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Zhao Y, Sun W, Fan Q, Huang Y, Ma Y, Zhang S, Gong C, Wang B, Zhang W, Yang Q, Lin S. Exploring the potential molecular intersection of stroke and major depression disorder. Biochem Biophys Res Commun 2024; 720:150079. [PMID: 38759300 DOI: 10.1016/j.bbrc.2024.150079] [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: 01/18/2024] [Revised: 04/22/2024] [Accepted: 05/07/2024] [Indexed: 05/19/2024]
Abstract
Stroke and major depression disorder are common neurological diseases, and a large number of clinical studies have shown that there is a close relationship between the two diseases, but whether the two diseases are linked at the genetic level needs to be further explored. The purpose of this study was to explore the comorbidity mechanism of stroke and major depression by using bioinformatics technology and animal experiments. From the GEO database, we gathered transcriptome data of stroke and depression mice (GSE104036, GSE131712, GSE81672, and GSE146845) and identified comorbid gene set through edgR and WGCNA analyses. Further analysis revealed that these genes were enriched in pathways associated with cell death. Programmed cell death gene sets (PCDGs) are generated from genes related to apoptosis, necroptosis, pyroptosis and autophagy. The intersection of PCDGs and comorbid gene set resulted in two hub genes, Mlkl and Nlrp3. Single-cell sequencing analysis indicated that Mlkl and Nlrp3 are mainly influential on endothelial cells and microglia, suggesting that the impairment of these two cell types may be a factor in the relationship between stroke and major depression. This was experimentally confirmed by RT-PCR and immunofluorescence staining. Our research revealed that two specific genes, namely, Mlkl and Nlrp3, play crucial roles in the complex mechanism that links stroke and major depression. Additionally, we have predicted six possible therapeutic agents and the outcomes of docking simulations of target proteins and drug molecules.
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Affiliation(s)
- Yuan Zhao
- Department of Neurology, Xinqiao Hospital, The Second Affiliated Hospital, Army Medical University, Chongqing, 400042, China
| | - Wenzhe Sun
- Department of Neurology, Xinqiao Hospital, The Second Affiliated Hospital, Army Medical University, Chongqing, 400042, China
| | - Qinlin Fan
- Department of Neurology, Xinqiao Hospital, The Second Affiliated Hospital, Army Medical University, Chongqing, 400042, China
| | - Yanjie Huang
- Department of Neurology, Xinqiao Hospital, The Second Affiliated Hospital, Army Medical University, Chongqing, 400042, China
| | - Yufan Ma
- Department of Neurology, Xinqiao Hospital, The Second Affiliated Hospital, Army Medical University, Chongqing, 400042, China
| | - Shuang Zhang
- Department of Neurology, Xinqiao Hospital, The Second Affiliated Hospital, Army Medical University, Chongqing, 400042, China
| | - Changxiong Gong
- Department of Neurology, Xinqiao Hospital, The Second Affiliated Hospital, Army Medical University, Chongqing, 400042, China
| | - Bingqiao Wang
- Department of Neurology, Xinqiao Hospital, The Second Affiliated Hospital, Army Medical University, Chongqing, 400042, China
| | - Wanyun Zhang
- Department of Neurology, Xinqiao Hospital, The Second Affiliated Hospital, Army Medical University, Chongqing, 400042, China
| | - Qingwu Yang
- Department of Neurology, Xinqiao Hospital, The Second Affiliated Hospital, Army Medical University, Chongqing, 400042, China; Chongqing Institute for Brain and Intelligence, Guangyang Bay Laboratory, Chongqing, 400064, China.
| | - Sen Lin
- Department of Neurology, Xinqiao Hospital, The Second Affiliated Hospital, Army Medical University, Chongqing, 400042, China; Chongqing Institute for Brain and Intelligence, Guangyang Bay Laboratory, Chongqing, 400064, China.
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2
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Li H, Liu J, Lai J, Su X, Wang X, Cao J, Mao S, Zhang T, Gu Q. The HHEX-ABI2/SLC17A9 axis induces cancer stem cell-like properties and tumorigenesis in HCC. J Transl Med 2024; 22:537. [PMID: 38844969 PMCID: PMC11155165 DOI: 10.1186/s12967-024-05324-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 05/20/2024] [Indexed: 06/10/2024] Open
Abstract
Accumulating evidence indicated that HHEX participated in the initiation and development of several cancers, but the potential roles and mechanisms of HHEX in hepatocellular carcinoma (HCC) were largely unclear. Cancer stem cells (CSCs) are responsible for cancer progression owing to their stemness characteristics. We reported that HHEX was a novel CSCs target for HCC. We found that HHEX was overexpressed in HCC tissues and high expression of HHEX was associated with poor survival. Subsequently, we found that HHEX promoted HCC cell proliferation, migration, and invasion. Moreover, bioinformatics analysis and experiments verified that HHEX promoted stem cell-like properties in HCC. Mechanistically, ABI2 serving as a co-activator of transcriptional factor HHEX upregulated SLC17A9 to promote HCC cancer stem cell-like properties and tumorigenesis. Collectively, the HHEX-mediated ABI2/SLC17A9 axis contributes to HCC growth and metastasis by maintaining the CSC population, suggesting that HHEX serves as a promising therapeutic target for HCC treatment.
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Affiliation(s)
- Huizi Li
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, 330006, Jiangxi, China.
| | - Jin Liu
- Department of Radiology, University of California, San Diego, The, USA
| | - Jie Lai
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, 330006, Jiangxi, China
| | - Xinyao Su
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, 330006, Jiangxi, China
| | - Xiaofeng Wang
- Department of Gastrointestinal Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Jiaqing Cao
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, 330006, Jiangxi, China
| | - Shengxun Mao
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, 330006, Jiangxi, China.
| | - Tong Zhang
- Department of Hepatic Surgery and Liver Transplantation Center, The Third Actuated Hospital of Sun Yat-sen University, Guangzhou, 510000, Guangdong, China.
- Department of General Surgery, School of Medicine, Organ Transplantation Clinical Medical Center of Xiamen University, Xiang'an Hospital of Xiamen University, Xiamen University, Xiamen, 361000, China.
- Department of Organ Transplantation, School of Medicine, Organ Transplantation Clinical Medical Center of Xiamen University, Xiang'an Hospital of Xiamen University, Xiamen University, Xiamen, 361005, Fujian, China.
| | - Qiuping Gu
- Department of Gastroenterology, Ganzhou People's Hospital, No. 16, Meiguan Avenue, Zhanggong District, Ganzhou City, 341000, Jiangxi Province, People's Republic of China.
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Aslanzadeh M, Stanicek L, Tarbier M, Mármol-Sánchez E, Biryukova I, Friedländer M. Malat1 affects transcription and splicing through distinct pathways in mouse embryonic stem cells. NAR Genom Bioinform 2024; 6:lqae045. [PMID: 38711862 PMCID: PMC11071118 DOI: 10.1093/nargab/lqae045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 03/14/2024] [Accepted: 04/30/2024] [Indexed: 05/08/2024] Open
Abstract
Malat1 is a long-noncoding RNA with critical roles in gene regulation and cancer metastasis, however its functional role in stem cells is largely unexplored. We here perform a nuclear knockdown of Malat1 in mouse embryonic stem cells, causing the de-regulation of 320 genes and aberrant splicing of 90 transcripts, some of which potentially affecting the translated protein sequence. We find evidence that Malat1 directly interacts with gene bodies and aberrantly spliced transcripts, and that it locates upstream of down-regulated genes at their putative enhancer regions, in agreement with functional genomics data. Consistent with this, we find these genes affected at both exon and intron levels, suggesting that they are transcriptionally regulated by Malat1. Besides, the down-regulated genes are regulated by specific transcription factors and bear both activating and repressive chromatin marks, suggesting that some of them might be regulated by bivalent promoters. We propose a model in which Malat1 facilitates the transcription of genes involved in chromatid dynamics and mitosis in one pathway, and affects the splicing of transcripts that are themselves involved in RNA processing in a distinct pathway. Lastly, we compare our findings with Malat1 perturbation studies performed in other cell systems and in vivo.
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Affiliation(s)
- Morteza Aslanzadeh
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Sweden
| | - Laura Stanicek
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Sweden
| | - Marcel Tarbier
- Science for Life Laboratory, Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Solna, Sweden
| | - Emilio Mármol-Sánchez
- Science for Life Laboratory and Center for Palaeogenetics. Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Sweden
| | - Inna Biryukova
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Sweden
| | - Marc R Friedländer
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Sweden
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Liu Z, Yu K, Chen K, Liu J, Dai K, Zhao P. HAS2 facilitates glioma cell malignancy and suppresses ferroptosis in an FZD7-dependent manner. Cancer Sci 2024. [PMID: 38816349 DOI: 10.1111/cas.16232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 05/07/2024] [Accepted: 05/14/2024] [Indexed: 06/01/2024] Open
Abstract
Glioma is the most common malignant tumor in the central nervous system, and it is crucial to uncover the factors that influence prognosis. In this study, we utilized Mfuzz to identify a gene set that showed a negative correlation with overall survival in patients with glioma. Gene Ontology (GO) enrichment analyses were then undertaken to gain insights into the functional characteristics and pathways associated with these genes. The expression distribution of Hyaluronan Synthase 2 (HAS2) was explored across multiple datasets, revealing its expression patterns. In vitro and in vivo experiments were carried out through gene knockdown and overexpression to validate the functionality of HAS2. Potential upstream transcription factors of HAS2 were predicted using transcriptional regulatory databases, and these predictions were experimentally validated using ChIP-PCR and dual-luciferase reporter gene assays. The results showed that elevated expression of HAS2 in glioma indicates poor prognosis. HAS2 was found to play a role in activating an antiferroptosis pathway in glioma cells. Inhibiting HAS2 significantly increased cellular sensitivity to ferroptosis-inducing agents. Finally, we determined that the oncogenic effect of HAS2 is mediated by the key receptor of the WNT pathway, FZD7.
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Affiliation(s)
- Zhiyuan Liu
- Department of Neurosurgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Kuo Yu
- Department of Neurosurgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Kaile Chen
- Department of Neurosurgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jinlai Liu
- Department of Neurosurgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
- Department of Neurosurgery, Yang Zhong, Jiangsu Province People's Hospital, Yangzhou, China
| | - Kexiang Dai
- Department of Neurosugery, Emergency General Hospital, Beijing, China
| | - Peng Zhao
- Department of Neurosurgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
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Li H, Wang L, Ruan Z, Li X, Yang Y, Fang J, Wang R. CSE1L as a prognostic biomarker associated with pan cancer immune infiltration and drug sensitivity. Expert Rev Clin Immunol 2024:1-13. [PMID: 38752776 DOI: 10.1080/1744666x.2024.2356747] [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: 11/06/2023] [Accepted: 05/13/2024] [Indexed: 05/24/2024]
Abstract
BACKGROUND Rising cancer-related mortality underscores the importance of biomarkers for treatment and prognosis, with Chromosome Segregation 1 Like (CSE1L) linked to various cancers yet its roles remain partially understood. This study investigates CSE1L's expression and oncogenic mechanisms in solid tumors. RESEARCH DESIGN AND METHODS We analyzed multi-omics data from 31 solid tumors, measured CSE1L in 41 head and neck carcinoma patients post-chemotherapy via qRT-PCR, and evaluated the impact of CSE1L knockdown on cell proliferation in A549 and HepG2 cells. RESULTS In this study, we observed significantly elevated levels of CSE1L RNA in 13 tumor tissues and protein levels in 8 tumor tissues compared to their corresponding adjacent normal tissues. Additionally, our investigation unveiled a correlation between heightened CSE1L expression in tumor tissues and worsened patient prognosis, poor response to immunotherapy, and diminished effectiveness of neoadjuvant chemotherapy. Through an analysis of CSE1L mechanisms, we discovered its potential involvement in promoting tumor cell proliferation, enhancing drug resistance, and influencing immune infiltration, thereby impacting patient prognosis and treatment outcomes. Finally, we delved into the potential mechanisms underlying upregulation of CSE1L in tumor tissues. CONCLUSION Our findings demonstrate that CSE1L promotes tumor development in various malignancies, highlighting its potential as both a therapeutic target and prognostic indicator.
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Affiliation(s)
- Haiyang Li
- Department of Otorhinolaryngology Head and Neck Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Lingwa Wang
- Department of Otorhinolaryngology Head and Neck Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Zhaohui Ruan
- Department of Major Emerging Infectious Diseases, Changping Laboratory, Beijing, China
| | - Xiaoyan Li
- Teaching and Research Section of Clinical Nursing, Xiangya Hospital of Central South University, Changsha, China
| | - Yifan Yang
- Department of Otorhinolaryngology Head and Neck Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Jugao Fang
- Department of Otorhinolaryngology Head and Neck Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Ru Wang
- Department of Otorhinolaryngology Head and Neck Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, China
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6
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Joosten SEP, Gregoricchio S, Stelloo S, Yapıcı E, Huang CCF, Yavuz K, Donaldson Collier M, Morova T, Altintaş UB, Kim Y, Canisius S, Moelans CB, van Diest PJ, Korkmaz G, Lack NA, Vermeulen M, Linn SC, Zwart W. Estrogen receptor 1 chromatin profiling in human breast tumors reveals high inter-patient heterogeneity with enrichment of risk SNPs and enhancer activity at most-conserved regions. Genome Res 2024; 34:539-555. [PMID: 38719469 PMCID: PMC11146591 DOI: 10.1101/gr.278680.123] [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: 10/30/2023] [Accepted: 04/11/2024] [Indexed: 06/05/2024]
Abstract
Estrogen Receptor 1 (ESR1; also known as ERα, encoded by ESR1 gene) is the main driver and prime drug target in luminal breast cancer. ESR1 chromatin binding is extensively studied in cell lines and a limited number of human tumors, using consensi of peaks shared among samples. However, little is known about inter-tumor heterogeneity of ESR1 chromatin action, along with its biological implications. Here, we use a large set of ESR1 ChIP-seq data from 70 ESR1+ breast cancers to explore inter-patient heterogeneity in ESR1 DNA binding to reveal a striking inter-tumor heterogeneity of ESR1 action. Of note, commonly shared ESR1 sites show the highest estrogen-driven enhancer activity and are most engaged in long-range chromatin interactions. In addition, the most commonly shared ESR1-occupied enhancers are enriched for breast cancer risk SNP loci. We experimentally confirm SNVs to impact chromatin binding potential for ESR1 and its pioneer factor FOXA1. Finally, in the TCGA breast cancer cohort, we can confirm these variations to associate with differences in expression for the target gene. Cumulatively, we reveal a natural hierarchy of ESR1-chromatin interactions in breast cancers within a highly heterogeneous inter-tumor ESR1 landscape, with the most common shared regions being most active and affected by germline functional risk SNPs for breast cancer development.
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Affiliation(s)
- Stacey E P Joosten
- Division of Oncogenomics, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
- Oncode Institute, The Netherlands
| | - Sebastian Gregoricchio
- Division of Oncogenomics, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
- Oncode Institute, The Netherlands
| | - Suzan Stelloo
- Oncode Institute, The Netherlands
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, 6500HB Nijmegen, The Netherlands
| | - Elif Yapıcı
- Koç University School of Medicine, 34450 Istanbul, Turkey
- Koç University Research Center for Translational Medicine (KUTTAM), 34450 Istanbul, Turkey
| | - Chia-Chi Flora Huang
- Vancouver Prostate Centre, University of British Columbia, Vancouver, British Columbia, V6H 3Z6 Canada
| | - Kerim Yavuz
- Vancouver Prostate Centre, University of British Columbia, Vancouver, British Columbia, V6H 3Z6 Canada
| | - Maria Donaldson Collier
- Division of Oncogenomics, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
- Oncode Institute, The Netherlands
| | - Tunç Morova
- Vancouver Prostate Centre, University of British Columbia, Vancouver, British Columbia, V6H 3Z6 Canada
| | - Umut Berkay Altintaş
- Vancouver Prostate Centre, University of British Columbia, Vancouver, British Columbia, V6H 3Z6 Canada
| | - Yongsoo Kim
- Department of Pathology, Amsterdam University Medical Center, Cancer Center Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - Sander Canisius
- Division of Molecular Pathology, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Cathy B Moelans
- Department of Pathology, Utrecht University Medical Centre, 3584 CX Utrecht, The Netherlands
| | - Paul J van Diest
- Department of Pathology, Utrecht University Medical Centre, 3584 CX Utrecht, The Netherlands
| | - Gozde Korkmaz
- Koç University School of Medicine, 34450 Istanbul, Turkey
- Koç University Research Center for Translational Medicine (KUTTAM), 34450 Istanbul, Turkey
| | - Nathan A Lack
- Koç University School of Medicine, 34450 Istanbul, Turkey
- Koç University Research Center for Translational Medicine (KUTTAM), 34450 Istanbul, Turkey
- Vancouver Prostate Centre, University of British Columbia, Vancouver, British Columbia, V6H 3Z6 Canada
| | - Michiel Vermeulen
- Oncode Institute, The Netherlands
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, 6500HB Nijmegen, The Netherlands
- Division of Molecular Genetics, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Sabine C Linn
- Division of Molecular Pathology, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
- Department of Pathology, Utrecht University Medical Centre, 3584 CX Utrecht, The Netherlands
- Department of Medical Oncology, Antoni van Leeuwenhoek Hospital, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Wilbert Zwart
- Division of Oncogenomics, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands;
- Oncode Institute, The Netherlands
- Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
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7
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Peng F, Lu J, Su K, Liu X, Luo H, He B, Wang C, Zhang X, An F, Lv D, Luo Y, Su Q, Jiang T, Deng Z, He B, Xu L, Guo T, Xiang J, Gu C, Wang L, Xu G, Xu Y, Li M, Kelley KW, Cui B, Liu Q. Oncogenic fatty acid oxidation senses circadian disruption in sleep-deficiency-enhanced tumorigenesis. Cell Metab 2024:S1550-4131(24)00138-4. [PMID: 38772364 DOI: 10.1016/j.cmet.2024.04.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 03/15/2024] [Accepted: 04/25/2024] [Indexed: 05/23/2024]
Abstract
Circadian disruption predicts poor cancer prognosis, yet how circadian disruption is sensed in sleep-deficiency (SD)-enhanced tumorigenesis remains obscure. Here, we show fatty acid oxidation (FAO) as a circadian sensor relaying from clock disruption to oncogenic metabolic signal in SD-enhanced lung tumorigenesis. Both unbiased transcriptomic and metabolomic analyses reveal that FAO senses SD-induced circadian disruption, as illustrated by continuously increased palmitoyl-coenzyme A (PA-CoA) catalyzed by long-chain fatty acyl-CoA synthetase 1 (ACSL1). Mechanistically, SD-dysregulated CLOCK hypertransactivates ACSL1 to produce PA-CoA, which facilitates CLOCK-Cys194 S-palmitoylation in a ZDHHC5-dependent manner. This positive transcription-palmitoylation feedback loop prevents ubiquitin-proteasomal degradation of CLOCK, causing FAO-sensed circadian disruption to maintain SD-enhanced cancer stemness. Intriguingly, timed β-endorphin resets rhythmic Clock and Acsl1 expression to alleviate SD-enhanced tumorigenesis. Sleep quality and serum β-endorphin are negatively associated with both cancer development and CLOCK/ACSL1 expression in patients with cancer, suggesting dawn-supplemented β-endorphin as a potential chronotherapeutic strategy for SD-related cancer.
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Affiliation(s)
- Fei Peng
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian, Liaoning, China
| | - Jinxin Lu
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian, Liaoning, China
| | - Keyu Su
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian, Liaoning, China; State Key Laboratory of Oncology in South China, Psychobehavioral Cancer Research Center, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - Xinyu Liu
- Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, Liaoning, China
| | - Huandong Luo
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian, Liaoning, China
| | - Bin He
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian, Liaoning, China
| | - Cenxin Wang
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian, Liaoning, China
| | - Xiaoyu Zhang
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian, Liaoning, China
| | - Fan An
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian, Liaoning, China
| | - Dekang Lv
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian, Liaoning, China
| | - Yuanyuan Luo
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian, Liaoning, China; Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, Liaoning, China
| | - Qitong Su
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian, Liaoning, China
| | - Tonghui Jiang
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian, Liaoning, China
| | - Ziqian Deng
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian, Liaoning, China
| | - Bin He
- State Key Laboratory of Oncology in South China, Psychobehavioral Cancer Research Center, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - Lingzhi Xu
- Department of Oncology, The Second Affiliated Hospital, Dalian Medical University, Dalian, Liaoning, China
| | - Tao Guo
- Department of Thoracic Surgery, The First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Jin Xiang
- State Key Laboratory of Oncology in South China, Psychobehavioral Cancer Research Center, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - Chundong Gu
- Department of Thoracic Surgery, The First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Ling Wang
- Department of Oncology, The First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Guowang Xu
- Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, Liaoning, China
| | - Ying Xu
- Cambridge-Soochow University Genomic Resource Center, Soochow University, Suzhou, Jiangsu, China
| | - Mindian Li
- Department of Cardiovascular Medicine, Center for Circadian Metabolism and Cardiovascular Disease, Southwest Hospital, Army Medical University, Chongqing, China
| | - Keith W Kelley
- Department of Pathology, College of Medicine and Department of Animal Sciences, College of ACES, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Bai Cui
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian, Liaoning, China; State Key Laboratory of Oncology in South China, Psychobehavioral Cancer Research Center, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China.
| | - Quentin Liu
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian, Liaoning, China; State Key Laboratory of Oncology in South China, Psychobehavioral Cancer Research Center, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China.
