tyrrell
- Department of Internal Medicine, Division of Cardiovascular Medicine, University of Michigan, Ann Arbor, Michigan, USA
- Department of Pathology, Heersink School of Medicine, University of Alabama at Birmingham, Alabama, USA
| | - Peter Sajjakulnukit
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, Michigan, USA
- University of Michigan Rogel Cancer Center
| | - Jane C. Deng
- Graduate Program in Immunology, and
- Department of Internal Medicine, Division of Pulmonary and Critical Care Medicine, University of Michigan, Ann Arbor, Michigan, USA
- Veterans Affairs Ann Arbor Healthcare System, Ann Arbor, Michigan, USA
| | - Costas A. Lyssiotis
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, Michigan, USA
- Veterans Affairs Ann Arbor Healthcare System, Ann Arbor, Michigan, USA
- Department of Internal Medicine, Division of Gastroenterology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Richard M. Mortensen
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, Michigan, USA
- Department of Pharmacology
- Department of Internal Medicine, Division of Metabolism, Endocrinology, and Diabetes
| | | | - Daniel R. Goldstein
- Department of Internal Medicine, Division of Cardiovascular Medicine, University of Michigan, Ann Arbor, Michigan, USA
- Graduate Program in Immunology, and
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
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14
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Ghobashi AH, Lanzloth R, Ladaika CA, O'Hagan HM. Single-cell profiling reveals the impact of genetic alterations on the differentiation of inflammation-induced colon tumors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.30.569463. [PMID: 38077052 PMCID: PMC10705473 DOI: 10.1101/2023.11.30.569463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Genetic mutations and chronic inflammation of the colon contribute to the development of colorectal cancer (CRC). Using a murine model of inflammation-induced colon tumorigenesis, we determined how genetic mutations alter colon tumor cell differentiation. Inflammation induced by enterotoxigenic Bacteroides fragilis (ETBF) colonization of multiple intestinal neoplasia (Min ApcΔ716/+ ) mice triggers loss of heterozygosity of Apc causing colon tumor formation. Here, we report that the addition of BRAF V600E mutation ( BRAF FV600E Lgr5 tm1(Cre/ERT2)Cle Min ApcΔ716/+ , BLM) or knocking out Msh2 ( Msh2 LoxP/LoxP Vil1-cre Min ApcΔ716/+ , MSH2KO) in the Min model altered colon tumor differentiation. Using single cell RNA-sequencing, we uncovered the differences between BLM, Min, and MSH2KO tumors at a single cell resolution. BLM tumors showed an increase in differentiated tumor epithelial cell lineages and a reduction in the stem cell population. In contrast, MSH2KO tumors were characterized by an increased stem cell population that had higher WNT signaling activity compared to Min tumors. Additionally, comparative analysis of single-cell transcriptomics revealed that BLM tumors had higher expression of transcription factors that drive differentiation, such as Cdx2, than Min tumors. Using RNA velocity, we were able to identify additional potential regulators of BLM tumor differentiation such as NDRG1. The role of CDX2 and NDRG1 as putative regulators for BLM tumor cell differentiation was verified using organoids derived from BLM tumors. Our results demonstrate the critical connections between genetic mutations and cell differentiation in inflammation-induced colon tumorigenesis. Understanding such roles will deepen our understanding of inflammation-associated colon cancer.
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15
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Nishino T, Ranade SS, Pelonero A, van Soldt BJ, Ye L, Alexanian M, Koback F, Huang Y, Sadagopan N, Lam A, Zholudeva LV, Li F, Padmanabhan A, Thomas R, van Bemmel JG, Gifford CA, Costa MW, Srivastava D. Single Cell Multimodal Analyses Reveal Epigenomic and Transcriptomic Basis for Birth Defects in Maternal Diabetes. NATURE CARDIOVASCULAR RESEARCH 2023; 2:1190-1203. [PMID: 39183978 PMCID: PMC11343316 DOI: 10.1038/s44161-023-00367-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 10/19/2023] [Indexed: 08/27/2024]
Abstract
Maternal diabetes mellitus is among the most frequent environmental contributors to congenital birth defects, including heart defects and craniofacial anomalies, yet the cell types affected and mechanisms of disruption are largely unknown. Using multi-modal single cell analyses, here we show that maternal diabetes affects the epigenomic landscape of specific subsets of cardiac and craniofacial progenitors during embryogenesis. A previously unrecognized cardiac progenitor subpopulation expressing the homeodomain-containing protein ALX3 showed prominent chromatin accessibility changes and acquired a more posterior identity. Similarly, a subpopulation of neural crest-derived cells in the second pharyngeal arch, which contributes to craniofacial structures, displayed abnormalities in the epigenetic landscape and axial patterning defects. Chromatin accessibility changes in both populations were associated with increased retinoic acid signaling, known to establish anterior-posterior identity. This work highlights how an environmental insult can have highly selective epigenomic consequences on discrete cell types leading to developmental patterning defects.
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Affiliation(s)
- Tomohiro Nishino
- Gladstone Institutes; San Francisco, CA, USA
- Roddenberry Center for Stem Cell Biology and Medicine at Gladstone; San Francisco, CA, USA
| | - Sanjeev S. Ranade
- Gladstone Institutes; San Francisco, CA, USA
- Roddenberry Center for Stem Cell Biology and Medicine at Gladstone; San Francisco, CA, USA
| | - Angelo Pelonero
- Gladstone Institutes; San Francisco, CA, USA
- Roddenberry Center for Stem Cell Biology and Medicine at Gladstone; San Francisco, CA, USA
| | - Benjamin J. van Soldt
- Gladstone Institutes; San Francisco, CA, USA
- Roddenberry Center for Stem Cell Biology and Medicine at Gladstone; San Francisco, CA, USA
| | - Lin Ye
- Gladstone Institutes; San Francisco, CA, USA
- Roddenberry Center for Stem Cell Biology and Medicine at Gladstone; San Francisco, CA, USA
| | - Michael Alexanian
- Gladstone Institutes; San Francisco, CA, USA
- Roddenberry Center for Stem Cell Biology and Medicine at Gladstone; San Francisco, CA, USA
| | - Frances Koback
- Gladstone Institutes; San Francisco, CA, USA
- Roddenberry Center for Stem Cell Biology and Medicine at Gladstone; San Francisco, CA, USA
| | - Yu Huang
- Gladstone Institutes; San Francisco, CA, USA
- Roddenberry Center for Stem Cell Biology and Medicine at Gladstone; San Francisco, CA, USA
| | - Nandhini Sadagopan
- Gladstone Institutes; San Francisco, CA, USA
- Roddenberry Center for Stem Cell Biology and Medicine at Gladstone; San Francisco, CA, USA
- Division of Cardiology, Department of Medicine, University of California, San Francisco; San Francisco, CA, USA
| | - Adrienne Lam
- Gladstone Institutes; San Francisco, CA, USA
- Roddenberry Center for Stem Cell Biology and Medicine at Gladstone; San Francisco, CA, USA
| | - Lyandysha V. Zholudeva
- Gladstone Institutes; San Francisco, CA, USA
- Roddenberry Center for Stem Cell Biology and Medicine at Gladstone; San Francisco, CA, USA
| | - Feiya Li
- Gladstone Institutes; San Francisco, CA, USA
- Roddenberry Center for Stem Cell Biology and Medicine at Gladstone; San Francisco, CA, USA
| | - Arun Padmanabhan
- Gladstone Institutes; San Francisco, CA, USA
- Roddenberry Center for Stem Cell Biology and Medicine at Gladstone; San Francisco, CA, USA
- Division of Cardiology, Department of Medicine, University of California, San Francisco; San Francisco, CA, USA
| | | | - Joke G. van Bemmel
- Gladstone Institutes; San Francisco, CA, USA
- Roddenberry Center for Stem Cell Biology and Medicine at Gladstone; San Francisco, CA, USA
| | - Casey A. Gifford
- Gladstone Institutes; San Francisco, CA, USA
- Roddenberry Center for Stem Cell Biology and Medicine at Gladstone; San Francisco, CA, USA
| | - Mauro W. Costa
- Gladstone Institutes; San Francisco, CA, USA
- Roddenberry Center for Stem Cell Biology and Medicine at Gladstone; San Francisco, CA, USA
| | - Deepak Srivastava
- Gladstone Institutes; San Francisco, CA, USA
- Roddenberry Center for Stem Cell Biology and Medicine at Gladstone; San Francisco, CA, USA
- Division of Cardiology, Department of Pediatrics, University of California, San Francisco; San Francisco, CA, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco; San Francisco, CA, USA
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16
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Teefy BB, Lemus AJJ, Adler A, Xu A, Bhala R, Hsu K, Benayoun BA. Widespread sex dimorphism across single-cell transcriptomes of adult African turquoise killifish tissues. Cell Rep 2023; 42:113237. [PMID: 37837621 PMCID: PMC10842523 DOI: 10.1016/j.celrep.2023.113237] [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: 05/05/2023] [Revised: 08/18/2023] [Accepted: 09/25/2023] [Indexed: 10/16/2023] Open
Abstract
The African turquoise killifish (Nothobranchius furzeri), the shortest-lived vertebrate that can be bred in captivity, is an emerging model organism for aging research. Here, we describe a multitissue, single-cell gene expression atlas of female and male blood, kidney, liver, and spleen. We annotate 22 cell types, define marker genes, and infer differentiation trajectories. We find pervasive sex-dimorphic gene expression across cell types. Sex-dimorphic genes tend to be linked to lipid metabolism, consistent with clear differences in lipid storage in female vs. male turquoise killifish livers. We use machine learning to predict sex using single-cell gene expression and identify potential markers for molecular sex identity. As a proof of principle, we show that our atlas can be used to deconvolute existing bulk RNA sequencing (RNA-seq) data to obtain accurate estimates of cell type proportions. This atlas can be a resource to the community that could be leveraged to develop cell-type-specific expression in transgenic animals.
