1
|
Van Wauwe J, Mahy A, Craps S, Ekhteraei-Tousi S, Vrancaert P, Kemps H, Dheedene W, Doñate Puertas R, Trenson S, Roderick HL, Beerens M, Luttun A. PRDM16 determines specification of ventricular cardiomyocytes by suppressing alternative cell fates. Life Sci Alliance 2024; 7:e202402719. [PMID: 39304345 PMCID: PMC11415600 DOI: 10.26508/lsa.202402719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 09/06/2024] [Accepted: 09/09/2024] [Indexed: 09/22/2024] Open
Abstract
PRDM16 is a transcription factor with histone methyltransferase activity expressed at the earliest stages of cardiac development. Pathogenic mutations in humans lead to cardiomyopathy, conduction abnormalities, and heart failure. PRDM16 is specifically expressed in ventricular but not atrial cardiomyocytes, and its expression declines postnatally. Because in other tissues PRDM16 is best known for its role in binary cell fate decisions, we hypothesized a similar decision-making function in cardiomyocytes. Here, we demonstrated that cardiomyocyte-specific deletion of Prdm16 during cardiac development results in contractile dysfunction and abnormal electrophysiology of the postnatal heart, resulting in premature death. By combined RNA+ATAC single-cell sequencing, we found that PRDM16 favors ventricular working cardiomyocyte identity, by opposing the activity of master regulators of ventricular conduction and atrial fate. Myocardial loss of PRDM16 during development resulted in hyperplasia of the (distal) ventricular conduction system. Hence, PRDM16 plays an indispensable role during cardiac development by driving ventricular working cardiomyocyte identity.
Collapse
Affiliation(s)
- Jore Van Wauwe
- https://ror.org/05f950310 Center for Molecular and Vascular Biology, Department of Cardiovascular Sciences, KU Leuven, Leuven, Belgium
| | - Alexia Mahy
- https://ror.org/05f950310 Center for Molecular and Vascular Biology, Department of Cardiovascular Sciences, KU Leuven, Leuven, Belgium
| | - Sander Craps
- https://ror.org/05f950310 Center for Molecular and Vascular Biology, Department of Cardiovascular Sciences, KU Leuven, Leuven, Belgium
| | - Samaneh Ekhteraei-Tousi
- https://ror.org/05f950310 Laboratory of Experimental Cardiology, Department of Cardiovascular Sciences, KU Leuven, Leuven, Belgium
| | - Pieter Vrancaert
- https://ror.org/05f950310 Center for Molecular and Vascular Biology, Department of Cardiovascular Sciences, KU Leuven, Leuven, Belgium
| | - Hannelore Kemps
- https://ror.org/05f950310 Center for Molecular and Vascular Biology, Department of Cardiovascular Sciences, KU Leuven, Leuven, Belgium
| | - Wouter Dheedene
- https://ror.org/05f950310 Center for Molecular and Vascular Biology, Department of Cardiovascular Sciences, KU Leuven, Leuven, Belgium
| | - Rosa Doñate Puertas
- https://ror.org/05f950310 Laboratory of Experimental Cardiology, Department of Cardiovascular Sciences, KU Leuven, Leuven, Belgium
| | - Sander Trenson
- https://ror.org/05f950310 Cardiology Lab, Department of Cardiovascular Sciences, KU Leuven, Leuven, Belgium
| | - H Llewelyn Roderick
- https://ror.org/05f950310 Laboratory of Experimental Cardiology, Department of Cardiovascular Sciences, KU Leuven, Leuven, Belgium
| | - Manu Beerens
- Institute for Clinical Chemistry and Laboratory Medicine, Medizinische Klinik und Poliklinik Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
- German Centre of Cardiovascular Research (DZHK), Partner Site Hamburg, Luebeck, Kiel, Hamburg, Germany
| | - Aernout Luttun
- https://ror.org/05f950310 Center for Molecular and Vascular Biology, Department of Cardiovascular Sciences, KU Leuven, Leuven, Belgium
| |
Collapse
|
2
|
Dhanasiri AK, Siciliani D, Kortner TM, Krogdahl Å. Epigenetic changes in pyloric caeca of Atlantic salmon fed diets containing increasing levels of lipids and choline. Epigenetics 2024; 19:2305079. [PMID: 38281164 PMCID: PMC10824149 DOI: 10.1080/15592294.2024.2305079] [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: 09/28/2023] [Accepted: 01/09/2024] [Indexed: 01/30/2024] Open
Abstract
An earlier study of ours investigating the effect of dietary lipid levels on the choline requirement of Atlantic salmon showed increasing severity of intestinal steatosis with increasing lipid levels. As choline is involved in epigenetic regulation by being the key methyl donor, pyloric caeca samples from the study were analysed for epigenetic effects of dietary lipid and choline levels. The diets varied in lipid levels between 16% and 28%, and choline levels between 1.9 and 2.3 g/kg. The diets were fed for 8 weeks to Atlantic salmon of 25 g of initial weight. Using reduced representation bisulfite sequencing (RRBS), this study revealed that increasing dietary lipid levels induced methylation differences in genes involved in membrane transport and signalling pathways, and in microRNAs important for the regulation of lipid homoeostasis. Increasing choline levels also affected genes involved in fatty acid biosynthesis and transport, lipolysis, and lipogenesis, as well as important immune genes. Our observations confirmed that choline is involved in epigenetic regulation in Atlantic salmon, as has been reported for higher vertebrates. This study showed the need for the inclusion of biomarkers of epigenetic processes in studies that must be conducted to define optimal choline levels in diets for Atlantic salmon.
Collapse
Affiliation(s)
- Anusha K.S. Dhanasiri
- Department of Paraclinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Daphne Siciliani
- Department of Paraclinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Trond M. Kortner
- Department of Paraclinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Åshild Krogdahl
- Department of Paraclinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences (NMBU), Ås, Norway
| |
Collapse
|
3
|
Lai J, Zhou Z, Hu K, Yu H, Su X, Niu X, Li H, Mao S. N6-methyladenosine methylation analysis of long noncoding RNAs and mRNAs in 5-FU-resistant colon cancer cells. Epigenetics 2024; 19:2298058. [PMID: 38145548 PMCID: PMC10761136 DOI: 10.1080/15592294.2023.2298058] [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: 07/03/2023] [Accepted: 12/13/2023] [Indexed: 12/27/2023] Open
Abstract
N6 methyladenosine (m6A), methylation at the sixth N atom of adenosine, is the most common and abundant modification in mammalian mRNAs and non-coding RNAs. Increasing evidence shows that the alteration of m6A modification level could regulate tumour proliferation, metastasis, self-renewal, and immune infiltration by regulating the related expression of tumour genes. However, the role of m6A modification in colorectal cancer (CRC) drug resistance is unclear. Here, MeRIP-seq and RNA-seq techniques were utilized to obtain mRNA, lncRNA expression, and their methylation profiles in 5-Fluorouracil (5-FU)-resistant colon cancer HCT-15 cells and control cells. In addition, we performed detailed bioinformatics analysis as well as in vitro experiments of lncRNA to explore the function of lncRNA with differential m6A in CRC progression and drug resistance. In this study, we obtained the m6A methylomic landscape of CRC cells and resistance group cells by MeRIP-seq and RNA-seq. We identified 3698 differential m6A peaks, of which 2224 were hypermethylated, and 1474 were hypomethylated. Among the lncRNAs, 60 were hypermethylated, and 38 were hypomethylated. GO and KEGG analysis annotations showed significant enrichment of endocytosis and MAPK signalling pathways. Moreover, knockdown of lncRNA ADIRF-AS1 and AL139035.1 promoted CRC proliferation and invasive metastasis in vitro. lncRNA- mRNA network showed that ADIRF-AS1 and AL139035.1 May play a key role in regulating drug resistance formation. We provide the first m6A methylation profile in 5-FU resistance CRC cells and analyse the functions of differential m6A-modified mRNAs and lncRNAs. Our results indicated that differential m6A RNAs were significantly associated with MAPK signalling and endocytosis after induction of 5-FU resistance. Knockdown of LncRNA ADIRF-AS1 and AL139035.1 promotes CRC progression and might be critical in regulating drug resistance formation.
Collapse
Affiliation(s)
- Jie Lai
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
- Department of General Surgery, Pingxiang People’s Hospital, Pingxiang, Jiangxi, China
| | - Zhiyong Zhou
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Kan Hu
- Department of General Surgery, Pingxiang People’s Hospital, Pingxiang, Jiangxi, China
| | - HongLong Yu
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Xingyao Su
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Xiaoqiang Niu
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Huizi Li
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Shengxun Mao
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| |
Collapse
|
4
|
Santana LS, Reyes A, Hoersch S, Ferrero E, Kolter C, Gaulis S, Steinhauser S. Benchmarking tools for transcription factor prioritization. Comput Struct Biotechnol J 2024; 23:2190-2199. [PMID: 38817966 PMCID: PMC11137382 DOI: 10.1016/j.csbj.2024.05.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Accepted: 05/09/2024] [Indexed: 06/01/2024] Open
Abstract
Spatiotemporal regulation of gene expression is controlled by transcription factor (TF) binding to regulatory elements, resulting in a plethora of cell types and cell states from the same genetic information. Due to the importance of regulatory elements, various sequencing methods have been developed to localise them in genomes, for example using ChIP-seq profiling of the histone mark H3K27ac that marks active regulatory regions. Moreover, multiple tools have been developed to predict TF binding to these regulatory elements based on DNA sequence. As altered gene expression is a hallmark of disease phenotypes, identifying TFs driving such gene expression programs is critical for the identification of novel drug targets. In this study, we curated 84 chromatin profiling experiments (H3K27ac ChIP-seq) where TFs were perturbed through e.g., genetic knockout or overexpression. We ran nine published tools to prioritize TFs using these real-world datasets and evaluated the performance of the methods in identifying the perturbed TFs. This allowed the nomination of three frontrunner tools, namely RcisTarget, MEIRLOP and monaLisa. Our analyses revealed opportunities and commonalities of tools that will help to guide further improvements and developments in the field.
Collapse
Affiliation(s)
| | | | | | | | | | - Swann Gaulis
- Novartis Biomedical Research, Basel, Switzerland
| | | |
Collapse
|
5
|
Liu X, Li J, Zhu L, Huang J, Zhang Q, Wang J, Xie J, Dong Q, Zou Z, Huang G, Gu Q, Wang J, Li J. Mechanistic insights into zinc oxide nanoparticles induced embryotoxicity via H3K9me3 modulation. Biomaterials 2024; 311:122679. [PMID: 38943823 DOI: 10.1016/j.biomaterials.2024.122679] [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: 02/08/2024] [Revised: 06/05/2024] [Accepted: 06/23/2024] [Indexed: 07/01/2024]
Abstract
The widespread application of nanoparticles (NPs) in various fields has raised health concerns, especially in reproductive health. Our research has shown zinc oxide nanoparticles (ZnONPs) exhibit the most significant toxicity to pre-implantation embryos in mice compared to other common NPs. In patients undergoing assisted reproduction technology (ART), a significant negative correlation was observed between Zn concentration and clinical outcomes. Therefore, this study explores the impact of ZnONPs exposure on pre-implantation embryonic development and its underlying mechanisms. We revealed that both in vivo and in vitro exposure to ZnONPs impairs pre-implantation embryonic development. Moreover, ZnONPs were found to reduce the pluripotency of mouse embryonic stem cells (mESCs), as evidenced by teratoma and diploid chimera assays. Employing multi-omics approaches, including RNA-Seq, CUT&Tag, and ATAC-seq, the embryotoxicity mechanisms of ZnONPs were elucidated. The findings indicate that ZnONPs elevate H3K9me3 levels, leading to increased heterochromatin and consequent inhibition of gene expression related to development and pluripotency. Notably, Chaetocin, a H3K9me3 inhibitor, sucessfully reversed the embryotoxicity effects induced by ZnONPs. Additionally, the direct interaction between ZnONPs and H3K9me3 was verified through pull-down and immunoprecipitation assays. Collectively, these findings offer new insights into the epigenetic mechanisms of ZnONPs toxicity, enhancing our understanding of their impact on human reproductive health.
Collapse
Affiliation(s)
- Xuemei Liu
- Chongqing Key Laboratory of Human Embryo Engineering and Precision Medicine, Center for Reproductive Medicine, Women and Children's Hospital of Chongqing Medical University, Chongqing, China; Chongqing Clinical Research Center for Reproductive Medicine, Chongqing Health Center for Women and Children, Chongqing, China
| | - Jie Li
- Molecular Biology Laboratory of Respiratory Disease, Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing, China
| | - Ling Zhu
- Chongqing Key Laboratory of Human Embryo Engineering and Precision Medicine, Center for Reproductive Medicine, Women and Children's Hospital of Chongqing Medical University, Chongqing, China; Chongqing Clinical Research Center for Reproductive Medicine, Chongqing Health Center for Women and Children, Chongqing, China
| | - Jiayu Huang
- Reproductive Medicine Center, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Qi Zhang
- Chongqing Key Laboratory of Human Embryo Engineering and Precision Medicine, Center for Reproductive Medicine, Women and Children's Hospital of Chongqing Medical University, Chongqing, China; Chongqing Clinical Research Center for Reproductive Medicine, Chongqing Health Center for Women and Children, Chongqing, China
| | - Jianwu Wang
- College of Life Science, Northeast Agricultural University, Harbin, China
| | - Juan Xie
- Chongqing Key Laboratory of Human Embryo Engineering and Precision Medicine, Center for Reproductive Medicine, Women and Children's Hospital of Chongqing Medical University, Chongqing, China; Chongqing Clinical Research Center for Reproductive Medicine, Chongqing Health Center for Women and Children, Chongqing, China
| | - Qiang Dong
- Chongqing Key Laboratory of Human Embryo Engineering and Precision Medicine, Center for Reproductive Medicine, Women and Children's Hospital of Chongqing Medical University, Chongqing, China; Chongqing Clinical Research Center for Reproductive Medicine, Chongqing Health Center for Women and Children, Chongqing, China
| | - Zhen Zou
- Molecular Biology Laboratory of Respiratory Disease, Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing, China
| | - Guoning Huang
- Chongqing Key Laboratory of Human Embryo Engineering and Precision Medicine, Center for Reproductive Medicine, Women and Children's Hospital of Chongqing Medical University, Chongqing, China; Chongqing Clinical Research Center for Reproductive Medicine, Chongqing Health Center for Women and Children, Chongqing, China.
| | - Qi Gu
- State Key Laboratory of Membrane Biology and the State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
| | - Jianyu Wang
- Molecular Biology Laboratory of Respiratory Disease, Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing, China.
| | - Jingyu Li
- Chongqing Key Laboratory of Human Embryo Engineering and Precision Medicine, Center for Reproductive Medicine, Women and Children's Hospital of Chongqing Medical University, Chongqing, China; Chongqing Clinical Research Center for Reproductive Medicine, Chongqing Health Center for Women and Children, Chongqing, China.
| |
Collapse
|
6
|
Madrid A, Koueik J, Papale LA, Chebel R, Renteria I, Cannon E, Hogan KJ, Alisch RS, Iskandar BJ. Folate-mediated transgenerational inheritance of sperm DNA methylation patterns correlate with spinal axon regeneration. Epigenetics 2024; 19:2380930. [PMID: 39066680 PMCID: PMC11285217 DOI: 10.1080/15592294.2024.2380930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2024] [Revised: 06/01/2024] [Accepted: 07/11/2024] [Indexed: 07/30/2024] Open
Abstract
In mammals, the molecular mechanisms underlying transgenerational inheritance of phenotypic traits in serial generations of progeny after ancestral environmental exposures, without variation in DNA sequence, remain elusive. We've recently described transmission of a beneficial trait in rats and mice, in which F0 supplementation of methyl donors, including folic acid, generates enhanced axon regeneration after sharp spinal cord injury in untreated F1 to F3 progeny linked to differential DNA methylation levels in spinal cord tissue. To test whether the transgenerational effect of folic acid is transmitted via the germline, we performed whole-genome methylation sequencing on sperm DNA from F0 mice treated with either folic acid or vehicle control, and their F1, F2, and F3 untreated progeny. Transgenerational differentially methylated regions (DMRs) are observed in each consecutive generation and distinguish folic acid from untreated lineages, predominate outside of CpG islands and in regions of the genome that regulate gene expression, including promoters, and overlap at both the differentially methylated position (DMP) and gene levels. These findings indicate that molecular changes between generations are caused by ancestral folate supplementation. In addition, 29,719 DMPs exhibit serial increases or decreases in DNA methylation levels in successive generations of untreated offspring, correlating with a serial increase in the phenotype across generations, consistent with a 'wash-in' effect. Sibship-specific DMPs annotate to genes that participate in axon- and synapse-related pathways.
Collapse
Affiliation(s)
- Andy Madrid
- Department of Neurological Surgery, University of Wisconsin School of Medicine and Public Health, Madison, USA
| | - Joyce Koueik
- Department of Neurological Surgery, University of Wisconsin School of Medicine and Public Health, Madison, USA
| | - Ligia A. Papale
- Department of Neurological Surgery, University of Wisconsin School of Medicine and Public Health, Madison, USA
| | - Roy Chebel
- Department of Neurological Surgery, University of Wisconsin School of Medicine and Public Health, Madison, USA
| | - Isabelle Renteria
- Department of Neurological Surgery, University of Wisconsin School of Medicine and Public Health, Madison, USA
| | - Emily Cannon
- Department of Neurological Surgery, University of Wisconsin School of Medicine and Public Health, Madison, USA
| | - Kirk J. Hogan
- Department of Anesthesiology, University of Wisconsin School of Medicine and Public Health, Madison, USA
| | - Reid S. Alisch
- Department of Neurological Surgery, University of Wisconsin School of Medicine and Public Health, Madison, USA
| | - Bermans J. Iskandar
- Department of Neurological Surgery, University of Wisconsin School of Medicine and Public Health, Madison, USA
| |
Collapse
|
7
|
Stoler-Barak L, Schmiedel D, Sarusi-Portuguez A, Rogel A, Blecher-Gonen R, Haimon Z, Stopka T, Shulman Z. SMARCA5-mediated chromatin remodeling is required for germinal center formation. J Exp Med 2024; 221:e20240433. [PMID: 39297882 PMCID: PMC11413417 DOI: 10.1084/jem.20240433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 06/19/2024] [Accepted: 08/15/2024] [Indexed: 09/26/2024] Open
Abstract
The establishment of long-lasting immunity against pathogens is facilitated by the germinal center (GC) reaction, during which B cells increase their antibody affinity and differentiate into antibody-secreting cells (ASC) and memory cells. These events involve modifications in chromatin packaging that orchestrate the profound restructuring of gene expression networks that determine cell fate. While several chromatin remodelers were implicated in lymphocyte functions, less is known about SMARCA5. Here, using ribosomal pull-down for analyzing translated genes in GC B cells, coupled with functional experiments in mice, we identified SMARCA5 as a key chromatin remodeler in B cells. While the naive B cell compartment remained unaffected following conditional depletion of Smarca5, effective proliferation during B cell activation, immunoglobulin class switching, and as a result GC formation and ASC differentiation were impaired. Single-cell multiomic sequencing analyses revealed that SMARCA5 is crucial for facilitating the transcriptional modifications and genomic accessibility of genes that support B cell activation and differentiation. These findings offer novel insights into the functions of SMARCA5, which can be targeted in various human pathologies.
Collapse
Affiliation(s)
- Liat Stoler-Barak
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Dominik Schmiedel
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Avital Sarusi-Portuguez
- Mantoux Bioinformatics Institute of the Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Adi Rogel
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Ronnie Blecher-Gonen
- The Crown Genomics Institute of the Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Zhana Haimon
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Tomas Stopka
- BIOCEV, First Faculty of Medicine, Charles University, Vestec, Czech Republic
| | - Ziv Shulman
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel
| |
Collapse
|
8
|
He Q, Zhang Y, Li W, Chen S, Xiong J, Zhao R, Yuan K, Hu Q, Liu S, Gao G, Bedford MT, Tang DG, Xu B, Zou C, Zhang D. Inhibition of PRMT5 moderately suppresses prostate cancer growth in vivo but enhances its response to immunotherapy. Cancer Lett 2024; 602:217214. [PMID: 39218291 DOI: 10.1016/j.canlet.2024.217214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 08/11/2024] [Accepted: 08/28/2024] [Indexed: 09/04/2024]
Abstract
Protein arginine methylation is a common post-translational modification (PTM) catalyzed by nine protein arginine methyltransferases (PRMTs). As the major symmetric arginine methyltransferase that methylates both histone and non-histone substrates, PRMT5 plays key roles in a number of biological processes critical for development and tumorigenesis. PRMT5 overexpression has been reported in multiple cancer types including prostate cancer (PCa), but the exact biological and mechanistic understanding of PRMT5 in aggressive PCa remains ill-defined. Here, we show that PRMT5 is upregulated in PCa, correlates with worse patient survival, promotes corrupted RNA splicing, and functionally cooperates with an array of pro-tumorigenic pathways to enhance oncogenesis. PRMT5 inhibition via either genetic knockdown or pharmacological inhibition reduces stemness with paralleled differentiation and arrests cell cycle progression without causing appreciable apoptosis. Strikingly, the severity of antitumor effect of PRMT5 inhibition correlates with disease aggressiveness, with AR+ PCa being less affected. Molecular characterization pinpoints MYC, but not (or at least to a lesser degree) AR, as the main partner of PRMT5 to form a positive feedback loop to exacerbate malignancy in both AR+ and AR- PCa cells. Inspired by the surprising finding that PRMT5 negatively correlates with tumor immune infiltration and transcriptionally suppresses an immune-gene program, we further show that although PRMT5 inhibitor (PRMT5i) EPZ015666 or anti-PD-1 immunotherapy alone exhibits limited antitumor effects, combination of PRMT5i with anti-PD-1 displays superior efficacy in inhibiting castration-resistant PCa (CRPC) in vivo. Finally, to expand the potential use of PRMT5i through a synthetic lethality concept, we also perform a global CRISPR/Cas9 knockout screen to unravel that many clinical-grade drugs of known oncogenic pathways can be repurposed to target CRPC when used in combination with PRMT5i at low doses. Collectively, our findings establish a rationale to exploit PRMT5i in combination with immunotherapy or other targeted therapies to treat aggressive PCa.