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8
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Li N, Jin K, Liu B, Yang M, Shi P, Heng D, Wang J, Liu L. Single-cell 3D genome structure reveals distinct human pluripotent states. Genome Biol 2024; 25:122. [PMID: 38741214 DOI: 10.1186/s13059-024-03268-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 05/05/2024] [Indexed: 05/16/2024] Open
Abstract
BACKGROUND Pluripotent states of embryonic stem cells (ESCs) with distinct transcriptional profiles affect ESC differentiative capacity and therapeutic potential. Although single-cell RNA sequencing has revealed additional subpopulations and specific features of naive and primed human pluripotent stem cells (hPSCs), the underlying mechanisms that regulate their specific transcription and that control their pluripotent states remain elusive. RESULTS By single-cell analysis of high-resolution, three-dimensional (3D) genomic structure, we herein demonstrate that remodeling of genomic structure is highly associated with the pluripotent states of human ESCs (hESCs). The naive pluripotent state is featured with specialized 3D genomic structures and clear chromatin compartmentalization that is distinct from the primed state. The naive pluripotent state is achieved by remodeling the active euchromatin compartment and reducing chromatin interactions at the nuclear center. This unique genomic organization is linked to enhanced chromatin accessibility on enhancers and elevated expression levels of naive pluripotent genes localized to this region. In contradistinction, the primed state exhibits intermingled genomic organization. Moreover, active euchromatin and primed pluripotent genes are distributed at the nuclear periphery, while repressive heterochromatin is densely concentrated at the nuclear center, reducing chromatin accessibility and the transcription of naive genes. CONCLUSIONS Our data provide insights into the chromatin structure of ESCs in their naive and primed states, and we identify specific patterns of modifications in transcription and chromatin structure that might explain the genes that are differentially expressed between naive and primed hESCs. Thus, the inversion or relocation of heterochromatin to euchromatin via compartmentalization is related to the regulation of chromatin accessibility, thereby defining pluripotent states and cellular identity.
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Affiliation(s)
- Niannian Li
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, 94 Weijin Road, Tianjin, 300071, China
- Weifang People's Hospital, Shandong, 261041, China
| | - Kairang Jin
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, 94 Weijin Road, Tianjin, 300071, China
- Department of Cell Biology and Genetics, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin, 300071, China
| | - Bin Liu
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, 94 Weijin Road, Tianjin, 300071, China
- Weifang People's Hospital, Shandong, 261041, China
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, 23 Hongda Street, TEDA, Tianjin, 300457, China
| | - Mingzhu Yang
- Key Laboratory for Stem Cells and Tissue Engineering (Sun Yat-Sen University), Ministry of Education, Guangzhou, 510080, China
- Department of Histology and Embryology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China
| | - PanPan Shi
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, 94 Weijin Road, Tianjin, 300071, China
- Department of Cell Biology and Genetics, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin, 300071, China
| | - Dai Heng
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, 94 Weijin Road, Tianjin, 300071, China
- Department of Cell Biology and Genetics, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin, 300071, China
| | - Jichang Wang
- Key Laboratory for Stem Cells and Tissue Engineering (Sun Yat-Sen University), Ministry of Education, Guangzhou, 510080, China.
- Department of Histology and Embryology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China.
| | - Lin Liu
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, 94 Weijin Road, Tianjin, 300071, China.
- Department of Cell Biology and Genetics, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin, 300071, China.
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9
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Hauck AK, Mehmood R, Carpenter BJ, Frankfurter MT, Tackenberg MC, Inoue SI, Krieg MK, Cassim Bawa FN, Midha MK, Zundell DM, Batmanov K, Lazar MA. Nuclear receptor corepressors non-canonically drive glucocorticoid receptor-dependent activation of hepatic gluconeogenesis. Nat Metab 2024; 6:825-836. [PMID: 38622413 DOI: 10.1038/s42255-024-01029-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 03/07/2024] [Indexed: 04/17/2024]
Abstract
Nuclear receptor corepressors (NCoRs) function in multiprotein complexes containing histone deacetylase 3 (HDAC3) to alter transcriptional output primarily through repressive chromatin remodelling at target loci1-5. In the liver, loss of HDAC3 causes a marked hepatosteatosis largely because of de-repression of genes involved in lipid metabolism6,7; however, the individual roles and contribution of other complex members to hepatic and systemic metabolic regulation are unclear. Here we show that adult loss of both NCoR1 and NCoR2 (double knockout (KO)) in hepatocytes phenocopied the hepatomegalic fatty liver phenotype of HDAC3 KO. In addition, double KO livers exhibited a dramatic reduction in glycogen storage and gluconeogenic gene expression that was not observed with hepatic KO of individual NCoRs or HDAC3, resulting in profound fasting hypoglycaemia. This surprising HDAC3-independent activation function of NCoR1 and NCoR2 is due to an unexpected loss of chromatin accessibility on deletion of NCoRs that prevented glucocorticoid receptor binding and stimulatory effect on gluconeogenic genes. These studies reveal an unanticipated, non-canonical activation function of NCoRs that is required for metabolic health.
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Affiliation(s)
- Amy K Hauck
- Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Rashid Mehmood
- Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Bryce J Carpenter
- Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Maxwell T Frankfurter
- Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Michael C Tackenberg
- Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Shin-Ichi Inoue
- Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Maria K Krieg
- Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Fathima N Cassim Bawa
- Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Mohit K Midha
- Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Delaine M Zundell
- Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Kirill Batmanov
- Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Mitchell A Lazar
- Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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10
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Zhao X, Lin S, Ren H, Sun S, Zheng L, Chen LF, Wang Z. The histone methyltransferase ASH1L protects against bone loss by inhibiting osteoclastogenesis. Cell Death Differ 2024; 31:605-617. [PMID: 38431690 PMCID: PMC11094046 DOI: 10.1038/s41418-024-01274-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 02/16/2024] [Accepted: 02/20/2024] [Indexed: 03/05/2024] Open
Abstract
Absent, small, or homeotic1-like (ASH1L) is a histone lysine methyltransferase that generally functions as a transcriptional activator in controlling cell fate. So far, its physiological relevance in bone homeostasis and osteoclast differentiation remains elusive. Here, by conditional deleting Ash1l in osteoclast progenitors of mice, we found ASH1L deficiency resulted in osteoporosis and potentiation of osteoclastogenesis in vivo and in vitro. Mechanistically, ASH1L binds the promoter of the Src homology 3 and cysteine-rich domain 2 (Stac2) and increases the gene's transcription via histone 3 lysine 4 (H3K4) trimethylation modification, thus augmenting the STAC2's protection against receptor activator of nuclear factor kB ligand (RANKL)-initiated inflammation during osteoclast formation. Collectively, we demonstrate the first piece of evidence to prove ASH1L as a critical checkpoint during osteoclastogenesis. The work sheds new light on our understanding about the biological function of ASH1L in bone homeostasis, therefore providing a valuable therapeutic target for the treatment of osteoporosis or inflammatory bone diseases.
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Affiliation(s)
- Xiaoli Zhao
- Department of Biochemistry, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Shuai Lin
- Department of Biochemistry, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Department of Orthodontics, School and Hospital of Stomatology, Peking University, Beijing, China
| | - Hangjiang Ren
- Department of Biochemistry, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Shenghui Sun
- Department of Biochemistry, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Liyun Zheng
- Department of Biochemistry, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Lin-Feng Chen
- Department of Biochemistry, School of Molecular and Cellular Biology, University of Illinois at Urbana-Champaign, Urbana, USA
| | - Zhen Wang
- Department of Biochemistry, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
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11
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Chen Z, Guo X, Tao R, Huyghe JR, Law PJ, Fernandez-Rozadilla C, Ping J, Jia G, Long J, Li C, Shen Q, Xie Y, Timofeeva MN, Thomas M, Schmit SL, Díez-Obrero V, Devall M, Moratalla-Navarro F, Fernandez-Tajes J, Palles C, Sherwood K, Briggs SEW, Svinti V, Donnelly K, Farrington SM, Blackmur J, Vaughan-Shaw PG, Shu XO, Lu Y, Broderick P, Studd J, Harrison TA, Conti DV, Schumacher FR, Melas M, Rennert G, Obón-Santacana M, Martín-Sánchez V, Oh JH, Kim J, Jee SH, Jung KJ, Kweon SS, Shin MH, Shin A, Ahn YO, Kim DH, Oze I, Wen W, Matsuo K, Matsuda K, Tanikawa C, Ren Z, Gao YT, Jia WH, Hopper JL, Jenkins MA, Win AK, Pai RK, Figueiredo JC, Haile RW, Gallinger S, Woods MO, Newcomb PA, Duggan D, Cheadle JP, Kaplan R, Kerr R, Kerr D, Kirac I, Böhm J, Mecklin JP, Jousilahti P, Knekt P, Aaltonen LA, Rissanen H, Pukkala E, Eriksson JG, Cajuso T, Hänninen U, Kondelin J, Palin K, Tanskanen T, Renkonen-Sinisalo L, Männistö S, Albanes D, Weinstein SJ, Ruiz-Narvaez E, Palmer JR, Buchanan DD, Platz EA, Visvanathan K, Ulrich CM, Siegel E, Brezina S, Gsur A, Campbell PT, Chang-Claude J, Hoffmeister M, Brenner H, Slattery ML, Potter JD, Tsilidis KK, Schulze MB, Gunter MJ, Murphy N, Castells A, Castellví-Bel S, Moreira L, Arndt V, Shcherbina A, Bishop DT, Giles GG, Southey MC, Idos GE, McDonnell KJ, Abu-Ful Z, Greenson JK, Shulman K, Lejbkowicz F, Offit K, Su YR, Steinfelder R, Keku TO, van Guelpen B, Hudson TJ, Hampel H, Pearlman R, Berndt SI, Hayes RB, Martinez ME, Thomas SS, Pharoah PDP, Larsson SC, Yen Y, Lenz HJ, White E, Li L, Doheny KF, Pugh E, Shelford T, Chan AT, Cruz-Correa M, Lindblom A, Hunter DJ, Joshi AD, Schafmayer C, Scacheri PC, Kundaje A, Schoen RE, Hampe J, Stadler ZK, Vodicka P, Vodickova L, Vymetalkova V, Edlund CK, Gauderman WJ, Shibata D, Toland A, Markowitz S, Kim A, Chanock SJ, van Duijnhoven F, Feskens EJM, Sakoda LC, Gago-Dominguez M, Wolk A, Pardini B, FitzGerald LM, Lee SC, Ogino S, Bien SA, Kooperberg C, Li CI, Lin Y, Prentice R, Qu C, Bézieau S, Yamaji T, Sawada N, Iwasaki M, Le Marchand L, Wu AH, Qu C, McNeil CE, Coetzee G, Hayward C, Deary IJ, Harris SE, Theodoratou E, Reid S, Walker M, Ooi LY, Lau KS, Zhao H, Hsu L, Cai Q, Dunlop MG, Gruber SB, Houlston RS, Moreno V, Casey G, Peters U, Tomlinson I, Zheng W. Fine-mapping analysis including over 254,000 East Asian and European descendants identifies 136 putative colorectal cancer susceptibility genes. Nat Commun 2024; 15:3557. [PMID: 38670944 PMCID: PMC11053150 DOI: 10.1038/s41467-024-47399-x] [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: 10/16/2023] [Accepted: 03/26/2024] [Indexed: 04/28/2024] Open
Abstract
Genome-wide association studies (GWAS) have identified more than 200 common genetic variants independently associated with colorectal cancer (CRC) risk, but the causal variants and target genes are mostly unknown. We sought to fine-map all known CRC risk loci using GWAS data from 100,204 cases and 154,587 controls of East Asian and European ancestry. Our stepwise conditional analyses revealed 238 independent association signals of CRC risk, each with a set of credible causal variants (CCVs), of which 28 signals had a single CCV. Our cis-eQTL/mQTL and colocalization analyses using colorectal tissue-specific transcriptome and methylome data separately from 1299 and 321 individuals, along with functional genomic investigation, uncovered 136 putative CRC susceptibility genes, including 56 genes not previously reported. Analyses of single-cell RNA-seq data from colorectal tissues revealed 17 putative CRC susceptibility genes with distinct expression patterns in specific cell types. Analyses of whole exome sequencing data provided additional support for several target genes identified in this study as CRC susceptibility genes. Enrichment analyses of the 136 genes uncover pathways not previously linked to CRC risk. Our study substantially expanded association signals for CRC and provided additional insight into the biological mechanisms underlying CRC development.
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Affiliation(s)
- Zhishan Chen
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt Epidemiology Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Xingyi Guo
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt Epidemiology Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Ran Tao
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, 37232, TN, USA
| | - Jeroen R Huyghe
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Philip J Law
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
| | - Ceres Fernandez-Rozadilla
- Edinburgh Cancer Research Centre, Institute of Genomics and Cancer, University of Edinburgh, Edinburgh, UK
- Genomic Medicine Group, Instituto de Investigacion Sanitaria de Santiago, Santiago de Compostela, Spain
| | - Jie Ping
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt Epidemiology Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Guochong Jia
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt Epidemiology Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jirong Long
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt Epidemiology Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Chao Li
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt Epidemiology Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Quanhu Shen
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Yuhan Xie
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, USA
| | - Maria N Timofeeva
- Colon Cancer Genetics Group, Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- Danish Institute for Advanced Study, Department of Public Health, University of Southern Denmark, Odense, Denmark
| | - Minta Thomas
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Stephanie L Schmit
- Genomic Medicine Institute, Cleveland Clinic, Cleveland, OH, USA
- Population and Cancer Prevention Program, Case Comprehensive Cancer Center, Cleveland, OH, USA
| | - Virginia Díez-Obrero
- Colorectal Cancer Group, ONCOBELL Program, Bellvitge Biomedical Research Institute, Barcelona, Spain
- Consortium for Biomedical Research in Epidemiology and Public Health, Madrid, Spain
- Department of Clinical Sciences, Faculty of Medicine, University of Barcelona, Barcelona, Spain
- Oncology Data Analytics Program, Catalan Institute of Oncology, Barcelona, Spain
| | - Matthew Devall
- Center for Public Health Genomics, Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA
| | - Ferran Moratalla-Navarro
- Colorectal Cancer Group, ONCOBELL Program, Bellvitge Biomedical Research Institute, Barcelona, Spain
- Consortium for Biomedical Research in Epidemiology and Public Health, Madrid, Spain
- Department of Clinical Sciences, Faculty of Medicine, University of Barcelona, Barcelona, Spain
- Oncology Data Analytics Program, Catalan Institute of Oncology, Barcelona, Spain
| | - Juan Fernandez-Tajes
- Edinburgh Cancer Research Centre, Institute of Genomics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Claire Palles
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Kitty Sherwood
- Edinburgh Cancer Research Centre, Institute of Genomics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Sarah E W Briggs
- Department of Public Health, Richard Doll Building, University of Oxford, Oxford, UK
| | - Victoria Svinti
- Colon Cancer Genetics Group, Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Kevin Donnelly
- Colon Cancer Genetics Group, Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Susan M Farrington
- Colon Cancer Genetics Group, Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - James Blackmur
- Colon Cancer Genetics Group, Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Peter G Vaughan-Shaw
- Colon Cancer Genetics Group, Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Xiao-Ou Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt Epidemiology Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Yingchang Lu
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt Epidemiology Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Peter Broderick
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
| | - James Studd
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
| | - Tabitha A Harrison
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - David V Conti
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Fredrick R Schumacher
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, USA
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Marilena Melas
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Gad Rennert
- Clalit National Cancer Control Center, Haifa, Israel
- Department of Community Medicine and Epidemiology, Lady Davis Carmel Medical Center, Haifa, Israel
- Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Mireia Obón-Santacana
- Colorectal Cancer Group, ONCOBELL Program, Bellvitge Biomedical Research Institute, Barcelona, Spain
- Consortium for Biomedical Research in Epidemiology and Public Health, Madrid, Spain
- Oncology Data Analytics Program, Catalan Institute of Oncology, Barcelona, Spain
| | - Vicente Martín-Sánchez
- Consortium for Biomedical Research in Epidemiology and Public Health, Madrid, Spain
- Biomedicine Institute, University of León, León, Spain
| | - Jae Hwan Oh
- Center for Colorectal Cancer, National Cancer Center Hospital, National Cancer Center, Gyeonggi-do, South Korea
| | - Jeongseon Kim
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Gyeonggi-do, South Korea
| | - Sun Ha Jee
- Department of Epidemiology and Health Promotion, Graduate School of Public Health, Yonsei University, Seoul, South Korea
| | - Keum Ji Jung
- Department of Epidemiology and Health Promotion, Graduate School of Public Health, Yonsei University, Seoul, South Korea
| | - Sun-Seog Kweon
- Department of Preventive Medicine, Chonnam National University Medical School, Gwangju, South Korea
| | - Min-Ho Shin
- Department of Preventive Medicine, Chonnam National University Medical School, Gwangju, South Korea
| | - Aesun Shin
- Cancer Research Institute, Seoul National University, Seoul, South Korea
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, South Korea
| | - Yoon-Ok Ahn
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, South Korea
| | - Dong-Hyun Kim
- Department of Social and Preventive Medicine, Hallym University College of Medicine, Okcheon-dong, South Korea
| | - Isao Oze
- Division of Cancer Epidemiology and Prevention, Aichi Cancer Center Research Institute, Nagoya, Japan
| | - Wanqing Wen
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt Epidemiology Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Keitaro Matsuo
- Department of Epidemiology, Nagoya University Graduate School of Medicine, Nagoya, Japan
- Division of Molecular and Clinical Epidemiology, Aichi Cancer Center Research Institute, Nagoya, Japan
| | - Koichi Matsuda
- Laboratory of Clinical Genome Sequencing, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, Tokyo, Japan
| | - Chizu Tanikawa
- Laboratory of Genome Technology, Human Genome Center, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Zefang Ren
- School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Yu-Tang Gao
- State Key Laboratory of Oncogenes and Related Genes and Department of Epidemiology, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Wei-Hua Jia
- State Key Laboratory of Oncology in South China, Cancer Center, Sun Yat-sen University, Guangzhou, China
| | - John L Hopper
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, VIC, Australia
- Department of Epidemiology, School of Public Health and Institute of Health and Environment, Seoul National University, Seoul, South Korea
| | - Mark A Jenkins
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, VIC, Australia
| | - Aung Ko Win
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, VIC, Australia
| | - Rish K Pai
- Department of Laboratory Medicine and Pathology, Mayo Clinic Arizona, Scottsdale, AZ, USA
| | - Jane C Figueiredo
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Department of Medicine, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Robert W Haile
- Division of Oncology, Department of Medicine, Cedars-Sinai Cancer Research Center for Health Equity, Los Angeles, CA, USA
| | - Steven Gallinger
- Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, University of Toronto, Toronto, ON, Canada
| | - Michael O Woods
- Division of Biomedical Sciences, Memorial University of Newfoundland, St. John, ON, Canada
| | - Polly A Newcomb
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- School of Public Health, University of Washington, Seattle, WA, USA
| | - David Duggan
- City of Hope National Medical Center, Translational Genomics Research Institute, Phoenix, AZ, USA
| | | | - Richard Kaplan
- MRC Clinical Trials Unit, Medical Research Council, Cardiff, UK
| | - Rachel Kerr
- Department of Oncology, University of Oxford, Oxford, UK
| | - David Kerr
- Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Iva Kirac
- Department of Surgical Oncology, University Hospital for Tumors, Sestre milosrdnice University Hospital Center, Zagreb, Croatia
| | - Jan Böhm
- Department of Pathology, Central Finland Health Care District, Jyväskylä, Finland
| | | | - Pekka Jousilahti
- Department of Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Paul Knekt
- Department of Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Lauri A Aaltonen
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
- Genome-Scale Biology Research Program, University of Helsinki, Helsinki, Finland
| | - Harri Rissanen
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Eero Pukkala
- Faculty of Social Sciences, Tampere University, Tampere, Finland
- Finnish Cancer Registry, Institute for Statistical and Epidemiological Cancer Research, Helsinki, Finland
| | - Johan G Eriksson
- Folkhälsan Research Centre, University of Helsinki, Helsinki, Finland
- Human Potential Translational Research Programme, National University of Singapore, Singapore, Singapore
- Unit of General Practice and Primary Health Care, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Tatiana Cajuso
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
- Genome-Scale Biology Research Program, University of Helsinki, Helsinki, Finland
| | - Ulrika Hänninen
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
- Genome-Scale Biology Research Program, University of Helsinki, Helsinki, Finland
| | - Johanna Kondelin
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
- Genome-Scale Biology Research Program, University of Helsinki, Helsinki, Finland
| | - Kimmo Palin
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
- Genome-Scale Biology Research Program, University of Helsinki, Helsinki, Finland
| | - Tomas Tanskanen
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
- Genome-Scale Biology Research Program, University of Helsinki, Helsinki, Finland
| | | | - Satu Männistö
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Demetrius Albanes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Stephanie J Weinstein
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Edward Ruiz-Narvaez
- Department of Nutritional Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Julie R Palmer
- Department of Medicine, Boston University School of Medicine, Boston, MA, USA
- Slone Epidemiology Center at Boston University, Boston, MA, USA
| | - Daniel D Buchanan
- Colorectal Oncogenomics Group, Department of Clinical Pathology, University of Melbourne, Parkville, VIC, Australia
- Genomic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, VIC, Australia
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, VIC, Australia
| | - Elizabeth A Platz
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Kala Visvanathan
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Cornelia M Ulrich
- Huntsman Cancer Institute and Department of Population Health Sciences, University of Utah, Salt Lake City, UT, USA
| | - Erin Siegel
- Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Stefanie Brezina
- Institute of Cancer Research, Department of Medicine I, Medical University Vienna, Vienna, Austria
| | - Andrea Gsur
- Institute of Cancer Research, Department of Medicine I, Medical University Vienna, Vienna, Austria