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Affiliation(s)
- Bryan B Teefy
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
| | - Aaron J J Lemus
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA; Molecular and Computational Biology Department, USC Dornsife College of Letters, Arts, and Sciences, Los Angeles, CA 90089, USA
| | - Ari Adler
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
| | - Alan Xu
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA; Quantitative & Computational Biology Department, USC Dornsife College of Letters, Arts, and Sciences, Los Angeles, CA 90089, USA
| | - Rajyk Bhala
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
| | - Katelyn Hsu
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA; Molecular and Computational Biology Department, USC Dornsife College of Letters, Arts, and Sciences, Los Angeles, CA 90089, USA
| | - Bérénice A Benayoun
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA; Molecular and Computational Biology Department, USC Dornsife College of Letters, Arts, and Sciences, Los Angeles, CA 90089, USA; Biochemistry and Molecular Medicine Department, USC Keck School of Medicine, Los Angeles, CA 90089, USA; Epigenetics and Gene Regulation, USC Norris Comprehensive Cancer Center, Los Angeles, CA 90089, USA; USC Stem Cell Initiative, Los Angeles, CA 90089, USA.
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17
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Wang L, Oill AT, Blanchard M, Wu M, Hibbard J, Sepulveda S, Peter L, Kilpatrick J, Munoz M, Stiller T, Shulkin N, Wagner J, Dolatabadi A, Nisis M, Shepphird J, Sanchez G, Lingaraju C, Manchanda M, Natri H, Kouakanou L, Sun G, Oliver-Cervantes C, Georges J, Aftabizadeh M, Forman S, Priceman S, Ressler J, Arvanitis L, Cotter J, D'Apuzzo M, Tamrazi B, Badie B, Davidson T, Banovich N, Brown C. Expansion of endogenous T cells in CSF of pediatric CNS tumor patients undergoing locoregional delivery of IL13R〿2-targeting CAR T cells: an interim analysis. RESEARCH SQUARE 2023:rs.3.rs-3454977. [PMID: 37961215 PMCID: PMC10635314 DOI: 10.21203/rs.3.rs-3454977/v1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Outcomes for pediatric brain tumor patients remain poor, and there is optimism that chimeric antigen receptor (CAR) T cell therapy can improve prognosis. Here, we present interim results from the first six pediatric patients treated on an ongoing phase I clinical trial (NCT04510051) of IL13BBζ-CAR T cells delivered weekly into the lateral cerebral ventricles, identifying clonal expansion of endogenous CAR-negative CD8+ T cells in the cerebrospinal fluid (CSF) over time. Additionally, of the five patients evaluable for disease response, three experienced transient radiographic and/or clinical benefit not meeting protocol criteria for response. The first three patients received CAR T cells alone; later patients received lymphodepletion before the first infusion. There were no dose limiting toxicities (DLTs). Aside from expected cytopenias in patients receiving lymphodepletion, serious adverse events possibly attributed to CAR T cell infusion were limited to one episode of headache and one of liver enzyme elevation. One patient withdrew from treatment during the DLT period due to a Grade 3 catheter-related infection and was not evaluable for disease response, although this was not attributed to CAR T cell infusion. Importantly, scRNA- and scTCR-sequence analyses provided insights into CAR T cell interaction with the endogenous immune system. In particular, clonally expanded endogenous CAR- T cells were recovered from the CSF, but not the peripheral blood, of patients who received intraventricular IL13BBζ-CAR T cell therapy. Additionally, although immune infiltrates in CSF and post-therapy tumor did not generally correlate, a fraction of expanded T cell receptors (TCRs) was seen to overlap between CSF and tumor. This has important implications for what samples are collected on these trials and how they are analyzed. These initial findings provide support for continued investigation into locoregionally-delivered IL13BBζ-CAR T cells for children with brain tumors.
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Affiliation(s)
| | | | | | - Melody Wu
- City of Hope National Medical Center
| | - Jonathan Hibbard
- Beckman Research Institute, City of Hope National Medical Center
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Heini Natri
- The Translational Genomics Research Institute
| | | | - Grace Sun
- City of Hope National Medical Center
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18
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Baby S, Shinde SD, Kulkarni N, Sahu B. Lysine-Specific Demethylase 1 (LSD1) Inhibitors: Peptides as an Emerging Class of Therapeutics. ACS Chem Biol 2023; 18:2144-2155. [PMID: 37812385 DOI: 10.1021/acschembio.3c00386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Aberrant expression of the epigenetic regulator lysine-specific demethylase 1 (LSD1) has been associated with the incidence of many diseases, particularly cancer, and it has evolved as a promising epigenetic target over the years for treatment. The advent of LSD1 inhibitor-based clinical utility began with tranylcypromine, and it is now considered an inevitable scaffold in the search for other irreversible novel LSD1 inhibitors (IMG-7289 or bomedemstat, ORY1001 or iadademstat, ORY-2001 or vafidemstat, GSK2879552, and INCB059872). Moreover, numerous reversible inhibitors for LSD1 have been reported in the literature, including clinical candidates CC-90011 (pulrodemstat) and SP-2577 (seclidemstat). There is parallel mining for peptide-based LSD1 inhibitors, which exploits the opportunities in the LSD1 substrate binding pocket. This Review highlights the research progress on reversible and irreversible peptide/peptide-derived LSD1 inhibitors. For the first time, we comprehensively organized the peptide-based LSD1 inhibitors from the design strategy. Peptide inhibitors of LSD1 are classified as H3 peptide and SNAIL1 peptide derivatives, along with miscellaneous peptides that include naturally occurring LSD1 inhibitors.
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Affiliation(s)
- Stephin Baby
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Ahmedabad, Gujarat 380054, India
| | - Suchita Dattatray Shinde
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Ahmedabad, Gujarat 380054, India
| | - Neeraj Kulkarni
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Ahmedabad, Gujarat 380054, India
| | - Bichismita Sahu
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Ahmedabad, Gujarat 380054, India
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19
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Mack KL, Talbott HE, Griffin MF, Parker JBL, Guardino NJ, Spielman AF, Davitt MF, Mascharak S, Downer M, Morgan A, Valencia C, Akras D, Berger MJ, Wan DC, Fraser HB, Longaker MT. Allele-specific expression reveals genetic drivers of tissue regeneration in mice. Cell Stem Cell 2023; 30:1368-1381.e6. [PMID: 37714154 PMCID: PMC10592051 DOI: 10.1016/j.stem.2023.08.010] [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: 08/05/2022] [Revised: 06/16/2023] [Accepted: 08/22/2023] [Indexed: 09/17/2023]
Abstract
In adult mammals, skin wounds typically heal by scarring rather than through regeneration. In contrast, "super-healer" Murphy Roths Large (MRL) mice have the unusual ability to regenerate ear punch wounds; however, the molecular basis for this regeneration remains elusive. Here, in hybrid crosses between MRL and non-regenerating mice, we used allele-specific gene expression to identify cis-regulatory variation associated with ear regeneration. Analyzing three major cell populations (immune, fibroblast, and endothelial), we found that genes with cis-regulatory differences specifically in fibroblasts were associated with wound-healing pathways and also co-localized with quantitative trait loci for ear wound-healing. Ectopic treatment with one of these proteins, complement factor H (CFH), accelerated wound repair and induced regeneration in typically fibrotic wounds. Through single-cell RNA sequencing (RNA-seq), we observed that CFH treatment dramatically reduced immune cell recruitment to wounds, suggesting a potential mechanism for CFH's effect. Overall, our results provide insights into the molecular drivers of regeneration with potential clinical implications.