Collapse
Affiliation(s)
- Qinju He
- Affiliated Hospital of Hunan University, School of Biomedical Sciences, Hunan University, Changsha, China; Hunan Key Laboratory of Animal Models and Molecular Medicine, Hunan University, Changsha, 410082, China
| | - Yuanzhen Zhang
- Affiliated Hospital of Hunan University, School of Biomedical Sciences, Hunan University, Changsha, China; Hunan Key Laboratory of Animal Models and Molecular Medicine, Hunan University, Changsha, 410082, China
| | - Wenchao Li
- Department of Urology, Affiliated Zhongda Hospital of Southeast University, Nanjing, 210009, China
| | - Saisai Chen
- Department of Urology, Affiliated Zhongda Hospital of Southeast University, Nanjing, 210009, China
| | - Jiangling Xiong
- Hunan Key Laboratory of Animal Models and Molecular Medicine, Hunan University, Changsha, 410082, China
| | - Ruizhe Zhao
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA; Current Address: Department of Urology, First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Kai Yuan
- Hunan Key Laboratory of Molecular Precision Medicine, Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, 410000, China
| | - Qiang Hu
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, 14263, New York, USA
| | - Song Liu
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, 14263, New York, USA
| | - Guozhen Gao
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Mark T Bedford
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Dean G Tang
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
| | - Bin Xu
- Department of Urology, Affiliated Zhongda Hospital of Southeast University, Nanjing, 210009, China.
| | - Cheng Zou
- Affiliated Hospital of Hunan University, School of Biomedical Sciences, Hunan University, Changsha, China; Hunan Key Laboratory of Animal Models and Molecular Medicine, Hunan University, Changsha, 410082, China; Shenzhen Research Institute, Hunan University, Shenzhen, 518000, China.
| | - Dingxiao Zhang
- Affiliated Hospital of Hunan University, School of Biomedical Sciences, Hunan University, Changsha, China; Hunan Key Laboratory of Animal Models and Molecular Medicine, Hunan University, Changsha, 410082, China; Shenzhen Research Institute, Hunan University, Shenzhen, 518000, China.
| |
Collapse
|
9
|
Davis E, Avniel-Polak S, Abu-Kamel S, Antman I, Saadoun T, Brim C, Jumaa M, Maron Y, Maimon O, Bel-Ange A, Atlan K, Tzur T, Abu Akar F, Wald O, Izhar U, Hecht M, Grozinsky-Glasberg S, Drier Y. Enhancer landscape of lung neuroendocrine tumors reveals regulatory and developmental signatures with potential theranostic implications. Proc Natl Acad Sci U S A 2024; 121:e2405001121. [PMID: 39361648 DOI: 10.1073/pnas.2405001121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Accepted: 09/05/2024] [Indexed: 10/05/2024] Open
Abstract
Well-differentiated low-grade lung neuroendocrine tumors (lung carcinoids or LNETs) are histopathologically classified as typical and atypical LNETs, but each subtype is still heterogeneous at both the molecular level and its clinical manifestation. Here, we report genome-wide profiles of primary LNETs' cis-regulatory elements by H3K27ac ChIP-seq with matching RNA-seq profiles. Analysis of these regulatory landscapes revealed three regulatory subtypes, independent of the typical/atypical classification. We identified unique differentiation signals that delineate each subtype. The "proneuronal" subtype emerges under the influence of ASCL1, SOX4, and TCF4 transcription factors, embodying a pronounced proneuronal signature. The "luminal-like" subtype is characterized by gain of acetylation at markers of luminal cells and GATA2 activation and loss of LRP5 and OTP. The "HNF+" subtype is characterized by a robust enhancer landscape driven by HNF1A, HNF4A, and FOXA3, with notable acetylation and expression of FGF signaling genes, especially FGFR3 and FGFR4, pivotal components of the FGF pathway. Our findings not only deepen the understanding of LNETs' regulatory and developmental diversity but also spotlight the HNF+ subtype's reliance on FGFR signaling. We demonstrate that targeting this pathway with FGF inhibitors curtails tumor growth both in vitro and in xenograft models, unveiling a potential vulnerability and paving the way for targeted therapies. Overall, our work provides an important resource for studying LNETs to reveal regulatory networks, differentiation signals, and therapeutically relevant dependencies.
Collapse
Affiliation(s)
- Ester Davis
- The Lautenberg Center for Immunology and Cancer Research, Institute for Medical Research Israel-Canada, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Shani Avniel-Polak
- The Neuroendocrine Tumor Unit, European Neuroendocrine Tumor Society Center of Excellence, Division of Internal Medicine, Hadassah Medical Center, Jerusalem 9112102, Israel
| | - Shahd Abu-Kamel
- The Lautenberg Center for Immunology and Cancer Research, Institute for Medical Research Israel-Canada, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Israel Antman
- The Lautenberg Center for Immunology and Cancer Research, Institute for Medical Research Israel-Canada, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Tsipora Saadoun
- The Lautenberg Center for Immunology and Cancer Research, Institute for Medical Research Israel-Canada, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Chava Brim
- The Lautenberg Center for Immunology and Cancer Research, Institute for Medical Research Israel-Canada, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Mohammad Jumaa
- Department of Pathology, Hadassah Medical Center, Jerusalem 9112102, Israel
| | - Yariv Maron
- Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Ofra Maimon
- Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 9112102, Israel
- Department of Oncology, Hadassah Medical Center, Jerusalem 9112102, Israel
| | - Anat Bel-Ange
- The Neuroendocrine Tumor Unit, European Neuroendocrine Tumor Society Center of Excellence, Division of Internal Medicine, Hadassah Medical Center, Jerusalem 9112102, Israel
| | - Karine Atlan
- Department of Pathology, Hadassah Medical Center, Jerusalem 9112102, Israel
- Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Tomer Tzur
- Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 9112102, Israel
- Department of Plastic and Reconstructive Surgery, Hadassah Medical Center, Jerusalem 9112102, Israel
| | - Firas Abu Akar
- The Edith Wolfson Medical Center, Holon 5822012, Israel
- Department of General Surgery, Faculty of Medicine, Al-Quds University, East Jerusalem, Palestinian Territories
- Department of Thoracic Surgery, Affiliated to the Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Ori Wald
- Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 9112102, Israel
- Department of General Surgery, Faculty of Medicine, Al-Quds University, East Jerusalem, Palestinian Territories
| | - Uzi Izhar
- Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 9112102, Israel
- Department of General Surgery, Faculty of Medicine, Al-Quds University, East Jerusalem, Palestinian Territories
| | - Merav Hecht
- The Lautenberg Center for Immunology and Cancer Research, Institute for Medical Research Israel-Canada, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Simona Grozinsky-Glasberg
- The Neuroendocrine Tumor Unit, European Neuroendocrine Tumor Society Center of Excellence, Division of Internal Medicine, Hadassah Medical Center, Jerusalem 9112102, Israel
- Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Yotam Drier
- The Lautenberg Center for Immunology and Cancer Research, Institute for Medical Research Israel-Canada, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| |
Collapse
|
10
|
Fogarty EA, Buchert EM, Ma Y, Nicely AB, Buttitta LA. Transcriptional repression and enhancer decommissioning silence cell cycle genes in postmitotic tissues. G3 (BETHESDA, MD.) 2024; 14:jkae203. [PMID: 39171889 DOI: 10.1093/g3journal/jkae203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Accepted: 08/16/2024] [Indexed: 08/23/2024]
Abstract
The mechanisms that maintain a non-cycling status in postmitotic tissues are not well understood. Many cell cycle genes have promoters and enhancers that remain accessible even when cells are terminally differentiated and in a non-cycling state, suggesting their repression must be maintained long term. In contrast, enhancer decommissioning has been observed for rate-limiting cell cycle genes in the Drosophila wing, a tissue where the cells die soon after eclosion, but it has been unclear if this also occurs in other contexts of terminal differentiation. In this study, we show that enhancer decommissioning also occurs at specific, rate-limiting cell cycle genes in the long-lived tissues of the Drosophila eye and brain, and we propose this loss of chromatin accessibility may help maintain a robust postmitotic state. We examined the decommissioned enhancers at specific rate-limiting cell cycle genes and showed that they encode for dynamic temporal and spatial expression patterns that include shared, as well as tissue-specific elements, resulting in broad gene expression with developmentally controlled temporal regulation. We extend our analysis to cell cycle gene expression and chromatin accessibility in the mammalian retina using a published dataset and find that the principles of cell cycle gene regulation identified in terminally differentiating Drosophila tissues are conserved in the differentiating mammalian retina. We propose a robust, non-cycling status is maintained in long-lived postmitotic tissues through a combination of stable repression at most cell cycle genes, alongside enhancer decommissioning at specific rate-limiting cell cycle genes.
Collapse
Affiliation(s)
- Elizabeth A Fogarty
- Molecular, Cellular and Developmental Biology, University of Michigan, 1105 N. University Ave., Ann Arbor, MI 48109, USA
| | - Elli M Buchert
- Molecular, Cellular and Developmental Biology, University of Michigan, 1105 N. University Ave., Ann Arbor, MI 48109, USA
| | - Yiqin Ma
- Molecular, Cellular and Developmental Biology, University of Michigan, 1105 N. University Ave., Ann Arbor, MI 48109, USA
| | - Ava B Nicely
- Molecular, Cellular and Developmental Biology, University of Michigan, 1105 N. University Ave., Ann Arbor, MI 48109, USA
| | - Laura A Buttitta
- Molecular, Cellular and Developmental Biology, University of Michigan, 1105 N. University Ave., Ann Arbor, MI 48109, USA
| |
Collapse
|
11
|
Angelis N, Baulies A, Hubl F, Kucharska A, Kelly G, Llorian M, Boeing S, Li VSW. Loss of ARID3A perturbs intestinal epithelial proliferation-differentiation ratio and regeneration. J Exp Med 2024; 221:e20232279. [PMID: 39150450 PMCID: PMC11329776 DOI: 10.1084/jem.20232279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 06/08/2024] [Accepted: 07/19/2024] [Indexed: 08/17/2024] Open
Abstract
Intestinal stem cells at the crypt divide and give rise to progenitor cells that proliferate and differentiate into various mature cell types in the transit-amplifying (TA) zone. Here, we showed that the transcription factor ARID3A regulates intestinal epithelial cell proliferation and differentiation at the TA progenitors. ARID3A forms an expression gradient from the villus tip to the upper crypt mediated by TGF-β and WNT. Intestinal-specific deletion of Arid3a reduces crypt proliferation, predominantly in TA cells. Bulk and single-cell transcriptomic analysis shows increased enterocyte and reduced secretory differentiation in the Arid3a cKO intestine, accompanied by enriched upper-villus gene signatures of both cell lineages. We find that the enhanced epithelial differentiation in the Arid3a-deficient intestine is caused by increased binding and transcription of HNF1 and HNF4. Finally, we show that loss of Arid3a impairs irradiation-induced regeneration with sustained cell death and reprogramming. Our findings imply that Arid3a functions to fine-tune the proliferation-differentiation dynamics at the TA progenitors, which are essential for injury-induced regeneration.
Collapse
Affiliation(s)
- Nikolaos Angelis
- Stem Cell and Cancer Biology Laboratory, The Francis Crick Institute , London, UK
| | - Anna Baulies
- Stem Cell and Cancer Biology Laboratory, The Francis Crick Institute , London, UK
| | - Florian Hubl
- Stem Cell and Cancer Biology Laboratory, The Francis Crick Institute , London, UK
| | - Anna Kucharska
- Stem Cell and Cancer Biology Laboratory, The Francis Crick Institute , London, UK
| | - Gavin Kelly
- Bioinformatics and Biostatistics Science Technology Platform, The Francis Crick Institute , London, UK
| | - Miriam Llorian
- Bioinformatics and Biostatistics Science Technology Platform, The Francis Crick Institute , London, UK
| | - Stefan Boeing
- Bioinformatics and Biostatistics Science Technology Platform, The Francis Crick Institute , London, UK
| | - Vivian S W Li
- Stem Cell and Cancer Biology Laboratory, The Francis Crick Institute , London, UK
| |
Collapse
|
12
|
Portelinha A, Wang S, Parsa S, Jiang M, Gorelick AN, Mohanty S, Sharma S, de Stanchina E, Berishaj M, Zhao C, Heward J, Aryal NK, Tavana O, Wen J, Fitzgibbon J, Dogan A, Younes A, Melnick AM, Wendel HG. SETD1B mutations confer apoptosis resistance and BCL2 independence in B cell lymphoma. J Exp Med 2024; 221:e20231143. [PMID: 39235528 PMCID: PMC11380151 DOI: 10.1084/jem.20231143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 03/05/2024] [Accepted: 08/02/2024] [Indexed: 09/06/2024] Open
Abstract
The translocation t(14;18) activates BCL2 and is considered the initiating genetic lesion in most follicular lymphomas (FL). Surprisingly, FL patients fail to respond to the BCL2 inhibitor, Venetoclax. We show that mutations and deletions affecting the histone lysine methyltransferase SETD1B (KMT2G) occur in 7% of FLs and 16% of diffuse large B cell lymphomas (DLBCL). Deficiency in SETD1B confers striking resistance to Venetoclax and an experimental MCL-1 inhibitor. SETD1B also acts as a tumor suppressor and cooperates with the loss of KMT2D in lymphoma development in vivo. Consistently, loss of SETD1B in human lymphomas typically coincides with loss of KMT2D. Mechanistically, SETD1B is required for the expression of several proapoptotic BCL2 family proteins. Conversely, inhibitors of the KDM5 histone H3K4 demethylases restore BIM and BIK expression and synergize with Venetoclax in SETD1B-deficient lymphomas. These results establish SETD1B as an epigenetic regulator of cell death and reveal a pharmacological strategy to augment Venetoclax sensitivity in lymphoma.
Collapse
MESH Headings
- Animals
- Humans
- Mice
- Apoptosis/genetics
- Bridged Bicyclo Compounds, Heterocyclic/pharmacology
- Cell Line, Tumor
- DNA-Binding Proteins/genetics
- DNA-Binding Proteins/metabolism
- Drug Resistance, Neoplasm/genetics
- Histone-Lysine N-Methyltransferase/genetics
- Histone-Lysine N-Methyltransferase/metabolism
- Lymphoma, B-Cell/genetics
- Lymphoma, B-Cell/pathology
- Lymphoma, B-Cell/metabolism
- Lymphoma, Large B-Cell, Diffuse/genetics
- Lymphoma, Large B-Cell, Diffuse/pathology
- Lymphoma, Large B-Cell, Diffuse/metabolism
- Mutation
- Neoplasm Proteins/genetics
- Neoplasm Proteins/metabolism
- Proto-Oncogene Proteins c-bcl-2/genetics
- Proto-Oncogene Proteins c-bcl-2/metabolism
- Sulfonamides/pharmacology
Collapse
Affiliation(s)
- Ana Portelinha
- Cancer Biology and Genetics Program, Memorial Sloan-Kettering Cancer Center , New York, NY, USA
| | - Shenqiu Wang
- Cancer Biology and Genetics Program, Memorial Sloan-Kettering Cancer Center , New York, NY, USA
| | - Sara Parsa
- Cancer Biology and Genetics Program, Memorial Sloan-Kettering Cancer Center , New York, NY, USA
| | - Man Jiang
- Cancer Biology and Genetics Program, Memorial Sloan-Kettering Cancer Center , New York, NY, USA
| | - Alexander N Gorelick
- Human Oncology and Pathogenesis Program, Memorial Sloan-Kettering Cancer Center , New York, NY, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Sagarajit Mohanty
- Cancer Biology and Genetics Program, Memorial Sloan-Kettering Cancer Center , New York, NY, USA
| | - Soumya Sharma
- Cancer Biology and Genetics Program, Memorial Sloan-Kettering Cancer Center , New York, NY, USA
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Elisa de Stanchina
- Antitumor Assessment Core, Memorial Sloan Kettering Cancer Center , New York, NY, USA
| | - Marjan Berishaj
- Cancer Biology and Genetics Program, Memorial Sloan-Kettering Cancer Center , New York, NY, USA
| | - Chunying Zhao
- Cancer Biology and Genetics Program, Memorial Sloan-Kettering Cancer Center , New York, NY, USA
| | | | - Neeraj K Aryal
- Bioscience, Early Oncology R&D, AstraZeneca , Waltham, MA, USA
| | - Omid Tavana
- Bioscience, Early Oncology R&D, AstraZeneca , Waltham, MA, USA
| | - Jiayu Wen
- Division of Genome Sciences and Cancer, The John Curtin School of Medical Research, The Australian National University and Australian Research Council Centre of Excellence for the Mathematical Analysis of Cellular Systems, Canberra, Australia
| | | | - Ahmet Dogan
- Departments of Pathology and Laboratory Medicine, Hematopathology Service, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Anas Younes
- Haematology R&D, AstraZeneca , New York, NY, USA
| | - Ari M Melnick
- Hematology and Oncology Division, Medicine Department, New York Presbyterian Hospital, Weill Cornell Medicine, New York, NY, USA
| | - Hans-Guido Wendel
- Cancer Biology and Genetics Program, Memorial Sloan-Kettering Cancer Center , New York, NY, USA
| |
Collapse
|
13
|
Feng Y, Li Z, Zhu J, Zou C, Tian Y, Xiong J, He Q, Li W, Xu H, Liu L, Xu B, Shi J, Zhang D. Stabilization of RRBP1 mRNA via an m 6A-dependent manner in prostate cancer constitutes a therapeutic vulnerability amenable to small-peptide inhibition of METTL3. Cell Mol Life Sci 2024; 81:414. [PMID: 39367907 DOI: 10.1007/s00018-024-05418-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 07/27/2024] [Accepted: 08/19/2024] [Indexed: 10/07/2024]
Abstract
Mounting evidence has implicated the RNA m6A methylation catalyzed by METTL3 in a wide range of physiological and pathological processes, including tumorigenesis. The detailed m6A landscape and molecular mechanism of METTL3 in prostate cancer (PCa) remains ill-defined. We find that METTL3 is overexpressed in PCa and correlates with worse patient survival. Functional studies establish METTL3 as an oncoprotein dependent on its m6A enzymatic activity in both AR+ and AR- PCa cells. To dissect the regulatory network of m6A pathway in PCa, we map the m6A landscape in clinical tumor samples using m6A-seq and identify genome-wide METTL3-binding transcripts via RIP-seq. Mechanistically, we discover RRBP1 as a direct METTL3 target in which METTL3 stabilizes RRBP1 mRNA in an m6A-dependent manner. RRBP1 positively correlates with METTL3 expression in PCa cohorts and exerts an oncogenic role in aggressive PCa cells. Leveraging the 3D structural protein-protein interaction between METTL3 and METTL14, we successfully develop two potential METTL3 peptide inhibitors (RM3 and RSM3) that effectively suppress cancer cell proliferation in vitro and tumor growth in vivo. Collectively, our study reveals a novel METTL3/m6A/RRBP1 axis in enhancing aggressive traits of PCa, which can be therapeutically targeted by small-peptide METTL3 antagonists.
Collapse
Affiliation(s)
- Yuqing Feng
- Affiliated Hospital of Hunan University, School of Biomedical Sciences, Hunan University, Changsha, China
- Hunan Key Laboratory of Animal Models and Molecular Medicine, School of Biomedical Sciences, Hunan University, Changsha, Hunan Province, 410082, China
- Shenzhen Research Institute, Hunan University, Shenzhen, 518000, China
| | - Zenghui Li
- Hunan Key Laboratory of Animal Models and Molecular Medicine, School of Biomedical Sciences, Hunan University, Changsha, Hunan Province, 410082, China
- Greater Bay Area Institute for Innovation, Hunan University, Guangzhou, 511300, China
| | - Jinwei Zhu
- Hunan Key Laboratory of Animal Models and Molecular Medicine, School of Biomedical Sciences, Hunan University, Changsha, Hunan Province, 410082, China
- Shenzhen Research Institute, Hunan University, Shenzhen, 518000, China
| | - Cheng Zou
- Hunan Key Laboratory of Animal Models and Molecular Medicine, School of Biomedical Sciences, Hunan University, Changsha, Hunan Province, 410082, China
- Shenzhen Research Institute, Hunan University, Shenzhen, 518000, China
| | - Yu Tian
- Hunan Key Laboratory of Animal Models and Molecular Medicine, School of Biomedical Sciences, Hunan University, Changsha, Hunan Province, 410082, China
| | - Jiangling Xiong
- Hunan Key Laboratory of Animal Models and Molecular Medicine, School of Biomedical Sciences, Hunan University, Changsha, Hunan Province, 410082, China
| | - Qinju He
- Hunan Key Laboratory of Animal Models and Molecular Medicine, School of Biomedical Sciences, Hunan University, Changsha, Hunan Province, 410082, China
| | - Wenjun Li
- Hunan Key Laboratory of Animal Models and Molecular Medicine, School of Biomedical Sciences, Hunan University, Changsha, Hunan Province, 410082, China
| | - Hao Xu
- Key Laboratory of Pesticides & Chemical Biology of Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, 430079, China
| | - Lu Liu
- Hunan Key Laboratory of Animal Models and Molecular Medicine, School of Biomedical Sciences, Hunan University, Changsha, Hunan Province, 410082, China
| | - Bin Xu
- Department of Urology, School of Medicine, Affiliated Zhongda Hospital of Southeast University, Nanjing, Jiangsu Province, 210009, China
| | - Junfeng Shi
- Affiliated Hospital of Hunan University, School of Biomedical Sciences, Hunan University, Changsha, China.
- Hunan Key Laboratory of Animal Models and Molecular Medicine, School of Biomedical Sciences, Hunan University, Changsha, Hunan Province, 410082, China.
- Shenzhen Research Institute, Hunan University, Shenzhen, 518000, China.
- Greater Bay Area Institute for Innovation, Hunan University, Guangzhou, 511300, China.
| | - Dingxiao Zhang
- Affiliated Hospital of Hunan University, School of Biomedical Sciences, Hunan University, Changsha, China.