| | - Peter T Campbell
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, New York, NY, USA
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center, Heidelberg, Germany
- University Medical Centre Hamburg-Eppendorf, University Cancer Centre Hamburg, Hamburg, Germany
| | - Michael Hoffmeister
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center, Heidelberg, Germany
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center, Heidelberg, Germany
- Division of Preventive Oncology, German Cancer Research Center and National Center for Tumor Diseases, Heidelberg, Germany
- German Cancer Consortium, German Cancer Research Center, Heidelberg, Germany
| | - Martha L Slattery
- Department of Internal Medicine, University of Utah, Salt Lake City, UT, USA
| | - John D Potter
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Research Centre for Hauora and Health, Massey University, Wellington, New Zealand
| | - Kostas K Tsilidis
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
- Department of Hygiene and Epidemiology, University of Ioannina School of Medicine, Ioannina, Greece
| | - Matthias B Schulze
- Department of Molecular Epidemiology, German Institute of Human Nutrition Potsdam-Rehbruecke, Nuthetal, Germany
- Institute of Nutritional Science, University of Potsdam, Potsdam, Germany
| | - Marc J Gunter
- Nutrition and Metabolism Branch, International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Neil Murphy
- Nutrition and Metabolism Branch, International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Antoni Castells
- Gastroenterology Department, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, University of Barcelona, Barcelona, Spain
| | - Sergi Castellví-Bel
- Gastroenterology Department, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, University of Barcelona, Barcelona, Spain
| | - Leticia Moreira
- Gastroenterology Department, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, University of Barcelona, Barcelona, Spain
| | - Volker Arndt
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center, Heidelberg, Germany
| | - Anna Shcherbina
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - D Timothy Bishop
- Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK
| | - Graham G Giles
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, VIC, Australia
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, VIC, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC, Australia
| | - Melissa C Southey
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, VIC, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC, Australia
- Department of Clinical Pathology, University of Melbourne, Melbourne, VIC, Australia
| | - Gregory E Idos
- Department of Medical Oncology and Center For Precision Medicine, City of Hope National Medical Center, Duarte, CA, USA
| | - Kevin J McDonnell
- Clalit National Cancer Control Center, Haifa, Israel
- Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
- Department of Medical Oncology and Center For Precision Medicine, City of Hope National Medical Center, Duarte, CA, USA
| | - Zomoroda Abu-Ful
- Department of Community Medicine and Epidemiology, Lady Davis Carmel Medical Center, Haifa, Israel
| | - Joel K Greenson
- Clalit National Cancer Control Center, Haifa, Israel
- Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Katerina Shulman
- Department of Community Medicine and Epidemiology, Lady Davis Carmel Medical Center, Haifa, Israel
| | - Flavio Lejbkowicz
- Clalit National Cancer Control Center, Haifa, Israel
- Department of Community Medicine and Epidemiology, Lady Davis Carmel Medical Center, Haifa, Israel
- Clalit Health Services, Personalized Genomic Service, Lady Davis Carmel Medical Center, Haifa, Israel
| | - Kenneth Offit
- Clinical Genetics Service, Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Yu-Ru Su
- Kaiser Permanente Washington Health Research Institute, Seattle, WA, USA
| | - Robert Steinfelder
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Temitope O Keku
- Center for Gastrointestinal Biology and Disease, University of North Carolina, Chapel Hill, NC, USA
| | - Bethany van Guelpen
- Department of Radiation Sciences, Oncology Unit, Umeå University, Umeå, Sweden
- Wallenberg Centre for Molecular Medicine, Umeå University, Umeå, Sweden
| | | | - Heather Hampel
- Division of Human Genetics, Department of Internal Medicine, Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Rachel Pearlman
- Division of Human Genetics, Department of Internal Medicine, Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Sonja I Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Richard B Hayes
- Division of Epidemiology, Department of Population Health, New York University School of Medicine, New York, NY, USA
| | - Marie Elena Martinez
- Department of Family Medicine and Public Health, University of California San Diego, La Jolla, CA, USA
- Population Sciences, Disparities and Community Engagement, University of California San Diego Moores Cancer Center, La Jolla, CA, USA
| | | | - Paul D P Pharoah
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Susanna C Larsson
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Yun Yen
- Taipei Medical University, Taipei, Taiwan
| | - Heinz-Josef Lenz
- Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Emily White
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Epidemiology, University of Washington School of Public Health, Seattle, WA, USA
| | - Li Li
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, USA
| | - Kimberly F Doheny
- Center for Inherited Disease Research, Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Elizabeth Pugh
- Center for Inherited Disease Research, Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Tameka Shelford
- Center for Inherited Disease Research, Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Andrew T Chan
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Marcia Cruz-Correa
- Comprehensive Cancer Center, University of Puerto Rico, San Juan, Puerto Rico
| | - Annika Lindblom
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - David J Hunter
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Amit D Joshi
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Clemens Schafmayer
- Department of General Surgery, University Hospital Rostock, Rostock, Germany
| | - Peter C Scacheri
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Anshul Kundaje
- Department of Genetics, Stanford University, Stanford, CA, USA
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Robert E Schoen
- Department of Medicine and Epidemiology, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Jochen Hampe
- Department of Medicine I, University Hospital Dresden, Technische Universität Dresden, Dresden, Germany
| | - Zsofia K Stadler
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
- Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Pavel Vodicka
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic
- Faculty of Medicine and Biomedical Center in Pilsen, Charles University, Pilsen, Czech Republic
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Ludmila Vodickova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic
- Faculty of Medicine and Biomedical Center in Pilsen, Charles University, Pilsen, Czech Republic
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Veronika Vymetalkova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic
- Faculty of Medicine and Biomedical Center in Pilsen, Charles University, Pilsen, Czech Republic
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Christopher K Edlund
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - W James Gauderman
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - David Shibata
- Department of Surgery, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Amanda Toland
- Departments of Cancer Biology and Genetics and Internal Medicine, Comprehensive Cancer Center, Ohio State University, Columbus, OH, USA
| | - Sanford Markowitz
- Departments of Medicine and Genetics, Case Comprehensive Cancer Center, Case Western Reserve University and University Hospitals of Cleveland, Cleveland, OH, USA
| | - Andre Kim
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Franzel van Duijnhoven
- Division of Human Nutrition and Health, Wageningen University and Research, Wageningen, The Netherlands
| | - Edith J M Feskens
- Division of Human Nutrition, Wageningen University and Research, Wageningen, The Netherlands
| | - Lori C Sakoda
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Manuela Gago-Dominguez
- Genomic Medicine Group, Galician Public Foundation of Genomic Medicine, Servicio Galego de Saude, Santiago de Compostela, Spain
- Instituto de Investigación Sanitaria de Santiago de Compostela, Santiago de Compostela, Spain
| | - Alicja Wolk
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Barbara Pardini
- Candiolo Cancer Institute FPO-IRCCS, Candiolo, (TO), Italy
- Italian Institute for Genomic Medicine, Candiolo Cancer Institute FPO-IRCCS, Candiolo, (TO), Italy
| | - Liesel M FitzGerald
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, VIC, Australia
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, Australia
| | - Soo Chin Lee
- National University Cancer Institute, Singapore, Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Shuji Ogino
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cancer Immunology Program, Dana-Farber Harvard Cancer Center, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Stephanie A Bien
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Charles Kooperberg
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Christopher I Li
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Yi Lin
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Ross Prentice
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Conghui Qu
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Stéphane Bézieau
- Service de Génétique Médicale, Centre Hospitalier Universitaire Nantes, Nantes, France
| | - Taiki Yamaji
- Division of Epidemiology, National Cancer Center Institute for Cancer Control, National Cancer Center, Tokyo, Japan
| | - Norie Sawada
- Division of Cohort Research, National Cancer Center Institute for Cancer Control, National Cancer Center, Tokyo, Japan
| | - Motoki Iwasaki
- Division of Epidemiology, National Cancer Center Institute for Cancer Control, National Cancer Center, Tokyo, Japan
- Division of Cohort Research, National Cancer Center Institute for Cancer Control, National Cancer Center, Tokyo, Japan
| | | | - Anna H Wu
- Preventative Medicine, University of Southern California, Los Angeles, CA, USA
| | - Chenxu Qu
- USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Caroline E McNeil
- USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | | | - Caroline Hayward
- MRC Human Genetics Unit, Institute of Genomics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Ian J Deary
- Lothian Birth Cohorts group, Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - Sarah E Harris
- Lothian Birth Cohorts group, Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - Evropi Theodoratou
- Centre for Global Health, Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Stuart Reid
- Colon Cancer Genetics Group, Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Marion Walker
- Colon Cancer Genetics Group, Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Li Yin Ooi
- Colon Cancer Genetics Group, Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- Department of Pathology, National University Hospital, National University Health System, Singapore, Singapore
| | - Ken S Lau
- Epithelial Biology Center and Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Hongyu Zhao
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, USA
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
| | - Li Hsu
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Biostatistics, School of Public Health, University of Washington, Seattle, WA, USA
| | - Qiuyin Cai
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt Epidemiology Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Malcolm G Dunlop
- Colon Cancer Genetics Group, Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Stephen B Gruber
- Department of Medical Oncology and Center For Precision Medicine, City of Hope National Medical Center, Duarte, CA, USA
| | - Richard S Houlston
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
| | - Victor Moreno
- Colorectal Cancer Group, ONCOBELL Program, Bellvitge Biomedical Research Institute, Barcelona, Spain
- Consortium for Biomedical Research in Epidemiology and Public Health, Madrid, Spain
- Department of Clinical Sciences, Faculty of Medicine, University of Barcelona, Barcelona, Spain
- Oncology Data Analytics Program, Catalan Institute of Oncology, Barcelona, Spain
| | - Graham Casey
- Center for Public Health Genomics, Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA
| | - Ulrike Peters
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - Ian Tomlinson
- Edinburgh Cancer Research Centre, Institute of Genomics and Cancer, University of Edinburgh, Edinburgh, UK
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt Epidemiology Center, Vanderbilt University Medical Center, Nashville, TN, USA.
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12
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Xu T, Li X, Zhao W, Wang X, Jin L, Feng Z, Li H, Zhang M, Tian Y, Hu G, Yue Y, Dai X, Shan C, Zhang W, Zhang C, Zhang Y. SF3B3-regulated mTOR alternative splicing promotes colorectal cancer progression and metastasis. J Exp Clin Cancer Res 2024; 43:126. [PMID: 38671459 PMCID: PMC11047005 DOI: 10.1186/s13046-024-03053-4] [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: 03/05/2024] [Accepted: 04/18/2024] [Indexed: 04/28/2024] Open
Abstract
BACKGROUND Aberrant alternative splicing (AS) is a pervasive event during colorectal cancer (CRC) development. SF3B3 is a splicing factor component of U2 small nuclear ribonucleoproteins which are crucial for early stages of spliceosome assembly. The role of SF3B3 in CRC remains unknown. METHODS SF3B3 expression in human CRCs was analyzed using publicly available CRC datasets, immunohistochemistry, qRT-PCR, and western blot. RNA-seq, RNA immunoprecipitation, and lipidomics were performed in SF3B3 knockdown or overexpressing CRC cell lines. CRC cell xenografts, patient-derived xenografts, patient-derived organoids, and orthotopic metastasis mouse models were utilized to determine the in vivo role of SF3B3 in CRC progression and metastasis. RESULTS SF3B3 was upregulated in CRC samples and associated with poor survival. Inhibition of SF3B3 by RNA silencing suppressed the proliferation and metastasis of CRC cells in vitro and in vivo, characterized by mitochondria injury, increased reactive oxygen species (ROS), and apoptosis. Mechanistically, silencing of SF3B3 increased mTOR exon-skipped splicing, leading to the suppression of lipogenesis via mTOR-SREBF1-FASN signaling. The combination of SF3B3 shRNAs and mTOR inhibitors showed synergistic antitumor activity in patient-derived CRC organoids and xenografts. Importantly, we identified SF3B3 as a critical regulator of mTOR splicing and autophagy in multiple cancers. CONCLUSIONS Our findings revealed that SF3B3 promoted CRC progression and metastasis by regulating mTOR alternative splicing and SREBF1-FASN-mediated lipogenesis, providing strong evidence to support SF3B3 as a druggable target for CRC therapy.
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Affiliation(s)
- Tong Xu
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, China
| | - Xichuan Li
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, Tianjin, 300382, China
| | - Wennan Zhao
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, China
| | - Xue Wang
- Cancer Biology Program, University of Hawaii Cancer Center, Honolulu, HI, 96813, USA
| | - Leixin Jin
- Department of Colorectal Surgery, Tianjin Union Medical Center, Tianjin, 30021, China
| | - Zhiqiang Feng
- Department of Colorectal Surgery, Tianjin Union Medical Center, Tianjin, 30021, China
| | - Huixiang Li
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, China
| | - Mingzhe Zhang
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, China
| | - Yiqing Tian
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, China
| | - Ge Hu
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, China
| | - Yuan Yue
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, Tianjin, 300382, China
| | - Xintong Dai
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, 300350, China
| | - Changliang Shan
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, 300350, China
| | | | - Chunze Zhang
- Department of Colorectal Surgery, Tianjin Union Medical Center, Tianjin, 30021, China.
| | - Youcai Zhang
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, China.
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13
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Cattaneo G, Ventin M, Arya S, Kontos F, Michelakos T, Sekigami Y, Cai L, Villani V, Sabbatino F, Chen F, Sadagopan A, Deshpande V, Moore PA, Ting DT, Bardeesy N, Wang X, Ferrone S, Ferrone CR. Interplay between B7-H3 and HLA class I in the clinical course of pancreatic ductal adenocarcinoma. Cancer Lett 2024; 587:216713. [PMID: 38364961 PMCID: PMC11146152 DOI: 10.1016/j.canlet.2024.216713] [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: 10/17/2023] [Revised: 01/16/2024] [Accepted: 02/05/2024] [Indexed: 02/18/2024]
Abstract
Human leukocyte antigen (HLA) class I defects are associated with cancer progression. However, their prognostic significance is controversial and may be modulated by immune checkpoints. Here, we investigated whether the checkpoint B7-H3 modulates the relationship between HLA class I and pancreatic ductal adenocarcinoma (PDAC) prognosis. PDAC tumors were analyzed for the expression of B7-H3, HLA class I, HLA class II molecules, and for the presence of tumor-infiltrating immune cells. We observed defective HLA class I and HLA class II expressions in 75% and 59% of PDAC samples, respectively. HLA class I and B7-H3 expression were positively related at mRNA and protein level, potentially because of shared regulation by RELA, a sub-unit of NF-kB. High B7-H3 expression and low CD8+ T cell density were indicators of poor survival, while HLA class I was not. Defective HLA class I expression was associated with unfavorable survival only in patients with low B7-H3 expression. Favorable survival was observed only when HLA class I expression was high and B7-H3 expression low. Our results provide the rationale for targeting B7-H3 in patients with PDAC tumors displaying high HLA class I levels.
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Affiliation(s)
- Giulia Cattaneo
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States. https://twitter.com/GCattaneoPhD
| | - Marco Ventin
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
| | - Shahrzad Arya
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
| | - Filippos Kontos
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
| | - Theodoros Michelakos
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
| | - Yurie Sekigami
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
| | - Lei Cai
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
| | - Vincenzo Villani
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
| | - Francesco Sabbatino
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
| | | | - Ananthan Sadagopan
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
| | - Vikram Deshpande
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
| | | | - David T Ting
- MassGeneral Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
| | - Nabeel Bardeesy
- MassGeneral Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
| | - Xinhui Wang
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
| | - Soldano Ferrone
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
| | - Cristina R Ferrone
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States; Department of Surgery, Cedars-Sinai Medical Center, Los Angeles, CA, United States.
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14
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Jiang Y, Peng Y, Tian Q, Cheng Z, Feng B, Hu J, Xia L, Guo H, Xia K, Zhou L, Hu Z. Intergenic sequences harboring potential enhancer elements contribute to Axenfeld-Rieger syndrome by regulating PITX2. JCI Insight 2024; 9:e177032. [PMID: 38592784 PMCID: PMC11141933 DOI: 10.1172/jci.insight.177032] [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: 11/01/2023] [Accepted: 03/27/2024] [Indexed: 04/11/2024] Open
Abstract
Recent studies have uncovered that noncoding sequence variants may relate to Axenfeld-Rieger syndrome (ARS), a rare developmental anomaly with genetic heterogeneity. However, how these genomic regions are functionally and structurally associated with ARS is still unclear. In this study, we performed genome-wide linkage analysis and whole-genome sequencing in a Chinese family with ARS and identified a heterozygous deletion of about 570 kb (termed LOH-1) in the intergenic sequence between paired-like homeodomain transcription factor 2 (PITX2) and family with sequence similarity 241 member A. Knockout of LOH-1 homologous sequences caused ARS phenotypes in mice. RNA-Seq and real-time quantitative PCR revealed a significant reduction in Pitx2 gene expression in LOH-1-/- mice, while forkhead box C1 expression remained unchanged. ChIP-Seq and bioinformatics analysis identified a potential enhancer region (LOH-E1) within LOH-1. Deletion of LOH-E1 led to a substantial downregulation of the PITX2 gene. Mechanistically, we found a sequence (hg38 chr4:111,399,594-111,399,691) that is on LOH-E1 could regulate PITX2 by binding to RAD21, a critical component of the cohesin complex. Knockdown of RAD21 resulted in reduced PITX2 expression. Collectively, our findings indicate that a potential enhancer sequence that is within LOH-1 may regulate PITX2 expression remotely through cohesin-mediated loop domains, leading to ARS when absent.
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Affiliation(s)
- Yizheng Jiang
- MOE Key Laboratory of Rare Pediatric Diseases & Hunan Key Laboratory of Medical Genetics of the School of Life Sciences and
| | - Yu Peng
- Department of Medical Genetics, The Affiliated Children’s Hospital of Xiangya School of Medicine, Central South University, Changsha, China
| | - Qi Tian
- MOE Key Laboratory of Rare Pediatric Diseases & Hunan Key Laboratory of Medical Genetics of the School of Life Sciences and
| | - Zhe Cheng
- MOE Key Laboratory of Rare Pediatric Diseases & Hunan Key Laboratory of Medical Genetics of the School of Life Sciences and
| | - Bei Feng
- MOE Key Laboratory of Rare Pediatric Diseases & Hunan Key Laboratory of Medical Genetics of the School of Life Sciences and
| | - Junping Hu
- MOE Key Laboratory of Rare Pediatric Diseases & Hunan Key Laboratory of Medical Genetics of the School of Life Sciences and
| | - Lu Xia
- MOE Key Laboratory of Rare Pediatric Diseases & Hunan Key Laboratory of Medical Genetics of the School of Life Sciences and
| | - Hui Guo
- MOE Key Laboratory of Rare Pediatric Diseases & Hunan Key Laboratory of Medical Genetics of the School of Life Sciences and
| | - Kun Xia
- MOE Key Laboratory of Rare Pediatric Diseases & Hunan Key Laboratory of Medical Genetics of the School of Life Sciences and
- MOE Key Laboratory of Rare Pediatric Diseases, Hengyang Medical School, University of South China, Hengyang, China
| | - Liang Zhou
- Department of Ophthalmology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Zhengmao Hu
- MOE Key Laboratory of Rare Pediatric Diseases & Hunan Key Laboratory of Medical Genetics of the School of Life Sciences and
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15
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Wang W, Gao R, Yang D, Ma M, Zang R, Wang X, Chen C, Kou X, Zhao Y, Chen J, Liu X, Lu J, Xu B, Liu J, Huang Y, Chen C, Wang H, Gao S, Zhang Y, Gao Y. ADNP modulates SINE B2-derived CTCF-binding sites during blastocyst formation in mice. Genes Dev 2024; 38:168-188. [PMID: 38479840 PMCID: PMC10982698 DOI: 10.1101/gad.351189.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 02/20/2024] [Indexed: 04/02/2024]
Abstract
CTCF is crucial for chromatin structure and transcription regulation in early embryonic development. However, the kinetics of CTCF chromatin occupation in preimplantation embryos have remained unclear. In this study, we used CUT&RUN technology to investigate CTCF occupancy in mouse preimplantation development. Our findings revealed that CTCF begins binding to the genome prior to zygotic genome activation (ZGA), with a preference for CTCF-anchored chromatin loops. Although the majority of CTCF occupancy is consistently maintained, we identified a specific set of binding sites enriched in the mouse-specific short interspersed element (SINE) family B2 that are restricted to the cleavage stages. Notably, we discovered that the neuroprotective protein ADNP counteracts the stable association of CTCF at SINE B2-derived CTCF-binding sites. Knockout of Adnp in the zygote led to impaired CTCF binding signal recovery, failed deposition of H3K9me3, and transcriptional derepression of SINE B2 during the morula-to-blastocyst transition, which further led to unfaithful cell differentiation in embryos around implantation. Our analysis highlights an ADNP-dependent restriction of CTCF binding during cell differentiation in preimplantation embryos. Furthermore, our findings shed light on the functional importance of transposable elements (TEs) in promoting genetic innovation and actively shaping the early embryo developmental process specific to mammals.