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Affiliation(s)
- Katya L Mack
- Stanford University, Department of Biology, Stanford, CA, USA
| | - Heather E Talbott
- Stanford School of Medicine, Department of Surgery, Division of Plastic and Reconstructive Surgery, Stanford, CA, USA; Stanford Institute for Stem Cell Biology and Regenerative Medicine, Stanford, CA, USA
| | - Michelle F Griffin
- Stanford School of Medicine, Department of Surgery, Division of Plastic and Reconstructive Surgery, Stanford, CA, USA
| | - Jennifer B L Parker
- Stanford School of Medicine, Department of Surgery, Division of Plastic and Reconstructive Surgery, Stanford, CA, USA; Stanford Institute for Stem Cell Biology and Regenerative Medicine, Stanford, CA, USA
| | - Nicholas J Guardino
- Stanford School of Medicine, Department of Surgery, Division of Plastic and Reconstructive Surgery, Stanford, CA, USA
| | - Amanda F Spielman
- Stanford School of Medicine, Department of Surgery, Division of Plastic and Reconstructive Surgery, Stanford, CA, USA
| | - Michael F Davitt
- Stanford School of Medicine, Department of Surgery, Division of Plastic and Reconstructive Surgery, Stanford, CA, USA
| | - Shamik Mascharak
- Stanford School of Medicine, Department of Surgery, Division of Plastic and Reconstructive Surgery, Stanford, CA, USA; Stanford Institute for Stem Cell Biology and Regenerative Medicine, Stanford, CA, USA
| | - Mauricio Downer
- Stanford School of Medicine, Department of Surgery, Division of Plastic and Reconstructive Surgery, Stanford, CA, USA
| | - Annah Morgan
- Stanford School of Medicine, Department of Surgery, Division of Plastic and Reconstructive Surgery, Stanford, CA, USA
| | - Caleb Valencia
- Stanford School of Medicine, Department of Surgery, Division of Plastic and Reconstructive Surgery, Stanford, CA, USA
| | - Deena Akras
- Stanford School of Medicine, Department of Surgery, Division of Plastic and Reconstructive Surgery, Stanford, CA, USA
| | - Mark J Berger
- Stanford University, Department of Computer Science, Stanford, CA 94305, USA
| | - Derrick C Wan
- Stanford School of Medicine, Department of Surgery, Division of Plastic and Reconstructive Surgery, Stanford, CA, USA
| | - Hunter B Fraser
- Stanford University, Department of Biology, Stanford, CA, USA.
| | - Michael T Longaker
- Stanford School of Medicine, Department of Surgery, Division of Plastic and Reconstructive Surgery, Stanford, CA, USA; Stanford Institute for Stem Cell Biology and Regenerative Medicine, Stanford, CA, USA.
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20
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Kaiser FMP, Janowska I, Menafra R, de Gier M, Korzhenevich J, Pico-Knijnenburg I, Khatri I, Schulz A, Kuijpers TW, Lankester AC, Konstantinidis L, Erlacher M, Kloet S, van Schouwenburg PA, Rizzi M, van der Burg M. IL-7 receptor signaling drives human B-cell progenitor differentiation and expansion. Blood 2023; 142:1113-1130. [PMID: 37369082 PMCID: PMC10644098 DOI: 10.1182/blood.2023019721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 05/18/2023] [Accepted: 06/05/2023] [Indexed: 06/29/2023] Open
Abstract
Although absence of interleukin-7 (IL-7) signaling completely abrogates T and B lymphopoiesis in mice, patients with severe combined immunodeficiency caused by mutations in the IL-7 receptor α chain (IL-7Rα) still generate peripheral blood B cells. Consequently, human B lymphopoiesis has been thought to be independent of IL-7 signaling. Using flow cytometric analysis and single-cell RNA sequencing of bone marrow samples from healthy controls and patients who are IL-7Rα deficient, in combination with in vitro modeling of human B-cell differentiation, we demonstrate that IL-7R signaling plays a crucial role in human B lymphopoiesis. IL-7 drives proliferation and expansion of early B-cell progenitors but not of pre-BII large cells and has a limited role in the prevention of cell death. Furthermore, IL-7 guides cell fate decisions by enhancing the expression of BACH2, EBF1, and PAX5, which jointly orchestrate the specification and commitment of early B-cell progenitors. In line with this observation, early B-cell progenitors of patients with IL-7Rα deficiency still expressed myeloid-specific genes. Collectively, our results unveil a previously unknown role for IL-7 signaling in promoting the B-lymphoid fate and expanding early human B-cell progenitors while defining important differences between mice and humans. Our results have implications for hematopoietic stem cell transplantation strategies in patients with T- B+ severe combined immunodeficiency and provide insights into the role of IL-7R signaling in leukemogenesis.
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Affiliation(s)
- Fabian M. P. Kaiser
- Department of Immunology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Iga Janowska
- Department of Rheumatology and Clinical Immunology, Freiburg University Medical Center, University of Freiburg, Freiburg, Germany
- Center for Chronic Immunodeficiency, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | | | - Melanie de Gier
- Department of Pediatrics, Laboratory for Pediatric Immunology, Willem-Alexander Children’s Hospital, Leiden University Medical Center, Leiden, The Netherlands
| | - Jakov Korzhenevich
- Division of Clinical and Experimental Immunology, Institute of Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Ingrid Pico-Knijnenburg
- Department of Pediatrics, Laboratory for Pediatric Immunology, Willem-Alexander Children’s Hospital, Leiden University Medical Center, Leiden, The Netherlands
| | - Indu Khatri
- Department of Immunology, Leiden University Medical Center, Leiden, The Netherlands
| | - Ansgar Schulz
- Department of Pediatrics and Adolescent Medicine, University Medical Center, University Ulm, Ulm, Germany
| | - Taco W. Kuijpers
- Department of Pediatrics, Amsterdam University Medical Center, Amsterdam, The Netherlands
| | - Arjan C. Lankester
- Department of Pediatrics, Hematology and Stem Cell Transplantation, Willem-Alexander Children’s Hospital, Leiden University Medical Center, Leiden, The Netherlands
| | - Lukas Konstantinidis
- Department of Orthopedics and Trauma Surgery, Freiburg University Medical Center, University of Freiburg, Freiburg, Germany
| | - Miriam Erlacher
- Division of Pediatric Hematology and Oncology, Department of Pediatrics and Adolescent Medicine, Freiburg University Medical Center, University of Freiburg, Freiburg, Germany
| | - Susan Kloet
- Leiden Genome Technology Center, Leiden, The Netherlands
| | - Pauline A. van Schouwenburg
- Department of Pediatrics, Laboratory for Pediatric Immunology, Willem-Alexander Children’s Hospital, Leiden University Medical Center, Leiden, The Netherlands
| | - Marta Rizzi
- Department of Rheumatology and Clinical Immunology, Freiburg University Medical Center, University of Freiburg, Freiburg, Germany
- Center for Chronic Immunodeficiency, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Division of Clinical and Experimental Immunology, Institute of Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
- Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany
| | - Mirjam van der Burg
- Department of Pediatrics, Laboratory for Pediatric Immunology, Willem-Alexander Children’s Hospital, Leiden University Medical Center, Leiden, The Netherlands
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21
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Lin CCJ, Herisson F, Le H, Jaafar N, Chetal K, Oram MK, Flynn KL, Gavrilles EP, Sadreyev RI, Schiffino FL, Tanzi RE. Mast cell deficiency improves cognition and enhances disease-associated microglia in 5XFAD mice. Cell Rep 2023; 42:113141. [PMID: 37713312 PMCID: PMC10634538 DOI: 10.1016/j.celrep.2023.113141] [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: 07/13/2022] [Revised: 06/20/2023] [Accepted: 08/30/2023] [Indexed: 09/17/2023] Open
Abstract
Emerging evidence suggests that peripheral immune cells contribute to Alzheimer's disease (AD) neuropathogenesis. Among these, mast cells are known for their functions in allergic reactions and neuroinflammation; however, little is known about their role in AD. Here, we crossed 5XFAD mice with mast cell-deficient strains and observed the effects on AD-related neuropathology and cognitive impairment. We found that mast cell depletion improved contextual fear conditioning in 5XFAD mice without affecting cued fear conditioning, anxiety-like behavior, or amyloid burden. Furthermore, mast cell depletion led to an upregulation of transcriptomic signatures for putatively protective disease-associated microglia and resulted in reduced markers indicative of reactive astrocytes. We hypothesize a system of bidirectional communication between dural mast cells and the brain, where mast cells respond to signals from the brain environment by expressing immune-regulatory mediators, impacting cognition and glial cell function. These findings highlight mast cells as potential therapeutic targets for AD.