- Hunan Key Laboratory of Animal Models and Molecular Medicine, School of Biomedical Sciences, Hunan University, Changsha, Hunan Province, 410082, China.
- Shenzhen Research Institute, Hunan University, Shenzhen, 518000, China.
| |
Collapse
|
14
|
Pudjihartono M, Pudjihartono N, O'Sullivan JM, Schierding W. Melanoma-specific mutation hotspots in distal, non-coding, promoter-interacting regions implicate novel candidate driver genes. Br J Cancer 2024:10.1038/s41416-024-02870-w. [PMID: 39367275 DOI: 10.1038/s41416-024-02870-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Revised: 09/23/2024] [Accepted: 09/26/2024] [Indexed: 10/06/2024] Open
Abstract
BACKGROUND To develop targeted treatments, it is crucial to identify the full spectrum of genetic drivers in melanoma, including those in non-coding regions. However, recent efforts to explore non-coding regions have primarily focused on gene-adjacent elements such as promoters and non-coding RNAs, leaving intergenic distal regulatory elements largely unexplored. METHODS We used Hi-C chromatin contact data from melanoma cells to map distal, non-coding, promoter-interacting regulatory elements genome-wide in melanoma. Using this "promoter-interaction network", alongside whole-genome sequence and gene expression data from the Pan Cancer Analysis of Whole Genomes, we developed multivariate linear regression models to identify distal somatic mutation hotspots that affect promoter activity. RESULTS We identified eight recurrently mutated hotspots that are novel, melanoma-specific, located in promoter-interacting distal regulatory elements, alter transcription factor binding motifs, and affect the expression of genes (e.g., HSPB7, CLDN1, ADCY9 and FDXR) previously implicated as tumour suppressors/oncogenes in various cancers. CONCLUSIONS Our study suggests additional non-coding drivers beyond the well-characterised TERT promoter in melanoma, offering new insights into the disruption of complex regulatory networks by non-coding mutations that may contribute to melanoma development. Furthermore, our study provides a framework for integrating multiple levels of biological data to uncover cancer-specific non-coding drivers.
Collapse
Affiliation(s)
- Michael Pudjihartono
- Liggins Institute, The University of Auckland, Auckland, New Zealand
- The Maurice Wilkins Centre, The University of Auckland, Auckland, New Zealand
| | | | - Justin M O'Sullivan
- Liggins Institute, The University of Auckland, Auckland, New Zealand.
- The Maurice Wilkins Centre, The University of Auckland, Auckland, New Zealand.
- Australian Parkinson's Mission, Garvan Institute of Medical Research, Sydney, NSW, Australia.
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, UK.
- Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.
| | - William Schierding
- Liggins Institute, The University of Auckland, Auckland, New Zealand.
- The Maurice Wilkins Centre, The University of Auckland, Auckland, New Zealand.
- Department of Ophthalmology, University of Auckland, Auckland, New Zealand.
| |
Collapse
|
15
|
Dupéré-Richer D, Riva A, Barwick BG, Maji S, Casellas Román H, Li J, De U, Sobh A, Quickstad G, Piper C, Kulis M, Ezponda T, Martín-Subero JI, Tonon G, Zhang W, Mitsiades CS, Boise LH, Bennett RL, Licht JD. KDM6A regulates immune response genes in multiple myeloma. Blood 2024; 144:1508-1520. [PMID: 39046770 DOI: 10.1182/blood.2024024518] [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: 03/07/2024] [Revised: 06/14/2024] [Accepted: 07/01/2024] [Indexed: 07/25/2024] Open
Abstract
ABSTRACT The histone H3 at lysine 27 (H3K27) demethylase lysine demethylase 6A (KDM6A) is a tumor suppressor in multiple cancers, including multiple myeloma (MM). We created isogenic MM cells disrupted for KDM6A and tagged the endogenous protein to facilitate genome-wide studies. KDM6A binds genes associated with immune recognition and cytokine signaling. Most importantly, KDM6A binds and activates NLRC5 and CIITA, which encode regulators of major histocompatibility complex genes. Patient data indicate that NLRC5 and CIITA are downregulated in MM with low KDM6A expression. Chromatin analysis shows that KDM6A binds poised and active enhancers and KDM6A loss led to decreased H3K27ac at enhancers, increased H3K27me3 levels in body of genes bound by KDM6A, and decreased gene expression. Reestablishing histone acetylation with an HDAC3 inhibitor leads to upregulation of major histocompatibility complex expression, offering a strategy to restore immunogenicity of KDM6A-deficient tumors. Loss of Kdm6a in Kirsten rat sarcoma virus (K-RAS)-transformed murine fibroblasts led to increased growth in vivo associated with decreased T-cell infiltration.
Collapse
Affiliation(s)
- Daphné Dupéré-Richer
- Division of Hematology/Oncology, University of Florida Health Cancer Center, University of Florida, Gainesville, FL
| | - Alberto Riva
- Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL
| | - Benjamin G Barwick
- Department of Hematology and Medical Oncology, School of Medicine, Emory University, Winship Cancer Institute, Atlanta, GA
| | - Sayantan Maji
- Division of Hematology/Oncology, University of Florida Health Cancer Center, University of Florida, Gainesville, FL
| | - Heidi Casellas Román
- Division of Hematology/Oncology, University of Florida Health Cancer Center, University of Florida, Gainesville, FL
- Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL
| | - Jianping Li
- Division of Hematology/Oncology, University of Florida Health Cancer Center, University of Florida, Gainesville, FL
| | - Umasankar De
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida Health Cancer Center, University of Florida, Gainesville, FL
| | - Amin Sobh
- Division of Hematology/Oncology, University of Florida Health Cancer Center, University of Florida, Gainesville, FL
| | - Gabrielle Quickstad
- Division of Hematology/Oncology, University of Florida Health Cancer Center, University of Florida, Gainesville, FL
| | - Crissandra Piper
- Division of Hematology/Oncology, University of Florida Health Cancer Center, University of Florida, Gainesville, FL
| | - Marta Kulis
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Universitat de Barcelona, Barcelona, Spain
| | - Teresa Ezponda
- Hemato-Oncology Department, Cima Universidad de Navarra, Instituto de Investigación Sanitaria de Navarra, Pamplona, Spain
- Centro de Investigación Biomédica en Red de Cáncer, Barcelona, Spain
| | - José Ignacio Martín-Subero
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Universitat de Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
- Departamento de Fundamentos Clínicos, Universitat de Barcelona, Barcelona, Spain
| | - Giovanni Tonon
- Center for Translational Genomics and Bioinformatics, IRCCS San Raffaele Scientific Institute, Milano, Italy
| | - Weizhou Zhang
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida Health Cancer Center, University of Florida, Gainesville, FL
| | | | - Lawrence H Boise
- Department of Hematology and Medical Oncology, School of Medicine, Emory University, Winship Cancer Institute, Atlanta, GA
| | - Richard L Bennett
- Division of Hematology/Oncology, University of Florida Health Cancer Center, University of Florida, Gainesville, FL
| | - Jonathan D Licht
- Division of Hematology/Oncology, University of Florida Health Cancer Center, University of Florida, Gainesville, FL
| |
Collapse
|
16
|
Barnada SM, Giner de Gracia A, Morenilla-Palao C, López-Cascales MT, Scopa C, Waltrich FJ, Mikkers HMM, Cicardi ME, Karlin J, Trotti D, Peterson KA, Brugmann SA, Santen GWE, McMahon SB, Herrera E, Trizzino M. ARID1A-BAF coordinates ZIC2 genomic occupancy for epithelial-to-mesenchymal transition in cranial neural crest specification. Am J Hum Genet 2024; 111:2232-2252. [PMID: 39226899 DOI: 10.1016/j.ajhg.2024.07.022] [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: 04/25/2024] [Revised: 07/30/2024] [Accepted: 07/30/2024] [Indexed: 09/05/2024] Open
Abstract
The BAF chromatin remodeler regulates lineage commitment including cranial neural crest cell (CNCC) specification. Variants in BAF subunits cause Coffin-Siris syndrome (CSS), a congenital disorder characterized by coarse craniofacial features and intellectual disability. Approximately 50% of individuals with CSS harbor variants in one of the mutually exclusive BAF subunits, ARID1A/ARID1B. While Arid1a deletion in mouse neural crest causes severe craniofacial phenotypes, little is known about the role of ARID1A in CNCC specification. Using CSS-patient-derived ARID1A+/- induced pluripotent stem cells to model CNCC specification, we discovered that ARID1A-haploinsufficiency impairs epithelial-to-mesenchymal transition (EMT), a process necessary for CNCC delamination and migration from the neural tube. Furthermore, wild-type ARID1A-BAF regulates enhancers associated with EMT genes. ARID1A-BAF binding at these enhancers is impaired in heterozygotes while binding at promoters is unaffected. At the sequence level, these EMT enhancers contain binding motifs for ZIC2, and ZIC2 binding at these sites is ARID1A-dependent. When excluded from EMT enhancers, ZIC2 relocates to neuronal enhancers, triggering aberrant neuronal gene activation. In mice, deletion of Zic2 impairs NCC delamination, while ZIC2 overexpression in chick embryos at post-migratory neural crest stages elicits ectopic delamination from the neural tube. These findings reveal an essential ARID1A-ZIC2 axis essential for EMT and CNCC delamination.
Collapse
Affiliation(s)
- Samantha M Barnada
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Aida Giner de Gracia
- Instituto de Neurociencias de Alicante (Consejo Superior de Investigaciones Científicas- Universidad Miguel Hernández, CSIC-UMH). Campus San Juan, Avd. Ramón y Cajal s/n, 03550 San Juan de Alicante, Spain
| | - Cruz Morenilla-Palao
- Instituto de Neurociencias de Alicante (Consejo Superior de Investigaciones Científicas- Universidad Miguel Hernández, CSIC-UMH). Campus San Juan, Avd. Ramón y Cajal s/n, 03550 San Juan de Alicante, Spain
| | - Maria Teresa López-Cascales
- Instituto de Neurociencias de Alicante (Consejo Superior de Investigaciones Científicas- Universidad Miguel Hernández, CSIC-UMH). Campus San Juan, Avd. Ramón y Cajal s/n, 03550 San Juan de Alicante, Spain
| | - Chiara Scopa
- Jefferson Weinberg ALS Center, Vickie and Jack Farber Institute for Neuroscience, Department of Neuroscience, Thomas Jefferson University, Philadelphia, PA, USA
| | - Francis J Waltrich
- Department of Pharmacology, Physiology, and Cancer Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Harald M M Mikkers
- Department of Cell & Chemical Biology, Leiden University Medical Center, Leiden, the Netherlands
| | - Maria Elena Cicardi
- Jefferson Weinberg ALS Center, Vickie and Jack Farber Institute for Neuroscience, Department of Neuroscience, Thomas Jefferson University, Philadelphia, PA, USA
| | - Jonathan Karlin
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Davide Trotti
- Jefferson Weinberg ALS Center, Vickie and Jack Farber Institute for Neuroscience, Department of Neuroscience, Thomas Jefferson University, Philadelphia, PA, USA
| | | | - Samantha A Brugmann
- Division of Developmental Biology, Department of Pediatrics at Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Gijs W E Santen
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Steven B McMahon
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Eloísa Herrera
- Instituto de Neurociencias de Alicante (Consejo Superior de Investigaciones Científicas- Universidad Miguel Hernández, CSIC-UMH). Campus San Juan, Avd. Ramón y Cajal s/n, 03550 San Juan de Alicante, Spain.
| | - Marco Trizzino
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, USA; Department of Life Sciences, Imperial College London, London, UK.
| |
Collapse
|
17
|
Erjavec E, Angée C, Hadjadj D, Passet B, David P, Kostic C, Dodé E, Zanlonghi X, Cagnard N, Nedelec B, Crippa SV, Bole-Feysot C, Zarhrate M, Creuzet S, Castille J, Vilotte JL, Calvas P, Plaisancié J, Chassaing N, Kaplan J, Rozet JM, Taie LF. Congenital microcoria deletion in mouse links Sox21 dysregulation to disease and suggests a role for TGFB2 in glaucoma and myopia. Am J Hum Genet 2024; 111:2265-2282. [PMID: 39293448 DOI: 10.1016/j.ajhg.2024.08.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 08/23/2024] [Accepted: 08/23/2024] [Indexed: 09/20/2024] Open
Abstract
Congenital microcoria (MCOR) is a rare hereditary developmental defect of the iris dilator muscle frequently associated with high axial myopia and high intraocular pressure (IOP) glaucoma. The condition is caused by submicroscopic rearrangements of chromosome 13q32.1. However, the mechanisms underlying the failure of iris development and the origin of associated features remain elusive. Here, we present a 3D architecture model of the 13q32.1 region, demonstrating that MCOR-related deletions consistently disrupt the boundary between two topologically associating domains (TADs). Deleting the critical MCOR-causing region in mice reveals ectopic Sox21 expression precisely aligning with Dct, each located in one of the two neighbor TADs. This observation is consistent with the TADs' boundary alteration and adoption of Dct regulatory elements by the Sox21 promoter. Additionally, we identify Tgfb2 as a target gene of SOX21 and show TGFΒ2 accumulation in the aqueous humor of an MCOR-affected subject. Accumulation of TGFB2 is recognized for its role in glaucoma and potential impact on axial myopia. Our results highlight the importance of SOX21-TGFB2 signaling in iris development and control of eye growth and IOP. Insights from MCOR studies may provide therapeutic avenues for this condition but also for glaucoma and high myopia conditions, affecting millions of people.
Collapse
Affiliation(s)
- Elisa Erjavec
- Laboratory of Genetics in Ophthalmology (LGO), INSERM UMR1163, Institute of Genetic Diseases, Imagine and Université Paris Cité, Paris, France
| | - Clémentine Angée
- Laboratory of Genetics in Ophthalmology (LGO), INSERM UMR1163, Institute of Genetic Diseases, Imagine and Université Paris Cité, Paris, France
| | - Djihad Hadjadj
- Institut Cochin, Inserm U1016, CNRS UMR8104, UFR de Pharmacie de Paris, Université Paris Cité, CARPEM, Paris, France
| | - Bruno Passet
- University of Paris-Saclay, INRAE, AgroParisTech, UMR1313 GABI, Jouy-en-Josas, France
| | - Pierre David
- Transgenesis Platform, Laboratoire d'Expérimentation Animale et Transgenèse (LEAT), Imagine Institute, Structure Fédérative de Recherche Necker INSERM US24/CNRS UMS3633, Paris, France
| | - Corinne Kostic
- Group for Retinal Disorder Research, Department of Ophthalmology, University of Lausanne, Jules-Gonin Eye Hospital, Fondation Asile des Aveugles, Lausanne, Switzerland
| | - Emmanuel Dodé
- Institut Ophtalmologique de L'Ouest-Clinique Jules VERNE, Nantes, France
| | - Xavier Zanlonghi
- Institut Ophtalmologique de L'Ouest-Clinique Jules VERNE, Nantes, France
| | - Nicolas Cagnard
- Université Paris Cité, Bioinformatics Core Facility, Imagine Institute, INSERM UMR 1163, Paris, France
| | - Brigitte Nedelec
- Laboratory of Genetics in Ophthalmology (LGO), INSERM UMR1163, Institute of Genetic Diseases, Imagine and Université Paris Cité, Paris, France
| | - Sylvain V Crippa
- Group for Retinal Disorder Research, Department of Ophthalmology, University of Lausanne, Jules-Gonin Eye Hospital, Fondation Asile des Aveugles, Lausanne, Switzerland
| | - Christine Bole-Feysot
- Université Paris Cité, Genomics Platform, Imagine Institute, INSERM UMR 1163, INSERM US24/CNRS UAR3633, Paris, France
| | - Mohammed Zarhrate
- Université Paris Cité, Genomics Platform, Imagine Institute, INSERM UMR 1163, INSERM US24/CNRS UAR3633, Paris, France
| | - Sophie Creuzet
- Paris-Saclay Institute of Neuroscience, NeuroPSI, CNRS, Paris-Saclay University, Campus CEA Saclay, Bât 151, 151 Route de la Rotonde, 91400 Saclay, France
| | - Johan Castille
- University of Paris-Saclay, INRAE, AgroParisTech, UMR1313 GABI, Jouy-en-Josas, France
| | - Jean-Luc Vilotte
- University of Paris-Saclay, INRAE, AgroParisTech, UMR1313 GABI, Jouy-en-Josas, France
| | - Patrick Calvas
- Centre de Référence pour les Affections Rares en Génétique Ophtalmologique (CARGO), CHU Toulouse, Toulouse, France
| | - Julie Plaisancié
- Centre de Référence pour les Affections Rares en Génétique Ophtalmologique (CARGO), CHU Toulouse, Toulouse, France
| | - Nicolas Chassaing
- Centre de Référence pour les Affections Rares en Génétique Ophtalmologique (CARGO), CHU Toulouse, Toulouse, France
| | - Josseline Kaplan
- Laboratory of Genetics in Ophthalmology (LGO), INSERM UMR1163, Institute of Genetic Diseases, Imagine and Université Paris Cité, Paris, France
| | - Jean-Michel Rozet
- Laboratory of Genetics in Ophthalmology (LGO), INSERM UMR1163, Institute of Genetic Diseases, Imagine and Université Paris Cité, Paris, France.
| | - Lucas Fares Taie
- Laboratory of Genetics in Ophthalmology (LGO), INSERM UMR1163, Institute of Genetic Diseases, Imagine and Université Paris Cité, Paris, France.
| |
Collapse
|
18
|
Gosztyla ML, Zhan L, Olson S, Wei X, Naritomi J, Nguyen G, Street L, Goda GA, Cavazos FF, Schmok JC, Jain M, Uddin Syed E, Kwon E, Jin W, Kofman E, Tankka AT, Li A, Gonzalez V, Lécuyer E, Dominguez D, Jovanovic M, Graveley BR, Yeo GW. Integrated multi-omics analysis of zinc-finger proteins uncovers roles in RNA regulation. Mol Cell 2024; 84:3826-3842.e8. [PMID: 39303722 DOI: 10.1016/j.molcel.2024.08.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 06/19/2024] [Accepted: 08/06/2024] [Indexed: 09/22/2024]
Abstract
RNA interactome studies have revealed that hundreds of zinc-finger proteins (ZFPs) are candidate RNA-binding proteins (RBPs), yet their RNA substrates and functional significance remain largely uncharacterized. Here, we present a systematic multi-omics analysis of the DNA- and RNA-binding targets and regulatory roles of more than 100 ZFPs representing 37 zinc-finger families. We show that multiple ZFPs are previously unknown regulators of RNA splicing, alternative polyadenylation, stability, or translation. The examined ZFPs show widespread sequence-specific RNA binding and preferentially bind proximal to transcription start sites. Additionally, several ZFPs associate with their targets at both the DNA and RNA levels. We highlight ZNF277, a C2H2 ZFP that binds thousands of RNA targets and acts as a multi-functional RBP. We also show that ZNF473 is a DNA/RNA-associated protein that regulates the expression and splicing of cell cycle genes. Our results reveal diverse roles for ZFPs in transcriptional and post-transcriptional gene regulation.
Collapse
Affiliation(s)
- Maya L Gosztyla
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92037, USA; Sanford Stem Cell Institute and UCSD Stem Cell Program, University of California San Diego, La Jolla, CA 92037, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - Lijun Zhan
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, UConn Health, Farmington, CT 06030, USA
| | - Sara Olson
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, UConn Health, Farmington, CT 06030, USA
| | - Xintao Wei
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, UConn Health, Farmington, CT 06030, USA
| | - Jack Naritomi
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92037, USA; Sanford Stem Cell Institute and UCSD Stem Cell Program, University of California San Diego, La Jolla, CA 92037, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - Grady Nguyen
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92037, USA; Sanford Stem Cell Institute and UCSD Stem Cell Program, University of California San Diego, La Jolla, CA 92037, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - Lena Street
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Grant A Goda
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA; Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Francisco F Cavazos
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Jonathan C Schmok
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92037, USA; Sanford Stem Cell Institute and UCSD Stem Cell Program, University of California San Diego, La Jolla, CA 92037, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - Manya Jain
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92037, USA; Sanford Stem Cell Institute and UCSD Stem Cell Program, University of California San Diego, La Jolla, CA 92037, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - Easin Uddin Syed
- Institut de Recherches Cliniques de Montréal (IRCM), Montreal, QC H2W 1R7, Canada; Department of Biochemistry and Molecular Medicine, Université de Montréal, Montreal, QC H3T 1J4, Canada; School of Pharmacy, Brac University, Dhaka 1212, Bangladesh
| | - Eunjeong Kwon
- Institut de Recherches Cliniques de Montréal (IRCM), Montreal, QC H2W 1R7, Canada
| | - Wenhao Jin
- Sanford Laboratories for Innovative Medicines, La Jolla, CA 92037, USA
| | - Eric Kofman
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92037, USA; Sanford Stem Cell Institute and UCSD Stem Cell Program, University of California San Diego, La Jolla, CA 92037, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - Alexandra T Tankka
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92037, USA; Sanford Stem Cell Institute and UCSD Stem Cell Program, University of California San Diego, La Jolla, CA 92037, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - Allison Li
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92037, USA; Sanford Stem Cell Institute and UCSD Stem Cell Program, University of California San Diego, La Jolla, CA 92037, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - Valerie Gonzalez
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92037, USA; Sanford Stem Cell Institute and UCSD Stem Cell Program, University of California San Diego, La Jolla, CA 92037, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - Eric Lécuyer
- Institut de Recherches Cliniques de Montréal (IRCM), Montreal, QC H2W 1R7, Canada; Department of Biochemistry and Molecular Medicine, Université de Montréal, Montreal, QC H3T 1J4, Canada; Division of Experimental Medicine, McGill University, Montreal, QC H3A 0G4, Canada
| | - Daniel Dominguez
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Marko Jovanovic
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Brenton R Graveley
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, UConn Health, Farmington, CT 06030, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92037, USA; Sanford Stem Cell Institute and UCSD Stem Cell Program, University of California San Diego, La Jolla, CA 92037, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92037, USA; Sanford Laboratories for Innovative Medicines, La Jolla, CA 92037, USA; Center for RNA Technologies and Therapeutics, University of California, San Diego, La Jolla, CA 92037, USA.
| |
Collapse
|
19
|
Xia Z, Zhang S, Guo H, Gao X, Hao K, Dong X, Guo J, Li J, Wang Z, An M, Wu Y, Zhou X. N 6-Methyladenosine RNA Modification Regulates Maize Resistance to Maize Chlorotic Mottle Virus Infection. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:21935-21945. [PMID: 39311423 DOI: 10.1021/acs.jafc.4c04832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/03/2024]
Abstract
Maize chlorotic mottle virus (MCMV) is one of the main viruses causing significant losses in maize. N6-methyladenosine (m6A) RNA modification has been proven to play important regulatory roles in plant development and stress response. In this study, we found that MCMV infection significantly up-regulated the m6A level in maize, and methylated RNA immunoprecipitation sequencing (MeRIP-seq) and RNA sequencing (RNA-seq) were performed to investigate the distribution of m6A modified peaks and gene expression patterns in MCMV-infected maize plants. The results showed that 1325 differentially methylated genes (DMGs) and 47 differentially methylated and expressed genes (DMEGs) were identified and analyzed. Moreover, the results of virus-induced gene silencing (VIGS) assays showed that ZmECT18 and ZmGST31 were required for MCMV infection, while silencing of ZmMTC, ZmSCI1 or ZmTIP1 significantly promoted MCMV infection in maize. Our findings provided novel insights into the regulatory roles of m6A modification in maize response to MCMV infection.