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Affiliation(s)
- Wen Wang
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
- State Key Laboratory of Cardiology and Medical Innovation Center, Institute for Regenerative Medicine, Shanghai East Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Rui Gao
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Dongxu Yang
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
- State Key Laboratory of Cardiology and Medical Innovation Center, Institute for Regenerative Medicine, Shanghai East Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Mingli Ma
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
- State Key Laboratory of Cardiology and Medical Innovation Center, Institute for Regenerative Medicine, Shanghai East Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Ruge Zang
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Xiangxiu Wang
- Key Laboratory of Biorheological and Technology of Ministry of Education, State and Local Joint Engineering Laboratory for Vascular Implants, Modern Life Science Experiment Teaching Center at Bioengineering College of Chongqing University, Chongqing 400030, China
| | - Chuan Chen
- Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310006, China
| | - Xiaochen Kou
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Yanhong Zhao
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Jiayu Chen
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
- Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai 200120, China
| | - Xuelian Liu
- State Key Laboratory of Cardiology and Medical Innovation Center, Institute for Regenerative Medicine, Shanghai East Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
- Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiaxu Lu
- State Key Laboratory of Cardiology and Medical Innovation Center, Institute for Regenerative Medicine, Shanghai East Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Ben Xu
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Juntao Liu
- State Key Laboratory of Cardiology and Medical Innovation Center, Institute for Regenerative Medicine, Shanghai East Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Yanxin Huang
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Chaoqun Chen
- State Key Laboratory of Cardiology and Medical Innovation Center, Institute for Regenerative Medicine, Shanghai East Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Hong Wang
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Shaorong Gao
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China;
- State Key Laboratory of Cardiology and Medical Innovation Center, Institute for Regenerative Medicine, Shanghai East Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
- Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai 200120, China
| | - Yong Zhang
- State Key Laboratory of Cardiology and Medical Innovation Center, Institute for Regenerative Medicine, Shanghai East Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China;
- Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai 200120, China
| | - Yawei Gao
- State Key Laboratory of Cardiology and Medical Innovation Center, Institute for Regenerative Medicine, Shanghai East Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China;
- Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai 200120, China
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16
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Jones T, Sigauke RF, Sanford L, Taatjes DJ, Allen MA, Dowell RD. A transcription factor (TF) inference method that broadly measures TF activity and identifies mechanistically distinct TF networks. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.15.585303. [PMID: 38559193 PMCID: PMC10980006 DOI: 10.1101/2024.03.15.585303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
TF profiler is a method of inferring transcription factor regulatory activity, i.e. when a TF is present and actively regulating transcription, directly directly from nascent sequencing assays such as PRO-seq and GRO-seq. Transcription factors orchestrate transcription and play a critical role in cellular maintenance, identity and response to external stimuli. While ChIP assays have measured DNA localization, they fall short of identifying when and where transcription factors are actively regulating transcription. Our method, on the other hand, uses RNA polymerase activity to infer TF activity across hundreds of data sets and transcription factors. Based on these classifications we identify three distinct classes of transcription factors: ubiquitous factors that play roles in cellular homeostasis, driving basal gene programs across tissues and cell types, tissue specific factors that act almost exclusively at enhancers and are themselves regulated at transcription, and stimulus responsive TFs which are regulated post-transcriptionally but act predominantly at enhancers. TF profiler is broadly applicable, providing regulatory insights on any PRO-seq sample for any transcription factor with a known binding motif.
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Li Y, Han M, Wei H, Huang W, Chen Z, Zhang T, Qian M, Jing L, Nan G, Sun X, Dai S, Wang K, Jiang J, Zhu P, Chen L. Id2 epigenetically controls CD8 + T-cell exhaustion by disrupting the assembly of the Tcf3-LSD1 complex. Cell Mol Immunol 2024; 21:292-308. [PMID: 38287103 PMCID: PMC10902300 DOI: 10.1038/s41423-023-01118-6] [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: 07/31/2022] [Accepted: 12/01/2023] [Indexed: 01/31/2024] Open
Abstract
CD8+ T-cell exhaustion is a state of dysfunction that promotes tumor progression and is marked by the generation of Slamf6+ progenitor exhausted (Texprog) and Tim-3+ terminally exhausted (Texterm) subpopulations. Inhibitor of DNA binding protein 2 (Id2) has been shown to play important roles in T-cell development and CD8+ T-cell immunity. However, the role of Id2 in CD8+ T-cell exhaustion is unclear. Here, we found that Id2 transcriptionally and epigenetically regulates the generation of Texprog cells and their conversion to Texterm cells. Genetic deletion of Id2 dampens CD8+ T-cell-mediated immune responses and the maintenance of stem-like CD8+ T-cell subpopulations, suppresses PD-1 blockade and increases tumor susceptibility. Mechanistically, through its HLH domain, Id2 binds and disrupts the assembly of the Tcf3-Tal1 transcriptional regulatory complex, and thus modulates chromatin accessibility at the Slamf6 promoter by preventing the interaction of Tcf3 with the histone lysine demethylase LSD1. Therefore, Id2 increases the abundance of the permissive H3K4me2 mark on the Tcf3-occupied E-boxes in the Slamf6 promoter, modulates chromatin accessibility at the Slamf6 promoter and epigenetically regulates the generation of Slamf6+ Texprog cells. An LSD1 inhibitor GSK2879552 can rescue the Id2 knockout phenotype in tumor-bearing mice. Inhibition of LSD1 increases the abundance of Slamf6+Tim-3- Texprog cells in tumors and the expression level of Tcf1 in Id2-deleted CD8+ T cells. This study demonstrates that Id2-mediated transcriptional and epigenetic modification drives hierarchical CD8+ T-cell exhaustion, and the mechanistic insights gained may have implications for therapeutic intervention with tumor immune evasion.
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Affiliation(s)
- Yiming Li
- Department of Cell Biology of National Translational Science Center for Molecular Medicine and Department of Clinical Immunology of Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi, 710032, China
- State Key Laboratory of New Targets Discovery and Drug Development for Major Diseases, Ganzhou, Jiangxi, 341000, Xi'an, Shaanxi, 710032, China
| | - Mingwei Han
- Department of Cell Biology of National Translational Science Center for Molecular Medicine and Department of Clinical Immunology of Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi, 710032, China
- State Key Laboratory of New Targets Discovery and Drug Development for Major Diseases, Ganzhou, Jiangxi, 341000, Xi'an, Shaanxi, 710032, China
| | - Haolin Wei
- Department of Cell Biology of National Translational Science Center for Molecular Medicine and Department of Clinical Immunology of Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi, 710032, China
- State Key Laboratory of New Targets Discovery and Drug Development for Major Diseases, Ganzhou, Jiangxi, 341000, Xi'an, Shaanxi, 710032, China
| | - Wan Huang
- Department of Cell Biology of National Translational Science Center for Molecular Medicine and Department of Clinical Immunology of Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi, 710032, China
- State Key Laboratory of New Targets Discovery and Drug Development for Major Diseases, Ganzhou, Jiangxi, 341000, Xi'an, Shaanxi, 710032, China
| | - Zhinan Chen
- Department of Cell Biology of National Translational Science Center for Molecular Medicine and Department of Clinical Immunology of Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi, 710032, China
- State Key Laboratory of New Targets Discovery and Drug Development for Major Diseases, Ganzhou, Jiangxi, 341000, Xi'an, Shaanxi, 710032, China
| | - Tianjiao Zhang
- Department of Cell Biology of National Translational Science Center for Molecular Medicine and Department of Clinical Immunology of Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi, 710032, China
- State Key Laboratory of New Targets Discovery and Drug Development for Major Diseases, Ganzhou, Jiangxi, 341000, Xi'an, Shaanxi, 710032, China
| | - Meirui Qian
- Department of Cell Biology of National Translational Science Center for Molecular Medicine and Department of Clinical Immunology of Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi, 710032, China
- State Key Laboratory of New Targets Discovery and Drug Development for Major Diseases, Ganzhou, Jiangxi, 341000, Xi'an, Shaanxi, 710032, China
| | - Lin Jing
- Department of Cell Biology of National Translational Science Center for Molecular Medicine and Department of Clinical Immunology of Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi, 710032, China
- State Key Laboratory of New Targets Discovery and Drug Development for Major Diseases, Ganzhou, Jiangxi, 341000, Xi'an, Shaanxi, 710032, China
| | - Gang Nan
- Department of Cell Biology of National Translational Science Center for Molecular Medicine and Department of Clinical Immunology of Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi, 710032, China
- State Key Laboratory of New Targets Discovery and Drug Development for Major Diseases, Ganzhou, Jiangxi, 341000, Xi'an, Shaanxi, 710032, China
| | - Xiuxuan Sun
- Department of Cell Biology of National Translational Science Center for Molecular Medicine and Department of Clinical Immunology of Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi, 710032, China
- State Key Laboratory of New Targets Discovery and Drug Development for Major Diseases, Ganzhou, Jiangxi, 341000, Xi'an, Shaanxi, 710032, China
| | - Shuhui Dai
- Department of Cell Biology of National Translational Science Center for Molecular Medicine and Department of Clinical Immunology of Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi, 710032, China
- State Key Laboratory of New Targets Discovery and Drug Development for Major Diseases, Ganzhou, Jiangxi, 341000, Xi'an, Shaanxi, 710032, China
| | - Kun Wang
- Department of Cell Biology of National Translational Science Center for Molecular Medicine and Department of Clinical Immunology of Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi, 710032, China
- State Key Laboratory of New Targets Discovery and Drug Development for Major Diseases, Ganzhou, Jiangxi, 341000, Xi'an, Shaanxi, 710032, China
| | - Jianli Jiang
- Department of Cell Biology of National Translational Science Center for Molecular Medicine and Department of Clinical Immunology of Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi, 710032, China.
- State Key Laboratory of New Targets Discovery and Drug Development for Major Diseases, Ganzhou, Jiangxi, 341000, Xi'an, Shaanxi, 710032, China.
| | - Ping Zhu
- Department of Cell Biology of National Translational Science Center for Molecular Medicine and Department of Clinical Immunology of Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi, 710032, China.
- State Key Laboratory of New Targets Discovery and Drug Development for Major Diseases, Ganzhou, Jiangxi, 341000, Xi'an, Shaanxi, 710032, China.
| | - Liang Chen
- State Key Laboratory of New Targets Discovery and Drug Development for Major Diseases, Ganzhou, Jiangxi, 341000, Xi'an, Shaanxi, 710032, China.
- School of Medicine, Shanghai University, Shanghai, 200444, China.
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18
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Hu XT, Wu XF, Sui LM, Ao LQ, Pu CX, Yuan M, Xing W, Xu X. The GRHL3-regulated long non-coding RNA lnc-DC modulates keratinocytes differentiation by interacting with IGF2BP2 and up-regulating ZNF750. J Dermatol Sci 2024; 113:93-102. [PMID: 38383230 DOI: 10.1016/j.jdermsci.2024.02.003] [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: 04/24/2023] [Revised: 01/18/2024] [Accepted: 02/09/2024] [Indexed: 02/23/2024]
Abstract
BACKGROUND Aberrant keratinocytes differentiation has been demonstrated to be associated with a number of skin diseases. The roles of lncRNAs in keratinocytes differentiation remain to be largely unknown. OBJECTIVE Here we aim to investigate the role of lnc-DC in regulating epidermal keratinocytes differentiation. METHODS Expression of lnc-DC in the skin was queried in AnnoLnc and verified by FISH. The lncRNA expression profiles during keratinocytes differentiation were reanalyzed and verified by qPCR and FISH. Gene knock-down and over-expression were used to explore the role of lnc-DC in keratinocytes differentiation. The downstream target of lnc-DC was screened by whole transcriptome sequencing. CUT&RUN assay and siRNAs transfection was used to reveal the regulatory effect of GRHL3 on lnc-DC. The mechanism of lnc-DC regulating ZNF750 was revealed by RIP assay and RNA stability assay. RESULTS Lnc-DC was biasedly expressed in skin and up-regulated during epidermal keratinocytes differentiation. Knockdown lnc-DC repressed epidermal keratinocytes differentiation while over-express lnc-DC showed the opposite effect. GRHL3, a well-known transcription factor regulating keratinocytes differentiation, could bind to the promoter of lnc-DC and regulate its expression. By whole transcriptome sequencing, we identified that ZNF750 was a downstream target of lnc-DC during keratinocytes differentiation. Mechanistically, lnc-DC interacted with RNA binding protein IGF2BP2 to stabilize ZNF750 mRNA and up- regulated its downstream targets TINCR and KLF4. CONCLUSION Our study revealed the novel role of GRHL3/lnc-DC/ZNF750 axis in regulating epidermal keratinocytes differentiation, which may provide new therapeutic targets of aberrant keratinocytes differentiation related skin diseases.
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Affiliation(s)
- Xue-Ting Hu
- Department of Stem Cell & Regenerative Medicine, State Key Laboratory of Trauma, Burn and Combined Injury, Daping Hosptial, Army Medical University, Chongqing, China; Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Army Medical University, Chongqing, China
| | - Xiao-Feng Wu
- Department of Stem Cell & Regenerative Medicine, State Key Laboratory of Trauma, Burn and Combined Injury, Daping Hosptial, Army Medical University, Chongqing, China
| | - Lu-Min Sui
- Department of Stem Cell & Regenerative Medicine, State Key Laboratory of Trauma, Burn and Combined Injury, Daping Hosptial, Army Medical University, Chongqing, China
| | - Luo-Quan Ao
- Department of Stem Cell & Regenerative Medicine, State Key Laboratory of Trauma, Burn and Combined Injury, Daping Hosptial, Army Medical University, Chongqing, China
| | - Cheng-Xiu Pu
- Department of Stem Cell & Regenerative Medicine, State Key Laboratory of Trauma, Burn and Combined Injury, Daping Hosptial, Army Medical University, Chongqing, China
| | - Mu Yuan
- Department of Stem Cell & Regenerative Medicine, State Key Laboratory of Trauma, Burn and Combined Injury, Daping Hosptial, Army Medical University, Chongqing, China
| | - Wei Xing
- Department of Stem Cell & Regenerative Medicine, State Key Laboratory of Trauma, Burn and Combined Injury, Daping Hosptial, Army Medical University, Chongqing, China.
| | - Xiang Xu
- Department of Stem Cell & Regenerative Medicine, State Key Laboratory of Trauma, Burn and Combined Injury, Daping Hosptial, Army Medical University, Chongqing, China; Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Army Medical University, Chongqing, China.
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19
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Zou D, Cai Y, Jin M, Zhang M, Liu Y, Chen S, Yang S, Zhang H, Zhu X, Huang C, Zhu Y, Miao X, Wei Y, Yang X, Tian J. A genetic variant in the immune-related gene ERAP1 affects colorectal cancer prognosis. Chin Med J (Engl) 2024; 137:431-440. [PMID: 37690994 PMCID: PMC10876254 DOI: 10.1097/cm9.0000000000002845] [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: 02/06/2023] [Indexed: 09/12/2023] Open
Abstract
BACKGROUND Findings on the association of genetic factors and colorectal cancer (CRC) survival are limited and inconsistent, and revealing the mechanism underlying their prognostic roles is of great importance. This study aimed to explore the relationship between functional genetic variations and the prognosis of CRC and further reveal the possible mechanism. METHODS We first systematically performed expression quantitative trait locus (eQTL) analysis using The Cancer Genome Atlas (TCGA) dataset. Then, the Kaplan-Meier analysis was used to filter out the survival-related eQTL target genes of CRC patients in two public datasets (TCGA and GSE39582 dataset from the Gene Expression Omnibus database). The seven most potentially functional eQTL single nucleotide polymorphisms (SNPs) associated with six survival-related eQTL target genes were genotyped in 907 Chinese CRC patients with clinical prognosis data. The regulatory mechanism of the survival-related SNP was further confirmed by functional experiments. RESULTS The rs71630754 regulating the expression of endoplasmic reticulum aminopeptidase 1 ( ERAP1 ) was significantly associated with the prognosis of CRC (additive model, hazard ratio [HR]: 1.43, 95% confidence interval [CI]: 1.08-1.88, P = 0.012). The results of dual-luciferase reporter assay and electrophoretic mobility shift assay showed that the A allele of the rs71630754 could increase the binding of transcription factor 3 (TCF3) and subsequently reduce the expression of ERAP1 . The results of bioinformatic analysis showed that lower expression of ERAP1 could affect the tumor immune microenvironment and was significantly associated with severe survival outcomes. CONCLUSION The rs71630754 could influence the prognosis of CRC patients by regulating the expression of the immune-related gene ERAP1 . TRIAL REGISTRATION No. NCT00454519 ( https://clinicaltrials.gov/ ).
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Affiliation(s)
- Danyi Zou
- Department of Clinical Laboratory, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, China
- Department of Epidemiology and Biostatistics, School of Public Health, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, Hubei 430071, China
- Department of Gastrointestinal Oncology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, China
| | - Yimin Cai
- Department of Epidemiology and Biostatistics, School of Public Health, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, Hubei 430071, China
- Department of Gastrointestinal Oncology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, China
| | - Meng Jin
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Ming Zhang
- Department of Epidemiology and Biostatistics, School of Public Health, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, Hubei 430071, China
- Department of Gastrointestinal Oncology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, China
| | - Yizhuo Liu
- Department of Epidemiology and Biostatistics, School of Public Health, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, Hubei 430071, China
- Department of Gastrointestinal Oncology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, China
| | - Shuoni Chen
- Department of Epidemiology and Biostatistics, School of Public Health, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, Hubei 430071, China
- Department of Gastrointestinal Oncology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, China
| | - Shuhui Yang
- Department of Epidemiology and Biostatistics, School of Public Health, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, Hubei 430071, China
- Department of Gastrointestinal Oncology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, China
| | - Heng Zhang
- Department of Epidemiology and Biostatistics, School of Public Health, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, Hubei 430071, China
- Department of Gastrointestinal Oncology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, China
| | - Xu Zhu
- Department of Gastrointestinal Surgery, Renmin Hospital of Wuhan University, Wuhan, Hubei 430071, China
| | - Chaoqun Huang
- Department of Gastrointestinal Surgery, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, Hubei 430071, China
| | - Ying Zhu
- Department of Epidemiology and Biostatistics, School of Public Health, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, Hubei 430071, China
- Department of Gastrointestinal Oncology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, China
| | - Xiaoping Miao
- Department of Epidemiology and Biostatistics, School of Public Health, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, Hubei 430071, China
- Department of Gastrointestinal Oncology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, China
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, Hubei 430030, China
- Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Yongchang Wei
- Department of Gastrointestinal Oncology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, China
| | - Xiaojun Yang
- Department of Gastrointestinal Surgery, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, Hubei 430071, China
| | - Jianbo Tian
- Department of Epidemiology and Biostatistics, School of Public Health, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, Hubei 430071, China
- Department of Gastrointestinal Oncology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, China
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20
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Xing M, Xiong Y, Zhang Y. Ku80 is indispensable for repairing DNA double-strand breaks at highly methylated sites in human HCT116 cells. DNA Repair (Amst) 2024; 134:103627. [PMID: 38219597 DOI: 10.1016/j.dnarep.2024.103627] [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: 09/16/2023] [Revised: 01/01/2024] [Accepted: 01/03/2024] [Indexed: 01/16/2024]
Abstract
DNA double-strand breaks (DSBs) are harmful to mammalian cells and a few of them can cause cell death. Accumulating DSBs in these cells to analyze their genomic distribution and their potential impact on chromatin structure is difficult. In this study, we used CRISPR to generate Ku80-/- human cells and arrested the cells in G1 phase to accumulate DSBs before conducting END-seq and Nanopore analysis. Our analysis revealed that DNA with high methylation level accumulates DSB hotspots in Ku80-/- human cells. Furthermore, we identified chromosome structural variants (SVs) using Nanopore sequencing and observed a higher number of SVs in Ku80-/- human cells. Based on our findings, we suggest that the high efficiency of Ku80 knockout in human HCT116 cells makes it a promising model for characterizing SVs in the context of 3D chromatin structure and studying the alternative-end joining (Alt-EJ) DSB repair pathway.
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Affiliation(s)
- Mengtan Xing
- Institute for Regenerative Medicine, Department of Neurosurgery, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Yanhong Xiong
- Institute for Regenerative Medicine, Department of Neurosurgery, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Yong Zhang
- Institute for Regenerative Medicine, Department of Neurosurgery, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China.
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21
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Zhang Z, Ruf-Zamojski F, Zamojski M, Bernard D, Chen X, Troyanskaya O, Sealfon S. Peak-agnostic high-resolution cis-regulatory circuitry mapping using single cell multiome data. Nucleic Acids Res 2024; 52:572-582. [PMID: 38084892 PMCID: PMC10810203 DOI: 10.1093/nar/gkad1166] [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: 07/07/2023] [Revised: 11/15/2023] [Accepted: 11/27/2023] [Indexed: 01/26/2024] Open
Abstract
Single same cell RNAseq/ATACseq multiome data provide unparalleled potential to develop high resolution maps of the cell-type specific transcriptional regulatory circuitry underlying gene expression. We present CREMA, a framework that recovers the full cis-regulatory circuitry by modeling gene expression and chromatin activity in individual cells without peak-calling or cell type labeling constraints. We demonstrate that CREMA overcomes the limitations of existing methods that fail to identify about half of functional regulatory elements which are outside the called chromatin 'peaks'. These circuit sites outside called peaks are shown to be important cell type specific functional regulatory loci, sufficient to distinguish individual cell types. Analysis of mouse pituitary data identifies a Gata2-circuit for the gonadotrope-enriched disease-associated Pcsk1 gene, which is experimentally validated by reduced gonadotrope expression in a gonadotrope conditional Gata2-knockout model. We present a web accessible human immune cell regulatory circuit resource, and provide CREMA as an R package.
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Affiliation(s)
- Zidong Zhang
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai (ISMMS), New York, NY, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Frederique Ruf-Zamojski
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai (ISMMS), New York, NY, USA
| | - Michel Zamojski
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai (ISMMS), New York, NY, USA
| | - Daniel J Bernard
- Department of Pharmacology and Therapeutics, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Xi Chen
- Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY, USA
| | - Olga G Troyanskaya
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY, USA
- Department of Computer Science, Princeton University, Princeton, NJ, USA
| | - Stuart C Sealfon
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai (ISMMS), New York, NY, USA
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22
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Xiang G, Guo Y, Bumcrot D, Sigova A. JMnorm: a novel joint multi-feature normalization method for integrative and comparative epigenomics. Nucleic Acids Res 2024; 52:e11. [PMID: 38055833 PMCID: PMC10810286 DOI: 10.1093/nar/gkad1146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 10/25/2023] [Accepted: 11/14/2023] [Indexed: 12/08/2023] Open
Abstract
Combinatorial patterns of epigenetic features reflect transcriptional states and functions of genomic regions. While many epigenetic features have correlated relationships, most existing data normalization approaches analyze each feature independently. Such strategies may distort relationships between functionally correlated epigenetic features and hinder biological interpretation. We present a novel approach named JMnorm that simultaneously normalizes multiple epigenetic features across cell types, species, and experimental conditions by leveraging information from partially correlated epigenetic features. We demonstrate that JMnorm-normalized data can better preserve cross-epigenetic-feature correlations across different cell types and enhance consistency between biological replicates than data normalized by other methods. Additionally, we show that JMnorm-normalized data can consistently improve the performance of various downstream analyses, which include candidate cis-regulatory element clustering, cross-cell-type gene expression prediction, detection of transcription factor binding and changes upon perturbations. These findings suggest that JMnorm effectively minimizes technical noise while preserving true biologically significant relationships between epigenetic datasets. We anticipate that JMnorm will enhance integrative and comparative epigenomics.