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Affiliation(s)
- Chih-Chung Jerry Lin
- Genetics and Aging Research Unit, Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA 02129, USA
| | - Fanny Herisson
- Genetics and Aging Research Unit, Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA 02129, USA
| | - Hoang Le
- Genetics and Aging Research Unit, Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA 02129, USA
| | - Nader Jaafar
- Genetics and Aging Research Unit, Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA 02129, USA
| | - Kashish Chetal
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Mary K Oram
- Genetics and Aging Research Unit, Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA 02129, USA
| | - Kelly L Flynn
- Genetics and Aging Research Unit, Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA 02129, USA
| | - Evan P Gavrilles
- Genetics and Aging Research Unit, Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA 02129, USA
| | - Ruslan I Sadreyev
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Felipe L Schiffino
- Genetics and Aging Research Unit, Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA 02129, USA
| | - Rudolph E Tanzi
- Genetics and Aging Research Unit, Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA 02129, USA; Henry and Allison McCance Center for Brain Health, Massachusetts General Hospital, Charlestown, MA 02129, USA.
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22
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Rzasa P, Whelan S, Farahmand P, Cai H, Guterman I, Palacios-Gallego R, Undru SS, Sandford L, Green C, Andreadi C, Mintseva M, Parrott E, Jin H, Hey F, Giblett S, Sylvius NB, Allcock NS, Straatman-Iwanowska A, Feuda R, Tufarelli C, Brown K, Pritchard C, Rufini A. BRAF V600E-mutated serrated colorectal neoplasia drives transcriptional activation of cholesterol metabolism. Commun Biol 2023; 6:962. [PMID: 37735514 PMCID: PMC10514332 DOI: 10.1038/s42003-023-05331-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 09/07/2023] [Indexed: 09/23/2023] Open
Abstract
BRAF mutations occur early in serrated colorectal cancers, but their long-term influence on tissue homeostasis is poorly characterized. We investigated the impact of short-term (3 days) and long-term (6 months) expression of BrafV600E in the intestinal tissue of an inducible mouse model. We show that BrafV600E perturbs the homeostasis of intestinal epithelial cells, with impaired differentiation of enterocytes emerging after prolonged expression of the oncogene. Moreover, BrafV600E leads to a persistent transcriptional reprogramming with enrichment of numerous gene signatures indicative of proliferation and tumorigenesis, and signatures suggestive of metabolic rewiring. We focused on the top-ranking cholesterol biosynthesis signature and confirmed its increased expression in human serrated lesions. Functionally, the cholesterol lowering drug atorvastatin prevents the establishment of intestinal crypt hyperplasia in BrafV600E-mutant mice. Overall, our work unveils the long-term impact of BrafV600E expression in intestinal tissue and suggests that colorectal cancers with mutations in BRAF might be prevented by statins.
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Affiliation(s)
- Paulina Rzasa
- Leicester Cancer Research Centre, University of Leicester, Leicester, UK
| | - Sarah Whelan
- Leicester Cancer Research Centre, University of Leicester, Leicester, UK
| | - Pooyeh Farahmand
- Leicester Cancer Research Centre, University of Leicester, Leicester, UK
| | - Hong Cai
- Leicester Cancer Research Centre, University of Leicester, Leicester, UK
| | - Inna Guterman
- Leicester Cancer Research Centre, University of Leicester, Leicester, UK
| | | | - Shanthi S Undru
- Leicester Cancer Research Centre, University of Leicester, Leicester, UK
| | - Lauren Sandford
- Leicester Cancer Research Centre, University of Leicester, Leicester, UK
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Caleb Green
- Leicester Cancer Research Centre, University of Leicester, Leicester, UK
| | - Catherine Andreadi
- Leicester Cancer Research Centre, University of Leicester, Leicester, UK
| | - Maria Mintseva
- Leicester Cancer Research Centre, University of Leicester, Leicester, UK
- Area of Neuroscience, International School for Advanced Studies (SISSA), Trieste, Italy
| | - Emma Parrott
- Leicester Cancer Research Centre, University of Leicester, Leicester, UK
| | - Hong Jin
- Leicester Cancer Research Centre, University of Leicester, Leicester, UK
| | - Fiona Hey
- Leicester Cancer Research Centre, University of Leicester, Leicester, UK
| | - Susan Giblett
- Leicester Cancer Research Centre, University of Leicester, Leicester, UK
| | - Nicolas B Sylvius
- NUCLEUS Genomics, Core Biotechnology Services, University of Leicester, Leicester, UK
| | - Natalie S Allcock
- University of Leicester Core Biotechnology Services Electron Microscopy Facility, Leicester, UK
| | | | - Roberto Feuda
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Cristina Tufarelli
- Leicester Cancer Research Centre, University of Leicester, Leicester, UK
| | - Karen Brown
- Leicester Cancer Research Centre, University of Leicester, Leicester, UK
| | - Catrin Pritchard
- Leicester Cancer Research Centre, University of Leicester, Leicester, UK
| | - Alessandro Rufini
- Leicester Cancer Research Centre, University of Leicester, Leicester, UK.
- Dipartimento di Bioscienze, University of Milan, Milan, Italy.
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23
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Ghobashi AH, Vuong TT, Kimani JW, Ladaika CA, Hollenhorst PC, O’Hagan HM. Activation of AKT induces EZH2-mediated β-catenin trimethylation in colorectal cancer. iScience 2023; 26:107630. [PMID: 37670785 PMCID: PMC10475482 DOI: 10.1016/j.isci.2023.107630] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 08/09/2023] [Accepted: 08/11/2023] [Indexed: 09/07/2023] Open
Abstract
Colorectal cancer (CRC) develops in part through the deregulation of different signaling pathways, including activation of the WNT/β-catenin and PI3K/AKT pathways. Additionally, the lysine methyltransferase enhancer of zeste homologue 2 (EZH2) is commonly overexpressed in CRC. EZH2 canonically represses gene transcription by trimethylating lysine 27 of histone H3, but also has non-histone substrates. Here, we demonstrated that in CRC, active AKT phosphorylated EZH2 on serine 21. Phosphorylation of EZH2 by AKT induced EZH2 to interact with and methylate β-catenin at lysine 49, which increased β-catenin's binding to the chromatin. Additionally, EZH2-mediated β-catenin trimethylation induced β-catenin to interact with TCF1 and RNA polymerase II and resulted in dramatic gains in genomic regions with β-catenin occupancy. EZH2 catalytic inhibition decreased stemness but increased migratory phenotypes of CRC cells with active AKT. Overall, we demonstrated that EZH2 modulates AKT-induced changes in gene expression through the AKT/EZH2/β-catenin axis in CRC.
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Affiliation(s)
- Ahmed H. Ghobashi
- Genome, Cell, and Developmental Biology Graduate Program, Department of Biology, Indiana University Bloomington, Bloomington, IN 47405, USA
- Medical Sciences Program, Indiana University School of Medicine, Bloomington, IN 47405, USA
| | - Truc T. Vuong
- Medical Sciences Program, Indiana University School of Medicine, Bloomington, IN 47405, USA
- Cell, Molecular and Cancer Biology Graduate Program, Indiana University School of Medicine, Bloomington, IN 47405, USA
| | - Jane W. Kimani
- Medical Sciences Program, Indiana University School of Medicine, Bloomington, IN 47405, USA
| | - Christopher A. Ladaika
- Genome, Cell, and Developmental Biology Graduate Program, Department of Biology, Indiana University Bloomington, Bloomington, IN 47405, USA
- Medical Sciences Program, Indiana University School of Medicine, Bloomington, IN 47405, USA
| | - Peter C. Hollenhorst
- Medical Sciences Program, Indiana University School of Medicine, Bloomington, IN 47405, USA
- Cell, Molecular and Cancer Biology Graduate Program, Indiana University School of Medicine, Bloomington, IN 47405, USA
- Tumor Microenvironment & Metastasis Program, Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indianapolis, IN 46202, USA
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Heather M. O’Hagan
- Medical Sciences Program, Indiana University School of Medicine, Bloomington, IN 47405, USA
- Cell, Molecular and Cancer Biology Graduate Program, Indiana University School of Medicine, Bloomington, IN 47405, USA
- Tumor Microenvironment & Metastasis Program, Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indianapolis, IN 46202, USA
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
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24
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Zhao YQ, Jin HR, Kim D, Jung SH, Liu S, Wan J, Lo HY, Fu XQ, Wang Q, Hao C, Bellail AC. SUMO1 degrader induces ER stress and ROS accumulation through deSUMOylation of TCF4 and inhibition of its transcription of StarD7 in colon cancer. Mol Carcinog 2023; 62:1249-1262. [PMID: 37191369 PMCID: PMC10524896 DOI: 10.1002/mc.23560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 02/09/2023] [Accepted: 05/04/2023] [Indexed: 05/17/2023]
Abstract
Small molecule degraders of small ubiquitin-related modifier 1 (SUMO1) induce SUMO1 degradation in colon cancer cells and inhibits the cancer cell growth; however, it is unclear how SUMO1 degradation leads to the anticancer activity of the degraders. Genome-wide CRISPR-Cas9 knockout screen has identified StAR-related lipid transfer domain containing 7 (StarD7) as a critical gene for the degrader's anticancer activity. Here, we show that both StarD7 mRNA and protein are overexpressed in human colon cancer and its knockout significantly reduces colon cancer cell growth and xenograft progression. The treatment with the SUMO1 degrader lead compound HB007 reduces StarD7 mRNA and protein levels and increases endoplasmic reticulum (ER) stress and reactive oxygen species (ROS) production in colon cancer cells and three-dimensional (3D) organoids. The study further provides a novel mechanism of the compound anticancer activity that SUMO1 degrader-induced decrease of StarD7 occur through degradation of SUMO1, deSUMOylation and degradation of T cell-specific transcription 4 (TCF4) and thereby inhibition of its transcription of StarD7 in colon cancer cells, 3D organoids and patient-derived xenografts (PDX).