Collapse
Affiliation(s)
- Zihao Xia
- Liaoning Key Laboratory of Plant Pathology, College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
- Key Laboratory of Major Agricultural Invasion Biological Monitoring and Control of Shenyang, Shenyang 110866, China
| | - Sijia Zhang
- Liaoning Key Laboratory of Plant Pathology, College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
- Key Laboratory of Major Agricultural Invasion Biological Monitoring and Control of Shenyang, Shenyang 110866, China
| | - Huiyan Guo
- Liaoning Key Laboratory of Plant Pathology, College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
- Key Laboratory of Major Agricultural Invasion Biological Monitoring and Control of Shenyang, Shenyang 110866, China
| | - Xinran Gao
- Liaoning Key Laboratory of Plant Pathology, College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
- Key Laboratory of Major Agricultural Invasion Biological Monitoring and Control of Shenyang, Shenyang 110866, China
| | - Kaiqiang Hao
- Liaoning Key Laboratory of Plant Pathology, College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
- Key Laboratory of Major Agricultural Invasion Biological Monitoring and Control of Shenyang, Shenyang 110866, China
| | - Xue Dong
- Liaoning Key Laboratory of Plant Pathology, College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
- Key Laboratory of Major Agricultural Invasion Biological Monitoring and Control of Shenyang, Shenyang 110866, China
| | - Jinxiu Guo
- Liaoning Key Laboratory of Plant Pathology, College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
- Key Laboratory of Major Agricultural Invasion Biological Monitoring and Control of Shenyang, Shenyang 110866, China
| | - Jian Li
- Liaoning Key Laboratory of Plant Pathology, College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
- Key Laboratory of Major Agricultural Invasion Biological Monitoring and Control of Shenyang, Shenyang 110866, China
| | - Zhiping Wang
- Liaoning Key Laboratory of Plant Pathology, College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
- Key Laboratory of Major Agricultural Invasion Biological Monitoring and Control of Shenyang, Shenyang 110866, China
| | - Mengnan An
- Liaoning Key Laboratory of Plant Pathology, College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
- Key Laboratory of Major Agricultural Invasion Biological Monitoring and Control of Shenyang, Shenyang 110866, China
| | - Yuanhua Wu
- Liaoning Key Laboratory of Plant Pathology, College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
- Key Laboratory of Major Agricultural Invasion Biological Monitoring and Control of Shenyang, Shenyang 110866, China
| | - Xueping Zhou
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
| |
Collapse
|
20
|
Patel S, Ganbold K, Cho CH, Siddiqui J, Yildiz R, Sparman N, Sadeh S, Nguyen CM, Wang J, Whitelegge JP, Fried SK, Waki H, Villanueva CJ, Seldin MM, Sakaguchi S, Ellmeier W, Tontonoz P, Rajbhandari P. Transcription factor PATZ1 promotes adipogenesis by controlling promoter regulatory loci of adipogenic factors. Nat Commun 2024; 15:8533. [PMID: 39358382 PMCID: PMC11447024 DOI: 10.1038/s41467-024-52917-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 09/25/2024] [Indexed: 10/04/2024] Open
Abstract
White adipose tissue (WAT) is essential for lipid storage and systemic energy homeostasis. Understanding adipocyte formation and stability is key to developing therapies for obesity and metabolic disorders. Through a high-throughput cDNA screen, we identified PATZ1, a POZ/BTB and AT-Hook Containing Zinc Finger 1 protein, as an important adipogenic transcription factor. PATZ1 is expressed in human and mouse adipocyte precursor cells (APCs) and adipocytes. In cellular models, PATZ1 promotes adipogenesis via protein-protein interactions and DNA binding. PATZ1 ablation in mouse adipocytes and APCs leads to a reduced APC pool, decreased fat mass, and hypertrophied adipocytes. ChIP-Seq and RNA-seq analyses show that PATZ1 supports adipogenesis by interacting with transcriptional machinery at the promoter regions of key early adipogenic factors. Mass-spec results show that PATZ1 associates with GTF2I, with GTF2I modulating PATZ1's function during differentiation. These findings underscore PATZ1's regulatory role in adipocyte differentiation and adiposity, offering insights into adipose tissue development.
Collapse
Affiliation(s)
- Sanil Patel
- Diabetes, Obesity, and Metabolism Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Khatanzul Ganbold
- Diabetes, Obesity, and Metabolism Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Chung Hwan Cho
- Diabetes, Obesity, and Metabolism Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Juwairriyyah Siddiqui
- Diabetes, Obesity, and Metabolism Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Ramazan Yildiz
- Diabetes, Obesity, and Metabolism Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Njeri Sparman
- Diabetes, Obesity, and Metabolism Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Shani Sadeh
- Diabetes, Obesity, and Metabolism Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Christy M Nguyen
- Department of Biological Chemistry, University of California, Irvine, CA, 92697, USA
| | - Jiexin Wang
- Department of Pathology and Laboratory Medicine and Department of Biological Chemistry, University of California, Los Angeles, CA, 90095, USA
| | - Julian P Whitelegge
- Pasarow Mass Spectrometry Laboratory, NPI-Semel Institute, University of California, Los Angeles, CA, 90095, USA
| | - Susan K Fried
- Diabetes, Obesity, and Metabolism Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Hironori Waki
- Department of Metabolism and Endocrinology, Graduate School of Medicine, Akita University, Akita, Japan
| | - Claudio J Villanueva
- Molecular, Cellular, and Integrative Physiology Program, and Department of Integrative Biology and Physiology, University of California, Los Angeles, CA, 90095, USA
| | - Marcus M Seldin
- Department of Biological Chemistry, University of California, Irvine, CA, 92697, USA
| | - Shinya Sakaguchi
- Medical University of Vienna, Center for Pathophysiology, Infectiology and Immunology, Institute of Immunology, Vienna, Austria
| | - Wilfried Ellmeier
- Medical University of Vienna, Center for Pathophysiology, Infectiology and Immunology, Institute of Immunology, Vienna, Austria
| | - Peter Tontonoz
- Department of Pathology and Laboratory Medicine and Department of Biological Chemistry, University of California, Los Angeles, CA, 90095, USA
| | - Prashant Rajbhandari
- Diabetes, Obesity, and Metabolism Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Disease Mechanism and Therapeutics Program, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
| |
Collapse
|
21
|
Yao XQ, Chen JY, Garcia-Segura ME, Wen ZH, Yu ZH, Huang ZC, Hamel R, Liu JH, Shen X, Huang ZP, Lu YM, Zhou ZT, Liu CT, Shi JM, Zhu QA, Peruzzotti-Jametti L, Chen JT. Integrated multi-omics analysis reveals molecular changes associated with chronic lipid accumulation following contusive spinal cord injury. Exp Neurol 2024; 380:114909. [PMID: 39097074 DOI: 10.1016/j.expneurol.2024.114909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Revised: 06/23/2024] [Accepted: 07/29/2024] [Indexed: 08/05/2024]
Abstract
Functional and pathological recovery after spinal cord injury (SCI) is often incomplete due to the limited regenerative capacity of the central nervous system (CNS), which is further impaired by several mechanisms that sustain tissue damage. Among these, the chronic activation of immune cells can cause a persistent state of local CNS inflammation and damage. However, the mechanisms that sustain this persistent maladaptive immune response in SCI have not been fully clarified yet. In this study, we integrated histological analyses with proteomic, lipidomic, transcriptomic, and epitranscriptomic approaches to study the pathological and molecular alterations that develop in a mouse model of cervical spinal cord hemicontusion. We found significant pathological alterations of the lesion rim with myelin damage and axonal loss that persisted throughout the late chronic phase of SCI. This was coupled by a progressive lipid accumulation in myeloid cells, including resident microglia and infiltrating monocyte-derived macrophages. At tissue level, we found significant changes of proteins indicative of glycolytic, tricarboxylic acid cycle (TCA), and fatty acid metabolic pathways with an accumulation of triacylglycerides with C16:0 fatty acyl chains in chronic SCI. Following transcriptomic, proteomic, and epitranscriptomic studies identified an increase of cholesterol and m6A methylation in lipid-droplet-accumulating myeloid cells as a core feature of chronic SCI. By characterizing the multiple metabolic pathways altered in SCI, our work highlights a key role of lipid metabolism in the chronic response of the immune and central nervous system to damage.
Collapse
Affiliation(s)
- Xin-Qiang Yao
- Division of Spine Surgery, Department of Orthopaedics, Nanfang hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Jia-Ying Chen
- Comprehensive Medical Treatment Ward, Nanfang hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Monica Emili Garcia-Segura
- Department of Metabolism, Digestion and Reproduction, Imperial College London, United Kingdom; Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - Zi-Han Wen
- Division of Spine Surgery, Department of Orthopaedics, Nanfang hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Zi-Han Yu
- Division of Spine Surgery, Department of Orthopaedics, Nanfang hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Zu-Cheng Huang
- Division of Spine Surgery, Department of Orthopaedics, Nanfang hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Regan Hamel
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - Jun-Hao Liu
- Division of Spine Surgery, Department of Orthopaedics, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong, China
| | - Xing Shen
- Division of Spine Surgery, Department of Orthopaedics, Nanfang hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Zhi-Ping Huang
- Division of Spine Surgery, Department of Orthopaedics, Nanfang hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Yan-Meng Lu
- Central Laboratory, Southern Medical University, Guangzhou, Guangdong, China
| | - Zhi-Tao Zhou
- Central Laboratory, Southern Medical University, Guangzhou, Guangdong, China
| | - Cui-Ting Liu
- Central Laboratory, Southern Medical University, Guangzhou, Guangdong, China
| | - Jun-Min Shi
- Central Laboratory, Southern Medical University, Guangzhou, Guangdong, China
| | - Qing-An Zhu
- Division of Spine Surgery, Department of Orthopaedics, Nanfang hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Luca Peruzzotti-Jametti
- Department of Metabolism, Digestion and Reproduction, Imperial College London, United Kingdom; Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - Jian-Ting Chen
- Division of Spine Surgery, Department of Orthopaedics, Nanfang hospital, Southern Medical University, Guangzhou, Guangdong, China.
| |
Collapse
|
22
|
Liu SX, Muelken P, Maxim ZL, Ramakrishnan A, Estill MS, LeSage MG, Smethells JR, Shen L, Tran PV, Harris AC, Gewirtz JC. Differential gene expression and chromatin accessibility in the medial prefrontal cortex associated with individual differences in rat behavioral models of opioid use disorder. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.29.582799. [PMID: 38979145 PMCID: PMC11230220 DOI: 10.1101/2024.02.29.582799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Opioid use disorder (OUD) is a neuropsychological disease that has a devastating impact on public health. Substantial individual differences in vulnerability exist, the neurobiological substrates of which remain unclear. To address this question, we investigated genome-wide gene transcription (RNA-seq) and chromatin accessibility (ATAC-seq) in the medial prefrontal cortex (mPFC) of male and female rats exhibiting differential vulnerability in behavioral paradigms modeling different phases of OUD: Withdrawal-Induced Anhedonia (WIA), Demand, and Reinstatement. Ingenuity Pathway Analysis (IPA) of RNA-seq revealed greater changes in canonical pathways in Resilient (vs. Saline) rats in comparison to Vulnerable (vs. Saline) rats across 3 paradigms, suggesting brain adaptations that might contribute to resilience to OUD across its trajectory. Analyses of gene networks and upstream regulators implicated processes involved in oligodendrocyte maturation and myelination in WIA, neuroinflammation in Demand, and metabolism in Reinstatement. Motif analysis of ATAC-seq showed changes in chromatin accessibility to a small set of transcription factor (TF) binding sites as a function either of opioid exposure (i.e., morphine versus saline) generally or of individual vulnerability specifically. Some of these were shared across the 3 paradigms and others were unique to each. In conclusion, we have identified changes in biological pathways, TFs, and their binding motifs that vary with paradigm and OUD vulnerability. These findings point to the involvement of distinct transcriptional and epigenetic mechanisms in response to opioid exposure, vulnerability to OUD, and different stages of the disorder.
Collapse
|
23
|
Kneuer JM, Grajek IA, Winkler M, Erbe S, Meinecke T, Weiss R, Garfias-Veitl T, Sheikh BN, König AC, Möbius-Winkler MN, Kogel A, Kresoja KP, Rosch S, Kokot KE, Filipova V, Gaul S, Thiele H, Lurz P, von Haehling S, Speer T, Laufs U, Boeckel JN. Novel Long Noncoding RNA HEAT4 Affects Monocyte Subtypes, Reducing Inflammation and Promoting Vascular Healing. Circulation 2024; 150:1101-1120. [PMID: 39005211 PMCID: PMC11444369 DOI: 10.1161/circulationaha.124.069315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Accepted: 06/11/2024] [Indexed: 07/16/2024]
Abstract
BACKGROUND Activation of the immune system contributes to cardiovascular diseases. The role of human-specific long noncoding RNAs in cardioimmunology is poorly understood. METHODS Single-cell sequencing in peripheral blood mononuclear cells revealed a novel human-specific long noncoding RNA called HEAT4 (heart failure-associated transcript 4). HEAT4 expression was assessed in several in vitro and ex vivo models of immune cell activation, as well as in the blood of patients with heart failure (HF), acute myocardial infarction, or cardiogenic shock. The transcriptional regulation of HEAT4 was verified through cytokine treatment and single-cell sequencing. Loss-of-function and gain-of-function studies and multiple RNA-protein interaction assays uncovered a mechanistic role of HEAT4 in the monocyte anti-inflammatory gene program. HEAT4 expression and function was characterized in a vascular injury model in NOD.CB17-Prkdc scid/Rj mice. RESULTS HEAT4 expression was increased in the blood of patients with HF, acute myocardial infarction, or cardiogenic shock. HEAT4 levels distinguished patients with HF from people without HF and predicted all-cause mortality in a cohort of patients with HF over 7 years of follow-up. Monocytes, particularly anti-inflammatory CD16+ monocytes, which are increased in patients with HF, are the primary source of HEAT4 expression in the blood. HEAT4 is transcriptionally activated by treatment with anti-inflammatory interleukin-10. HEAT4 activates anti-inflammatory and inhibits proinflammatory gene expression. Increased HEAT4 levels result in a shift toward more CD16+ monocytes. HEAT4 binds to S100A9, causing a monocyte subtype switch, thereby reducing inflammation. As a result, HEAT4 improves endothelial barrier integrity during inflammation and promotes vascular healing after injury in mice. CONCLUSIONS These results characterize a novel endogenous anti-inflammatory pathway that involves the conversion of monocyte subtypes into anti-inflammatory CD16+ monocytes. The data identify a novel function for the class of long noncoding RNAs by preventing protein secretion and suggest long noncoding RNAs as potential targets for interventions in the field of cardioimmunology.
Collapse
Affiliation(s)
- Jasmin M. Kneuer
- Klinik und Poliklinik für Kardiologie, Universitätsklinikum Leipzig, Germany (J.M.K., I.A.G., M.W., S.E., T.M., M.N.M.-W., A.K., K.E.K., V.F., S.G., U.L., J.-N.B.)
- Central German Heart Alliance (J.M.K., I.A.G., M.W., S.E., T.M., M.N.M.-W., A.K., K.E.K., V.F., S.G., H.T., U.L., J.-N.B.)
| | - Ignacy A. Grajek
- Klinik und Poliklinik für Kardiologie, Universitätsklinikum Leipzig, Germany (J.M.K., I.A.G., M.W., S.E., T.M., M.N.M.-W., A.K., K.E.K., V.F., S.G., U.L., J.-N.B.)
- Central German Heart Alliance (J.M.K., I.A.G., M.W., S.E., T.M., M.N.M.-W., A.K., K.E.K., V.F., S.G., H.T., U.L., J.-N.B.)
| | - Melanie Winkler
- Klinik und Poliklinik für Kardiologie, Universitätsklinikum Leipzig, Germany (J.M.K., I.A.G., M.W., S.E., T.M., M.N.M.-W., A.K., K.E.K., V.F., S.G., U.L., J.-N.B.)
- Central German Heart Alliance (J.M.K., I.A.G., M.W., S.E., T.M., M.N.M.-W., A.K., K.E.K., V.F., S.G., H.T., U.L., J.-N.B.)
| | - Stephan Erbe
- Klinik und Poliklinik für Kardiologie, Universitätsklinikum Leipzig, Germany (J.M.K., I.A.G., M.W., S.E., T.M., M.N.M.-W., A.K., K.E.K., V.F., S.G., U.L., J.-N.B.)
- Central German Heart Alliance (J.M.K., I.A.G., M.W., S.E., T.M., M.N.M.-W., A.K., K.E.K., V.F., S.G., H.T., U.L., J.-N.B.)
| | - Tim Meinecke
- Klinik und Poliklinik für Kardiologie, Universitätsklinikum Leipzig, Germany (J.M.K., I.A.G., M.W., S.E., T.M., M.N.M.-W., A.K., K.E.K., V.F., S.G., U.L., J.-N.B.)
- Central German Heart Alliance (J.M.K., I.A.G., M.W., S.E., T.M., M.N.M.-W., A.K., K.E.K., V.F., S.G., H.T., U.L., J.-N.B.)
| | - Ronald Weiss
- Institute of Clinical Immunology, University of Leipzig, Germany (R.W.)
| | - Tania Garfias-Veitl
- Department of Cardiology and Pneumology, University Medical Center of Göttingen (UMG), Germany (T.G.-V., S.v.H.)
- German Center for Cardiovascular Research (DZHK), Partner Site Göttingen, Germany (T.G.-V., S.v.H.)
| | - Bilal N. Sheikh
- Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG) of the Helmholtz Zentrum München at the University of Leipzig and University Hospital Leipzig, Germany (B.N.S.)
| | - Ann-Christine König
- German Research Center for Environmental Health (GmbH), Metabolomics and Proteomics Core, Helmholtz Zentrum München, Germany (A.-C.K.)
| | - Maximilian N. Möbius-Winkler
- Klinik und Poliklinik für Kardiologie, Universitätsklinikum Leipzig, Germany (J.M.K., I.A.G., M.W., S.E., T.M., M.N.M.-W., A.K., K.E.K., V.F., S.G., U.L., J.-N.B.)
- Central German Heart Alliance (J.M.K., I.A.G., M.W., S.E., T.M., M.N.M.-W., A.K., K.E.K., V.F., S.G., H.T., U.L., J.-N.B.)
| | - Alexander Kogel
- Klinik und Poliklinik für Kardiologie, Universitätsklinikum Leipzig, Germany (J.M.K., I.A.G., M.W., S.E., T.M., M.N.M.-W., A.K., K.E.K., V.F., S.G., U.L., J.-N.B.)
- Central German Heart Alliance (J.M.K., I.A.G., M.W., S.E., T.M., M.N.M.-W., A.K., K.E.K., V.F., S.G., H.T., U.L., J.-N.B.)
| | - Karl-Patrik Kresoja
- Department of Cardiology, Heart Center at University of Leipzig, Germany (K.-P.K., S.R., H.T., P.L.)
- Department of Cardiology, Universitätsmedizin Johannes Gutenberg-University, Mainz, Germany (K.-P.K., S.R., P.L.)
| | - Sebastian Rosch
- Department of Cardiology, Heart Center at University of Leipzig, Germany (K.-P.K., S.R., H.T., P.L.)
- Department of Cardiology, Universitätsmedizin Johannes Gutenberg-University, Mainz, Germany (K.-P.K., S.R., P.L.)
| | - Karoline E. Kokot
- Klinik und Poliklinik für Kardiologie, Universitätsklinikum Leipzig, Germany (J.M.K., I.A.G., M.W., S.E., T.M., M.N.M.-W., A.K., K.E.K., V.F., S.G., U.L., J.-N.B.)
- Central German Heart Alliance (J.M.K., I.A.G., M.W., S.E., T.M., M.N.M.-W., A.K., K.E.K., V.F., S.G., H.T., U.L., J.-N.B.)
| | - Vanina Filipova
- Klinik und Poliklinik für Kardiologie, Universitätsklinikum Leipzig, Germany (J.M.K., I.A.G., M.W., S.E., T.M., M.N.M.-W., A.K., K.E.K., V.F., S.G., U.L., J.-N.B.)
- Central German Heart Alliance (J.M.K., I.A.G., M.W., S.E., T.M., M.N.M.-W., A.K., K.E.K., V.F., S.G., H.T., U.L., J.-N.B.)
| | - Susanne Gaul
- Klinik und Poliklinik für Kardiologie, Universitätsklinikum Leipzig, Germany (J.M.K., I.A.G., M.W., S.E., T.M., M.N.M.-W., A.K., K.E.K., V.F., S.G., U.L., J.-N.B.)