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Affiliation(s)
- Guanjue Xiang
- CAMP4 Therapeutics Corp., One Kendall Square, Building 1400 West, Cambridge, MA 02139, USA
| | - Yuchun Guo
- CAMP4 Therapeutics Corp., One Kendall Square, Building 1400 West, Cambridge, MA 02139, USA
| | - David Bumcrot
- CAMP4 Therapeutics Corp., One Kendall Square, Building 1400 West, Cambridge, MA 02139, USA
| | - Alla Sigova
- CAMP4 Therapeutics Corp., One Kendall Square, Building 1400 West, Cambridge, MA 02139, USA
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23
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Taing L, Dandawate A, L’Yi S, Gehlenborg N, Brown M, Meyer C. Cistrome Data Browser: integrated search, analysis and visualization of chromatin data. Nucleic Acids Res 2024; 52:D61-D66. [PMID: 37971305 PMCID: PMC10767960 DOI: 10.1093/nar/gkad1069] [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: 09/15/2023] [Revised: 10/14/2023] [Accepted: 11/02/2023] [Indexed: 11/19/2023] Open
Abstract
The Cistrome Data Browser is a resource of ChIP-seq, ATAC-seq and DNase-seq data from humans and mice. It provides maps of the genome-wide locations of transcription factors, cofactors, chromatin remodelers, histone post-translational modifications and regions of chromatin accessible to endonuclease activity. Cistrome DB v3.0 contains approximately 45 000 human and 44 000 mouse samples with about 32 000 newly collected datasets compared to the previous release. The Cistrome DB v3.0 user interface is implemented as a single page application that unifies menu driven and data driven search functions and provides an embedded genome browser, which allows users to find and visualize data more effectively. Users can find informative chromatin profiles through keyword, menu, and data-driven search tools. Browser search functions can predict the regulators of query genes as well as the cell type and factor dependent functionality of potential cis-regulatory elements. Cistrome DB v3.0 expands the display of quality control statistics, incorporates sequence logos into motif enrichment displays and includes more expansive sample metadata. Cistrome DB v3.0 is available at http://db3.cistrome.org/browser.
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Affiliation(s)
- Len Taing
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Ariaki Dandawate
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Sehi L’Yi
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Nils Gehlenborg
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Myles Brown
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA
| | - Clifford A Meyer
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
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24
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Zhu X, Li C, Gao Y, Zhang Q, Wang T, Zhou H, Bu F, Chen J, Mao X, He Y, Wu K, Li N, Luo H. The feedback loop of EFTUD2/c-MYC impedes chemotherapeutic efficacy by enhancing EFTUD2 transcription and stabilizing c-MYC protein in colorectal cancer. J Exp Clin Cancer Res 2024; 43:7. [PMID: 38163859 PMCID: PMC10759692 DOI: 10.1186/s13046-023-02873-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 10/27/2023] [Indexed: 01/03/2024] Open
Abstract
BACKGROUND Chemoresistance presents a significant obstacle in the treatment of colorectal cancer (CRC), yet the molecular basis underlying CRC chemoresistance remains poorly understood, impeding the development of new therapeutic interventions. Elongation factor Tu GTP binding domain containing 2 (EFTUD2) has emerged as a potential oncogenic factor implicated in various cancer types, where it fosters tumor growth and survival. However, its specific role in modulating the sensitivity of CRC cells to chemotherapy is still unclear. METHODS Public dataset analysis and in-house sample validation were conducted to assess the expression of EFTUD2 in 5-fluorouracil (5-FU) chemotherapy-resistant CRC cells and the potential of EFTUD2 as a prognostic indicator for CRC. Experiments both in vitro, including MTT assay, EdU cell proliferation assay, TUNEL assay, and clone formation assay and in vivo, using cell-derived xenograft models, were performed to elucidate the function of EFTUD2 in sensitivity of CRC cells to 5-FU treatment. The molecular mechanism on the reciprocal regulation between EFTUD2 and the oncogenic transcription factor c-MYC was investigated through molecular docking, ubiquitination assay, chromatin immunoprecipitation (ChIP), dual luciferase reporter assay, and co-immunoprecipitation (Co-IP). RESULTS We found that EFTUD2 expression was positively correlated with 5-FU resistance, higher pathological grade, and poor prognosis in CRC patients. We also demonstrated both in vitro and in vivo that knockdown of EFTUD2 sensitized CRC cells to 5-FU treatment, whereas overexpression of EFTUD2 impaired such sensitivity. Mechanistically, we uncovered that EFTUD2 physically interacted with and stabilized c-MYC protein by preventing its ubiquitin-mediated proteasomal degradation. Intriguingly, we found that c-MYC directly bound to the promoter region of EFTUD2 gene, activating its transcription. Leveraging rescue experiments, we further confirmed that the effect of EFTUD2 on 5-FU resistance was dependent on c-MYC stabilization. CONCLUSION Our findings revealed a positive feedback loop involving an EFTUD2/c-MYC axis that hampers the efficacy of 5-FU chemotherapy in CRC cells by increasing EFTUD2 transcription and stabilizing c-MYC oncoprotein. This study highlights the potential of EFTUD2 as a promising therapeutic target to surmount chemotherapy resistance in CRC patients.
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Affiliation(s)
- Xiaojian Zhu
- Tomas Lindahl Nobel Laureate Laboratory, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, 518107, China
| | - Changxue Li
- Tomas Lindahl Nobel Laureate Laboratory, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, 518107, China
- Digestive Diseases Center, Guangdong Provincial Key Laboratory of Digestive Cancer Research, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, 518107, China
| | - Yunfei Gao
- Tomas Lindahl Nobel Laureate Laboratory, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, 518107, China
- Department of Otolaryngology, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, 518107, China
| | - Qingyuan Zhang
- Tomas Lindahl Nobel Laureate Laboratory, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, 518107, China
- Digestive Diseases Center, Guangdong Provincial Key Laboratory of Digestive Cancer Research, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, 518107, China
| | - Tao Wang
- Tomas Lindahl Nobel Laureate Laboratory, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, 518107, China
| | - Huaixiang Zhou
- Tomas Lindahl Nobel Laureate Laboratory, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, 518107, China
| | - Fanqin Bu
- Department of Gastroenterology, Beijing Friendship Hospital, National Clinical Research Center for Digestive Disease, Capital Medical University, Beijing, 100050, China
| | - Jia Chen
- Tomas Lindahl Nobel Laureate Laboratory, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, 518107, China
- Digestive Diseases Center, Guangdong Provincial Key Laboratory of Digestive Cancer Research, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, 518107, China
| | - Xinjun Mao
- Department of Anesthesiology, The Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, 533000, China
| | - Yulong He
- Tomas Lindahl Nobel Laureate Laboratory, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, 518107, China.
- Digestive Diseases Center, Guangdong Provincial Key Laboratory of Digestive Cancer Research, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, 518107, China.
| | - Kaiming Wu
- Tomas Lindahl Nobel Laureate Laboratory, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, 518107, China.
- Digestive Diseases Center, Guangdong Provincial Key Laboratory of Digestive Cancer Research, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, 518107, China.
| | - Ningning Li
- Tomas Lindahl Nobel Laureate Laboratory, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, 518107, China.
- China-UK Institute for Frontier Science, Shenzhen, 518107, China.
| | - Hongliang Luo
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, 330006, China.
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25
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Lin Y, Jiang H, Li J, Ren F, Wang Y, Qiu Y, Li J, Li M, Wang Y, Yang L, Song Y, Jia H, Zhai W, Kuang Y, Yu H, Zhu W, Liu S, Morii E, Ensinger C, David C, Zheng H, Ji J, Wang H, Chang Z. Microenvironment-induced CREPT expression by cancer-derived small extracellular vesicles primes field cancerization. Theranostics 2024; 14:662-680. [PMID: 38169511 PMCID: PMC10758052 DOI: 10.7150/thno.87344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 12/02/2023] [Indexed: 01/05/2024] Open
Abstract
Rationale: Cancer local recurrence increases the mortality of patients, and might be caused by field cancerization, a pre-malignant alteration of normal epithelial cells. It has been suggested that cancer-derived small extracellular vesicles (CDEs) may contribute to field cancerization, but the underlying mechanisms remain poorly understood. In this study, we aim to identify the key regulatory factors within recipient cells under the instigation of CDEs. Methods: In vitro experiments were performed to demonstrate that CDEs promote the expression of CREPT in normal epithelial cells. TMT-based quantitative mass spectrometry was employed to investigate the proteomic differences between normal cells and tumor cells. Loss-of-function approaches by CRISPR-Cas9 system were used to assess the role of CREPT in CDEs-induced field cancerization. RNA-seq was performed to explore the genes regulated by CREPT during field cancerization. Results: CDEs promote field cancerization by inducing the expression of CREPT in non-malignant epithelial cells through activating the ERK signaling pathway. Intriguingly, CDEs failed to induce field cancerization when CREPT was deleted, highlighting the importance of CREPT. Transcriptomic analyses revealed that CDEs elicited inflammatory responses, primarily through activation of the TNF signaling pathway. CREPT, in turn, regulates the transduction of downstream signals of TNF by modulating the expression of TNFR2 and PI3K, thereby promoting inflammation-to-cancer transition. Conclusion: CREPT not only serves as a biomarker for field cancerization, but also emerges as a target for preventing the cancer local recurrence.
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Affiliation(s)
- Yuting Lin
- State Key Laboratory of Membrane Biology, School of Medicine, National Engineering Laboratory for Anti-tumor Therapeutics, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Joint Center for Life Sciences, School of Medicine, School of Life Science, Tsinghua University, Beijing 100084, China
| | - Hanguo Jiang
- State Key Laboratory of Membrane Biology, School of Medicine, National Engineering Laboratory for Anti-tumor Therapeutics, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Joint Center for Life Sciences, School of Medicine, School of Life Science, Tsinghua University, Beijing 100084, China
| | - Jun Li
- State Key Laboratory of Membrane Biology, School of Medicine, National Engineering Laboratory for Anti-tumor Therapeutics, Tsinghua University, Beijing 100084, China
| | - Fangli Ren
- State Key Laboratory of Membrane Biology, School of Medicine, National Engineering Laboratory for Anti-tumor Therapeutics, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Joint Center for Life Sciences, School of Medicine, School of Life Science, Tsinghua University, Beijing 100084, China
| | - Yinyin Wang
- State Key Laboratory of Membrane Biology, School of Medicine, National Engineering Laboratory for Anti-tumor Therapeutics, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Joint Center for Life Sciences, School of Medicine, School of Life Science, Tsinghua University, Beijing 100084, China
| | - Ying Qiu
- State Key Laboratory of Membrane Biology, School of Medicine, National Engineering Laboratory for Anti-tumor Therapeutics, Tsinghua University, Beijing 100084, China
| | - Jianghua Li
- State Key Laboratory of Membrane Biology, School of Medicine, National Engineering Laboratory for Anti-tumor Therapeutics, Tsinghua University, Beijing 100084, China
| | - Mengdi Li
- State Key Laboratory of Membrane Biology, School of Medicine, National Engineering Laboratory for Anti-tumor Therapeutics, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Joint Center for Life Sciences, School of Medicine, School of Life Science, Tsinghua University, Beijing 100084, China
| | - Ying Wang
- State Key Laboratory of Membrane Biology, School of Medicine, National Engineering Laboratory for Anti-tumor Therapeutics, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Joint Center for Life Sciences, School of Medicine, School of Life Science, Tsinghua University, Beijing 100084, China
| | - Liu Yang
- State Key Laboratory of Membrane Biology, School of Medicine, National Engineering Laboratory for Anti-tumor Therapeutics, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Joint Center for Life Sciences, School of Medicine, School of Life Science, Tsinghua University, Beijing 100084, China
| | - Yunhao Song
- State Key Laboratory of Membrane Biology, School of Medicine, National Engineering Laboratory for Anti-tumor Therapeutics, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Joint Center for Life Sciences, School of Medicine, School of Life Science, Tsinghua University, Beijing 100084, China
| | - Huihui Jia
- State Key Laboratory of Membrane Biology, School of Medicine, National Engineering Laboratory for Anti-tumor Therapeutics, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Joint Center for Life Sciences, School of Medicine, School of Life Science, Tsinghua University, Beijing 100084, China
| | - Wanli Zhai
- State Key Laboratory of Membrane Biology, School of Medicine, National Engineering Laboratory for Anti-tumor Therapeutics, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Joint Center for Life Sciences, School of Medicine, School of Life Science, Tsinghua University, Beijing 100084, China
| | - Yanshen Kuang
- Department of General Surgery, General Hospital of PLA, Beijing 100700, China
| | - Hanyang Yu
- State Key Laboratory of Membrane Biology, School of Medicine, National Engineering Laboratory for Anti-tumor Therapeutics, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Joint Center for Life Sciences, School of Medicine, School of Life Science, Tsinghua University, Beijing 100084, China
| | - Wenyuan Zhu
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Suling Liu
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Shanghai Medical College, Key Laboratory of Breast Cancer in Shanghai, Innovation Center for Cell Signaling Network, Cancer Institutes, Fudan University, Shanghai 200032, China
| | - Eiichi Morii
- Department of Pathology, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Christian Ensinger
- Institute of Pathology, Medical University of Innsbruck, A-6020 Innsbruck, Austria
| | - Charles David
- State Key Laboratory of Membrane Biology, School of Medicine, National Engineering Laboratory for Anti-tumor Therapeutics, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Joint Center for Life Sciences, School of Medicine, School of Life Science, Tsinghua University, Beijing 100084, China
| | - Hanqiu Zheng
- State Key Laboratory of Membrane Biology, School of Medicine, National Engineering Laboratory for Anti-tumor Therapeutics, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Joint Center for Life Sciences, School of Medicine, School of Life Science, Tsinghua University, Beijing 100084, China
| | - Jianguo Ji
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Hongxia Wang
- Department of Oncology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, China
| | - Zhijie Chang
- State Key Laboratory of Membrane Biology, School of Medicine, National Engineering Laboratory for Anti-tumor Therapeutics, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Joint Center for Life Sciences, School of Medicine, School of Life Science, Tsinghua University, Beijing 100084, China
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26
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Cai Y, Chen M, Gong Y, Tang G, Shu Z, Chen J, Zhou H, He Y, Long Z, Gan Y. Androgen-repressed lncRNA LINC01126 drives castration-resistant prostate cancer by regulating the switch between O-GlcNAcylation and phosphorylation of androgen receptor. Clin Transl Med 2024; 14:e1531. [PMID: 38214432 PMCID: PMC10785194 DOI: 10.1002/ctm2.1531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 12/16/2023] [Accepted: 12/23/2023] [Indexed: 01/13/2024] Open
Abstract
BACKGROUND Prostate cancer (PCa) initially shows satisfactory response to therapies targeting the androgen receptor (AR). However, progression to a castration-resistant stage indicates poor prognosis in PCa patients. AR signalling still plays a central role in most castration-resistant prostate cancers (CRPC). Therefore, unveiling the mechanisms of AR reactivation under androgen-deprived conditions is imperative to discover novel therapeutic targets for CRPC. METHODS Using an integrative analysis of the transcriptomics of three independent PCa cohorts and a published landscape of AR-regulated long non-coding RNA (lncRNA), lncRNA LINC01126 was selected as a candidate gene that could drive CRPC progression for further study. Quantitative reverse transcription polymerase chain reaction, in situ hybridisation (ISH) and fluorescent ISH were performed to detect LINC01126 in PCa tissues and cells. The functional role and mechanism of LINC01126 were further investigated using in vitro and in vivo gain and loss of function assays. RESULTS LINC01126, identified as an AR-repressed lncRNA, was significantly upregulated after AR-targeted therapies. In addition, we found that LINC01126 was upregulated in CRPC and was associated with poor prognosis. We also proved that LINC01126 stabilised AR protein and enhanced AR nuclear translocation and transactivation by promoting the transition from O-GlcNAcylation at threonine 80 to phosphorylation at serine 81 (S81) within the AR protein. Mechanism analysis revealed that LINC01126 facilitates the interaction of CDK9 with AR and impedes the binding of O-linked N-acetylglucosamine (O-GlcNAc) transferase to AR. Consequently, LINC01126 expression was sufficient to activate AR signalling without androgen. LINC01126 overexpression increased, whereas LINC01126 knockdown decreased castration resistance traits in PCa cells in vitro and in vivo. Furthermore, our data showed that LINC01126-targeting antisense oligonucleotides (ASO) substantially inhibited CRPC cells in vitro. CONCLUSIONS Our research expands the functions of AR-regulated lncRNA in sustaining androgen-independent AR activity and promoting CRPC progression and reveals that LINC01126 may be a new therapeutic target for PCa.
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Affiliation(s)
- Yi Cai
- Department of UrologyDisorders of Prostate Cancer Multidisciplinary TeamNational Clinical Research Center for Geriatric DisordersXiangya HospitalCentral South UniversityChangshaHunanP.R. China
| | - Minfeng Chen
- Department of UrologyDisorders of Prostate Cancer Multidisciplinary TeamNational Clinical Research Center for Geriatric DisordersXiangya HospitalCentral South UniversityChangshaHunanP.R. China
| | - Yuchen Gong
- Department of UrologyDisorders of Prostate Cancer Multidisciplinary TeamNational Clinical Research Center for Geriatric DisordersXiangya HospitalCentral South UniversityChangshaHunanP.R. China
| | - Guyu Tang
- Department of UrologyDisorders of Prostate Cancer Multidisciplinary TeamNational Clinical Research Center for Geriatric DisordersXiangya HospitalCentral South UniversityChangshaHunanP.R. China
| | - Zhiwei Shu
- Department of UrologyDisorders of Prostate Cancer Multidisciplinary TeamNational Clinical Research Center for Geriatric DisordersXiangya HospitalCentral South UniversityChangshaHunanP.R. China
| | - Jiaxian Chen
- Department of UrologyDisorders of Prostate Cancer Multidisciplinary TeamNational Clinical Research Center for Geriatric DisordersXiangya HospitalCentral South UniversityChangshaHunanP.R. China
| | - Hengfeng Zhou
- Andrology CenterDepartment of UrologyThe Third Xiangya HospitalCentral South UniversityChangshaHunanP.R. China
| | - Yao He
- Department of UrologyDisorders of Prostate Cancer Multidisciplinary TeamNational Clinical Research Center for Geriatric DisordersXiangya HospitalCentral South UniversityChangshaHunanP.R. China
| | - Zhi Long
- Andrology CenterDepartment of UrologyThe Third Xiangya HospitalCentral South UniversityChangshaHunanP.R. China
| | - Yu Gan
- Department of UrologyDisorders of Prostate Cancer Multidisciplinary TeamNational Clinical Research Center for Geriatric DisordersXiangya HospitalCentral South UniversityChangshaHunanP.R. China
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27
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Feng Y, Zhang Z, Hong Y, Ding Y, Liu L, Gao S, Fang H, Shi J. A DNA methylation haplotype block landscape in human tissues and preimplantation embryos reveals regulatory elements defined by comethylation patterns. Genome Res 2023; 33:gr.278146.123. [PMID: 37940553 PMCID: PMC10760529 DOI: 10.1101/gr.278146.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 11/03/2023] [Indexed: 11/10/2023]
Abstract
DNA methylation and associated regulatory elements play a crucial role in gene expression regulation. Previous studies have focused primarily on the distribution of mean methylation levels. Advances in whole-genome bisulfite sequencing (WGBS) have enabled the characterization of DNA methylation haplotypes (MHAPs), representing CpG sites from the same read fragment on a single chromosome, and the subsequent identification of methylation haplotype blocks (MHBs), in which adjacent CpGs on the same fragment are comethylated. Using our expert-curated WGBS data sets, we report comprehensive landscapes of MHBs in 17 representative normal somatic human tissues and during early human embryonic development. Integrative analysis reveals MHBs as a distinctive type of regulatory element characterized by comethylation patterns rather than mean methylation levels. We show the enrichment of MHBs in open chromatin regions, tissue-specific histone marks, and enhancers, including super-enhancers. Moreover, we find that MHBs tend to localize near tissue-specific genes and show an association with differential gene expression that is independent of mean methylation. Similar findings are observed in the context of human embryonic development, highlighting the dynamic nature of MHBs during early development. Collectively, our comprehensive MHB landscapes provide valuable insights into the tissue specificity and developmental dynamics of DNA methylation.
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Affiliation(s)
- Yan Feng
- Key Laboratory of RNA Science and Engineering, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Zhiqiang Zhang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Yuyang Hong
- Key Laboratory of RNA Science and Engineering, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yi Ding
- Key Laboratory of RNA Science and Engineering, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Leiqin Liu
- Key Laboratory of RNA Science and Engineering, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Siqi Gao
- Key Laboratory of RNA Science and Engineering, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Hai Fang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Jiantao Shi
- Key Laboratory of RNA Science and Engineering, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China;
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28
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Su H, Shu S, Tang W, Zheng C, Zhao L, Fan H. ETV4 facilitates angiogenesis in hepatocellular carcinoma by upregulating MMP14 expression. Biochem Biophys Res Commun 2023; 684:149137. [PMID: 37897911 DOI: 10.1016/j.bbrc.2023.149137] [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: 08/31/2023] [Revised: 10/17/2023] [Accepted: 10/18/2023] [Indexed: 10/30/2023]
Abstract
Abnormal vascularization plays a crucial role in cell proliferation, tumor invasion and metastasis of hepatocellular carcinoma (HCC). It has been reported that ETV4 functions as an oncogenic gene in driving the carcinogenesis and progression, and promoting invasion and metastasis of HCC. However, the function of ETV4 on angiogenesis in HCC remains unclear. In the current study, immunohistochemistry showed that knockdown of ETV4 reduced angiogenesis in HCC xenograft tumor tissues. In vitro, tube formation assay verified that ETV4 expression promoted angiogenesis through simulating the angiogenic environment in HCC cells. Transcriptome sequencing indicated that MMP14 was one of the differentially expressed genes enriched in angiogenesis process. Subsequently, it was confirmed that MMP14 was regulated by ETV4 at the transcription level in HCC cells, clinical tissue samples and online databases. Further, we demonstrated that MMP14 induced angiogenesis in ETV4-mediated HCC microenvironment. Collectively, this research further reveals the biological mechanism of ETV4 in promoting the migration and invasion of HCC, and provides novel mechanistic insights and strategic guidance for anti-angiogenic therapy in HCC.