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Affiliation(s)
- Yin Quan Zhao
- Department of Gastric and Colorectal Surgery, General Surgery Center, The First Hospital of Jilin University, Changchun, Jilin Province, 130021, China
- School of Life Sciences, Jilin University, Changchun, Jilin Province, 130012, China
- Department of Pathology & Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Hong Ri Jin
- Department of Pathology & Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Daeho Kim
- Department of Pathology & Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Sung Han Jung
- Department of Pathology & Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Sheng Liu
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Jun Wan
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Ho-Yin Lo
- Synovel Laboratory LLC, Danbury, CT 06811, USA
| | - Xue Qi Fu
- School of Life Sciences, Jilin University, Changchun, Jilin Province, 130012, China
| | - Quan Wang
- Department of Gastric and Colorectal Surgery, General Surgery Center, The First Hospital of Jilin University, Changchun, Jilin Province, 130021, China
| | - Chunhai Hao
- Department of Pathology & Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Anita C. Bellail
- Department of Pathology & Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- HB Therapeutics Inc. Indianapolis, IN 46202, USA
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25
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Yoon H, Dean LS, Jiyarom B, Khadka V, Deng Y, Nerurukar VR, Chow DC, Shikuma CM, Devendra G, Koh Y, Park J. Single-cell RNA sequencing reveals characteristics of myeloid cells in pulmonary post-acute sequelae of SARS-CoV-2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.31.551349. [PMID: 37577518 PMCID: PMC10418075 DOI: 10.1101/2023.07.31.551349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Background Although our understanding of the immunopathology and subsequent risk and severity of COVID-19 disease is evolving, a detailed account of immune responses that contribute to the long-term consequences of pulmonary complication in COVID-19 infection remain unclear. Few studies have detailed the immune and cytokine profiles associated with post-acute sequalae of SARS-CoV-2 infection with persistent pulmonary symptoms (PPASC). However, the dysregulation of the immune system that drives pulmonary sequelae in COVID-19 survivors and PASC sufferers remains largely unknown. Results To characterize the immunological features of pulmonary PASC (PPASC), we performed droplet-based single-cell RNA sequencing to study the transcriptomic profiles of peripheral blood mononuclear cells (PBMCs) from participants naïve to SARS-CoV-2 (Control) and infected with SARS-CoV-2 with chronic pulmonary symptoms (PPASC). We analyzed more than 34,139 PBMCs by integrating our dataset with previously reported control datasets (GSM4509024) cell distribution. In total, 11 distinct cell populations were identified based on the expression of canonical markers. The proportion of myeloid-lineage cells ([MLCs]; CD14 + /CD16 + monocytes and dendritic cells) was increased in PPASC compared to controls. MLCs from PPASC displayed up-regulation of genes associated with pulmonary symptoms/fibrosis, while glycolysis metabolism-related genes were downregulated. Similarly, pathway analysis showed that fibrosis- related ( VEGF , WNT , and SMAD ) and cell death pathways were up-regulated, but immune pathways were down-regulated in PPASC. In PPASC, we observed interactive VEGF ligand- receptor pairs among MLCs, and network modules in CD14 + (cluster 4) and CD16 + (Cluster 5) monocytes displayed a significant enrichment for biological pathways linked to adverse COVID- 19 outcomes, fibrosis, and angiogenesis. Further analysis revealed a distinct metabolic alteration in MLCs with a down-regulation of glycolysis/gluconeogenesis in PPASC compared to SARS- CoV-2 naïve samples. Conclusion This study offers valuable insights into the immune response and cellular landscape in PPASC. The presence of elevated MLC levels and their corresponding gene signatures associated with fibrosis, immune response suppression, and altered metabolic states suggests their potential role as a driver of PPASC.
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26
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Coulombe P, Cole G, Fentiman A, Parker JDK, Yung E, Bilenky M, Degefie L, Lac P, Ling MYM, Tam D, Humphries RK, Karsan A. Meis1 establishes the pre-hemogenic endothelial state prior to Runx1 expression. Nat Commun 2023; 14:4537. [PMID: 37500618 PMCID: PMC10374625 DOI: 10.1038/s41467-023-40283-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 07/20/2023] [Indexed: 07/29/2023] Open
Abstract
Hematopoietic stem and progenitor cells (HSPCs) originate from an endothelial-to-hematopoietic transition (EHT) during embryogenesis. Characterization of early hemogenic endothelial (HE) cells is required to understand what drives hemogenic specification and to accurately define cells capable of undergoing EHT. Using Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-seq), we define the early subpopulation of pre-HE cells based on both surface markers and transcriptomes. We identify the transcription factor Meis1 as an essential regulator of hemogenic cell specification in the embryo prior to Runx1 expression. Meis1 is expressed at the earliest stages of EHT and distinguishes pre-HE cells primed towards the hemogenic trajectory from the arterial endothelial cells that continue towards a vascular fate. Endothelial-specific deletion of Meis1 impairs the formation of functional Runx1-expressing HE which significantly impedes the emergence of pre-HSPC via EHT. Our findings implicate Meis1 in a critical fate-determining step for establishing EHT potential in endothelial cells.
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Affiliation(s)
- Patrick Coulombe
- Michael Smith Genome Sciences Centre, BC Cancer, 675 West 10th Avenue, Vancouver, BC, V5Z 1L3, Canada
- Department of Experimental Medicine, University of British Columbia, Vancouver, BC, V6T 2B5, Canada
| | - Grace Cole
- Michael Smith Genome Sciences Centre, BC Cancer, 675 West 10th Avenue, Vancouver, BC, V5Z 1L3, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, V6T 2B5, Canada
| | - Amanda Fentiman
- Michael Smith Genome Sciences Centre, BC Cancer, 675 West 10th Avenue, Vancouver, BC, V5Z 1L3, Canada
- Interdisciplinary Oncology Program, University of British Columbia, Vancouver, BC, V6T 2B5, Canada
| | - Jeremy D K Parker
- Michael Smith Genome Sciences Centre, BC Cancer, 675 West 10th Avenue, Vancouver, BC, V5Z 1L3, Canada
| | - Eric Yung
- Terry Fox Laboratory, BC Cancer, 675 West 10th Avenue, Vancouver, BC, V5Z 1L3, Canada
| | - Misha Bilenky
- Michael Smith Genome Sciences Centre, BC Cancer, 675 West 10th Avenue, Vancouver, BC, V5Z 1L3, Canada
| | - Lemlem Degefie
- Michael Smith Genome Sciences Centre, BC Cancer, 675 West 10th Avenue, Vancouver, BC, V5Z 1L3, Canada
| | - Patrick Lac
- Michael Smith Genome Sciences Centre, BC Cancer, 675 West 10th Avenue, Vancouver, BC, V5Z 1L3, Canada
| | - Maggie Y M Ling
- Michael Smith Genome Sciences Centre, BC Cancer, 675 West 10th Avenue, Vancouver, BC, V5Z 1L3, Canada
| | - Derek Tam
- Michael Smith Genome Sciences Centre, BC Cancer, 675 West 10th Avenue, Vancouver, BC, V5Z 1L3, Canada
| | - R Keith Humphries
- Terry Fox Laboratory, BC Cancer, 675 West 10th Avenue, Vancouver, BC, V5Z 1L3, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, V6T 2B5, Canada
| | - Aly Karsan
- Michael Smith Genome Sciences Centre, BC Cancer, 675 West 10th Avenue, Vancouver, BC, V5Z 1L3, Canada.