- Central German Heart Alliance (J.M.K., I.A.G., M.W., S.E., T.M., M.N.M.-W., A.K., K.E.K., V.F., S.G., H.T., U.L., J.-N.B.)
| | - Holger Thiele
- Central German Heart Alliance (J.M.K., I.A.G., M.W., S.E., T.M., M.N.M.-W., A.K., K.E.K., V.F., S.G., H.T., U.L., J.-N.B.)
- Department of Cardiology, Heart Center at University of Leipzig, Germany (K.-P.K., S.R., H.T., P.L.)
| | - Philipp Lurz
- Department of Cardiology, Heart Center at University of Leipzig, Germany (K.-P.K., S.R., H.T., P.L.)
- Department of Cardiology, Universitätsmedizin Johannes Gutenberg-University, Mainz, Germany (K.-P.K., S.R., P.L.)
| | - Stephan von Haehling
- Department of Cardiology and Pneumology, University Medical Center of Göttingen (UMG), Germany (T.G.-V., S.v.H.)
- German Center for Cardiovascular Research (DZHK), Partner Site Göttingen, Germany (T.G.-V., S.v.H.)
| | - Thimoteus Speer
- Medizinische Klinik 4: Nephrologie, Universitätsklinikum Frankfurt, Frankfurt am Main, Germany (T.S.)
- Else Kroener-Fresenius Center for Nephrological Research, Goethe University, Frankfurt, Germany (T.S.)
| | - Ulrich Laufs
- Klinik und Poliklinik für Kardiologie, Universitätsklinikum Leipzig, Germany (J.M.K., I.A.G., M.W., S.E., T.M., M.N.M.-W., A.K., K.E.K., V.F., S.G., U.L., J.-N.B.)
- Central German Heart Alliance (J.M.K., I.A.G., M.W., S.E., T.M., M.N.M.-W., A.K., K.E.K., V.F., S.G., H.T., U.L., J.-N.B.)
| | - Jes-Niels Boeckel
- Klinik und Poliklinik für Kardiologie, Universitätsklinikum Leipzig, Germany (J.M.K., I.A.G., M.W., S.E., T.M., M.N.M.-W., A.K., K.E.K., V.F., S.G., U.L., J.-N.B.)
- Central German Heart Alliance (J.M.K., I.A.G., M.W., S.E., T.M., M.N.M.-W., A.K., K.E.K., V.F., S.G., H.T., U.L., J.-N.B.)
| |
Collapse
|
24
|
Khadka S, Dziadowicz SA, Xu X, Wang L, Hu G, Carrero JA, DiPaolo RJ, Busada JT. Endogenous glucocorticoids are required for normal macrophage activation and gastric Helicobacter pylori immunity. Am J Physiol Gastrointest Liver Physiol 2024; 327:G531-G544. [PMID: 39041676 DOI: 10.1152/ajpgi.00114.2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 07/03/2024] [Accepted: 07/18/2024] [Indexed: 07/24/2024]
Abstract
Glucocorticoids are steroid hormones well known for their potent anti-inflammatory effects. However, their immunomodulatory properties are multifaceted. Increasing evidence suggests that glucocorticoid signaling promotes effective immunity and that disruption of glucocorticoid signaling impairs immune function. In this study, we conditionally deleted the glucocorticoid receptor (GR) in the myeloid lineage using the LysM-Cre driver (myGRKO). We examined the impact on macrophage activation and gastric immune responses to Helicobacter pylori, the best-known risk factor of gastric cancer. Our results indicate that, compared with wild type (WT), glucocorticoid receptor knockout (GRKO) macrophages exhibited higher expression of proinflammatory genes in steroid-free conditions. However, when challenged in vivo, GRKO macrophages exhibited aberrant chromatin landscapes and impaired proinflammatory gene expression profiles. Moreover, gastric colonization with H. pylori revealed impaired gastric immune responses and reduced T cell recruitment in myGRKO mice. As a result, myGRKO mice were protected from atrophic gastritis and pyloric metaplasia development. These results demonstrate a dual role for glucocorticoid signaling in preparing macrophages to respond to bacterial infection but limiting their pathogenic activation. In addition, our results support that macrophages are critical for gastric H. pylori immunity.NEW & NOTEWORTHY Signaling by endogenous glucocorticoids primes macrophages toward more robust responses to pathogens. Disruption of glucocorticoid signaling caused dysregulation of the chromatin landscape, blunted proinflammatory gene activation upon bacterial challenge, and impaired the gastric inflammatory response to Helicobacter pylori infection.
Collapse
Affiliation(s)
- Stuti Khadka
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University School of Medicine, Morgantown, West Virginia, United States
| | - Sebastian A Dziadowicz
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University School of Medicine, Morgantown, West Virginia, United States
| | - Xiaojiang Xu
- Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, New Orleans, Louisiana, United States
| | - Lei Wang
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University School of Medicine, Morgantown, West Virginia, United States
| | - Gangqing Hu
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University School of Medicine, Morgantown, West Virginia, United States
| | - Javier A Carrero
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, Saint Louis, Missouri, United States
| | - Richard J DiPaolo
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, Saint Louis, Missouri, United States
| | - Jonathan T Busada
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University School of Medicine, Morgantown, West Virginia, United States
| |
Collapse
|
25
|
Chen H, Su S, Yang S, Zhao T, Tang P, Luo Q, Zhong Y, Yang J. Effector MoSDT1 enhances Magnaporthe oryzae virulence and plays a dual role in regulating rice defense. PLANT PHYSIOLOGY 2024; 196:1042-1063. [PMID: 39046202 DOI: 10.1093/plphys/kiae364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Accepted: 05/16/2024] [Indexed: 07/25/2024]
Abstract
C2H2 zinc effectors are a class of pathogen proteins that play a dual role in plant-pathogen interactions, promoting pathogenicity and enhancing plant defense. In our previous research, we identified Magnaporthe oryzae Systemic Defense Trigger 1 (MoSDT1) as a C2H2 zinc effector that activates rice (Oryza sativa) defense when overexpressed in rice. However, its regulatory roles in pathogenicity and defense require further investigation. In this study, we generated an MoSDT1 overexpressing strain and 2 knockout strains of M. oryzae to assess the impact of MoSDT1 on pathogenicity, rice defense, and phenotypic characteristics. Our analyses revealed that MoSDT1 substantially influenced vegetative growth, conidia size, and conidiation, and was crucial for the virulence of M. oryzae while suppressing rice defense. MoSDT1 localized to the nucleus and cytoplasm of rice, either dependent or independent of M. oryzae delivery. Through RNA-seq, scRNA-seq, and ChIP-seq, we identified that MoSDT1 modulates rice defense by regulating the phosphorylation and ubiquitination of various rice signaling proteins, including transcription factors, transcription repressors, kinases, phosphatases, and the ubiquitin system. These findings provide valuable insights into the regulatory mechanisms of C2H2 zinc finger effector proteins and offer important foundational information for utilizing their target genes in disease resistance breeding and the design of targets for disease management.
Collapse
Affiliation(s)
- Hongfeng Chen
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Ministry of Education, Yunnan Agricultural University, Kunming 650201, China
| | - Shunyu Su
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Ministry of Education, Yunnan Agricultural University, Kunming 650201, China
| | - Shumin Yang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Ministry of Education, Yunnan Agricultural University, Kunming 650201, China
| | - Tianqi Zhao
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Ministry of Education, Yunnan Agricultural University, Kunming 650201, China
| | - Ping Tang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Ministry of Education, Yunnan Agricultural University, Kunming 650201, China
| | - Qiong Luo
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Ministry of Education, Yunnan Agricultural University, Kunming 650201, China
| | - Yuanyuan Zhong
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Ministry of Education, Yunnan Agricultural University, Kunming 650201, China
| | - Jing Yang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Ministry of Education, Yunnan Agricultural University, Kunming 650201, China
| |
Collapse
|
26
|
Chen EX, Hu SC, Xu JQ, Liu KY, Tang J, Shen XP, Liang X, Xie YL, Ge LX, Luo X, Wang YX, Xiang YL, Ding YB. Suppression of GATA3 promotes epithelial-mesenchymal transition and simultaneous cellular senescence in human extravillous trophoblasts. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2024; 1871:119768. [PMID: 38838858 DOI: 10.1016/j.bbamcr.2024.119768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Revised: 05/16/2024] [Accepted: 05/27/2024] [Indexed: 06/07/2024]
Abstract
The regulatory mechanism of the transcription factor GATA3 in the differentiation and maturation process of extravillous trophoblasts (EVT) in early pregnancy placenta, as well as its relevance to the occurrence of pregnancy disorders, remains poorly understood. This study leveraged single-cell RNA sequencing data from placental organoid models and placental tissue to explore the dynamic changes in GATA3 expression during EVT maturation. The expression pattern exhibited an initial upregulation followed by subsequent downregulation, with aberrant GATA3 localization observed in cases of recurrent miscarriage (RM). By identifying global targets regulated by GATA3 in primary placental EVT cells, JEG3, and HTR8/SVneo cell lines, this study offered insights into its regulatory mechanisms across different EVT cell models. Shared regulatory targets among these cell types and activation of trophoblast cell marker genes emphasized the importance of GATA3 in EVT differentiation and maturation. Knockdown of GATA3 in JEG3 cells led to repression of GATA3-induced epithelial-mesenchymal transition (EMT), as evidenced by changes in marker gene expression levels and enhanced migration ability. Additionally, interference with GATA3 accelerated cellular senescence, as indicated by reduced proliferation rates and increased activity levels for senescence-associated β-galactosidase enzyme, along with elevated expression levels for senescence-associated genes. This study provides comprehensive insights into the dual role of GATA3 in regulating EMT and cellular senescence during EVT differentiation, shedding light on the dynamic changes in GATA3 expression in normal and pathological placental conditions.
Collapse
Affiliation(s)
- En-Xiang Chen
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, China; Department of Toxicology, Joint International Research Laboratory of Reproduction and Development of the Ministry of Education of China, School of Public Health, Chongqing Medical University, Chongqing 400016, China; Hunan Provincial University Key Laboratory of the Fundamental and Clinical Research on Functional Nucleic Acid, Department of Basic Medical Sciences, Changsha Medical University, Hunan 410219, China
| | - Si-Chen Hu
- Department of Toxicology, Joint International Research Laboratory of Reproduction and Development of the Ministry of Education of China, School of Public Health, Chongqing Medical University, Chongqing 400016, China
| | - Jia-Qi Xu
- Department of Toxicology, Joint International Research Laboratory of Reproduction and Development of the Ministry of Education of China, School of Public Health, Chongqing Medical University, Chongqing 400016, China
| | - Kun-Yan Liu
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, China
| | - Jing Tang
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, China; Department of Toxicology, Joint International Research Laboratory of Reproduction and Development of the Ministry of Education of China, School of Public Health, Chongqing Medical University, Chongqing 400016, China
| | - Xi-Peng Shen
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, China
| | - Xiao Liang
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, China
| | - You-Long Xie
- Department of Toxicology, Joint International Research Laboratory of Reproduction and Development of the Ministry of Education of China, School of Public Health, Chongqing Medical University, Chongqing 400016, China
| | - Lu-Xin Ge
- Department of Toxicology, Joint International Research Laboratory of Reproduction and Development of the Ministry of Education of China, School of Public Health, Chongqing Medical University, Chongqing 400016, China; Hunan Provincial Key Laboratory of the Traditional Chinese Medicine Agricultural Biogenomics, Changsha Medical University. Hunan 410219, China
| | - Xin Luo
- Department of Obstetrics, the First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Ying-Xiong Wang
- Department of Toxicology, Joint International Research Laboratory of Reproduction and Development of the Ministry of Education of China, School of Public Health, Chongqing Medical University, Chongqing 400016, China.
| | - Yun-Long Xiang
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, China.
| | - Yu-Bin Ding
- Department of Obstetrics and Gynecology, Women and Children's Hospital of Chongqing Medical University, Chongqing 401147, China; Department of Toxicology, Joint International Research Laboratory of Reproduction and Development of the Ministry of Education of China, School of Public Health, Chongqing Medical University, Chongqing 400016, China.
| |
Collapse
|
27
|
Spathopoulou A, Sauerwein GA, Marteau V, Podlesnic M, Lindlbauer T, Kipura T, Hotze M, Gabassi E, Kruszewski K, Koskuvi M, Réthelyi JM, Apáti Á, Conti L, Ku M, Koal T, Müller U, Talmazan RA, Ojansuu I, Vaurio O, Lähteenvuo M, Lehtonen Š, Mertens J, Kwiatkowski M, Günther K, Tiihonen J, Koistinaho J, Trajanoski Z, Edenhofer F. Integrative metabolomics-genomics analysis identifies key networks in a stem cell-based model of schizophrenia. Mol Psychiatry 2024; 29:3128-3140. [PMID: 38684795 PMCID: PMC11449784 DOI: 10.1038/s41380-024-02568-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 04/12/2024] [Accepted: 04/17/2024] [Indexed: 05/02/2024]
Abstract
Schizophrenia (SCZ) is a neuropsychiatric disorder, caused by a combination of genetic and environmental factors. The etiology behind the disorder remains elusive although it is hypothesized to be associated with the aberrant response to neurotransmitters, such as dopamine and glutamate. Therefore, investigating the link between dysregulated metabolites and distorted neurodevelopment holds promise to offer valuable insights into the underlying mechanism of this complex disorder. In this study, we aimed to explore a presumed correlation between the transcriptome and the metabolome in a SCZ model based on patient-derived induced pluripotent stem cells (iPSCs). For this, iPSCs were differentiated towards cortical neurons and samples were collected longitudinally at various developmental stages, reflecting neuroepithelial-like cells, radial glia, young and mature neurons. The samples were analyzed by both RNA-sequencing and targeted metabolomics and the two modalities were used to construct integrative networks in silico. This multi-omics analysis revealed significant perturbations in the polyamine and gamma-aminobutyric acid (GABA) biosynthetic pathways during rosette maturation in SCZ lines. We particularly observed the downregulation of the glutamate decarboxylase encoding genes GAD1 and GAD2, as well as their protein product GAD65/67 and their biochemical product GABA in SCZ samples. Inhibition of ornithine decarboxylase resulted in further decrease of GABA levels suggesting a compensatory activation of the ornithine/putrescine pathway as an alternative route for GABA production. These findings indicate an imbalance of cortical excitatory/inhibitory dynamics occurring during early neurodevelopmental stages in SCZ. Our study supports the hypothesis of disruption of inhibitory circuits to be causative for SCZ and establishes a novel in silico approach that enables for integrative correlation of metabolic and transcriptomic data of psychiatric disease models.
Collapse
Affiliation(s)
- Angeliki Spathopoulou
- Institute of Molecular Biology & CMBI, Department of Genomics, Stem Cell & Regenerative Medicine, University of Innsbruck, Innsbruck, Austria
| | - Gabriella A Sauerwein
- Institute of Molecular Biology & CMBI, Department of Genomics, Stem Cell & Regenerative Medicine, University of Innsbruck, Innsbruck, Austria
| | - Valentin Marteau
- Institute of Molecular Biology & CMBI, Department of Genomics, Stem Cell & Regenerative Medicine, University of Innsbruck, Innsbruck, Austria
| | - Martina Podlesnic
- Institute of Molecular Biology & CMBI, Department of Genomics, Stem Cell & Regenerative Medicine, University of Innsbruck, Innsbruck, Austria
| | - Theresa Lindlbauer
- Institute of Molecular Biology & CMBI, Department of Genomics, Stem Cell & Regenerative Medicine, University of Innsbruck, Innsbruck, Austria
| | - Tobias Kipura
- Institute of Biochemistry and Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck, Austria
| | - Madlen Hotze
- Institute of Biochemistry and Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck, Austria
| | - Elisa Gabassi
- Institute of Molecular Biology & CMBI, Department of Genomics, Stem Cell & Regenerative Medicine, University of Innsbruck, Innsbruck, Austria
| | - Katharina Kruszewski
- Institute of Molecular Biology & CMBI, Department of Genomics, Stem Cell & Regenerative Medicine, University of Innsbruck, Innsbruck, Austria
| | - Marja Koskuvi
- Neuroscience Center, University of Helsinki, Helsinki, Finland
| | - János M Réthelyi
- Department of Psychiatry and Psychotherapy, Semmelweis University, Budapest, Hungary
| | - Ágota Apáti
- HUN-REN RCNS, Institute of Molecular Life Sciences, Budapest, Hungary
| | - Luciano Conti
- Department of Cellular, Computational and Integrative Biology-CIBIO, University of Trento, Trento, Italy
| | - Manching Ku
- Department of Pediatrics and Adolescent Medicine, Division of Pediatric Hematology and Oncology, Faculty of Medicine, Medical Center - University of Freiburg, Freiburg, Germany
| | | | - Udo Müller
- biocrates life sciences AG, Innsbruck, Austria
| | | | - Ilkka Ojansuu
- Department of Forensic Psychiatry, University of Kuopio, Niuvanniemi Hospital, Kuopio, Finland
| | - Olli Vaurio
- Department of Forensic Psychiatry, University of Kuopio, Niuvanniemi Hospital, Kuopio, Finland
| | - Markku Lähteenvuo
- Department of Forensic Psychiatry, University of Kuopio, Niuvanniemi Hospital, Kuopio, Finland
| | - Šárka Lehtonen
- Neuroscience Center, University of Helsinki, Helsinki, Finland
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Jerome Mertens
- Institute of Molecular Biology & CMBI, Department of Genomics, Stem Cell & Regenerative Medicine, University of Innsbruck, Innsbruck, Austria
- Department of Neurosciences, Sanford Consortium for Regenerative Medicine, University of California San Diego, San Diego, USA
| | - Marcel Kwiatkowski
- Institute of Biochemistry and Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck, Austria
| | - Katharina Günther
- Institute of Molecular Biology & CMBI, Department of Genomics, Stem Cell & Regenerative Medicine, University of Innsbruck, Innsbruck, Austria
| | - Jari Tiihonen
- Department of Forensic Psychiatry, University of Kuopio, Niuvanniemi Hospital, Kuopio, Finland
- Department of Clinical Neuroscience, Karolinska Institutet, and Center for Psychiatry Research, Stockholm City Council, Stockholm, Sweden
| | - Jari Koistinaho
- Institute of Life Science, University of Helsinki, FI-00014, Helsinki, Finland
- Drug Research Program, Division of Pharmacology and Pharmacotherapy, University of Helsinki, Helsinki, Finland
| | - Zlatko Trajanoski
- Institute of Bioinformatics, Biocenter, Medical University Innsbruck, Innsbruck, Austria
| | - Frank Edenhofer
- Institute of Molecular Biology & CMBI, Department of Genomics, Stem Cell & Regenerative Medicine, University of Innsbruck, Innsbruck, Austria.
| |
Collapse
|
28
|
Rahman R, Rahaman MH, Hanson AR, Choo N, Xie J, Townley SL, Shrestha R, Hassankhani R, Islam S, Ramm S, Simpson KJ, Risbridger GP, Best G, Centenera MM, Balk SP, Kichenadasse G, Taylor RA, Butler LM, Tilley WD, Conn SJ, Lawrence MG, Wang S, Selth LA. CDK9 inhibition inhibits multiple oncogenic transcriptional and epigenetic pathways in prostate cancer. Br J Cancer 2024; 131:1092-1105. [PMID: 39117800 PMCID: PMC11405875 DOI: 10.1038/s41416-024-02810-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 07/18/2024] [Accepted: 07/25/2024] [Indexed: 08/10/2024] Open
Abstract
BACKGROUND Cyclin-dependent kinase 9 (CDK9) stimulates oncogenic transcriptional pathways in cancer and CDK9 inhibitors have emerged as promising therapeutic candidates. METHODS The activity of an orally bioavailable CDK9 inhibitor, CDKI-73, was evaluated in prostate cancer cell lines, a xenograft mouse model, and patient-derived tumor explants and organoids. Expression of CDK9 was evaluated in clinical specimens by mining public datasets and immunohistochemistry. Effects of CDKI-73 on prostate cancer cells were determined by cell-based assays, molecular profiling and transcriptomic/epigenomic approaches. RESULTS CDKI-73 inhibited proliferation and enhanced cell death in diverse in vitro and in vivo models of androgen receptor (AR)-driven and AR-independent models. Mechanistically, CDKI-73-mediated inhibition of RNA polymerase II serine 2 phosphorylation resulted in reduced expression of BCL-2 anti-apoptotic factors and transcriptional defects. Transcriptomic and epigenomic approaches revealed that CDKI-73 suppressed signaling pathways regulated by AR, MYC, and BRD4, key drivers of dysregulated transcription in prostate cancer, and reprogrammed cancer-associated super-enhancers. These latter findings prompted the evaluation of CDKI-73 with the BRD4 inhibitor AZD5153, a combination that was synergistic in patient-derived organoids and in vivo. CONCLUSION Our work demonstrates that CDK9 inhibition disrupts multiple oncogenic pathways and positions CDKI-73 as a promising therapeutic agent for prostate cancer, particularly aggressive, therapy-resistant subtypes.