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Affiliation(s)
- Hongmeng Su
- Department of Medical Genetics and Developmental Biology, School of Medicine, The Key Laboratory of Developmental Genes and Human Diseases, Ministry of Education, Southeast University, Nanjing, China.
| | - Shihui Shu
- School of Life Science and Technology, Southeast University, Nanjing, China.
| | - Wenqing Tang
- School of Life Science and Technology, Southeast University, Nanjing, China.
| | - Chuqian Zheng
- Department of Medical Genetics and Developmental Biology, School of Medicine, The Key Laboratory of Developmental Genes and Human Diseases, Ministry of Education, Southeast University, Nanjing, China.
| | - Luyu Zhao
- Department of Medical Genetics and Developmental Biology, School of Medicine, The Key Laboratory of Developmental Genes and Human Diseases, Ministry of Education, Southeast University, Nanjing, China.
| | - Hong Fan
- Department of Medical Genetics and Developmental Biology, School of Medicine, The Key Laboratory of Developmental Genes and Human Diseases, Ministry of Education, Southeast University, Nanjing, China.
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Wang A, Shen J, Rodriguez AA, Saunders EJ, Chen F, Janivara R, Darst BF, Sheng X, Xu Y, Chou AJ, Benlloch S, Dadaev T, Brook MN, Plym A, Sahimi A, Hoffman TJ, Takahashi A, Matsuda K, Momozawa Y, Fujita M, Laisk T, Figuerêdo J, Muir K, Ito S, Liu X, Uchio Y, Kubo M, Kamatani Y, Lophatananon A, Wan P, Andrews C, Lori A, Choudhury PP, Schleutker J, Tammela TL, Sipeky C, Auvinen A, Giles GG, Southey MC, MacInnis RJ, Cybulski C, Wokolorczyk D, Lubinski J, Rentsch CT, Cho K, Mcmahon BH, Neal DE, Donovan JL, Hamdy FC, Martin RM, Nordestgaard BG, Nielsen SF, Weischer M, Bojesen SE, Røder A, Stroomberg HV, Batra J, Chambers S, Horvath L, Clements JA, Tilly W, Risbridger GP, Gronberg H, Aly M, Szulkin R, Eklund M, Nordstrom T, Pashayan N, Dunning AM, Ghoussaini M, Travis RC, Key TJ, Riboli E, Park JY, Sellers TA, Lin HY, Albanes D, Weinstein S, Cook MB, Mucci LA, Giovannucci E, Lindstrom S, Kraft P, Hunter DJ, Penney KL, Turman C, Tangen CM, Goodman PJ, Thompson IM, Hamilton RJ, Fleshner NE, Finelli A, Parent MÉ, Stanford JL, Ostrander EA, Koutros S, Beane Freeman LE, Stampfer M, Wolk A, Håkansson N, Andriole GL, Hoover RN, Machiela MJ, Sørensen KD, Borre M, Blot WJ, Zheng W, Yeboah ED, Mensah JE, Lu YJ, Zhang HW, Feng N, Mao X, Wu Y, Zhao SC, Sun Z, Thibodeau SN, McDonnell SK, Schaid DJ, West CM, Barnett G, Maier C, Schnoeller T, Luedeke M, Kibel AS, Drake BF, Cussenot O, Cancel-Tassin G, Menegaux F, Truong T, Koudou YA, John EM, Grindedal EM, Maehle L, Khaw KT, Ingles SA, Stern MC, Vega A, Gómez-Caamaño A, Fachal L, Rosenstein BS, Kerns SL, Ostrer H, Teixeira MR, Paulo P, Brandão A, Watya S, Lubwama A, Bensen JT, Butler EN, Mohler JL, Taylor JA, Kogevinas M, Dierssen-Sotos T, Castaño-Vinyals G, Cannon-Albright L, Teerlink CC, Huff CD, Pilie P, Yu Y, Bohlender RJ, Gu J, Strom SS, Multigner L, Blanchet P, Brureau L, Kaneva R, Slavov C, Mitev V, Leach RJ, Brenner H, Chen X, Holleczek B, Schöttker B, Klein EA, Hsing AW, Kittles RA, Murphy AB, Logothetis CJ, Kim J, Neuhausen SL, Steele L, Ding YC, Isaacs WB, Nemesure B, Hennis AJ, Carpten J, Pandha H, Michael A, Ruyck KD, Meerleer GD, Ost P, Xu J, Razack A, Lim J, Teo SH, Newcomb LF, Lin DW, Fowke JH, Neslund-Dudas CM, Rybicki BA, Gamulin M, Lessel D, Kulis T, Usmani N, Abraham A, Singhal S, Parliament M, Claessens F, Joniau S, den Broeck TV, Gago-Dominguez M, Castelao JE, Martinez ME, Larkin S, Townsend PA, Aukim-Hastie C, Bush WS, Aldrich MC, Crawford DC, Srivastava S, Cullen J, Petrovics G, Casey G, Wang Y, Tettey Y, Lachance J, Tang W, Biritwum RB, Adjei AA, Tay E, Truelove A, Niwa S, Yamoah K, Govindasami K, Chokkalingam AP, Keaton JM, Hellwege JN, Clark PE, Jalloh M, Gueye SM, Niang L, Ogunbiyi O, Shittu O, Amodu O, Adebiyi AO, Aisuodionoe-Shadrach OI, Ajibola HO, Jamda MA, Oluwole OP, Nwegbu M, Adusei B, Mante S, Darkwa-Abrahams A, Diop H, Gundell SM, Roobol MJ, Jenster G, van Schaik RH, Hu JJ, Sanderson M, Kachuri L, Varma R, McKean-Cowdin R, Torres M, Preuss MH, Loos RJ, Zawistowski M, Zöllner S, Lu Z, Van Den Eeden SK, Easton DF, Ambs S, Edwards TL, Mägi R, Rebbeck TR, Fritsche L, Chanock SJ, Berndt SI, Wiklund F, Nakagawa H, Witte JS, Gaziano JM, Justice AC, Mancuso N, Terao C, Eeles RA, Kote-Jarai Z, Madduri RK, Conti DV, Haiman CA. Characterizing prostate cancer risk through multi-ancestry genome-wide discovery of 187 novel risk variants. Nat Genet 2023; 55:2065-2074. [PMID: 37945903 PMCID: PMC10841479 DOI: 10.1038/s41588-023-01534-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Accepted: 09/15/2023] [Indexed: 11/12/2023]
Abstract
The transferability and clinical value of genetic risk scores (GRSs) across populations remain limited due to an imbalance in genetic studies across ancestrally diverse populations. Here we conducted a multi-ancestry genome-wide association study of 156,319 prostate cancer cases and 788,443 controls of European, African, Asian and Hispanic men, reflecting a 57% increase in the number of non-European cases over previous prostate cancer genome-wide association studies. We identified 187 novel risk variants for prostate cancer, increasing the total number of risk variants to 451. An externally replicated multi-ancestry GRS was associated with risk that ranged from 1.8 (per standard deviation) in African ancestry men to 2.2 in European ancestry men. The GRS was associated with a greater risk of aggressive versus non-aggressive disease in men of African ancestry (P = 0.03). Our study presents novel prostate cancer susceptibility loci and a GRS with effective risk stratification across ancestry groups.
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Affiliation(s)
- Anqi Wang
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Jiayi Shen
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | | | | | - Fei Chen
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Rohini Janivara
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Burcu F. Darst
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Xin Sheng
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Yili Xu
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Alisha J. Chou
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Sara Benlloch
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology,University of Cambridge, Cambridge, UK
| | | | | | - Anna Plym
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
- Urology Division, Department of Surgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Ali Sahimi
- Department of Population and Public Health Sciences, Keck School of Medicine,University of Southern California, Los Angeles, CA, USA
| | - Thomas J. Hoffman
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
| | - Atushi Takahashi
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Department of Genomic Medicine, National Cerebral and Cardiovascular Center Research Institute, Suita, Japan
| | - Koichi Matsuda
- Department of Computational Biology and Medical Sciences, Laboratory of Clinical Genome Sequencing,Graduate school of Frontier Sciences,The University of Tokyo, Tokyo, Japan
| | - Yukihide Momozawa
- Laboratory for Genotyping Development, RIKEN Center of Integrative Medical Sciences, Yokohama, Japan
| | - Masashi Fujita
- Laboratory for Cancer Genomics, RIKEN Center of Integrative Medical Sciences, Yokohama, Japan
| | - Triin Laisk
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Jéssica Figuerêdo
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Kenneth Muir
- Division of Population Health, Health Services Research and Primary Care, School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
- Warwick Medical School, University of Warwick, Coventry, UK
| | - Shuji Ito
- Department of Orthopaedics, Shimane University, Izumo, Shimane, Japan
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Xiaoxi Liu
- Laboratory for Statistical and Translational Genetics, Center for Integrative Medical Sciences, RIKEN, Yokohama, Japan
| | - The Biobank Japan Project
- Corresponding Author: Christopher A. Haiman, Harlyne J. Norris Cancer Research Tower, USC Norris Comprehensive Cancer Center, 1450 Biggy Street, Rm 1504, Los Angeles, CA 90033 or
| | - Yuji Uchio
- Department of Orthopaedics, Shimane University, Izumo, Shimane, Japan
| | - Michiaki Kubo
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Yoichiro Kamatani
- Laboratory for Statistical and Translational Genetics, Center for Integrative Medical Sciences, RIKEN, Yokohama, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Artitaya Lophatananon
- Division of Population Health, Health Services Research and Primary Care, School of Health Sciences, Faculty of Biology, Medicine and Health, Manchester, UK
| | - Peggy Wan
- Department of Population and Public Health Sciences, Keck School of Medicine,University of Southern California, Los Angeles, CA, USA
| | - Caroline Andrews
- Harvard TH Chan School of Public Health and Division of Population Sciences,Dana Farber Cancer Institute, Boston, MA, USA
| | - Adriana Lori
- Department of Population Science, American Cancer Society, Kennesaw, GA, USA
| | | | - Johanna Schleutker
- Institute of Biomedicine, University of Turku, Turku, Finland
- Department of Medical Genetics, Genomics, Laboratory Division, Turku University Hospital, Turku, Finland
| | | | - Csilla Sipeky
- Institute of Biomedicine, University of Turku, Turku, Finland
| | - Anssi Auvinen
- Unit of Health Sciences, Faculty of Social Sciences, Tampere University, Tampere, Finland
| | - Graham G. Giles
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health,The University of Melbourne, Victoria, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia
| | - Melissa C. Southey
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia
| | - Robert J. MacInnis
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health,The University of Melbourne, Victoria, Australia
| | - Cezary Cybulski
- International Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Dominika Wokolorczyk
- International Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Jan Lubinski
- International Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Christopher T. Rentsch
- Yale School of Medicine, New Haven, CT, USA
- Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, UK
- VA Connecticut Healthcare System, West Haven, CT, USA
| | - Kelly Cho
- Division of Aging, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- VA Boston Healthcare System, Boston, MA, USA
| | | | - David E. Neal
- Nuffield Department of Surgical Sciences, University of Oxford, John Radcliffe Hospital, Headington, Oxford, UK
- University of Cambridge, Department of Oncology, Addenbrooke’s Hospital, Cambridge, UK
- Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Cambridge, UK
| | - Jenny L. Donovan
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Freddie C. Hamdy
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
- Faculty of Medical Science, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Richard M. Martin
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- NIHR Bristol Biomedical Research Centre at University Hospitals Bristol and Weston NHS Foundation Trust and the University of Bristol, Bristol, UK
- Medical Research Council (MRC) Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - Borge G. Nordestgaard
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Copenhagen, Denmark
| | - Sune F. Nielsen
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Copenhagen, Denmark
| | - Maren Weischer
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Copenhagen, Denmark
| | - Stig E. Bojesen
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Copenhagen, Denmark
| | - Andreas Røder
- Copenhagen Prostate Cancer Center, Department of Urology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Hein V. Stroomberg
- Copenhagen Prostate Cancer Center, Department of Urology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Jyotsna Batra
- Australian Prostate Cancer Research Centre-Qld, Institute of Health and Biomedical Innovation and School of Biomedical Sciences, Queensland University of Technology, Brisbane, Australia
- Translational Research Institute, Brisbane, Queensland, Australia
| | | | - Lisa Horvath
- Chris O’Brien Lifehouse (COBLH), Camperdown, Sydney, NSW, Australia, Sydney, Australia
- Garvan Institute of Medical Research, Sydney, Australia
| | - Judith A. Clements
- Australian Prostate Cancer Research Centre-Qld, Institute of Health and Biomedical Innovation and School of Biomedical Sciences, Queensland University of Technology, Brisbane, Australia
- Translational Research Institute, Brisbane, Queensland, Australia
| | - Wayne Tilly
- Dame Roma Mitchell Cancer Research Laboratories, University of Adelaide, Adelaide, Australia
| | - Gail P. Risbridger
- Department of Anatomy and Developmental Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia
- Prostate Cancer Translational Research Program, Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Henrik Gronberg
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
| | - Markus Aly
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
- Department of Molecular Medicine and Surgery, Karolinska Institutet, and Department of Urology, Karolinska University Hospital, Solna, Stockholm, Sweden
- Department of Urology, Karolinska University Hospital, Stockholm, Sweden
| | - Robert Szulkin
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
- SDS Life Sciences, Stockholm, Sweden
| | - Martin Eklund
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
| | - Tobias Nordstrom
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
- Department of Clinical Sciences at Danderyd Hospital, Karolinska Institutet, Stockholm, Sweden
| | - Nora Pashayan
- University College London, Department of Applied Health Research, London, UK
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Strangeways Laboratory, Cambridge, UK
- Department of Applied Health Research, University College London, London, UK
| | - Alison M. Dunning
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Strangeways Laboratory, Cambridge, UK
| | - Maya Ghoussaini
- Open Targets, Wellcome Sanger Institute, Hinxton, Saffron Walden, Hinxton, UK
| | - Ruth C. Travis
- Cancer Epidemiology Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Tim J. Key
- Cancer Epidemiology Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Elio Riboli
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
| | - Jong Y. Park
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, FL, USA
| | - Thomas A. Sellers
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, FL, USA
| | - Hui-Yi Lin
- School of Public Health, Louisiana State University Health Sciences Center, New Orleans, LA, USA
| | - Demetrius Albanes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Stephanie Weinstein
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Michael B. Cook
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH,, Bethesda, MD, USA
| | - Lorelei A. Mucci
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Edward Giovannucci
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Sara Lindstrom
- Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - Peter Kraft
- Program in Genetic Epidemiology and Statistical Genetics, Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - David J. Hunter
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Kathryn L. Penney
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital/Harvard Medical School, Boston, MA, USA
| | - Constance Turman
- Program in Genetic Epidemiology and Statistical Genetics, Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Catherine M. Tangen
- SWOG Statistical Center, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Phyllis J. Goodman
- SWOG Statistical Center, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Ian M. Thompson
- CHRISTUS Santa Rosa Hospital – Medical Center, San Antonio, TX, USA
| | - Robert J. Hamilton
- Dept. of Surgical Oncology, Princess Margaret Cancer Centre, Toronto, Canada
- Dept. of Surgery (Urology), University of Toronto, Toronto, Canada
| | - Neil E. Fleshner
- Dept. of Surgical Oncology, Princess Margaret Cancer Centre, Toronto, Canada
| | - Antonio Finelli
- Division of Urology, Princess Margaret Cancer Centre, Toronto, Canada
| | - Marie-Élise Parent
- Epidemiology and Biostatistics Unit, Centre Armand-Frappier Santé Biotechnologie, Laval, QC, Canada
| | - Janet L. Stanford
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Elaine A. Ostrander
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Stella Koutros
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Laura E. Beane Freeman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Meir Stampfer
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital/Harvard Medical School, Boston, MA, USA
| | - Alicja Wolk
- Division of Nutritional Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Niclas Håkansson
- Division of Nutritional Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Gerald L. Andriole
- Brady Urological Institute in National Capital Region, Johns Hopkins University, Baltimore, MD, USA
| | - Robert N. Hoover
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Mitchell J. Machiela
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Karina Dalsgaard Sørensen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Michael Borre
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Urology, Aarhus University Hospital, Aarhus, Denmark
| | - William J. Blot
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- International Epidemiology Institute, Rockville, MD, USA
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | | | - James E. Mensah
- University of Ghana Medical School, Accra, Ghana
- Korle Bu Teaching Hospital, Accra, Ghana
| | - Yong-Jie Lu
- Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, London, UK
| | | | - Ninghan Feng
- Wuxi Second Hospital, Nanjing Medical University, Wuxi, Jiangzhu Province, China
| | - Xueying Mao
- Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, London, UK
| | - Yudong Wu
- Department of Urology, First Affiliated Hospital, The Academy of Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Shan-Chao Zhao
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Zan Sun
- The People’s Hospital of Liaoning Proviouce, The People’s Hospital of China Medical University, Shenyang, China, Shenyang, China
| | - Stephen N. Thibodeau
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | | | - Daniel J. Schaid
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | - Catharine M.L. West
- Division of Cancer Sciences, University of Manchester, Manchester Academic Health Science Centre, Radiotherapy Related Research, The Christie Hospital NHS Foundation Trust, Manchester, UK
| | - Gill Barnett
- University of Cambridge Department of Oncology, Oncology Centre, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | | | | | | | - Adam S. Kibel
- Division of Urologic Surgery, Brigham and Womens Hospital, Boston, MA, USA
| | | | - Olivier Cussenot
- GRC 5 Predictive Onco-Urology, Sorbonne Université, Paris, France
- CeRePP, Paris, France
| | | | - Florence Menegaux
- Exposome and Heredity, CESP (UMR 1018), Paris-Saclay Medical School, Paris-Saclay University, Inserm, Gustave Roussy, Villejuif, France
| | - Thérèse Truong
- Exposome and Heredity, CESP (UMR 1018), Paris-Saclay Medical School, Paris-Saclay University, Inserm, Gustave Roussy, Villejuif, France
| | - Yves Akoli Koudou
- Cancer & Environment Group, Center for Research in Epidemiology and Population Health (CESP), INSERM, University Paris-Sud, University Paris-Saclay, Villejuif Cédex, France
| | - Esther M. John
- Department of Medicine, Stanford Cancer Institute,Stanford University School of Medicine, Stanford, CA, USA
| | | | - Lovise Maehle
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Kay-Tee Khaw
- Clinical Gerontology Unit, University of Cambridge, Cambridge, UK
| | - Sue A. Ingles
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California/Norris Comprehensive Cancer Center, Los Angeles, CA, USA
| | - Mariana C Stern
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California/Norris Comprehensive Cancer Center, Los Angeles, CA, USA
| | - Ana Vega
- Fundación Pública Galega Medicina Xenómica, Santiago De Compostela, Spain
- Instituto de Investigación Sanitaria de Santiago de Compostela, Santiago De Compostela, Spain
- Centro de Investigación en Red de Enfermedades Raras (CIBERER), Spain
| | - Antonio Gómez-Caamaño
- Department of Radiation Oncology, Complexo Hospitalario Universitario de Santiago, SERGAS, Santiago de Compostela, Spain
| | - Laura Fachal
- Instituto de Investigación Sanitaria de Santiago de Compostela, Santiago De Compostela, Spain
- Centro de Investigación en Red de Enfermedades Raras (CIBERER), Spain
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Strangeways Research Laboratory, Cambridge, UK
- Fundación Pública Galega Medicina Xenómica, Santiago de Compostela, Spain
| | - Barry S. Rosenstein
- Department of Radiation Oncology and Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sarah L. Kerns
- Department of Radiation Oncology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Harry Ostrer
- Professor of Pathology and Pediatrics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Manuel R. Teixeira
- Department of Laboratory Genetics, Portuguese Oncology Institute of Porto (IPO Porto) / Porto Comprehensive Cancer Center, Porto, Portugal
- Cancer Genetics Group, IPO Porto Research Center (CI-IPOP) / RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto) / Porto Comprehensive Cancer Center, Porto, Portugal
- School of Medicine and Biomedical Sciences (ICBAS), University of Porto, Porto, Portugal
| | - Paula Paulo
- Cancer Genetics Group, IPO Porto Research Center (CI-IPOP) / RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto) / Porto Comprehensive Cancer Center, Porto, Portugal
| | - Andreia Brandão
- Cancer Genetics Group, IPO Porto Research Center (CI-IPOP) / RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto) / Porto Comprehensive Cancer Center, Porto, Portugal
| | | | | | - Jeannette T. Bensen
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ebonee N. Butler
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - James L. Mohler
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Urology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Jack A. Taylor
- Epidemiology Branch, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
- Laboratory of Molecular Carcinogenesis, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Manolis Kogevinas
- ISGlobal, Barcelona, Spain
- IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Trinidad Dierssen-Sotos
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- University of Cantabria-IDIVAL, Santander, Spain
| | - Gemma Castaño-Vinyals
- ISGlobal, Barcelona, Spain
- IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Lisa Cannon-Albright
- Division of Epidemiology, Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, UT, USA
- George E. Wahlen Department of Veterans Affairs Medical Center, Salt Lake City, UT, USA
| | - Craig C. Teerlink
- Division of Epidemiology, Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, UT, USA
- George E. Wahlen Department of Veterans Affairs Medical Center, Salt Lake City, UT, USA
| | - Chad D. Huff
- Department of Epidemiology, University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Patrick Pilie
- Department of Genitourinary Medical Oncology, University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Yao Yu
- Department of Epidemiology, University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Ryan J. Bohlender
- Department of Epidemiology, University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Jian Gu
- Department of Epidemiology, University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Sara S. Strom
- The University of Texas M. D. Anderson Cancer Center, Houston, TX, USA
| | - Luc Multigner
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail), Rennes, France
| | - Pascal Blanchet
- CHU de Pointe-à-Pitre, Univ Antilles, Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail), Pointe-à-Pitre, France
| | - Laurent Brureau
- CHU de Pointe-à-Pitre, Univ Antilles, Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail), Pointe-à-Pitre, France
| | - Radka Kaneva
- Molecular Medicine Center, Department of Medical Chemistry and Biochemistry, Medical University of Sofia, Sofia, Bulgaria
| | - Chavdar Slavov
- Department of Urology and Alexandrovska University Hospital, Medical University of Sofia, Sofia, Bulgaria