- Department of Experimental Medicine, University of British Columbia, Vancouver, BC, V6T 2B5, Canada.
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, V6T 2B5, Canada.
- Interdisciplinary Oncology Program, University of British Columbia, Vancouver, BC, V6T 2B5, Canada.
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Teefy BB, Lemus AJ, Adler A, Xu A, Bhala R, Hsu K, Benayoun BA. Widespread sex-dimorphism across single-cell transcriptomes of adult African turquoise killifish tissues. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.05.539616. [PMID: 37214847 PMCID: PMC10197525 DOI: 10.1101/2023.05.05.539616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The African turquoise killifish (Nothobranchius furzeri), the shortest-lived vertebrate that can be bred in captivity, is an emerging model organism to study vertebrate aging. Here we describe the first multi-tissue, single-cell gene expression atlas of female and male turquoise killifish tissues comprising immune and metabolic cells from the blood, kidney, liver, and spleen. We were able to annotate 22 distinct cell types, define associated marker genes, and infer differentiation trajectories. Using this dataset, we found pervasive sex-dimorphic gene expression across cell types, especially in the liver. Sex-dimorphic genes tended to be involved in processes related to lipid metabolism, and indeed, we observed clear differences in lipid storage in female vs. male turquoise killifish livers. Importantly, we use machine-learning to predict sex using single-cell gene expression in our atlas and identify potential transcriptional markers for molecular sex identity in this species. As proof-of-principle, we show that our atlas can be used to deconvolute existing liver bulk RNA-seq data in this species to obtain accurate estimates of cell type proportions across biological conditions. We believe that this single-cell atlas can be a resource to the community that could notably be leveraged to identify cell type-specific genes for cell type-specific expression in transgenic animals.
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Affiliation(s)
- Bryan B. Teefy
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
| | - Aaron J.J. Lemus
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
- Molecular and Computational Biology Department, USC Dornsife College of Letters, Arts and Sciences, Los Angeles, CA 90089, USA
| | - Ari Adler
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
| | - Alan Xu
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
- Quantitative & Computational Biology Department, USC Dornsife College of Letters, Arts and Sciences, Los Angeles, CA 90089, USA
| | - Rajyk Bhala
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
| | - Katelyn Hsu
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
- Molecular and Computational Biology Department, USC Dornsife College of Letters, Arts and Sciences, Los Angeles, CA 90089, USA
| | - Bérénice A. Benayoun
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
- Molecular and Computational Biology Department, USC Dornsife College of Letters, Arts and Sciences, Los Angeles, CA 90089, USA
- Biochemistry and Molecular Medicine Department, USC Keck School of Medicine, Los Angeles, CA 90089, USA
- USC Norris Comprehensive Cancer Center, Epigenetics and Gene Regulation, Los Angeles, CA 90089, USA
- USC Stem Cell Initiative, Los Angeles, CA 90089, USA
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28
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Lu Y, Cao Q, Yu Y, Sun Y, Jiang X, Li X. Pan-cancer analysis revealed H3K4me1 at bivalent promoters premarks DNA hypermethylation during tumor development and identified the regulatory role of DNA methylation in relation to histone modifications. BMC Genomics 2023; 24:235. [PMID: 37138231 PMCID: PMC10157937 DOI: 10.1186/s12864-023-09341-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 04/27/2023] [Indexed: 05/05/2023] Open
Abstract
BACKGROUND DNA hypermethylation at promoter CpG islands (CGIs) is a hallmark of cancers and could lead to dysregulation of gene expression in the development of cancers, however, its dynamics and regulatory mechanisms remain elusive. Bivalent genes, that direct development and differentiation of stem cells, are found to be frequent targets of hypermethylation in cancers. RESULTS Here we performed comprehensive analysis across multiple cancer types and identified that the decrease in H3K4me1 levels coincides with DNA hypermethylation at the bivalent promoter CGIs during tumorigenesis. Removal of DNA hypermethylation leads to increment of H3K4me1 at promoter CGIs with preference for bivalent genes. Nevertheless, the alteration of H3K4me1 by overexpressing or knockout LSD1, the demethylase of H3K4, doesn't change the level or pattern of DNA methylation. Moreover, LSD1 was found to regulate the expression of a bivalent gene OVOL2 to promote tumorigenesis. Knockdown of OVOL2 in LSD1 knockout HCT116 cells restored the cancer cell phenotype. CONCLUSION In summary, our work identified a universal indicator that can pre-mark DNA hypermethylation in cancer cells, and dissected the interplay between H3K4me1 and DNA hypermethylation in detail. Current study also reveals a novel mechanism underlying the oncogenic role of LSD1, providing clues for cancer therapies.
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Affiliation(s)
- Yang Lu
- School of Medicine, Shenzhen Campus of Sun Yat-Sen University, Shenzhen, China
| | - Qiang Cao
- School of Medicine, Shenzhen Campus of Sun Yat-Sen University, Shenzhen, China
| | - Yue Yu
- School of Medicine, Shenzhen Campus of Sun Yat-Sen University, Shenzhen, China
| | - Yazhou Sun
- The Seventh Affiliated Hospital of Sun Yat-Sen University, Shenzhen, China
| | - Xuan Jiang
- School of Medicine, Shenzhen Campus of Sun Yat-Sen University, Shenzhen, China.
| | - Xin Li
- School of Medicine, Shenzhen Campus of Sun Yat-Sen University, Shenzhen, China.
- Guangdong Provincial Key Laboratory of Digestive Cancer Research, The Seventh Affiliated Hospital of Sun Yat-Sen University, Shenzhen, China.
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29
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Weigel B, Tegethoff JF, Grieder SD, Lim B, Nagarajan B, Liu YC, Truberg J, Papageorgiou D, Adrian-Segarra JM, Schmidt LK, Kaspar J, Poisel E, Heinzelmann E, Saraswat M, Christ M, Arnold C, Ibarra IL, Campos J, Krijgsveld J, Monyer H, Zaugg JB, Acuna C, Mall M. MYT1L haploinsufficiency in human neurons and mice causes autism-associated phenotypes that can be reversed by genetic and pharmacologic intervention. Mol Psychiatry 2023; 28:2122-2135. [PMID: 36782060 PMCID: PMC10575775 DOI: 10.1038/s41380-023-01959-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 12/30/2022] [Accepted: 01/11/2023] [Indexed: 02/15/2023]
Abstract
MYT1L is an autism spectrum disorder (ASD)-associated transcription factor that is expressed in virtually all neurons throughout life. How MYT1L mutations cause neurological phenotypes and whether they can be targeted remains enigmatic. Here, we examine the effects of MYT1L deficiency in human neurons and mice. Mutant mice exhibit neurodevelopmental delays with thinner cortices, behavioural phenotypes, and gene expression changes that resemble those of ASD patients. MYT1L target genes, including WNT and NOTCH, are activated upon MYT1L depletion and their chemical inhibition can rescue delayed neurogenesis in vitro. MYT1L deficiency also causes upregulation of the main cardiac sodium channel, SCN5A, and neuronal hyperactivity, which could be restored by shRNA-mediated knockdown of SCN5A or MYT1L overexpression in postmitotic neurons. Acute application of the sodium channel blocker, lamotrigine, also rescued electrophysiological defects in vitro and behaviour phenotypes in vivo. Hence, MYT1L mutation causes both developmental and postmitotic neurological defects. However, acute intervention can normalise resulting electrophysiological and behavioural phenotypes in adulthood.