Collapse
Affiliation(s)
- Razia Rahman
- Flinders University, College of Medicine and Public Health, Flinders Health and Medical Research Institute, Bedford Park, SA, Australia
| | - Muhammed H Rahaman
- Drug Discovery and Development, Clinical and Health Sciences, University of South Australia, Adelaide, SA, Australia
| | - Adrienne R Hanson
- Flinders University, College of Medicine and Public Health, Flinders Health and Medical Research Institute, Bedford Park, SA, Australia
| | - Nicholas Choo
- Biomedicine Discovery Institute Cancer Program, Prostate Cancer Research Group, Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC, Australia
| | - Jianling Xie
- Flinders University, College of Medicine and Public Health, Flinders Health and Medical Research Institute, Bedford Park, SA, Australia
| | - Scott L Townley
- Flinders University, College of Medicine and Public Health, Flinders Health and Medical Research Institute, Bedford Park, SA, Australia
| | - Raj Shrestha
- Flinders University, College of Medicine and Public Health, Flinders Health and Medical Research Institute, Bedford Park, SA, Australia
- Flinders University, Freemasons Centre for Male Health and Wellbeing, Bedford Park, SA, Australia
| | - Ramin Hassankhani
- Drug Discovery and Development, Clinical and Health Sciences, University of South Australia, Adelaide, SA, Australia
| | - Saiful Islam
- Drug Discovery and Development, Clinical and Health Sciences, University of South Australia, Adelaide, SA, Australia
| | - Susanne Ramm
- Victorian Centre for Functional Genomics, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, Australia
| | - Kaylene J Simpson
- Victorian Centre for Functional Genomics, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, Australia
- Department of Biochemistry and Pharmacology, University of Melbourne, Parkville, VIC, Australia
| | - Gail P Risbridger
- Biomedicine Discovery Institute Cancer Program, Prostate Cancer Research Group, Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC, Australia
- The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, Australia
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Cabrini Institute, Cabrini Health, Malvern, Melbourne, VIC, Australia
- Melbourne Urological Research Alliance (MURAL), Monash Biomedicine Discovery Institute Cancer Program, Monash University, Clayton, VIC, Australia
| | - Giles Best
- Flinders University, College of Medicine and Public Health, Flinders Health and Medical Research Institute, Bedford Park, SA, Australia
| | - Margaret M Centenera
- South Australian Health and Medical Research Institute, Adelaide, SA, Australia
- Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, SA, Australia
| | - Steven P Balk
- Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Ganessan Kichenadasse
- Flinders University, College of Medicine and Public Health, Flinders Health and Medical Research Institute, Bedford Park, SA, Australia
- Department of Medical Oncology, Flinders Medical Centre, Southern Adelaide Local Health Network, Adelaide, SA, South Australia
| | - Renea A Taylor
- The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, Australia
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Cabrini Institute, Cabrini Health, Malvern, Melbourne, VIC, Australia
- Melbourne Urological Research Alliance (MURAL), Monash Biomedicine Discovery Institute Cancer Program, Monash University, Clayton, VIC, Australia
- Biomedicine Discovery Institute Cancer Program, Department of Physiology, Monash University, Clayton, VIC, Australia
| | - Lisa M Butler
- South Australian Health and Medical Research Institute, Adelaide, SA, Australia
- Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, SA, Australia
| | - Wayne D Tilley
- Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, SA, Australia
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical School, The University of Adelaide, Adelaide, SA, Australia
| | - Simon J Conn
- Flinders University, College of Medicine and Public Health, Flinders Health and Medical Research Institute, Bedford Park, SA, Australia
| | - Mitchell G Lawrence
- Biomedicine Discovery Institute Cancer Program, Prostate Cancer Research Group, Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC, Australia
- The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, Australia
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Cabrini Institute, Cabrini Health, Malvern, Melbourne, VIC, Australia
- Melbourne Urological Research Alliance (MURAL), Monash Biomedicine Discovery Institute Cancer Program, Monash University, Clayton, VIC, Australia
| | - Shudong Wang
- Drug Discovery and Development, Clinical and Health Sciences, University of South Australia, Adelaide, SA, Australia
| | - Luke A Selth
- Flinders University, College of Medicine and Public Health, Flinders Health and Medical Research Institute, Bedford Park, SA, Australia.
- Flinders University, Freemasons Centre for Male Health and Wellbeing, Bedford Park, SA, Australia.
- Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, SA, Australia.
| |
Collapse
|
29
|
Saeki K, Pan R, Lee E, Kurotaki D, Ozato K. IRF8 defines the epigenetic landscape in postnatal microglia, thereby directing their transcriptome programs. Nat Immunol 2024; 25:1928-1942. [PMID: 39313544 DOI: 10.1038/s41590-024-01962-2] [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: 08/14/2023] [Accepted: 08/12/2024] [Indexed: 09/25/2024]
Abstract
Microglia are innate immune cells in the brain. Transcription factor IRF8 (interferon regulatory factor 8) is highly expressed in microglia. However, its role in postnatal microglia development is unknown. We demonstrate that IRF8 binds stepwise to enhancer regions of postnatal microglia along with Sall1 and PU.1, reaching a maximum after day 14. IRF8 binding correlated with a stepwise increase in chromatin accessibility, which preceded the initiation of microglia-specific transcriptome. Constitutive and postnatal Irf8 deletion led to a loss of microglia identity and gain of disease-associated microglia (DAM)-like genes. Combined analysis of single-cell (sc)RNA sequencing and single-cell transposase-accessible chromatin with sequencing (scATAC-seq) revealed a correlation between chromatin accessibility and transcriptome at a single-cell level. IRF8 was also required for microglia-specific DNA methylation patterns. Last, in the 5xFAD model, constitutive and postnatal Irf8 deletion reduced the interaction of microglia with amyloidβ plaques and the size of plaques, lessening neuronal loss. Together, IRF8 sets the epigenetic landscape, which is required for postnatal microglia gene expression.
Collapse
Affiliation(s)
- Keita Saeki
- Division of Developmental Biology, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA.
| | - Richard Pan
- Division of Developmental Biology, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
- Department of Neuroscience, Columbia University, School of Medicine, New York, NY, USA
| | - Eunju Lee
- Division of Developmental Biology, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Daisuke Kurotaki
- Laboratory of Chromatin Organization in Immune Cell Development, International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Keiko Ozato
- Division of Developmental Biology, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA.
| |
Collapse
|
30
|
Schlachetzki JC, Gianella S, Ouyang Z, Lana AJ, Yang X, O'Brien S, Challacombe JF, Gaskill PJ, Jordan-Sciutto KL, Chaillon A, Moore D, Achim CL, Ellis RJ, Smith DM, Glass CK. Gene expression and chromatin conformation of microglia in virally suppressed people with HIV. Life Sci Alliance 2024; 7:e202402736. [PMID: 39060113 PMCID: PMC11282357 DOI: 10.26508/lsa.202402736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 07/14/2024] [Accepted: 07/15/2024] [Indexed: 07/28/2024] Open
Abstract
The presence of HIV in sequestered reservoirs is a central impediment to a functional cure, allowing HIV to persist despite life-long antiretroviral therapy (ART), and driving a variety of comorbid conditions. Our understanding of the latent HIV reservoir in the central nervous system is incomplete, because of difficulties in accessing human central nervous system tissues. Microglia contribute to HIV reservoirs, but the molecular phenotype of HIV-infected microglia is poorly understood. We leveraged the unique "Last Gift" rapid autopsy program, in which people with HIV are closely followed until days or even hours before death. Microglial populations were heterogeneous regarding their gene expression profiles but showed similar chromatin accessibility landscapes. Despite ART, we detected occasional microglia containing cell-associated HIV RNA and HIV DNA integrated into open regions of the host's genome (∼0.005%). Microglia with detectable HIV RNA showed an inflammatory phenotype. These results demonstrate a distinct myeloid cell reservoir in the brains of people with HIV despite suppressive ART. Strategies for curing HIV and neurocognitive impairment will need to consider the myeloid compartment to be successful.
Collapse
Affiliation(s)
- Johannes Cm Schlachetzki
- https://ror.org/01vf2g217 Department of Cellular and Molecular Medicine, University of California San Diego, San Diego, CA, USA
- https://ror.org/01vf2g217 Department of Neurosciences, University of California San Diego, San Diego, CA, USA
| | - Sara Gianella
- https://ror.org/01vf2g217 Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California San Diego, San Diego, CA, USA
| | - Zhengyu Ouyang
- https://ror.org/01vf2g217 Department of Cellular and Molecular Medicine, University of California San Diego, San Diego, CA, USA
| | - Addison J Lana
- https://ror.org/01vf2g217 Department of Cellular and Molecular Medicine, University of California San Diego, San Diego, CA, USA
| | - Xiaoxu Yang
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
| | - Sydney O'Brien
- https://ror.org/01vf2g217 Department of Cellular and Molecular Medicine, University of California San Diego, San Diego, CA, USA
| | - Jean F Challacombe
- https://ror.org/01vf2g217 Department of Cellular and Molecular Medicine, University of California San Diego, San Diego, CA, USA
| | - Peter J Gaskill
- Department of Pharmacology and Physiology, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Kelly L Jordan-Sciutto
- Department of Oral Medicine, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Antoine Chaillon
- https://ror.org/01vf2g217 Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California San Diego, San Diego, CA, USA
| | - David Moore
- https://ror.org/01vf2g217 Department of Psychiatry, University of California San Diego, San Diego, CA, USA
| | - Cristian L Achim
- https://ror.org/01vf2g217 Department of Pathology, University of California San Diego, San Diego, CA, USA
| | - Ronald J Ellis
- https://ror.org/01vf2g217 Department of Neurosciences, University of California San Diego, San Diego, CA, USA
| | - Davey M Smith
- https://ror.org/01vf2g217 Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California San Diego, San Diego, CA, USA
| | - Christopher K Glass
- https://ror.org/01vf2g217 Department of Cellular and Molecular Medicine, University of California San Diego, San Diego, CA, USA
| |
Collapse
|
31
|
Yoon HS, Fujino K, Liu S, Takano T, Tsugama D. VIP1 and its close homologs confer mechanical stress tolerance in Arabidopsis leaves. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 215:109021. [PMID: 39137679 DOI: 10.1016/j.plaphy.2024.109021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Revised: 07/19/2024] [Accepted: 08/05/2024] [Indexed: 08/15/2024]
Abstract
VIP1, an Arabidopsis thaliana basic leucine zipper transcription factor, and its close homologs are imported from the cytoplasm to the nucleus when cells are exposed to mechanical stress. They bind to AGCTG (G/T) and regulate mechanical stress responses in roots. However, their role in leaves is unclear. To clarify this, mutant lines (QM1 and QM2) that lack the functions of VIP1 and its close homologs (bZIP29, bZIP30 and PosF21) were generated. Brushing more severely damaged QM1 and QM2 leaves than wild-type leaves. Genes regulating stress responses and cell wall properties were downregulated in brushed QM2 leaves and upregulated in brushed VIP1-GFP-overexpressing (VIP1-GFPox) leaves compared to wild-type leaves in a transcriptome analysis. The VIP1-binding sequence AGCTG (G/T) was enriched in the promoters of genes downregulated in brushed QM2 leaves compared to wild-type leaves and in those upregulated in brushed VIP1-GFPox leaves. Calmodulin-binding transcription activators (CAMTAs) are known regulators of mechanical stress responses, and the CAMTA-binding sequence CGCGT was enriched in the promoters of genes upregulated in the brushed QM2 leaves and in those downregulated in the brushed VIP1-GFPox leaves. These findings suggest that VIP1 and its homologs upregulate genes via AGCTG (G/T) and influence CAMTA-dependent gene expression to enhance mechanical stress tolerance in leaves.
Collapse
Affiliation(s)
- Hyuk Sung Yoon
- Asian Research Center for Bioresource and Environmental Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Midori-cho, Nishitokyo-shi, Tokyo, 188-0002, Japan.
| | - Kaien Fujino
- Laboratory of Crop Physiology, Research Faculty of Agriculture, Hokkaido University, Kita 9 Nishi 9 Kita-ku, Sapporo-shi, Hokkaido, 060-8589, Japan.
| | - Shenkui Liu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Lin'an, Hangzhou, 311300, PR China.
| | - Tetsuo Takano
- Asian Research Center for Bioresource and Environmental Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Midori-cho, Nishitokyo-shi, Tokyo, 188-0002, Japan.
| | - Daisuke Tsugama
- Asian Research Center for Bioresource and Environmental Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Midori-cho, Nishitokyo-shi, Tokyo, 188-0002, Japan.
| |
Collapse
|
32
|
Qazi M, Gupta SK, Takano T, Tsugama D. Overexpression of a pearl millet WRKY transcription factor gene, PgWRKY74, in Arabidopsis retards shoot growth under dehydration and salinity-stressed conditions. Biotechnol Lett 2024; 46:851-860. [PMID: 38717664 DOI: 10.1007/s10529-024-03492-1] [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: 11/24/2023] [Revised: 02/26/2024] [Accepted: 04/14/2024] [Indexed: 09/21/2024]
Abstract
Pearl millet (Cenchrus americanus) is a cereal crop that can tolerate high temperatures, drought, and low-fertility conditions where other crops lose productivity. However, genes regulating this ability are largely unknown. Transcription factors (TFs) regulate transcription of their target genes, regulate downstream biological processes, and thus are candidates for regulators of such tolerance of pearl millet. PgWRKY74 encodes a group IIc WRKY TF in pearl millet and is downregulated by drought. PgWRKY74 may have a role in drought tolerance. The objective of this study was to gain insights into the physiological and biochemical functions of PgWRKY74. Yeast one-hybrid and gel shift assays were performed to examine transcriptional activation potential and deoxyribonucleic acid (DNA)-binding ability, respectively. Transgenic Arabidopsis thaliana plants overexpressing PgWRKY74-green fluorescent protein (GFP) fusion gene were generated and tested for growth and stress-responsive gene expression under mannitol and NaCl-stressed conditions. A construct with PgWRKY74 enabled yeast reporter cells to survive on test media in the yeast one-hybrid assays. The electrophoretic mobility of DNA with putative WRKY TF-binding motifs was lower in the presence of a recombinant PgWRKY74 protein than its absence. The PgWRKY74-GFP-overexpressing Arabidopsis plants exhibited smaller rosette areas than did wild-type plants under mannitol-stressed and NaCl-stressed conditions, and exhibited weaker expression of RD29B, which is induced by the stress-related phytohormone abscisic acid (ABA), under the mannitol-stressed condition. PgWRKY74 have transcriptional activation potential and DNA-binding ability, and can negatively regulate plant responses to mannitol and NaCl stresses, possibly by decreasing ABA levels or ABA sensitivity.
Collapse
Affiliation(s)
- Maimuna Qazi
- Asian Research Center for Bioresource and Environmental Sciences (ARC-BRES), Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Midori-Cho, Nishi-Tokyo-Shi, Tokyo, 188-0002, Japan
| | - Shashi Kumar Gupta
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Telangana, India
| | - Tetsuo Takano
- Asian Research Center for Bioresource and Environmental Sciences (ARC-BRES), Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Midori-Cho, Nishi-Tokyo-Shi, Tokyo, 188-0002, Japan
| | - Daisuke Tsugama
- Asian Research Center for Bioresource and Environmental Sciences (ARC-BRES), Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Midori-Cho, Nishi-Tokyo-Shi, Tokyo, 188-0002, Japan.
| |
Collapse
|
33
|
Kumagai Y. BootCellNet, a resampling-based procedure, promotes unsupervised identification of cell populations via robust inference of gene regulatory networks. PLoS Comput Biol 2024; 20:e1012480. [PMID: 39348410 DOI: 10.1371/journal.pcbi.1012480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 09/11/2024] [Indexed: 10/02/2024] Open
Abstract
Recent advances in measurement technologies, particularly single-cell RNA sequencing (scRNA-seq), have revolutionized our ability to acquire large amounts of omics-level data on cellular states. As measurement techniques evolve, there has been an increasing need for data analysis methodologies, especially those focused on cell-type identification and inference of gene regulatory networks (GRNs). We have developed a new method named BootCellNet, which employs smoothing and resampling to infer GRNs. Using the inferred GRNs, BootCellNet further infers the minimum dominating set (MDS), a set of genes that determines the dynamics of the entire network. We have demonstrated that BootCellNet robustly infers GRNs and their MDSs from scRNA-seq data and facilitates unsupervised identification of cell clusters using scRNA-seq datasets of peripheral blood mononuclear cells and hematopoiesis. It has also identified COVID-19 patient-specific cells and their potential regulatory transcription factors. BootCellNet not only identifies cell types in an unsupervised and explainable way but also provides insights into the characteristics of identified cell types through the inference of GRNs and MDS.
Collapse
Affiliation(s)
- Yutaro Kumagai
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, Higashi, Tsukuba, Ibaraki, Japan
| |
Collapse
|
34
|
Zhang X, Huang G, Jiang T, Meng L, Li T, Zhang G, Wu N, Chen X, Zhao B, Li N, Wu S, Guo J, Zheng R, Ji Z, Xu Z, Wang Z, Deng D, Tan Y, Xu W. CEP112 coordinates translational regulation of essential fertility genes during spermiogenesis through phase separation in humans and mice. Nat Commun 2024; 15:8465. [PMID: 39349455 PMCID: PMC11443074 DOI: 10.1038/s41467-024-52705-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Accepted: 09/19/2024] [Indexed: 10/02/2024] Open
Abstract
Spermiogenesis, the complex transformation of haploid spermatids into mature spermatozoa, relies on precise spatiotemporal regulation of gene expression at the post-transcriptional level. The mechanisms underlying this critical process remain incompletely understood. Here, we identify centrosomal protein 112 (CEP112) as an essential regulator of mRNA translation during this critical developmental process. Mutations in CEP112 are discovered in oligoasthenoteratospermic patients, and Cep112-deficient male mice recapitulate key phenotypes of human asthenoteratozoospermia. CEP112 localizes to the neck and atypical centrioles of mature sperm and forms RNA granules during spermiogenesis, enriching target mRNAs such as Fsip2, Cfap61, and Cfap74. Through multi-omics analyses and the TRICK reporter assay, we demonstrate that CEP112 orchestrates the translation of target mRNAs. Co-immunoprecipitation and mass spectrometry identify CEP112's interactions with translation-related proteins, including hnRNPA2B1, EEF1A1, and EIF4A1. In vitro, CEP112 undergoes liquid-liquid phase separation, forming condensates that recruit essential proteins and mRNAs. Moreover, variants in patient-derived CEP112 disrupt phase separation and impair translation efficiency. Our results suggest that CEP112 mediates the assembly of RNA granules through liquid-liquid phase separation to control the post-transcriptional expression of fertility-related genes. This study not only clarifies CEP112's role in spermatogenesis but also highlights the role of phase separation in translational regulation, providing insights into male infertility and suggesting potential therapeutic targets.
Collapse
Affiliation(s)
- Xueguang Zhang
- Joint Lab of Reproductive Medicine of SCU-CUHK, Lab of Reproductive genetics and Epigenetics, Department of Obstetrics/Gynecology, Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, West China Second University Hospital, Sichuan University, 610041, Chengdu, China
| | - Gelin Huang
- Joint Lab of Reproductive Medicine of SCU-CUHK, Lab of Reproductive genetics and Epigenetics, Department of Obstetrics/Gynecology, Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, West China Second University Hospital, Sichuan University, 610041, Chengdu, China
| | - Ting Jiang
- Joint Lab of Reproductive Medicine of SCU-CUHK, Lab of Reproductive genetics and Epigenetics, Department of Obstetrics/Gynecology, Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, West China Second University Hospital, Sichuan University, 610041, Chengdu, China
| | - Lanlan Meng
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive & Genetic Hospital of CITIC-Xiangya, 410008, Changsha, China
| | - Tongtong Li
- Joint Lab of Reproductive Medicine of SCU-CUHK, Lab of Reproductive genetics and Epigenetics, Department of Obstetrics/Gynecology, Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, West China Second University Hospital, Sichuan University, 610041, Chengdu, China
| | - Guohui Zhang
- Key Laboratory of Reproductive Medicine, Sichuan Provincial Maternity and Child Health Care Hospital, 610041, Chengdu, China
| | - Nan Wu
- State Key Laboratory of Cellular Stress Biology, National Institute for Data Science in Health and Medicine, School of Life Sciences, Xiamen University, 361005, Xiamen, China
| | - Xinyi Chen
- Department of Obstetrics, Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University, Chengdu, 610041, China
| | - Bingwang Zhao
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, 100101, Beijing, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Nana Li
- Shandong Provincial Key Laboratory of Animal Cell and Developmental Biology, School of Life Sciences, Shandong University, 266237, Qingdao, China
| | - Sixian Wu
- Joint Lab of Reproductive Medicine of SCU-CUHK, Lab of Reproductive genetics and Epigenetics, Department of Obstetrics/Gynecology, Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, West China Second University Hospital, Sichuan University, 610041, Chengdu, China
| | - Junceng Guo
- Joint Lab of Reproductive Medicine of SCU-CUHK, Lab of Reproductive genetics and Epigenetics, Department of Obstetrics/Gynecology, Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, West China Second University Hospital, Sichuan University, 610041, Chengdu, China
| | - Rui Zheng
- Joint Lab of Reproductive Medicine of SCU-CUHK, Lab of Reproductive genetics and Epigenetics, Department of Obstetrics/Gynecology, Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, West China Second University Hospital, Sichuan University, 610041, Chengdu, China
| | - Zhiliang Ji
- State Key Laboratory of Cellular Stress Biology, National Institute for Data Science in Health and Medicine, School of Life Sciences, Xiamen University, 361005, Xiamen, China
| | - Zhigang Xu
- Shandong Provincial Key Laboratory of Animal Cell and Developmental Biology, School of Life Sciences, Shandong University, 266237, Qingdao, China
| | - Zhenbo Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, 100101, Beijing, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Dong Deng
- Department of Obstetrics, Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University, Chengdu, 610041, China
| | - Yueqiu Tan
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive & Genetic Hospital of CITIC-Xiangya, 410008, Changsha, China.
| | - Wenming Xu
- Joint Lab of Reproductive Medicine of SCU-CUHK, Lab of Reproductive genetics and Epigenetics, Department of Obstetrics/Gynecology, Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, West China Second University Hospital, Sichuan University, 610041, Chengdu, China.
| |
Collapse
|
35
|
Ma Z, Huang X, Kuang J, Wang Q, Qin Y, Huang T, Liang Z, Li W, Fu Y, Li P, Fan Y, Zhai Z, Wang X, Ming J, Zhao C, Wang B, Pei D. Cpt1a Drives primed-to-naïve pluripotency transition through lipid remodeling. Commun Biol 2024; 7:1223. [PMID: 39349670 PMCID: PMC11442460 DOI: 10.1038/s42003-024-06874-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Accepted: 09/10/2024] [Indexed: 10/04/2024] Open
Abstract
Metabolism has been implicated in cell fate determination, particularly through epigenetic modifications. Similarly, lipid remodeling also plays a role in regulating cell fate. Here, we present comprehensive lipidomics analysis during BMP4-driven primed to naive pluripotency transition or BiPNT and demonstrate that lipid remodeling plays an essential role. We further identify Cpt1a as a rate-limiting factor in BiPNT, driving lipid remodeling and metabolic reprogramming while simultaneously increasing intracellular acetyl-CoA levels and enhancing H3K27ac at chromatin open sites. Perturbation of BiPNT by histone acetylation inhibitors suppresses lipid remodeling and pluripotency transition. Together, our study suggests that lipid remodeling promotes pluripotency transitions and further regulates cell fate decisions, implicating Cpt1a as a critical regulator between primed-naive cell fate control.