| | - Vanio Mitev
- Molecular Medicine Center, Department of Medical Chemistry and Biochemistry, Medical University of Sofia, Sofia, Bulgaria
| | - Robin J. Leach
- Department of Cell Systems and Anatomy and Mays Cancer Center, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Xuechen Chen
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Ben Schöttker
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Eric A. Klein
- Cleveland Clinic Lerner Research Institute, Cleveland, OH, USA
- Glickman Urological & Kidney Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Ann W. Hsing
- Department of Medicine and Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Adam B. Murphy
- Department of Urology, Northwestern University, Chicago, IL, USA
| | - Christopher J. Logothetis
- The University of Texas M. D. Anderson Cancer Center, Department of Genitourinary Medical Oncology, Houston, TX, USA
| | - Jeri Kim
- The University of Texas M. D. Anderson Cancer Center, Department of Genitourinary Medical Oncology, Houston, TX, USA
| | - Susan L. Neuhausen
- Department of Population Sciences, Beckman Research Institute of the City of Hope, Duarte, CA, USA
| | - Linda Steele
- Department of Population Sciences, Beckman Research Institute of the City of Hope, Duarte, CA, USA
| | - Yuan Chun Ding
- Department of Population Sciences, Beckman Research Institute of the City of Hope, Duarte, CA, USA
| | - William B. Isaacs
- James Buchanan Brady Urological Institute, Johns Hopkins Hospital and Medical Institution, Baltimore, MD, USA
| | - Barbara Nemesure
- Department of Family, Population and Preventive Medicine, Stony Brook University, Stony Brook, NY, USA
| | - Anselm J.M. Hennis
- Department of Family, Population and Preventive Medicine, Stony Brook University, Stony Brook, NY, USA
- Chronic Disease Research Centre and Faculty of Medical Sciences, University of the West Indies, Bridgetown, Barbados
| | - John Carpten
- Department of Translational Genomics, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | | | | | - Kim De Ruyck
- Ghent University, Faculty of Medicine and Health Sciences, Basic Medical Sciences, Ghent, Belgium
| | - Gert De Meerleer
- Ghent University Hospital, Department of Radiotherapy, Ghent, Belgium
| | - Piet Ost
- Ghent University Hospital, Department of Radiotherapy, Ghent, Belgium
| | - Jianfeng Xu
- Program for Personalized Cancer Care and Department of Surgery, NorthShore University HealthSystem, Evanston, IL, USA
| | - Azad Razack
- Department of Surgery, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Jasmine Lim
- Department of Surgery, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Soo-Hwang Teo
- Cancer Research Malaysia (CRM), Outpatient Centre, Subang Jaya Medical Centre, Subang Jaya, Selangor, Malaysia
| | - Lisa F. Newcomb
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Urology, University of Washington, Seattle, WA, USA
| | - Daniel W. Lin
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Urology, University of Washington, Seattle, WA, USA
| | - Jay H. Fowke
- Department of Preventive Medicine, Division of Epidemiology,The University of Tennessee Health Science Center, Memphis, TN, USA
| | | | - Benjamin A. Rybicki
- Department of Public Health Sciences, Henry Ford Hospital, Detroit, Detroit, MI, USA
| | - Marija Gamulin
- Division of Medical Oncology, Urogenital Unit, Department of Oncology, University Hospital Centre Zagreb, Zagreb, Croatia
| | - Davor Lessel
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Tomislav Kulis
- Department of Urology, University Hospital Center Zagreb, University of Zagreb School of Medicine, Zagreb, Croatia
| | - Nawaid Usmani
- Department of Oncology, Cross Cancer Institute, University of Alberta, Edmonton, Alberta, Canada
- Division of Radiation Oncology, Cross Cancer Institute, Edmonton, Alberta, Canada
| | - Aswin Abraham
- Department of Oncology, Cross Cancer Institute, University of Alberta, Edmonton, Alberta, Canada
- Division of Radiation Oncology, Cross Cancer Institute, Edmonton, Alberta, Canada
| | - Sandeep Singhal
- Department of Oncology, Cross Cancer Institute, University of Alberta, Edmonton, Alberta, Canada
| | - Matthew Parliament
- Department of Oncology, Cross Cancer Institute, University of Alberta, Edmonton, Alberta, Canada
- Division of Radiation Oncology, Cross Cancer Institute, Edmonton, Alberta, Canada
| | - Frank Claessens
- Molecular Endocrinology Laboratory, Department of Cellular and Molecular Medicine, Leuven, Belgium
| | - Steven Joniau
- Department of Urology, University Hospitals Leuven, Leuven, Belgium
| | - Thomas Van den Broeck
- Molecular Endocrinology Laboratory, Department of Cellular and Molecular Medicine, Leuven, Belgium
- Department of Urology, University Hospitals Leuven, Leuven, Belgium
| | - Manuela Gago-Dominguez
- Genomic Medicine Group, Galician Foundation of Genomic Medicine, Instituto de Investigacion Sanitaria de Santiago de Compostela (IDIS), Complejo Hospitalario Universitario de Santiago, Servicio Galego de Saúde, SERGAS, Santiago de Compostela, Spain
- University of California San Diego, Moores Cancer Center, La Jolla, CA, USA
| | - Jose Esteban Castelao
- Genetic Oncology Unit, CHUVI Hospital, Complexo Hospitalario Universitario de Vigo, Instituto de Investigación Biomédica Galicia Sur (IISGS), Vigo (Pontevedra), Spain
| | - Maria Elena Martinez
- University of California San Diego, Moores Cancer Center, Department of Family Medicine and Public Health, University of California San Diego, La Jolla, CA, USA
| | - Samantha Larkin
- Scientific Education Support, Thames Ditton, Surrey, Formerly Cancer Sciences, University of Southampton, Southampton, UK
| | - Paul A. Townsend
- School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Surrey, UK
| | | | - William S. Bush
- Department of Population and Quantitative Health Sciences, Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, USA
| | - Melinda C. Aldrich
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Dana C. Crawford
- Department of Population and Quantitative Health Sciences, Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, USA
| | - Shiv Srivastava
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University Medical Center, Washington, DC, USA
| | - Jennifer Cullen
- Department of Population and Quantitative Health Sciences, Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, USA
- Department of Surgery, Center for Prostate Disease Research,Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Gyorgy Petrovics
- Department of Surgery, Center for Prostate Disease Research,Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Graham Casey
- Department of Public Health Science, Center for Public Health Genomics,University of Virginia, Charlottesville, VA, USA
| | - Ying Wang
- Department of Population Science, American Cancer Society, Kennesaw, GA, USA
| | - Yao Tettey
- Korle Bu Teaching Hospital, Accra, Ghana
- Department of Pathology, University of Ghana, Accra, Ghana
| | - Joseph Lachance
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Wei Tang
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | | | - Andrew A. Adjei
- Department of Pathology, University of Ghana Medical School, Accra, Ghana
| | - Evelyn Tay
- Korle Bu Teaching Hospital, Accra, Ghana
| | | | | | - Kosj Yamoah
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, FL, USA
- Department of Radiation Oncology, Moffitt Cancer Center, Tampa, FL, USA
| | | | | | - Jacob M. Keaton
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jacklyn N. Hellwege
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Division of Genetic Medicine, Department of Medicine, Vanderbilt Genetics Institute, Nashville, TN, USA
| | - Peter E. Clark
- Atrium Health/Levine Cancer Institute, Charlotte, NC, USA
| | | | | | | | - Olufemi Ogunbiyi
- Department of Pathology, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Olayiwola Shittu
- Department of Surgery, College of Medicine, University of Ibadan and Univerity College Hospital, Ibadan, Nigeria
| | - Olukemi Amodu
- Institute of Child Health, College of Medicine, University of Ibadan and University College Hospital, Ibadan, Nigeria
| | - Akindele O. Adebiyi
- Clinical Epidemiology Unit, Department of Community Medicine, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Oseremen I. Aisuodionoe-Shadrach
- College of Health Sciences, University of Abuja, University of Abuja Teaching Hospital and Cancer Science Center, Abuja, Nigeria
| | - Hafees O. Ajibola
- College of Health Sciences, University of Abuja, University of Abuja Teaching Hospital and Cancer Science Center, Abuja, Nigeria
| | - Mustapha A. Jamda
- College of Health Sciences, University of Abuja, University of Abuja Teaching Hospital and Cancer Science Center, Abuja, Nigeria
| | - Olabode P. Oluwole
- College of Health Sciences, University of Abuja, University of Abuja Teaching Hospital and Cancer Science Center, Abuja, Nigeria
| | - Maxwell Nwegbu
- College of Health Sciences, University of Abuja, University of Abuja Teaching Hospital and Cancer Science Center, Abuja, Nigeria
| | | | | | | | - Halimatou Diop
- Laboratoires Bacteriologie et Virologie, Hôpital Aristide Le Dantec, Dakar, Senegal
| | - Susan M. Gundell
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Monique J. Roobol
- Department of Urology, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Guido Jenster
- Department of Urology, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Ron H.N. van Schaik
- Department of Clinical Chemistry, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Jennifer J. Hu
- The University of Miami School of Medicine, Sylvester Comprehensive Cancer Center, Miami, FL, USA
| | - Maureen Sanderson
- Department of Family and Community Medicine, Meharry Medical College, Nashville, TN, USA
| | - Linda Kachuri
- Department of Epidemiology and Population Health, Stanford Cancer Institute, Stanford, CA, USA
| | - Rohit Varma
- Southern California Eye Institute, CHA Hollywood Presbyterian Medical Center, Los Angeles, CA, USA
| | - Roberta McKean-Cowdin
- Department of Population and Public Health Sciences, Keck School of Medicine,University of Southern California, Los Angeles, CA, USA
| | - Mina Torres
- Southern California Eye Institute, CHA Hollywood Presbyterian Medical Center, Los Angeles, CA, USA
| | - Michael H. Preuss
- The Charles Bronfman Institute for Personalized Medicine,Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ruth J.F. Loos
- The Charles Bronfman Institute for Personalized Medicine,Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Matthew Zawistowski
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
- Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Sebastian Zöllner
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
- Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI, USA
- Department of Psychiatry, University of Michigan, Ann Arbor, MI, USA
| | - Zeyun Lu
- Department of Population and Public Health Sciences, Keck School of Medicine,University of Southern California, Los Angeles, CA, USA
| | | | - Douglas F. Easton
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology,, Cambridge, UK
| | - Stefan Ambs
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Todd L. Edwards
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Reedik Mägi
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Timothy R. Rebbeck
- Harvard TH Chan School of Public Health and Division of Population Sciences, Dana Farber Cancer Institute, Boston, MA, USA
| | - Lars Fritsche
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Stephen J. Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Sonja I. Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Fredrik Wiklund
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
| | - Hidewaki Nakagawa
- Laboratory for Cancer Genomics, RIKEN Center of Integrative Medical Sciences, Yokohama, Japan
| | - John S. Witte
- Department of Epidemiology and Population Health, Stanford Cancer Institute, Stanford, CA, USA
- Departments of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - J. Michael Gaziano
- Division of Aging, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- VA Boston Healthcare System, Boston, MA, USA
| | | | - Nick Mancuso
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Chikashi Terao
- Laboratory for Statistical and Translational Genetics, Center for Integrative Medical Sciences, RIKEN, Yokohama, Japan
- Clinical Research Center, Shizuoka General Hospital, Shizuoka, Japan
- The Department of Applied Genetics, School of Pharmaceutical Sciences, Shizuoka, Japan
| | - Rosalind A. Eeles
- The Institute of Cancer Research, London, UK
- Royal Marsden NHS Foundation Trust, London, UK
| | | | | | - David V. Conti
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Christopher A. Haiman
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
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Chaudhry KA, Jacobi JJ, Gillard BM, Karasik E, Martin JC, da Silva Fernandes T, Hurley E, Feltri ML, Attwood KM, Twist CJ, Smiraglia DJ, Long MD, Bianchi-Smiraglia A. Aryl hydrocarbon receptor is a tumor promoter in MYCN-amplified neuroblastoma cells through suppression of differentiation. iScience 2023; 26:108303. [PMID: 38026169 PMCID: PMC10654598 DOI: 10.1016/j.isci.2023.108303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 09/25/2023] [Accepted: 10/20/2023] [Indexed: 12/01/2023] Open
Abstract
Neuroblastoma is the most common extracranial solid tumor in children. MYCN amplification is detected in almost half of high-risk cases and is associated with poorly differentiated tumors, poor patient prognosis and poor response to therapy, including retinoids. We identify the aryl hydrocarbon receptor (AhR) as a transcription factor promoting the growth and suppressing the differentiation of MYCN-amplified neuroblastoma. A neuroblastoma specific AhR transcriptional signature reveals an inverse correlation of AhR activity with patients' outcome, suggesting AhR activity is critical for disease progression. AhR modulates chromatin structures, reducing accessibility to regions responsive to retinoic acid. Genetic and pharmacological inhibition of AhR results in induction of differentiation. Importantly, AhR antagonism with clofazimine synergizes with retinoic acid in inducing differentiation both in vitro and in vivo. Thus, we propose AhR as a target for MYCN-amplified neuroblastoma and that its antagonism, combined with current standard-of-care, may result in a more durable response in patients.
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Affiliation(s)
- Kanita A. Chaudhry
- Department of Cell Stress Biology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Justine J. Jacobi
- Department of Cell Stress Biology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Bryan M. Gillard
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Ellen Karasik
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Jeffrey C. Martin
- Department of Cell Stress Biology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | | | - Edward Hurley
- Department of Biochemistry and Neurology, Institute for Myelin and Glia Exploration, State University of New York at Buffalo, Buffalo, NY, USA
| | - Maria Laura Feltri
- Department of Biochemistry and Neurology, Institute for Myelin and Glia Exploration, State University of New York at Buffalo, Buffalo, NY, USA
- Department of Medical Biotechnology and Translational Medicine, University of Milan, Foundation I.R.C.C.S. Carlo Besta Neurological Institute Milan, Italy
| | - Kristopher M. Attwood
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Clare J. Twist
- Department of Pediatric Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Dominic J. Smiraglia
- Department of Cell Stress Biology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Mark D. Long
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Anna Bianchi-Smiraglia
- Department of Cell Stress Biology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
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31
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Madan V, Shyamsunder P, Dakle P, Woon TW, Han L, Cao Z, Nordin HBM, Jizhong S, Shuizhou Y, Hossain MZ, Koeffler HP. Dissecting the role of SWI/SNF component ARID1B in steady-state hematopoiesis. Blood Adv 2023; 7:6553-6566. [PMID: 37611161 PMCID: PMC10632677 DOI: 10.1182/bloodadvances.2023009946] [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: 02/10/2023] [Revised: 08/10/2023] [Accepted: 08/11/2023] [Indexed: 08/25/2023] Open
Abstract
The adenosine triphosphate (ATP)-dependent chromatin remodeling complex, SWItch/Sucrose Non-Fermentable (SWI/SNF), has been implicated in normal hematopoiesis. The AT-rich interaction domain 1B (ARID1B) and its paralog, ARID1A, are mutually exclusive, DNA-interacting subunits of the BRG1/BRM-associated factor (BAF) subclass of SWI/SNF complex. Although the role of several SWI/SNF components in hematopoietic differentiation and stem cell maintenance has been reported, the function of ARID1B in hematopoietic development has not been defined. To this end, we generated a mouse model of Arid1b deficiency specifically in the hematopoietic compartment. Unlike the extensive phenotype observed in mice deficient in its paralog, ARID1A, Arid1b knockout (KO) mice exhibited a modest effect on steady-state hematopoiesis. Nonetheless, transplantation experiments showed that the reconstitution of myeloid cells in irradiated recipient mice was dependent on ARID1B. Furthermore, to assess the effect of the complete loss of ARID1 proteins in the BAF complex, we generated mice lacking both ARID1A and ARID1B in the hematopoietic compartment. The double-KO mice succumbed to acute bone marrow failure resulting from complete loss of BAF-mediated chromatin remodeling activity. Our Assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) analyses revealed that >80% of loci regulated by ARID1B were distinct from those regulated by ARID1A; and ARID1B controlled expression of genes crucial in myelopoiesis. Overall, loss of ARID1B affected chromatin dynamics in murine hematopoietic stem and progenitor cells, albeit to a lesser extent than cells lacking ARID1A.
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Affiliation(s)
- Vikas Madan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Pavithra Shyamsunder
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore
| | - Pushkar Dakle
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Teoh Weoi Woon
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore
| | - Lin Han
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Zeya Cao
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | | | - Shi Jizhong
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Yu Shuizhou
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Md Zakir Hossain
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - H. Phillip Koeffler
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
- Division of Hematology/Oncology, Cedars-Sinai Medical Center, UCLA School of Medicine, Los Angeles, CA
- Department of Hematology-Oncology, National University Cancer Institute of Singapore, National University Hospital, Singapore
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32
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Yang H, Wang Y, Zhang Y. Characterization of H3K9me3 and DNA methylation co-marked CpG-rich regions during mouse development. BMC Genomics 2023; 24:663. [PMID: 37924034 PMCID: PMC10623782 DOI: 10.1186/s12864-023-09758-8] [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: 06/27/2023] [Accepted: 10/20/2023] [Indexed: 11/06/2023] Open
Abstract
BACKGROUND H3K9me3 and DNA methylation co-marked CpG-rich regions (CHMs) are functionally important in mouse pre-implantation embryos, but their characteristics in other biological processes are still largely unknown. RESULTS In this study, we performed a comprehensive analysis to characterize CHMs during 6 mouse developmental processes, identifying over 2,600 CHMs exhibiting stable co-mark of H3K9me3 and DNA methylation patterns at CpG-rich regions. We revealed the distinctive features of CHMs, including elevated H3K9me3 signals and a significant presence in euchromatin and the potential role in silencing younger long terminal repeats (LTRs), especially in some ERVK subfamilies. The results highlight the distinct nature of universal CHMs compared to CpG-rich nonCHMs in terms of location, LTR enrichment, and DNA sequence features, enhancing our understanding of CpG-rich regions' regulatory roles. CONCLUSIONS This study characterizes the features of CHMs in multiple developmental processes and broadens our understanding of the regulatory roles of CpG-rich regions.
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Affiliation(s)
- Hui Yang
- Institute for Regenerative Medicine, Department of Neurosurgery, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Yiman Wang
- Institute for Regenerative Medicine, Department of Neurosurgery, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Yong Zhang
- Institute for Regenerative Medicine, Department of Neurosurgery, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China.
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33
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Joosten SE, Gregoricchio S, Stelloo S, Yapıcı E, Huang CCF, Collier MD, Morova T, Altintas B, Kim Y, Canisius S, Korkmaz G, Lack N, Vermeulen M, Linn SC, Zwart W. Breast cancer risk SNPs converge on estrogen receptor binding sites commonly shared between breast tumors to locally alter estrogen signalling output. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.30.564691. [PMID: 37961147 PMCID: PMC10634999 DOI: 10.1101/2023.10.30.564691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Estrogen Receptor alpha (ERα) is the main driver and prime drug target in luminal breast. ERα chromatin binding is extensively studied in cell lines and a limited number of human tumors, using consensi of peaks shared among samples. However, little is known about inter-tumor heterogeneity of ERα chromatin action, along with its biological implications. Here, we use a large set of ERα ChIP-seq data from 70 ERα+ breast cancers to explore inter-patient heterogeneity in ERα DNA binding, to reveal a striking inter-tumor heterogeneity of ERα action. Interestingly, commonly-shared ERα sites showed the highest estrogen-driven enhancer activity and were most-engaged in long-range chromatin interactions. In addition, the most-commonly shared ERα-occupied enhancers were enriched for breast cancer risk SNP loci. We experimentally confirm SNVs to impact chromatin binding potential for ERα and its pioneer factor FOXA1. Finally, in the TCGA breast cancer cohort, we could confirm these variations to associate with differences in expression for the target gene. Cumulatively, we reveal a natural hierarchy of ERα-chromatin interactions in breast cancers within a highly heterogeneous inter-tumor ERα landscape, with the most-common shared regions being most active and affected by germline functional risk SNPs for breast cancer development.
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34
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Li X, Zhao Y, Kong H, Song C, Liu J, Xia J. Identification of region-specific splicing QTLs in human hippocampal tissue and its distinctive role in brain disorders. iScience 2023; 26:107958. [PMID: 37810239 PMCID: PMC10558811 DOI: 10.1016/j.isci.2023.107958] [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: 05/07/2023] [Revised: 06/28/2023] [Accepted: 09/14/2023] [Indexed: 10/10/2023] Open
Abstract
Alternative splicing (AS) regulation has an essential role in complex diseases. However, the AS profiles in the hippocampal (HIPPO) region of human brain are underexplored. Here, we investigated cis-acting sQTLs of HIPPO region in 264 samples and identified thousands of significant sQTLs. By enrichment analysis and functional characterization of these sQTLs, we found that the HIPPO sQTLs were enriched among histone-marked regions, transcription factors binding sites, RNA binding proteins sites, and brain disorders-associated loci. Comparative analyses with the dorsolateral prefrontal cortex revealed the importance of AS regulation in HIPPO (rg = 0.87). Furthermore, we performed a transcriptome-wide association study of Alzheimer's disease and identified 16 significant genes whose genetically regulated splicing levels may have a causal role in Alzheimer. Overall, our study improves our knowledge of the transcriptome gene regulation in the HIPPO region and provides novel insights into elucidating the pathogenesis of potential genes associated with brain disorders.