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Affiliation(s)
- Bettina Weigel
- Cell Fate Engineering and Disease Modeling Group, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, 69120, Heidelberg, Germany
- HITBR Hector Institute for Translational Brain Research gGmbH, 69120, Heidelberg, Germany
- Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, 68159, Mannheim, Germany
- Faculty of Biosciences, Heidelberg University, 69120, Heidelberg, Germany
| | - Jana F Tegethoff
- Cell Fate Engineering and Disease Modeling Group, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, 69120, Heidelberg, Germany
- HITBR Hector Institute for Translational Brain Research gGmbH, 69120, Heidelberg, Germany
- Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, 68159, Mannheim, Germany
- Faculty of Biosciences, Heidelberg University, 69120, Heidelberg, Germany
| | - Sarah D Grieder
- Cell Fate Engineering and Disease Modeling Group, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, 69120, Heidelberg, Germany
- HITBR Hector Institute for Translational Brain Research gGmbH, 69120, Heidelberg, Germany
- Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, 68159, Mannheim, Germany
| | - Bryce Lim
- Cell Fate Engineering and Disease Modeling Group, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, 69120, Heidelberg, Germany
- HITBR Hector Institute for Translational Brain Research gGmbH, 69120, Heidelberg, Germany
- Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, 68159, Mannheim, Germany
- Faculty of Biosciences, Heidelberg University, 69120, Heidelberg, Germany
| | - Bhuvaneswari Nagarajan
- Cell Fate Engineering and Disease Modeling Group, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, 69120, Heidelberg, Germany
- HITBR Hector Institute for Translational Brain Research gGmbH, 69120, Heidelberg, Germany
- Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, 68159, Mannheim, Germany
| | - Yu-Chao Liu
- Department of Clinical Neurobiology, University Hospital Heidelberg and DKFZ, Heidelberg, Germany
| | - Jule Truberg
- Cell Fate Engineering and Disease Modeling Group, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, 69120, Heidelberg, Germany
- HITBR Hector Institute for Translational Brain Research gGmbH, 69120, Heidelberg, Germany
- Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, 68159, Mannheim, Germany
- Faculty of Biosciences, Heidelberg University, 69120, Heidelberg, Germany
| | - Dimitris Papageorgiou
- Division of Proteomics of Stem Cells and Cancer, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
- Medical Faculty, Heidelberg University, 69120, Heidelberg, Germany
| | - Juan M Adrian-Segarra
- Cell Fate Engineering and Disease Modeling Group, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, 69120, Heidelberg, Germany
- HITBR Hector Institute for Translational Brain Research gGmbH, 69120, Heidelberg, Germany
- Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, 68159, Mannheim, Germany
| | - Laura K Schmidt
- Cell Fate Engineering and Disease Modeling Group, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, 69120, Heidelberg, Germany
- HITBR Hector Institute for Translational Brain Research gGmbH, 69120, Heidelberg, Germany
- Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, 68159, Mannheim, Germany
| | - Janina Kaspar
- Cell Fate Engineering and Disease Modeling Group, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, 69120, Heidelberg, Germany
- HITBR Hector Institute for Translational Brain Research gGmbH, 69120, Heidelberg, Germany
- Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, 68159, Mannheim, Germany
| | - Eric Poisel
- Cell Fate Engineering and Disease Modeling Group, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, 69120, Heidelberg, Germany
- HITBR Hector Institute for Translational Brain Research gGmbH, 69120, Heidelberg, Germany
- Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, 68159, Mannheim, Germany
| | - Elisa Heinzelmann
- Cell Fate Engineering and Disease Modeling Group, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, 69120, Heidelberg, Germany
- HITBR Hector Institute for Translational Brain Research gGmbH, 69120, Heidelberg, Germany
- Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, 68159, Mannheim, Germany
| | - Manu Saraswat
- Cell Fate Engineering and Disease Modeling Group, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, 69120, Heidelberg, Germany
- HITBR Hector Institute for Translational Brain Research gGmbH, 69120, Heidelberg, Germany
- Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, 68159, Mannheim, Germany
- Faculty of Biosciences, Heidelberg University, 69120, Heidelberg, Germany
| | - Marleen Christ
- Cell Fate Engineering and Disease Modeling Group, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, 69120, Heidelberg, Germany
- HITBR Hector Institute for Translational Brain Research gGmbH, 69120, Heidelberg, Germany
- Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, 68159, Mannheim, Germany
| | - Christian Arnold
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69115, Heidelberg, Germany
| | - Ignacio L Ibarra
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69115, Heidelberg, Germany
- Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764, Neuherberg, Germany
| | - Joaquin Campos
- Chica and Heinz Schaller Research Group, Institute for Anatomy and Cell Biology, Heidelberg University, 69120, Heidelberg, Germany
| | - Jeroen Krijgsveld
- Division of Proteomics of Stem Cells and Cancer, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
- Medical Faculty, Heidelberg University, 69120, Heidelberg, Germany
| | - Hannah Monyer
- Department of Clinical Neurobiology, University Hospital Heidelberg and DKFZ, Heidelberg, Germany
| | - Judith B Zaugg
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69115, Heidelberg, Germany
| | - Claudio Acuna
- Chica and Heinz Schaller Research Group, Institute for Anatomy and Cell Biology, Heidelberg University, 69120, Heidelberg, Germany
| | - Moritz Mall
- Cell Fate Engineering and Disease Modeling Group, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, 69120, Heidelberg, Germany.
- HITBR Hector Institute for Translational Brain Research gGmbH, 69120, Heidelberg, Germany.
- Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, 68159, Mannheim, Germany.
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Smirnov A, Melino G, Candi E. Gene expression in organoids: an expanding horizon. Biol Direct 2023; 18:11. [PMID: 36964575 PMCID: PMC10038780 DOI: 10.1186/s13062-023-00360-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 02/20/2023] [Indexed: 03/26/2023] Open
Abstract
Recent development of human three-dimensional organoid cultures has opened new doors and opportunities ranging from modelling human development in vitro to personalised cancer therapies. These new in vitro systems are opening new horizons to the classic understanding of human development and disease. However, the complexity and heterogeneity of these models requires cutting-edge techniques to capture and trace global changes in gene expression to enable identification of key players and uncover the underlying molecular mechanisms. Rapid development of sequencing approaches made possible global transcriptome analyses and epigenetic profiling. Despite challenges in organoid culture and handling, these techniques are now being adapted to embrace organoids derived from a wide range of human tissues. Here, we review current state-of-the-art multi-omics technologies, such as single-cell transcriptomics and chromatin accessibility assays, employed to study organoids as a model for development and a platform for precision medicine.
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Affiliation(s)
- Artem Smirnov
- Department of Experimental Medicine, Torvergata Oncoscience Research, University of Rome "Tor Vergata", Via Montpellier 1, 00133, Rome, Italy
| | - Gerry Melino
- Department of Experimental Medicine, Torvergata Oncoscience Research, University of Rome "Tor Vergata", Via Montpellier 1, 00133, Rome, Italy
| | - Eleonora Candi
- Department of Experimental Medicine, Torvergata Oncoscience Research, University of Rome "Tor Vergata", Via Montpellier 1, 00133, Rome, Italy.
- Biochemistry Laboratory, Istituto Dermopatico Immacolata (IDI-IRCCS), 00166, Rome, Italy.
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31
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Ghobashi AH, Vuong TT, Kimani JW, O'Hagan HM. Activation of AKT induces EZH2-mediated β-catenin trimethylation in colorectal cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.31.526429. [PMID: 36778289 PMCID: PMC9915619 DOI: 10.1101/2023.01.31.526429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Colorectal cancer (CRC) develops in part through the deregulation of different signaling pathways, including activation of the WNT/β-catenin and PI3K/AKT pathways. Enhancer of zeste homolog 2 (EZH2) is a lysine methyltransferase that is involved in regulating stem cell development and differentiation and is overexpressed in CRC. However, depending on the study EZH2 has been found to be both positively and negatively correlated with the survival of CRC patients suggesting that EZH2's role in CRC may be context specific. In this study, we explored how PI3K/AKT activation alters EZH2's role in CRC. We found that activation of AKT by PTEN knockdown or by hydrogen peroxide treatment induced EZH2 phosphorylation at serine 21. Phosphorylation of EZH2 resulted in EZH2-mediated methylation of β-catenin and an associated increased interaction between β-catenin, TCF1, and RNA polymerase II. AKT activation increased β-catenin's enrichment across the genome and EZH2 inhibition reduced this enrichment by reducing the methylation of β-catenin. Furthermore, PTEN knockdown increased the expression of epithelial-mesenchymal transition (EMT)-related genes, and somewhat unexpectedly EZH2 inhibition further increased the expression of these genes. Consistent with these findings, EZH2 inhibition enhanced the migratory phenotype of PTEN knockdown cells. Overall, we demonstrated that EZH2 modulates AKT-induced changes in gene expression through the AKT/EZH2/ β-catenin axis in CRC with active PI3K/AKT signaling. Therefore, it is important to consider the use of EZH2 inhibitors in CRC with caution as these inhibitors will inhibit EZH2-mediated methylation of histone and non-histone targets such as β-catenin, which can have tumor-promoting effects.