Collapse
Affiliation(s)
- Zhaoyi Ma
- College of Life Sciences, Zhejiang University, Hangzhou, China
- Laboratory of Cell Fate Control, School of Life Sciences, Westlake University, Hangzhou, China
| | - Xingnan Huang
- Laboratory of Cell Fate Control, School of Life Sciences, Westlake University, Hangzhou, China
| | - Junqi Kuang
- Laboratory of Cell Fate Control, School of Life Sciences, Westlake University, Hangzhou, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
| | - Qiannan Wang
- Laboratory of Cell Fate Control, School of Life Sciences, Westlake University, Hangzhou, China
| | - Yue Qin
- Laboratory of Cell Fate Control, School of Life Sciences, Westlake University, Hangzhou, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
| | - Tao Huang
- College of Life Sciences, Zhejiang University, Hangzhou, China
- Laboratory of Cell Fate Control, School of Life Sciences, Westlake University, Hangzhou, China
| | - Zechuan Liang
- College of Life Sciences, Zhejiang University, Hangzhou, China
- Laboratory of Cell Fate Control, School of Life Sciences, Westlake University, Hangzhou, China
| | - Wei Li
- Laboratory on Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yu Fu
- Laboratory of Cell Fate Control, School of Life Sciences, Westlake University, Hangzhou, China
| | - Pengli Li
- Laboratory on Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yixin Fan
- Laboratory on Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ziwei Zhai
- Laboratory on Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiaomin Wang
- Laboratory of Cell Fate Control, School of Life Sciences, Westlake University, Hangzhou, China
| | - Jin Ming
- Laboratory of Cell Fate Control, School of Life Sciences, Westlake University, Hangzhou, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, China
| | - Chengchen Zhao
- Laboratory of Cell Fate Control, School of Life Sciences, Westlake University, Hangzhou, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- Zhejiang Key Laboratory of Biomedical Intelligent Computing Technology, Hangzhou, China
| | - Bo Wang
- Laboratory of Cell Fate Control, School of Life Sciences, Westlake University, Hangzhou, China
- Zhejiang Key Laboratory of Biomedical Intelligent Computing Technology, Hangzhou, China
- Zhejiang University of Science and Technology School of Information and Electronic Engineering, Hangzhou, China
| | - Duanqing Pei
- Laboratory of Cell Fate Control, School of Life Sciences, Westlake University, Hangzhou, China.
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China.
| |
Collapse
|
36
|
Hisler V, Bardot P, Detilleux D, Bernardini A, Stierle M, Sanchez EG, Richard C, Arab LH, Ehrhard C, Morlet B, Hadzhiev Y, Jung M, Le Gras S, Négroni L, Müller F, Tora L, Vincent SD. RNA polymerase II transcription initiation in holo-TFIID-depleted mouse embryonic stem cells. Cell Rep 2024; 43:114791. [PMID: 39352809 DOI: 10.1016/j.celrep.2024.114791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 07/09/2024] [Accepted: 09/07/2024] [Indexed: 10/04/2024] Open
Abstract
The recognition of core promoter sequences by TFIID is the first step in RNA polymerase II (Pol II) transcription initiation. Metazoan holo-TFIID is a trilobular complex, composed of the TATA binding protein (TBP) and 13 TBP-associated factors (TAFs). Why and how TAFs are necessary for the formation of TFIID domains and how they contribute to transcription initiation remain unclear. Inducible TAF7 or TAF10 depletion, followed by comprehensive analysis of TFIID subcomplex formation, chromatin binding, and nascent transcription in mouse embryonic stem cells, result in the formation of a TAF7-lacking TFIID or a minimal core-TFIID complex, respectively. These partial complexes support TBP recruitment at promoters and nascent Pol II transcription at most genes early after depletion, but importantly, TAF10 is necessary for efficient Pol II pausing. We show that partially assembled TFIID complexes can sustain Pol II transcription initiation but cannot replace holo-TFIID over several cell divisions and/or development.
Collapse
Affiliation(s)
- Vincent Hisler
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67400 Illkirch, France; CNRS, UMR7104, 67400 Illkirch, France; INSERM, U1258, 67400 Illkirch, France; Université de Strasbourg, 67400 Illkirch, France
| | - Paul Bardot
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67400 Illkirch, France; CNRS, UMR7104, 67400 Illkirch, France; INSERM, U1258, 67400 Illkirch, France; Université de Strasbourg, 67400 Illkirch, France
| | - Dylane Detilleux
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67400 Illkirch, France; CNRS, UMR7104, 67400 Illkirch, France; INSERM, U1258, 67400 Illkirch, France; Université de Strasbourg, 67400 Illkirch, France
| | - Andrea Bernardini
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67400 Illkirch, France; CNRS, UMR7104, 67400 Illkirch, France; INSERM, U1258, 67400 Illkirch, France; Université de Strasbourg, 67400 Illkirch, France
| | - Matthieu Stierle
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67400 Illkirch, France; CNRS, UMR7104, 67400 Illkirch, France; INSERM, U1258, 67400 Illkirch, France; Université de Strasbourg, 67400 Illkirch, France
| | - Emmanuel Garcia Sanchez
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67400 Illkirch, France; CNRS, UMR7104, 67400 Illkirch, France; INSERM, U1258, 67400 Illkirch, France; Université de Strasbourg, 67400 Illkirch, France
| | - Claire Richard
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67400 Illkirch, France; CNRS, UMR7104, 67400 Illkirch, France; INSERM, U1258, 67400 Illkirch, France; Université de Strasbourg, 67400 Illkirch, France
| | - Lynda Hadj Arab
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67400 Illkirch, France; CNRS, UMR7104, 67400 Illkirch, France; INSERM, U1258, 67400 Illkirch, France; Université de Strasbourg, 67400 Illkirch, France
| | - Cynthia Ehrhard
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67400 Illkirch, France; CNRS, UMR7104, 67400 Illkirch, France; INSERM, U1258, 67400 Illkirch, France; Université de Strasbourg, 67400 Illkirch, France
| | - Bastien Morlet
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67400 Illkirch, France; CNRS, UMR7104, 67400 Illkirch, France; INSERM, U1258, 67400 Illkirch, France; Université de Strasbourg, 67400 Illkirch, France; Proteomics Platform (IGBMC), 67400 Illkirch, France
| | - Yavor Hadzhiev
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Matthieu Jung
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67400 Illkirch, France; CNRS, UMR7104, 67400 Illkirch, France; INSERM, U1258, 67400 Illkirch, France; Université de Strasbourg, 67400 Illkirch, France; GenomEast (IGBMC), 67400 Illkirch, France
| | - Stéphanie Le Gras
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67400 Illkirch, France; CNRS, UMR7104, 67400 Illkirch, France; INSERM, U1258, 67400 Illkirch, France; Université de Strasbourg, 67400 Illkirch, France; GenomEast (IGBMC), 67400 Illkirch, France
| | - Luc Négroni
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67400 Illkirch, France; CNRS, UMR7104, 67400 Illkirch, France; INSERM, U1258, 67400 Illkirch, France; Université de Strasbourg, 67400 Illkirch, France; Proteomics Platform (IGBMC), 67400 Illkirch, France
| | - Ferenc Müller
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - László Tora
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67400 Illkirch, France; CNRS, UMR7104, 67400 Illkirch, France; INSERM, U1258, 67400 Illkirch, France; Université de Strasbourg, 67400 Illkirch, France
| | - Stéphane D Vincent
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67400 Illkirch, France; CNRS, UMR7104, 67400 Illkirch, France; INSERM, U1258, 67400 Illkirch, France; Université de Strasbourg, 67400 Illkirch, France.
| |
Collapse
|
37
|
Xiong J, Zhou Z, Jiang Y, Li Q, Geng Z, Guo J, Yan C, Zhang J. Hypoxic stabilization of RIPOR3 mRNA via METTL3-mediated m 6A methylation drives breast cancer progression and metastasis. Oncogene 2024:10.1038/s41388-024-03180-4. [PMID: 39341989 DOI: 10.1038/s41388-024-03180-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 09/22/2024] [Accepted: 09/24/2024] [Indexed: 10/01/2024]
Abstract
Dysregulated N6-methyladenosine (m6A) modification has been associated with breast cancer pathogenesis. Hypoxia which characterizes solid tumors is known to reprogram the m6A epitranscriptome, but the underlying mechanisms of how this process contributes to breast cancer progression remain poorly understood. Through integrative analyses of m6A-RIP sequencing and RNA sequencing databases, we reveal a cluster of mRNAs with upregulated m6A methylation and expression under hypoxia, that are enriched by many oncogenic pathways, including PI3K-Akt signaling. Furthermore, we identify the mRNA, RIPOR3, as a target of METTL3-mediated m6A methylation in response to hypoxia. We find that m6A methylation stabilizes RIPOR3, increasing its protein expression in a METTL3 catalytic activity-dependent manner, and consequently driving breast tumor growth and metastasis. RIPOR3 is found to be overexpressed in breast cancer cell lines and tumor tissues from breast cancer patients, in whom elevated RIPOR3 is associated with a worse prognosis. Mechanistically, we show that RIPOR3 interacts with EGFR and is essential for the PI3K-Akt pathway activation. In conclusion, we identify RIPOR3 as a hypoxia-stabilized oncogenic driver via METTL3-mediated m6A methylation, thus provide a potential therapeutic target for breast cancer.
Collapse
Affiliation(s)
- Jingjing Xiong
- Department of Urology, Zhongnan Hospital of Wuhan University, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Wuhan University, Wuhan, China
| | - Zirui Zhou
- Department of Urology, Zhongnan Hospital of Wuhan University, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Wuhan University, Wuhan, China
| | - Yulong Jiang
- Department of Urology, Zhongnan Hospital of Wuhan University, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Wuhan University, Wuhan, China
| | - Qifang Li
- Department of Urology, Zhongnan Hospital of Wuhan University, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Wuhan University, Wuhan, China
| | - Zuhan Geng
- Department of Thoracic Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jiahao Guo
- Department of Urology, Zhongnan Hospital of Wuhan University, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Wuhan University, Wuhan, China
| | - Chaojun Yan
- Department of Urology, Zhongnan Hospital of Wuhan University, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Wuhan University, Wuhan, China.
| | - Jing Zhang
- Department of Urology, Zhongnan Hospital of Wuhan University, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Wuhan University, Wuhan, China.
| |
Collapse
|
38
|
Banerjee A, Zhang S, Bahar I. Genome structural dynamics: insights from Gaussian network analysis of Hi-C data. Brief Funct Genomics 2024; 23:525-537. [PMID: 38654598 PMCID: PMC11428154 DOI: 10.1093/bfgp/elae014] [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: 11/02/2023] [Revised: 03/11/2024] [Accepted: 04/02/2024] [Indexed: 04/26/2024] Open
Abstract
Characterization of the spatiotemporal properties of the chromatin is essential to gaining insights into the physical bases of gene co-expression, transcriptional regulation and epigenetic modifications. The Gaussian network model (GNM) has proven in recent work to serve as a useful tool for modeling chromatin structural dynamics, using as input high-throughput chromosome conformation capture data. We focus here on the exploration of the collective dynamics of chromosomal structures at hierarchical levels of resolution, from single gene loci to topologically associating domains or entire chromosomes. The GNM permits us to identify long-range interactions between gene loci, shedding light on the role of cross-correlations between distal regions of the chromosomes in regulating gene expression. Notably, GNM analysis performed across diverse cell lines highlights the conservation of the global/cooperative movements of the chromatin across different types of cells. Variations driven by localized couplings between genomic loci, on the other hand, underlie cell differentiation, underscoring the significance of the four-dimensional properties of the genome in defining cellular identity. Finally, we demonstrate the close relation between the cell type-dependent mobility profiles of gene loci and their gene expression patterns, providing a clear demonstration of the role of chromosomal 4D features in defining cell-specific differential expression of genes.
Collapse
Affiliation(s)
- Anupam Banerjee
- Laufer Center for Physical & Quantitative Biology, Stony Brook University, NY 11794, USA
| | - She Zhang
- OpenEye, Cadence Molecular Sciences, Santa Fe, NM 87508, USA
| | - Ivet Bahar
- Laufer Center for Physical & Quantitative Biology, Stony Brook University, NY 11794, USA
- Department of Biochemistry and Cell Biology, Renaissance School of Medicine, Stony Brook University, NY 11794, USA
| |
Collapse
|
39
|
Kumar Halder A, Agarwal A, Jodkowska K, Plewczynski D. A systematic analyses of different bioinformatics pipelines for genomic data and its impact on deep learning models for chromatin loop prediction. Brief Funct Genomics 2024; 23:538-548. [PMID: 38555493 DOI: 10.1093/bfgp/elae009] [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: 11/28/2023] [Revised: 02/07/2024] [Accepted: 03/04/2024] [Indexed: 04/02/2024] Open
Abstract
Genomic data analysis has witnessed a surge in complexity and volume, primarily driven by the advent of high-throughput technologies. In particular, studying chromatin loops and structures has become pivotal in understanding gene regulation and genome organization. This systematic investigation explores the realm of specialized bioinformatics pipelines designed specifically for the analysis of chromatin loops and structures. Our investigation incorporates two protein (CTCF and Cohesin) factor-specific loop interaction datasets from six distinct pipelines, amassing a comprehensive collection of 36 diverse datasets. Through a meticulous review of existing literature, we offer a holistic perspective on the methodologies, tools and algorithms underpinning the analysis of this multifaceted genomic feature. We illuminate the vast array of approaches deployed, encompassing pivotal aspects such as data preparation pipeline, preprocessing, statistical features and modelling techniques. Beyond this, we rigorously assess the strengths and limitations inherent in these bioinformatics pipelines, shedding light on the interplay between data quality and the performance of deep learning models, ultimately advancing our comprehension of genomic intricacies.
Collapse
Affiliation(s)
- Anup Kumar Halder
- Laboratory of Bioinformatics and Computational Genomics, Faculty of Mathematics and Information Science, Warsaw University of Technology, Koszykowa 75, 00-662 Warsaw, Poland
- Laboratory of Functional and Structural Genomics, Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
| | - Abhishek Agarwal
- Laboratory of Functional and Structural Genomics, Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
| | - Karolina Jodkowska
- Laboratory of Functional and Structural Genomics, Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
| | - Dariusz Plewczynski
- Laboratory of Bioinformatics and Computational Genomics, Faculty of Mathematics and Information Science, Warsaw University of Technology, Koszykowa 75, 00-662 Warsaw, Poland
- Laboratory of Functional and Structural Genomics, Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
| |
Collapse
|
40
|
Chen Z, Yang J, Zhang W, Qian Y, Zhang N, Chen Z, Lu M, Ge L, Liu C, Tian X, Jia G, Ma L, Li B. Understanding m6A changes in chromophobe renal cell carcinoma and predicting patient outcomes survival. BMC Cancer 2024; 24:1187. [PMID: 39334021 PMCID: PMC11438101 DOI: 10.1186/s12885-024-12956-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Accepted: 09/17/2024] [Indexed: 09/30/2024] Open
Abstract
N6-methyladenosine (m6A) is a prevalent mRNA modification known for its implications in various cancer types, yet its role in chromophobe renal cell carcinoma (chRCC) remains largely unexplored. In this study, we performed m6A-SEAL-seq and RNA-seq analyses on tissues from three chRCC subjects, aiming to uncover m6A alterations in chRCC. Our findings revealed reduced expression levels of four m6A regulators in chRCC tissues and highlighted differences in m6A levels compared to normal tissues. Furthermore, we identified specific genes and cancer-related pathways affected by these differences, including notable candidates like NOTCH1 and FGFR1, implicated in chRCC development. Additionally, we developed a predictive model based on the expression level of m6A associated genes, demonstrating promising prognostic capabilities for patient survival prediction. Overall, our study provides valuable insights into the role of m6A in chRCC and its potential as a prognostic indicator.
Collapse
Affiliation(s)
- Zhigang Chen
- Department of Urology, Beijing Haidian Hospital (Haidian Section of Peking University Third Hospital), Beijing, 100080, China
| | - Junbo Yang
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Wei Zhang
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Yang Qian
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Nan Zhang
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Zixin Chen
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Min Lu
- Department of Urology, Peking University Third Hospital, Beijing, 100191, China
- Department of Pathology, Peking University Third Hospital, Beijing, 100191, China
| | - Liyuan Ge
- Department of Urology, Peking University Third Hospital, Beijing, 100191, China
| | - Cheng Liu
- Department of Urology, Peking University Third Hospital, Beijing, 100191, China
| | - Xiaojun Tian
- Department of Urology, Peking University Third Hospital, Beijing, 100191, China
| | - Guifang Jia
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China.
| | - Lulin Ma
- Department of Urology, Peking University Third Hospital, Beijing, 100191, China.
| | - Baoguo Li
- Department of Urology, Beijing Haidian Hospital (Haidian Section of Peking University Third Hospital), Beijing, 100080, China.
| |
Collapse
|
41
|
Poudel SP, Behura SK. Relevance of the regulation of the brain-placental axis to the nocturnal bottleneck of mammals. Placenta 2024; 155:11-21. [PMID: 39121583 DOI: 10.1016/j.placenta.2024.08.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/23/2024] [Revised: 08/02/2024] [Accepted: 08/03/2024] [Indexed: 08/12/2024]
Abstract
INTRODUCTION Evolutionary theory suggests that the ancestors of all placental animals were nocturnal. Visual perceptive function of mammalian brain has evolved extensively, but nearly 70 % of today's mammals are still nocturnal. While placental influence on brain development is known, if placenta plays a role in the visual perceptive function of mammalian brain remains untested. The present study aims to test this hypothesis. METHODS In this study, single-nuclei RNA sequencing was performed to identify genes expressed in the pig placenta and fetal brain, and then compared with the orthologous genes expressed in the placenta and fetal brain cells of mouse. Differential gene expression analysis was performed to identify placental genes regulated differentially between nocturnal and diurnal animals. Phylogenetic modeling was performed to test correlated evolution between placenta type, and the nocturnal or diurnal activity among different mammals. RESULTS The results showed that genes differentially regulated in the fetal brain were related to visual perception whereas the placental genes were related to the nocturnal or diurnal activity in placental animals. Phylogenetic modeling of these genes in thirty-four diverse mammalian species showed evidence for evolutionary link between placenta and the nocturnal/diurnal activity in animals. DISCUSSION The findings of this study suggest that the placenta plays a role in the evolution of visual perceptive function of brain to shape the nocturnal or diurnal activity of placental animals.
Collapse
Affiliation(s)
- Shankar P Poudel
- Division of Animal Sciences, University of Missouri, 920 East Campus Drive, Columbia, MO, 65211, USA
| | - Susanta K Behura
- Division of Animal Sciences, University of Missouri, 920 East Campus Drive, Columbia, MO, 65211, USA; MU Institute for Data Science and Informatics, University of Missouri, 920 East Campus Drive, Columbia, MO, 65211, USA; Interdisciplinary Reproduction and Health Group, University of Missouri, 920 East Campus Drive, Columbia, MO, 65211, USA; Interdisciplinary Neuroscience Program, University of Missouri, 920 East Campus Drive, Columbia, MO, 65211, USA.
| |
Collapse
|
42
|
El Omri-Charai R, Rwigemera A, Gilbert I, Langford A, Robert C, Sloboda DM, McGraw S, Delbes G. Erasure of DNA methylation in rat fetal germ cells is sex-specific and sensitive to maternal high-fat diet. J Dev Orig Health Dis 2024; 15:e19. [PMID: 39324180 DOI: 10.1017/s2040174424000230] [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] [Indexed: 09/27/2024]
Abstract
In mammals, DNA methylation (DNAme) erasure and reinstatement during embryo development and germline establishment are sensitive to the intrauterine environment. Maternal intake of a high-fat diet (HFD), associated with excessive gestational weight gain, has transgenerational effects on offspring health, which may be mediated by changes in DNAme in the germline. Here, we tested the impact of a maternal HFD on embryonic germline DNAme erasure using a rat strain that expresses green fluorescent protein specifically in germ cells. DNAme was analysed by methyl-seq capture in germ cells collected from male and female F1 gonads at gestational day 16. Our data show that although HFD induced global hypomethylation in both sexes, DNAme erasure in female germ cells was more advanced compared to male germ cells. The delay in DNAme erasure in males and the greater impact of HFD suggest that male germ cells are more vulnerable to alterations by exogenous factors.
Collapse
Affiliation(s)
- R El Omri-Charai
- Centre Armand Frappier Santé Biotechnologie, Institut national de la recherche scientifique, Laval, QC, Canada
| | - A Rwigemera
- Centre Armand Frappier Santé Biotechnologie, Institut national de la recherche scientifique, Laval, QC, Canada
| | - I Gilbert
- Department of Animal Sciences, Faculty of Agricultural and Food Sciences, Université Laval, Quebec, QC, Canada
| | - A Langford
- Department of Obstetrics and Gynecology, Faculty of Medicine, Université de Montréal, Montreal, QC, Canada
| | - C Robert
- Department of Animal Sciences, Faculty of Agricultural and Food Sciences, Université Laval, Quebec, QC, Canada
| | - D M Sloboda
- Departments of Biochemistry and Biomedical Sciences, Obstetrics and Gynecology and Pediatrics, McMaster University, Hamilton, ON, Canada
- Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, ON, Canada
| | - S McGraw
- Department of Obstetrics and Gynecology, Faculty of Medicine, Université de Montréal, Montreal, QC, Canada
- Centre de Recherche Azrieli du Centre Hospitalier Universitaire Sainte-Justine, Montréal, QC, Canada
| | - G Delbes
- Centre Armand Frappier Santé Biotechnologie, Institut national de la recherche scientifique, Laval, QC, Canada
| |
Collapse
|
43
|
Cui S, Chen T, Xin D, Chen F, Zhong X, Dong C, Chen X, Chen H, Zhou W, Lin Y, Lu QR. Zinc-Finger Protein ZFP488 Regulates the Timing of Oligodendrocyte Myelination and Remyelination. J Neurosci 2024; 44:e0141242024. [PMID: 39151953 PMCID: PMC11426379 DOI: 10.1523/jneurosci.0141-24.2024] [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: 01/20/2024] [Revised: 07/28/2024] [Accepted: 08/07/2024] [Indexed: 08/19/2024] Open
Abstract
Oligodendrocyte myelination and remyelination after injury are intricately regulated by various intrinsic and extrinsic factors, including transcriptional regulators. Among these, the zinc-finger protein ZFP488 is an oligodendrocyte-enriched transcriptional regulator that promotes oligodendrocyte differentiation in the developing neural tube and in oligodendroglial cell lines. However, the specific in vivo genetic requirements for ZFP488 during oligodendrocyte development and remyelination have not been defined. To address this gap, we generated a lineage-traceable ZFP488 knock-out mouse line, wherein an H2b-GFP reporter replaces the ZFP488-coding region. Using these mice of either sex, we examined the dynamics of ZFP488 expression from the endogenous promoter in the developing central nervous system (CNS). We observed a unique expression pattern in the oligodendrocyte lineage, with ZFP488 expression particularly enriched in differentiated oligodendrocytes. ZFP488 loss resulted in delayed myelination in the developing CNS and impaired remyelination after demyelinating injury in the brain. Integrated transcriptomic and genomic profiling further revealed that ZFP488 loss decreased the expression of myelination-associated genes but not oligodendrocyte progenitor-associated genes, suggesting that ZFP488 serves as a positive regulator of myelination by regulating maturation programs. Thus, our genetic loss-of-function study revealed that ZFP488 regulates a stage-dependent differentiation program that controls the timing of CNS myelination and remyelination.
Collapse
Affiliation(s)
- Siying Cui
- Key Laboratory of Birth Defects, Children's Hospital of Fudan University, Shanghai 201102, China
| | - Tong Chen
- Key Laboratory of Birth Defects, Children's Hospital of Fudan University, Shanghai 201102, China
| | - Dazhuan Xin
- Department of Pediatrics, Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio 45229
| | - Fangbing Chen
- Key Laboratory of Birth Defects, Children's Hospital of Fudan University, Shanghai 201102, China
| | - Xiaowen Zhong
- Department of Pediatrics, Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio 45229
| | - Chen Dong
- Key Laboratory of Birth Defects, Children's Hospital of Fudan University, Shanghai 201102, China
| | - Xiang Chen
- Key Laboratory of Birth Defects, Children's Hospital of Fudan University, Shanghai 201102, China
| | - Huiyao Chen
- Key Laboratory of Birth Defects, Children's Hospital of Fudan University, Shanghai 201102, China
| | - Wenhao Zhou
- Key Laboratory of Birth Defects, Children's Hospital of Fudan University, Shanghai 201102, China
| | - Yifeng Lin
- Key Laboratory of Birth Defects, Children's Hospital of Fudan University, Shanghai 201102, China
| | - Q Richard Lu
- Department of Pediatrics, Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio 45229
| |
Collapse
|
44
|
Wang W, Dernst A, Martin B, Lorenzi L, Cadefau-Fabregat M, Phulphagar K, Wagener A, Budden C, Stair N, Wagner T, Färber H, Jaensch A, Stahl R, Duthie F, Schmidt SV, Coll RC, Meissner F, Cuartero S, Latz E, Mangan MSJ. Butyrate and propionate are microbial danger signals that activate the NLRP3 inflammasome in human macrophages upon TLR stimulation. Cell Rep 2024; 43:114736. [PMID: 39277863 DOI: 10.1016/j.celrep.2024.114736] [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: 12/20/2023] [Revised: 03/06/2024] [Accepted: 08/23/2024] [Indexed: 09/17/2024] Open
Abstract
Short-chain fatty acids (SCFAs) are immunomodulatory compounds produced by the microbiome through dietary fiber fermentation. Although generally considered beneficial for gut health, patients suffering from inflammatory bowel disease (IBD) display poor tolerance to fiber-rich diets, suggesting that SCFAs may have contrary effects under inflammatory conditions. To investigate this, we examined the effect of SCFAs on human macrophages in the presence of Toll-like receptor (TLR) agonists. In contrast to anti-inflammatory effects under steady-state conditions, we found that butyrate and propionate activated the NOD-, LRR-, and pyrin domain-containing protein 3 (NLRP3) inflammasome in the presence of TLR agonists. Mechanistically, these SCFAs prevented transcription of FLICE-like inhibitory protein (cFLIP) and interleukin-10 (IL-10) through histone deacetylase (HDAC) inhibition, triggering caspase-8-dependent NLRP3 inflammasome activation. SCFA-driven NLRP3 activation was potassium efflux independent and did not result in cell death but rather triggered hyperactivation and IL-1β release. Our findings demonstrate that butyrate and propionate are bacterially derived danger signals that regulate NLRP3 inflammasome activation through epigenetic modulation of the inflammatory response.
Collapse
Affiliation(s)
- Wei Wang
- Institute of Innate Immunity, University Hospital Bonn, University of Bonn, 53127 Bonn, Germany; Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast BT9 7BL, UK
| | - Alesja Dernst
- Institute of Innate Immunity, University Hospital Bonn, University of Bonn, 53127 Bonn, Germany
| | - Bianca Martin
- Institute of Innate Immunity, University Hospital Bonn, University of Bonn, 53127 Bonn, Germany
| | - Lucia Lorenzi
- Josep Carreras Leukemia Research Institute (IJC), 08916 Badalona, Barcelona, Spain
| | | | - Kshiti Phulphagar
- Institute of Innate Immunity, University Hospital Bonn, University of Bonn, 53127 Bonn, Germany
| | - Antonia Wagener
- Institute of Innate Immunity, University Hospital Bonn, University of Bonn, 53127 Bonn, Germany
| | - Christina Budden
- Institute of Innate Immunity, University Hospital Bonn, University of Bonn, 53127 Bonn, Germany
| | - Neil Stair
- Institute for Genetics, CECAD Research Center, University of Cologne, 50931 Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging-associated Diseases (CECAD), University of Cologne, 50931 Cologne, Germany
| | - Theresa Wagner
- Institute of Innate Immunity, University Hospital Bonn, University of Bonn, 53127 Bonn, Germany
| | - Harald Färber
- Institute for Hygiene and Public Health, University Hospital Bonn, University of Bonn, 53127 Bonn, Germany
| | - Andreas Jaensch
- Institute for Hygiene and Public Health, University Hospital Bonn, University of Bonn, 53127 Bonn, Germany
| | - Rainer Stahl
- Institute of Innate Immunity, University Hospital Bonn, University of Bonn, 53127 Bonn, Germany
| | - Fraser Duthie
- Institute of Innate Immunity, University Hospital Bonn, University of Bonn, 53127 Bonn, Germany
| | - Susanne V Schmidt
- Institute of Innate Immunity, University Hospital Bonn, University of Bonn, 53127 Bonn, Germany
| | - Rebecca C Coll
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast BT9 7BL, UK
| | - Felix Meissner
- Institute of Innate Immunity, University Hospital Bonn, University of Bonn, 53127 Bonn, Germany
| | - Sergi Cuartero
- Josep Carreras Leukemia Research Institute (IJC), 08916 Badalona, Barcelona, Spain
| | - Eicke Latz
- Institute of Innate Immunity, University Hospital Bonn, University of Bonn, 53127 Bonn, Germany; German Center for Neurodegenerative Diseases, 53127 Bonn, Germany; Department of Infectious Diseases & Immunology, UMass Medical School, Worcester, MA 01605, USA; Deutsches Rheuma Forschungszentrum Berlin (DRFZ), 10117 Berlin, Germany.
| | - Matthew S J Mangan
- Institute of Innate Immunity, University Hospital Bonn, University of Bonn, 53127 Bonn, Germany; German Center for Neurodegenerative Diseases, 53127 Bonn, Germany.
| |
Collapse
|
45
|
Miao L, Weidemann DE, Ngo K, Unruh BA, Kojima S. A Comparative Study of Algorithms Detecting Differential Rhythmicity in Transcriptomic Data. Bioinform Biol Insights 2024; 18:11779322241281188. [PMID: 39351295 PMCID: PMC11440551 DOI: 10.1177/11779322241281188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 08/19/2024] [Indexed: 10/04/2024] Open
Abstract
Rhythmic transcripts play pivotal roles in driving the daily oscillations of various biological processes. Genetic or environmental disruptions can lead to alterations in the rhythmicity of transcripts, ultimately impacting downstream circadian outputs, including metabolic processes and even behavior. To statistically compare the differences in transcript rhythms between 2 or more conditions, several algorithms have been developed to analyze circadian transcriptomic data, each with distinct features. In this study, we compared the performance of 7 algorithms that were specifically designed to detect differential rhythmicity (DODR, LimoRhyde, CircaCompare, compareRhythms, diffCircadian, dryR, and RepeatedCircadian). We found that even when applying the same statistical threshold, these algorithms yielded varying numbers of differentially rhythmic transcripts, most likely because each algorithm defines rhythmic and differentially rhythmic transcripts differently. Nevertheless, the output for the differential phase and amplitude were identical between dryR and compareRhyhms, and diffCircadian and CircaCompare, while the output from LimoRhyde2 was highly correlated with that from diffCircadian and CircaCompare. Because each algorithm has unique requirements for input data and reports different information as an output, it is crucial to ensure the compatibility of input data with the chosen algorithm and assess whether the algorithm's output fits the user's needs when selecting an algorithm for analysis.
Collapse
Affiliation(s)
- Lin Miao
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA
- Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA, USA
| | - Douglas E Weidemann
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA
- Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA, USA
| | - Katherine Ngo
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA
- Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA, USA
| | - Benjamin A Unruh
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA
- Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA, USA
| | - Shihoko Kojima
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA
- Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA, USA
| |
Collapse
|
46
|
Zhong J, O'Brien A, Patel M, Eiser D, Mobaraki M, Collins I, Wang L, Guo K, TruongVo T, Jermusyk A, O'Neill M, Dill CD, Wells AD, Leonard ME, Pippin JA, Grant SFA, Zhang T, Andresson T, Connelly KE, Shi J, Arda HE, Hoskins JW, Amundadottir LT. Large-scale multi-omic analysis identifies noncoding somatic driver mutations and nominates ZFP36L2 as a driver gene for pancreatic ductal adenocarcinoma. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.09.22.24314165. [PMID: 39371173 PMCID: PMC11451821 DOI: 10.1101/2024.09.22.24314165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/08/2024]
Abstract
Identification of somatic driver mutations in the noncoding genome remains challenging. To comprehensively characterize noncoding driver mutations for pancreatic ductal adenocarcinoma (PDAC), we first created genome-scale maps of accessible chromatin regions (ACRs) and histone modification marks (HMMs) in pancreatic cell lines and purified pancreatic acinar and duct cells. Integration with whole-genome mutation calls from 506 PDACs revealed 314 ACRs/HMMs significantly enriched with 3,614 noncoding somatic mutations (NCSMs). Functional assessment using massively parallel reporter assays (MPRA) identified 178 NCSMs impacting reporter activity (19.45% of those tested). Focused luciferase validation confirmed negative effects on gene regulatory activity for NCSMs near CDKN2A and ZFP36L2 . For the latter, CRISPR interference (CRISPRi) further identified ZFP36L2 as a target gene (16.0 - 24.0% reduced expression, P = 0.023-0.0047) with disrupted KLF9 binding likely mediating the effect. Our integrative approach provides a catalog of potentially functional noncoding driver mutations and nominates ZFP36L2 as a PDAC driver gene.
Collapse
|
47
|
Sakai H, Uno H, Yamakawa H, Tanaka K, Ikedo A, Uezumi A, Ohkawa Y, Imai Y. The androgen receptor in mesenchymal progenitors regulates skeletal muscle mass via Igf1 expression in male mice. Proc Natl Acad Sci U S A 2024; 121:e2407768121. [PMID: 39292748 PMCID: PMC11441553 DOI: 10.1073/pnas.2407768121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Accepted: 08/20/2024] [Indexed: 09/20/2024] Open
Abstract
Androgens exert their effects primarily by binding to the androgen receptor (AR), a ligand-dependent nuclear receptor. While androgens have anabolic effects on skeletal muscle, previous studies reported that AR functions in myofibers to regulate skeletal muscle quality, rather than skeletal muscle mass. Therefore, the anabolic effects of androgens are exerted via nonmyofiber cells. In this context, the cellular and molecular mechanisms of AR in mesenchymal progenitors, which play a crucial role in maintaining skeletal muscle homeostasis, remain largely unknown. In this study, we demonstrated expression of AR in mesenchymal progenitors and found that targeted AR ablation in mesenchymal progenitors reduced limb muscle mass in mature adult, but not young or aged, male mice, although fatty infiltration of muscle was not affected. The absence of AR in mesenchymal progenitors led to remarkable perineal muscle hypotrophy, regardless of age, due to abnormal regulation of transcripts associated with cell death and extracellular matrix organization. Additionally, we revealed that AR in mesenchymal progenitors regulates the expression of insulin-like growth factor 1 (Igf1) and that IGF1 administration prevents perineal muscle atrophy in a paracrine manner. These findings indicate that the anabolic effects of androgens regulate skeletal muscle mass via, at least in part, AR signaling in mesenchymal progenitors.
Collapse
Affiliation(s)
- Hiroshi Sakai
- Division of Integrative Pathophysiology, Proteo-Science Center, Ehime University, Toon, Ehime791-0295, Japan
- Department of Pathophysiology, Ehime University Graduate School of Medicine, Toon, Ehime791-0295, Japan
| | - Hideaki Uno
- Department of Pathophysiology, Ehime University Graduate School of Medicine, Toon, Ehime791-0295, Japan
| | - Harumi Yamakawa
- Department of Pathophysiology, Ehime University Graduate School of Medicine, Toon, Ehime791-0295, Japan
| | - Kaori Tanaka
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, Higashi-ku, Fukuoka812-0054, Japan
| | - Aoi Ikedo
- Division of Integrative Pathophysiology, Proteo-Science Center, Ehime University, Toon, Ehime791-0295, Japan
| | - Akiyoshi Uezumi
- Division of Cell Heterogeneity, Medical Institute of Bioregulation, Kyushu University, Higashi-ku, Fukuoka812-0054, Japan
| | - Yasuyuki Ohkawa
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, Higashi-ku, Fukuoka812-0054, Japan
| | - Yuuki Imai
- Division of Integrative Pathophysiology, Proteo-Science Center, Ehime University, Toon, Ehime791-0295, Japan
- Department of Pathophysiology, Ehime University Graduate School of Medicine, Toon, Ehime791-0295, Japan
| |
Collapse
|
48
|
Hu X, Zhang X, Sun W, Liu C, Deng P, Cao Y, Zhang C, Xu N, Zhang T, Zhang Y, Liu JJ, Wang H. Systematic discovery of DNA-binding tandem repeat proteins. Nucleic Acids Res 2024; 52:10464-10489. [PMID: 39189466 PMCID: PMC11417379 DOI: 10.1093/nar/gkae710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 07/30/2024] [Accepted: 08/07/2024] [Indexed: 08/28/2024] Open
Abstract
Tandem repeat proteins (TRPs) are widely distributed and bind to a wide variety of ligands. DNA-binding TRPs such as zinc finger (ZNF) and transcription activator-like effector (TALE) play important roles in biology and biotechnology. In this study, we first conducted an extensive analysis of TRPs in public databases, and found that the enormous diversity of TRPs is largely unexplored. We then focused our efforts on identifying novel TRPs possessing DNA-binding capabilities. We established a protein language model for DNA-binding protein prediction (PLM-DBPPred), and predicted a large number of DNA-binding TRPs. A subset was then selected for experimental screening, leading to the identification of 11 novel DNA-binding TRPs, with six showing sequence specificity. Notably, members of the STAR (Short TALE-like Repeat proteins) family can be programmed to target specific 9 bp DNA sequences with high affinity. Leveraging this property, we generated artificial transcription factors using reprogrammed STAR proteins and achieved targeted activation of endogenous gene sets. Furthermore, the members of novel families such as MOON (Marine Organism-Originated DNA binding protein) and pTERF (prokaryotic mTERF-like protein) exhibit unique features and distinct DNA-binding characteristics, revealing interesting biological clues. Our study expands the diversity of DNA-binding TRPs, and demonstrates that a systematic approach greatly enhances the discovery of new biological insights and tools.
Collapse
Affiliation(s)
- Xiaoxuan Hu
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Xuechun Zhang
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Wen Sun
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Chunhong Liu
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Pujuan Deng
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yuanwei Cao
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Chenze Zhang
- National Key Laboratory of Efficacy and Mechanism on Chinese Medicine for Metabolic Diseases, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Ning Xu
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Tongtong Zhang
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Yong E Zhang
- University of Chinese Academy of Sciences, Beijing 100049, China
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jun-Jie Gogo Liu
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - Haoyi Wang
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| |
Collapse
|
49
|
Luo C, Xu H, Yu Z, Liu D, Zhong D, Zhou S, Zhang B, Zhan J, Sun F. Meiotic chromatin-associated HSF5 is indispensable for pachynema progression and male fertility. Nucleic Acids Res 2024; 52:10255-10275. [PMID: 39162221 PMCID: PMC11417359 DOI: 10.1093/nar/gkae701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Revised: 07/04/2024] [Accepted: 08/07/2024] [Indexed: 08/21/2024] Open
Abstract
Pachynema progression contributes to the completion of prophase I. Nevertheless, the regulation of this significant meiotic process remains poorly understood. In this study, we identified a novel testis-specific protein HSF5, which regulates pachynema progression during male meiosis in a manner dependent on chromatin-binding. Deficiency of HSF5 results in meiotic arrest and male infertility, characterized as unconventional pachynema arrested at the mid-to-late stage, with extensive spermatocyte apoptosis. Our scRNA-seq data confirmed consistent expressional alterations of certain driver genes (Sycp1, Msh4, Meiob, etc.) crucial for pachynema progression in Hsf5-/- individuals. HSF5 was revealed to primarily bind to promoter regions of such key divers by CUT&Tag analysis. Also, our results demonstrated that HSF5 biologically interacted with SMARCA5, SMARCA4 and SMARCE1, and it could function as a transcription factor for pachynema progression during meiosis. Therefore, our study underscores the importance of the chromatin-associated HSF5 for the differentiation of spermatocytes, improving the protein regulatory network of the pachynema progression.
Collapse
Affiliation(s)
- Chunhai Luo
- Department of Urology & Andrology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310016, China
| | - Haoran Xu
- Department of Urology & Andrology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310016, China
| | - Ziqi Yu
- Department of Urology & Andrology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310016, China
| | - Dalin Liu
- Department of Urology & Andrology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310016, China
| | - Danyang Zhong
- Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310016, China
| | - Shumin Zhou
- Department of Urology & Andrology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310016, China
| | - Beibei Zhang
- Department of Urology & Andrology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310016, China
| | - Junfeng Zhan
- Department of Urology & Andrology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310016, China
| | - Fei Sun
- Department of Urology & Andrology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310016, China
| |
Collapse
|
50
|
Peng P, Yin Q, Sun W, Han J, Guo H, Cheng C, Liu D. Global RNA Interaction and Transcriptome Profiles Demonstrate the Potential Anti-Oncogenic Targets and Pathways of RBM6 in HeLa Cells. FRONT BIOSCI-LANDMRK 2024; 29:330. [PMID: 39344314 DOI: 10.31083/j.fbl2909330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 06/01/2024] [Accepted: 06/11/2024] [Indexed: 10/01/2024]
Abstract
BACKGROUND The fate and functions of RNAs are coordinately regulated by RNA-binding proteins (RBPs), which are often dysregulated in various cancers. Known as a splicing regulator, RNA-binding motif protein 6 (RBM6) harbors tumor-suppressor activity in many cancers; however, there is a lack of research on the molecular targets and regulatory mechanisms of RBM6. METHODS In this study, we constructed an RBM6 knock-down (shRBM6) model in the HeLa cell line to investigate its functions and molecular targets. Then we applied improved RNA immunoprecipitation coupled with sequencing (iRIP-seq) and whole transcriptome sequencing approaches to investigate the potential role and RNA targets of RBM6. RESULTS Using The Cancer Genome Atlas dataset, we found that higher expression of RBM6 is associated with a better prognosis in many cancer types. In addition, we found that RBM6 knockdown promoted cell proliferation and inhibited apoptosis, demonstrating that RBM6 may act as an anti-oncogenic protein in cancer cells. RBM6 can regulate the alternative splicing (AS) of genes involved in DNA damage response, proliferation, and apoptosis-associated pathways. Meanwhile, RBM6 knockdown activated type I interferon signaling pathways and inhibited the expression of genes involved in the cell cycle, cellular responses to DNA damage, and DNA repair pathways. The differentially expressed genes (DEGs) by shRBM6 and their involved pathways were likely regulated by the transcription factors undergoing aberrant AS by RBM6 knockdown. For iRIP-seq analysis, we found that RBM6 could interact with a large number of mRNAs, with a tendency for binding motifs GGCGAUG and CUCU. RBM6 bound to the mRNA of cell proliferation- and apoptosis-associated genes with dysregulated AS after RBM6 knockdown. CONCLUSIONS In summary, our study highlights the important role of RBM6, as well as the downstream targets and regulated pathways, suggesting the potential regulatory mechanisms of RBM6 in the development of cancer.
Collapse
Affiliation(s)
- Ping Peng
- Cancer Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430030 Wuhan, Hubei, China
| | - Qingqing Yin
- Center for Genome Analysis, Wuhan Ruixing Biotechnology Co., Ltd., 430075 Wuhan, Hubei, China
| | - Wei Sun
- Cancer Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430030 Wuhan, Hubei, China
| | - Jing Han
- Cancer Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430030 Wuhan, Hubei, China
| | - Hao Guo
- Center for Genome Analysis, Wuhan Ruixing Biotechnology Co., Ltd., 430075 Wuhan, Hubei, China
| | - Chao Cheng
- Center for BioBigData Analysis, ABLife BioBigData Institute, 430075 Wuhan, Hubei, China
| | - Dongbo Liu
- Cancer Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430030 Wuhan, Hubei, China
| |
Collapse
|