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Antitumor Effect of Demethylzeylasteral (T-96) on Triple-Negative Breast Cancer via LSD1-Mediate Epigenetic Mechanisms. Anal Cell Pathol (Amst) 2022; 2022:2522597. [PMID: 36276611 PMCID: PMC9581660 DOI: 10.1155/2022/2522597] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 09/12/2022] [Accepted: 09/29/2022] [Indexed: 11/18/2022] Open
Abstract
Background and Purpose. Breast cancer ranks first in the incidence of female tumors. Triple-negative breast cancer (TNBC), one type of breast cancer, is more aggressive and has a worse prognosis. Demethylzeylasteral (T-96) is isolated from Tripterygium wilfordii Hook F. Our previous study found that T96 could inhibit TNBC invasion via suppressing the canonical and noncanonical TGF-β signaling pathways. However, the antitumor effects and mechanisms of T-96 on TNBC have not been studied. This study is aimed at investigating the antitumor effect and mechanism of T-96 on breast cancer. Experimental approach. MTT assay, Live and Dead cell assay, and TUNEL were used to observe the antitumor effect of breast cancer cells treated with T-96. siRNA of LSD1, Co-IP, and molecular docking were used to explore the direct target and mechanism of T-96. Subcutaneous murine xenograft models were used to detect the efficacy of T-96 antitumor activity in vivo. Key Results. T-96 was more susceptible to inducing the apoptosis of highly metastatic TNBC cell lines (SUM-1315). An abnormal level of histone methylation is a crucial characteristic of metastatic cancer cells. LSD1 is a histone demethylase. We found that T-96 could significantly decrease the protein expression of LSD1, increase its target protein PTEN expression and enhance histone methylation. T-96 could also down-regulate the PI3K/AKT signaling pathway, which could be blocked by PTEN. Knockdown of LSD1 by siRNA blocked the pharmacological activity of T-96. And the molecular docking predicted T-96 processed affinity toward LSD1 through hydrogen bonding. Finally, T-96 was evaluated in a murine xenograft model of SUM-1315 cells. And T-96 could significantly inhibit tumor growth without showing marked toxicity. Conclusions & Implications. The results illustrated that T-96 exerted antitumor activity in highly metastatic TNBC by inactivating the LSD1 function.
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Sriramkumar S, Metcalfe TX, Lai T, Zong X, Fang F, O’Hagan HM, Nephew KP. Single-cell analysis of a high-grade serous ovarian cancer cell line reveals transcriptomic changes and cell subpopulations sensitive to epigenetic combination treatment. PLoS One 2022; 17:e0271584. [PMID: 35921335 PMCID: PMC9348737 DOI: 10.1371/journal.pone.0271584] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 07/01/2022] [Indexed: 11/19/2022] Open
Abstract
Ovarian cancer (OC) is a lethal gynecological malignancy with a five-year survival rate of only 46%. Development of resistance to platinum-based chemotherapy is a common cause of high mortality rates among OC patients. Tumor and transcriptomic heterogeneity are drivers of platinum resistance in OC. Platinum-based chemotherapy enriches for ovarian cancer stem cells (OCSCs) that are chemoresistant and contribute to disease recurrence and relapse. Studies examining the effect of different treatments on subpopulations of HGSOC cell lines are limited. Having previously demonstrated that combined treatment with an enhancer of zeste homolog 2 inhibitor (EZH2i) and a RAC1 GTPase inhibitor (RAC1i) inhibited survival of OCSCs, we investigated EZH2i and RAC1i combination effects on HGSOC heterogeneity using single cell RNA sequencing. We demonstrated that RAC1i reduced expression of stemness and early secretory marker genes, increased expression of an intermediate secretory marker gene and induced inflammatory gene expression. Importantly, RAC1i alone and in combination with EZH2i significantly reduced oxidative phosphorylation and upregulated Sirtuin signaling pathways. Altogether, we demonstrated that combining a RAC1i with an EZH2i promoted differentiation of subpopulations of HGSOC cells, supporting the future development of epigenetic drug combinations as therapeutic approaches in OC.
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Affiliation(s)
- Shruthi Sriramkumar
- Cell, Molecular and Cancer Biology Graduate Program and Medical Sciences Program, Indiana University School of Medicine, Bloomington, Indiana, United States of America
| | - Tara X. Metcalfe
- Cell, Molecular and Cancer Biology Graduate Program and Medical Sciences Program, Indiana University School of Medicine, Bloomington, Indiana, United States of America
| | - Tim Lai
- Luddy School of Informatics, Computing, and Engineering, Indiana University, Bloomington, Indiana, United States of America
- Department of Mathematics, Indiana University, Bloomington, Indiana, United States of America
| | - Xingyue Zong
- Cell, Molecular and Cancer Biology Graduate Program and Medical Sciences Program, Indiana University School of Medicine, Bloomington, Indiana, United States of America
| | - Fang Fang
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Heather M. O’Hagan
- Cell, Molecular and Cancer Biology Graduate Program and Medical Sciences Program, Indiana University School of Medicine, Bloomington, Indiana, United States of America
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
- Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indianapolis, Indiana, United States of America
- * E-mail: (KPN); (HMO)
| | - Kenneth P. Nephew
- Cell, Molecular and Cancer Biology Graduate Program and Medical Sciences Program, Indiana University School of Medicine, Bloomington, Indiana, United States of America
- Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indianapolis, Indiana, United States of America
- Department of Anatomy, Cell Biology and Physiology; Department of Obstetrics and Gynecology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
- * E-mail: (KPN); (HMO)
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Yang C, Li D, Zang S, Zhang L, Zhong Z, Zhou Y. Mechanisms of carcinogenic activity triggered by lysine-specific demethylase 1A. Front Pharmacol 2022; 13:955218. [PMID: 36059955 PMCID: PMC9428822 DOI: 10.3389/fphar.2022.955218] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Accepted: 06/29/2022] [Indexed: 12/23/2022] Open
Abstract
Epigenetics has emerged as a prime focus area in the field of cancer research. Lysine-specific demethylase 1A (LSD1), the first discovered histone demethylase, is mainly responsible for catalysing demethylation of histone 3 lysine 4 (H3K4) and H3K9 to activate or inhibit gene transcription. LSD1 is abnormally expressed in various cancers and participates in cancer proliferation, apoptosis, metastasis, invasion, drug resistance and other processes by interacting with regulatory factors. Therefore, it may serve as a potential therapeutic target for cancer. This review summarises the major oncogenic mechanisms mediated by LSD1 and provides a reference for developing novel and efficient anticancer strategies targeting LSD1.
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Affiliation(s)
- Chao Yang
- National Engineering Research Center for Marine Aquaculture, Institute of Innovation and Application, Zhejiang Ocean University, Zhoushan, China
| | - Dan Li
- State Key Laboratory of Southwestern Chinese Medicine Resource, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Shaohong Zang
- National Engineering Research Center for Marine Aquaculture, Institute of Innovation and Application, Zhejiang Ocean University, Zhoushan, China
| | - Lei Zhang
- Department of Chemical Engineering, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, ON, Canada
| | - Zhangfeng Zhong
- Macau Centre for Research and Development in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macao SAR, China
- *Correspondence: Zhangfeng Zhong, ; Yingtang Zhou,
| | - Yingtang Zhou
- National Engineering Research Center for Marine Aquaculture, Institute of Innovation and Application, Zhejiang Ocean University, Zhoushan, China
- *Correspondence: Zhangfeng Zhong, ; Yingtang Zhou,
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Malagraba G, Yarmohammadi M, Javed A, Barceló C, Rubio-Tomás T. The Role of LSD1 and LSD2 in Cancers of the Gastrointestinal System: An Update. Biomolecules 2022; 12:462. [PMID: 35327654 PMCID: PMC8946813 DOI: 10.3390/biom12030462] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 03/11/2022] [Accepted: 03/15/2022] [Indexed: 02/07/2023] Open
Abstract
Epigenetic mechanisms are known to play a key role in cancer progression. Specifically, histone methylation involves reversible post-translational modification of histones that govern chromatin structure remodelling, genomic imprinting, gene expression, DNA damage repair, and meiotic crossover recombination, among other chromatin-based activities. Demethylases are enzymes that catalyse the demethylation of their substrate using a flavin adenine dinucleotide-dependent amine oxidation process. Lysine-specific demethylase 1 (LSD1) and its homolog, lysine-specific demethylase 2 (LSD2), are overexpressed in a variety of human cancer types and, thus, regulate tumour progression. In this review, we focus on the literature from the last 5 years concerning the role of LSD1 and LSD2 in the main gastrointestinal cancers (i.e., gastric cancer, liver cancer, pancreatic cancer, and colorectal cancer).
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Affiliation(s)
- Gianluca Malagraba
- Translational Pancreatic Cancer Oncogenesis Group, Health Research Institute of the Balearic Islands (IdISBA), 07120 Palma de Mallorca, Spain;
| | - Mahdieh Yarmohammadi
- Central Tehran Branch, Department of Biology, Faculty of Sciences, Islamic Azad University, Tehran 1955847881, Iran;
| | - Aadil Javed
- Cancer Biology Laboratory, Department of Bioengineering, Faculty of Engineering, Ege University, Izmir 35040, Turkey;
| | - Carles Barceló
- Translational Pancreatic Cancer Oncogenesis Group, Health Research Institute of the Balearic Islands (IdISBA), 07120 Palma de Mallorca, Spain;
| | - Teresa Rubio-Tomás
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain
- School of Medicine, University of Crete, 70013 Herakleion, Crete, Greece
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