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Affiliation(s)
- Xiaoyan Li
- Information Materials and Intelligent Sensing Laboratory of Anhui Province and Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education, Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui 230601, China
| | - Yiran Zhao
- Information Materials and Intelligent Sensing Laboratory of Anhui Province and Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education, Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui 230601, China
| | - Hui Kong
- Information Materials and Intelligent Sensing Laboratory of Anhui Province and Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education, Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui 230601, China
| | - Chengcheng Song
- Information Materials and Intelligent Sensing Laboratory of Anhui Province and Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education, Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui 230601, China
| | - Jie Liu
- Information Materials and Intelligent Sensing Laboratory of Anhui Province and Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education, Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui 230601, China
| | - Junfeng Xia
- Information Materials and Intelligent Sensing Laboratory of Anhui Province and Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education, Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui 230601, China
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35
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Li GS, Huang ZG, He RQ, Zhang W, Tang YX, Liu ZS, Gan XY, Tang D, Li DM, Tang YL, Zhan YT, Dang YW, Zhou HF, Zheng JH, Jin MH, Tian J, Chen G. ITGB4 Serves as an Identification and Prognosis Marker Associated with Immune Infiltration in Small Cell Lung Carcinoma. Mol Biotechnol 2023:10.1007/s12033-023-00912-x. [PMID: 37847361 DOI: 10.1007/s12033-023-00912-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 09/15/2023] [Indexed: 10/18/2023]
Abstract
Integrin beta 4 (ITGB4) is a vital factor for numerous cancers. However, no reports regarding ITGB4 in small cell lung carcinoma (SCLC) have been found in the existing literature. This study systematically investigated the expression and clinical value of ITGB4 in SCLC using multi-center and large-sample (n = 963) data. The ITGB4 expression levels between SCLC and control tissues were compared using standardized mean difference and Wilcoxon rank-sum test. The clinical significance of the gene in SCLC was observed using Cox regression and Kaplan-Meier curves. ITGB4 is overexpressed in multiple cancers and represents significant value in distinguishing among cancer samples (AUC = 0.91) and predicting the prognoses (p < 0.05) of patients with different cancers. In contrast, decreased ITGB4 mRNA expression was determined in SCLC (SMD < 0), and this finding was further confirmed at protein levels using in-house specimens (p < 0.05). This decrease in expression may be attributed to the regulatory role of estrogen receptor 1. ITGB4 may participate in the progression of SCLC by affecting several signaling pathways (e.g., tumor necrosis factor signaling pathway) and a series of immune cells (e.g., dendritic cells) (p < 0.05). The gene may serve as a potential marker for predicting the disease status (AUC = 0.97) and prognoses (p < 0.05) of patients with SCLC. Collectively, ITGB4 was identified as an identification and prognosis marker associated with immune infiltration in SCLC.
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Affiliation(s)
- Guo-Sheng Li
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, People's Republic of China
| | - Zhi-Guang Huang
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, People's Republic of China
| | - Rong-Quan He
- Department of Medical Oncology, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, People's Republic of China
| | - Wei Zhang
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, People's Republic of China
| | - Yu-Xing Tang
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, People's Republic of China
| | - Zhi-Su Liu
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, People's Republic of China
| | - Xiang-Yu Gan
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, People's Republic of China
| | - Deng Tang
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, People's Republic of China
| | - Dong-Ming Li
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, People's Republic of China
| | - Yu-Lu Tang
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, People's Republic of China
| | - Yan-Ting Zhan
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, People's Republic of China
| | - Yi-Wu Dang
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, People's Republic of China
| | - Hua-Fu Zhou
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, People's Republic of China
| | - Jin-Hua Zheng
- Department of Pathology, The Affiliated Hospital of Guilin Medical University, Guilin, 541001, People's Republic of China
| | - Mei-Hua Jin
- Department of Pathology, The Affiliated Hospital of Guilin Medical University, Guilin, 541001, People's Republic of China
| | - Jia Tian
- Department of Pathology, The Affiliated Hospital of Guilin Medical University, Guilin, 541001, People's Republic of China
| | - Gang Chen
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, People's Republic of China.
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Chen Y, Lin B, Yang S, Huang J. IRF1 suppresses colon cancer proliferation by reducing SPI1-mediated transcriptional activation of GPX4 and promoting ferroptosis. Exp Cell Res 2023; 431:113733. [PMID: 37517591 DOI: 10.1016/j.yexcr.2023.113733] [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: 04/16/2023] [Revised: 07/24/2023] [Accepted: 07/26/2023] [Indexed: 08/01/2023]
Abstract
IRF1 is a tumor suppressor gene in colon cancer. This study aimed to explore the potential regulation of IRF1 on the ferroptosis of colon cancer and the mechanisms underlying its regulation of GPX4 transcription. IRF1 interacting transcription factors regulating GPX4 transcription were predicted and validated. The role of the IRF1/SPI1-GPX4 axis on the ferroptosis of colon cancer cells was explored. Results showed that IRF1 overexpression reduced GPX4 transcription, increased reactive oxygen species (ROS) and lipid ROS accumulation, and enhanced erastin-induced colon cancer cell growth in vitro and in vivo. SPI1 could directly bind to the GPX4 promoter (-414 to -409) and activate its transcription. IRF1 could bind to SPI1 and suppress its transcriptional activating effects on GPX4 expression. SPI1 overexpression reduced ROS and lipid ROS accumulation and increased colon cancer cell viability and colony formation upon erastin induction. These trends were reversed by IRF1 overexpression. In conclusion, this study revealed a novel oncogenic mechanism of SPI1 by reducing erastin-induced ferroptosis in colon cancer. IRF1 interacts with SPI1 and suppresses its transcriptional activating effect on GPX4 expression. Through this mechanism, IRF1 can enhance erastin-induced ferroptosis of colon cancer. The IRF1/SPI1-GPX4 axis might play a crucial role in modulating ferroptosis in colon cancer and might serve as a potential therapeutic target in the future.
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Affiliation(s)
- Yilin Chen
- Department of General Surgery, The Second Affiliated Hospital of Fujian Medical University, Fujian, China
| | - Beian Lin
- Department of General Surgery, The Second Affiliated Hospital of Fujian Medical University, Fujian, China
| | - Shiyu Yang
- Department of General Surgery, The Second Affiliated Hospital of Fujian Medical University, Fujian, China
| | - Jingshan Huang
- Department of General Surgery, The Second Affiliated Hospital of Fujian Medical University, Fujian, China.
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37
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Suthon S, Lin J, Perkins RS, Miranda-Carboni GA, Krum SA. Regulation and Function of FOXC1 in Osteoblasts. J Dev Biol 2023; 11:38. [PMID: 37754840 PMCID: PMC10531946 DOI: 10.3390/jdb11030038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 09/11/2023] [Accepted: 09/15/2023] [Indexed: 09/28/2023] Open
Abstract
Estrogens, which bind to estrogen receptor alpha (ERα), are important for proper bone mineral density. When women go through menopause, estrogen levels decrease, and there is a decrease in bone quality, along with an increased risk for fractures. We previously identified an enhancer near FOXC1 as the most significantly enriched binding site for estrogen receptor alpha (ERα) in osteoblasts. FOXC1 is a transcription factor belonging to a large group of proteins known as forkhead box genes and is an important regulator of bone formation. Here, we demonstrate that 17β-estradiol (E2) increases the mRNA and protein levels of FOXC1 in primary mouse and human osteoblasts. GATA4 is a pioneer factor for ERα and it is also recruited to enhancers near Foxc1. Knockdown of Gata4 in mouse osteoblasts in vitro decreases Foxc1 expression as does knockout of Gata4 in vivo. Functionally, GATA4 and FOXC1 interact and regulate osteoblast proteins such as RUNX2, as demonstrated by ChIP-reChIP and luciferase assays. The most enriched motif in GATA4 binding sites from ChIP-seq is for FOXC1, supporting the notion that GATA4 and FOXC1 cooperate in regulating osteoblast differentiation. Together, these data demonstrate the interactions of the transcription factors ERα, GATA4, and FOXC1 to regulate each other's expression and other osteoblast differentiation genes.
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Affiliation(s)
- Sarocha Suthon
- Department of Orthopaedic Surgery and Biomedical Engineering, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Jianjian Lin
- Department of Orthopaedic Surgery and Biomedical Engineering, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Rachel S. Perkins
- Department of Orthopaedic Surgery and Biomedical Engineering, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Gustavo A. Miranda-Carboni
- Department of Medicine, University of Tennessee Health Science Center, Memphis, TN 38163, USA
- Center for Cancer Research, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Susan A. Krum
- Department of Orthopaedic Surgery and Biomedical Engineering, University of Tennessee Health Science Center, Memphis, TN 38163, USA
- Center for Cancer Research, University of Tennessee Health Science Center, Memphis, TN 38163, USA
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38
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Zhang Y, Shen Y, Zhao L, Zhao Q, Zhao L, Yi S. Transcription Factor BCL11A Regulates Schwann Cell Behavior During Peripheral Nerve Regeneration. Mol Neurobiol 2023; 60:5352-5365. [PMID: 37316757 DOI: 10.1007/s12035-023-03432-6] [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: 02/16/2023] [Accepted: 06/05/2023] [Indexed: 06/16/2023]
Abstract
Nerve injury-induced Schwann cell dedifferentiation helps to construct a favorable microenvironment for axon growth. Transcription factors regulate cell reprogramming and thus may be critical for Schwann cell phenotype switch during peripheral nerve regeneration. Here, we show that transcription factor B-cell lymphoma/leukemia 11A (BCL11A) is up-regulated in Schwann cells of injured peripheral nerves. Bcl11a silencing suppresses Schwann cell viability, decreases Schwann cell proliferation and migration rates, and impairs the debris clearance ability of Schwann cells. Reduced Bcl11a in injured peripheral nerves results in restricted axon elongation and myelin wrapping, leading to recovery failure. Mechanistically, we demonstrate that BCL11A may mediate Schwann cell activity through binding to the promoter of nuclear receptor subfamily 2 group F member 2 (Nr2f2) and regulating Nr2f2 expression. Collectively, we conclude that BCL11A is essential for Schwann cell activation and peripheral nerve regeneration, providing a potential therapeutic target for the treatment of peripheral nerve injury.
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Affiliation(s)
- Yunsong Zhang
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University, Nantong, Jiangsu, China
| | - Yinying Shen
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University, Nantong, Jiangsu, China
| | - Li Zhao
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University, Nantong, Jiangsu, China
| | - Qian Zhao
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University, Nantong, Jiangsu, China
| | - Lili Zhao
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University, Nantong, Jiangsu, China.
| | - Sheng Yi
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University, Nantong, Jiangsu, China.
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Tabrizian N, Nouruzi S, Cui CJ, Kobelev M, Namekawa T, Lodhia I, Talal A, Sivak O, Ganguli D, Zoubeidi A. ASCL1 is activated downstream of the ROR2/CREB signaling pathway to support lineage plasticity in prostate cancer. Cell Rep 2023; 42:112937. [PMID: 37552603 DOI: 10.1016/j.celrep.2023.112937] [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: 02/22/2023] [Revised: 07/16/2023] [Accepted: 07/20/2023] [Indexed: 08/10/2023] Open
Abstract
Lineage plasticity is a form of therapy-induced drug resistance. In prostate cancer, androgen receptor (AR) pathway inhibitors potentially lead to the accretion of tumor relapse with loss of AR signaling and a shift from a luminal state to an alternate program. However, the molecular and signaling mechanisms orchestrating the development of lineage plasticity under the pressure of AR-targeted therapies are not fully understood. Here, a survey of receptor tyrosine kinases (RTKs) identifies ROR2 as the top upregulated RTK following AR pathway inhibition, which feeds into lineage plasticity by promoting stem-cell-like and neuronal networks. Mechanistically, ROR2 activates the ERK/CREB signaling pathway to modulate the expression of the lineage commitment transcription factor ASCL1. Collectively, our findings nominate ROR2 as a potential therapeutic target to reverse the ENZ-induced plastic phenotype and potentially re-sensitize tumors to AR pathway inhibitors.
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Affiliation(s)
- Nakisa Tabrizian
- Department of Urologic Sciences, The University of British Columbia, Vancouver, BC V5Z 1M9, Canada; Vancouver Prostate Centre, Vancouver, BC V6H 3Z6, Canada
| | - Shaghayegh Nouruzi
- Department of Urologic Sciences, The University of British Columbia, Vancouver, BC V5Z 1M9, Canada; Vancouver Prostate Centre, Vancouver, BC V6H 3Z6, Canada
| | - Cassandra Jingjing Cui
- Department of Urologic Sciences, The University of British Columbia, Vancouver, BC V5Z 1M9, Canada; Vancouver Prostate Centre, Vancouver, BC V6H 3Z6, Canada
| | - Maxim Kobelev
- Department of Urologic Sciences, The University of British Columbia, Vancouver, BC V5Z 1M9, Canada; Vancouver Prostate Centre, Vancouver, BC V6H 3Z6, Canada
| | - Takeshi Namekawa
- Department of Urologic Sciences, The University of British Columbia, Vancouver, BC V5Z 1M9, Canada; Vancouver Prostate Centre, Vancouver, BC V6H 3Z6, Canada
| | - Ishana Lodhia
- Vancouver Prostate Centre, Vancouver, BC V6H 3Z6, Canada
| | - Amina Talal
- Vancouver Prostate Centre, Vancouver, BC V6H 3Z6, Canada
| | - Olena Sivak
- Vancouver Prostate Centre, Vancouver, BC V6H 3Z6, Canada
| | | | - Amina Zoubeidi
- Department of Urologic Sciences, The University of British Columbia, Vancouver, BC V5Z 1M9, Canada; Vancouver Prostate Centre, Vancouver, BC V6H 3Z6, Canada.
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40
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Jiang Q, Chen Z, Meng F, Zhang H, Chen H, Xue J, Shen X, Liu T, Dong L, Zhang S, Xue R. CD36-BATF2\MYB Axis Predicts Anti-PD-1 Immunotherapy Response in Gastric Cancer. Int J Biol Sci 2023; 19:4476-4492. [PMID: 37781029 PMCID: PMC10535701 DOI: 10.7150/ijbs.87635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 08/11/2023] [Indexed: 10/03/2023] Open
Abstract
Despite the utilization of anti-PD-1 therapy in gastric cancer (GC), the absence of a reliable predictive biomarker continues to pose a challenge. In this study, we utilized bioinformatic analysis and immunohistochemistry to develop a prediction model for activated CD4+ memory T cells, considering both mRNA and protein levels. An elevation of activated CD4+ memory T cells in GC was noted, which exhibited a strong association with the patients' overall survival. By utilizing WGCNA and DEG analysis, we discovered that BATF2, MYB, and CD36 are genes that exhibit differential expression and are linked to activated CD4+ memory T cells. Afterwards, a forecast model was built utilizing Stepwise regression and immunohistochemistry relying on the three genes. The model's high-risk score showed significant associations with a suppressive immune microenvironment. Moreover, our model exhibited encouraging prognostic value and superior performance in predicting response to immune checkpoint blockade therapy compared with the conventional CD8+PD-L1 model. In terms of mechanism, CD36 could function as a receptor upstream that identifies Helicobacter pylori and fatty acids. This recognition then results in the reduction of the BATF2-MYB protein complex and subsequent alterations in the transcription of genes associated with classical T cell activation. As a result, the activation state of CD4+ memory T cells is ultimately suppressed. The CD36-BATF2/MYB signature serves as a robust predictor of anti-PD-1 immunotherapy response in GC.
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Affiliation(s)
- Qiuyu Jiang
- Department of Gastroenterology and Hepatology, Shanghai Institute of Liver Diseases, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Zhixue Chen
- Department of Gastroenterology and Hepatology, Shanghai Institute of Liver Diseases, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Fansheng Meng
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Hao Zhang
- Department of Oncology, Minhang Hospital, Fudan University, China
- Key Laboratory of Whole-Period Monitoring and Precise Intervention of Digestive Cancer (SMHC), Minhang Hospital & AHS, Fudan University, China
| | - He Chen
- Department of Gastroenterology and Hepatology, Shanghai Institute of Liver Diseases, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Jindan Xue
- School of Medicine, Anhui University of Science and Technology, Anhui, 232000, China
| | - Xizhong Shen
- Department of Gastroenterology and Hepatology, Shanghai Institute of Liver Diseases, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Tianshu Liu
- Department of Medical Oncology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Ling Dong
- Department of Gastroenterology and Hepatology, Shanghai Institute of Liver Diseases, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Si Zhang
- NHC Key Laboratory of Glycoconjugate Research, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Ruyi Xue
- Department of Gastroenterology and Hepatology, Shanghai Institute of Liver Diseases, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
- Shanghai Baoshan District Wusong Central Hospital (Zhongshan Hospital Wusong Branch, Fudan University), Shanghai 200940, China
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Mangoni D, Simi A, Lau P, Armaos A, Ansaloni F, Codino A, Damiani D, Floreani L, Di Carlo V, Vozzi D, Persichetti F, Santoro C, Pandolfini L, Tartaglia GG, Sanges R, Gustincich S. LINE-1 regulates cortical development by acting as long non-coding RNAs. Nat Commun 2023; 14:4974. [PMID: 37591988 PMCID: PMC10435495 DOI: 10.1038/s41467-023-40743-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 08/07/2023] [Indexed: 08/19/2023] Open
Abstract
Long Interspersed Nuclear Elements-1s (L1s) are transposable elements that constitute most of the genome's transcriptional output yet have still largely unknown functions. Here we show that L1s are required for proper mouse brain corticogenesis operating as regulatory long non-coding RNAs. They contribute to the regulation of the balance between neuronal progenitors and differentiation, the migration of post-mitotic neurons and the proportions of different cell types. In cortical cultured neurons, L1 RNAs are mainly associated to chromatin and interact with the Polycomb Repressive Complex 2 (PRC2) protein subunits enhancer of Zeste homolog 2 (Ezh2) and suppressor of zeste 12 (Suz12). L1 RNA silencing influences PRC2's ability to bind a portion of its targets and the deposition of tri-methylated histone H3 (H3K27me3) marks. Our results position L1 RNAs as crucial signalling hubs for genome-wide chromatin remodelling, enabling the fine-tuning of gene expression during brain development and evolution.
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Affiliation(s)
- Damiano Mangoni
- Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), Genova, Italy
| | - Alessandro Simi
- Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), Genova, Italy
| | - Pierre Lau
- Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), Genova, Italy
| | - Alexandros Armaos
- Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), Genova, Italy
| | - Federico Ansaloni
- Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), Genova, Italy
| | - Azzurra Codino
- Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), Genova, Italy
| | - Devid Damiani
- Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), Genova, Italy
| | - Lavinia Floreani
- Area of Neuroscience, International School for Advanced Studies (SISSA), Trieste, Italy
| | - Valerio Di Carlo
- Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), Genova, Italy
| | - Diego Vozzi
- Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), Genova, Italy
| | - Francesca Persichetti
- Department of Health Sciences and Research Center on Autoimmune and Allergic Diseases (CAAD), University of Piemonte Orientale (UPO), Novara, Italy
| | - Claudio Santoro
- Department of Health Sciences and Research Center on Autoimmune and Allergic Diseases (CAAD), University of Piemonte Orientale (UPO), Novara, Italy
| | - Luca Pandolfini
- Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), Genova, Italy
| | | | - Remo Sanges
- Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), Genova, Italy.
- Area of Neuroscience, International School for Advanced Studies (SISSA), Trieste, Italy.
| | - Stefano Gustincich
- Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), Genova, Italy.
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Kupkova K, Shetty SJ, Pray-Grant MG, Grant PA, Haque R, Petri WA, Auble DT. Globally elevated levels of histone H3 lysine 9 trimethylation in early infancy are associated with poor growth trajectory in Bangladeshi children. Clin Epigenetics 2023; 15:129. [PMID: 37568218 PMCID: PMC10422758 DOI: 10.1186/s13148-023-01548-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 08/06/2023] [Indexed: 08/13/2023] Open
Abstract
BACKGROUND Stunting is a global health problem affecting hundreds of millions of children worldwide and contributing to 45% of deaths in children under the age of five. Current therapeutic interventions have limited efficacy. Understanding the epigenetic changes underlying stunting will elucidate molecular mechanisms and likely lead to new therapies. RESULTS We profiled the repressive mark histone H3 lysine 9 trimethylation (H3K9me3) genome-wide in peripheral blood mononuclear cells (PBMCs) from 18-week-old infants (n = 15) and mothers (n = 14) enrolled in the PROVIDE study established in an urban slum in Bangladesh. We associated H3K9me3 levels within individual loci as well as genome-wide with anthropometric measurements and other biomarkers of stunting and performed functional annotation of differentially affected regions. Despite the relatively small number of samples from this vulnerable population, we observed globally elevated H3K9me3 levels were associated with poor linear growth between birth and one year of age. A large proportion of the differentially methylated genes code for proteins targeting viral mRNA and highly significant regions were enriched in transposon elements with potential regulatory roles in immune system activation and cytokine production. Maternal data show a similar trend with child's anthropometry; however, these trends lack statistical significance to infer an intergenerational relationship. CONCLUSIONS We speculate that high H3K9me3 levels may result in poor linear growth by repressing genes involved in immune system activation. Importantly, changes to H3K9me3 were detectable before the overt manifestation of stunting and therefore may be valuable as new biomarkers of stunting.
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Affiliation(s)
- Kristyna Kupkova
- Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, VA, 22908, USA
- Center for Public Health Genomics, University of Virginia Health System, Charlottesville, VA, 22908, USA
| | - Savera J Shetty
- Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, VA, 22908, USA
| | - Marilyn G Pray-Grant
- Department of Biomedical Science, Charles E. Schmidt College of Medicine, Florida Atlantic University, Boca Raton, FL, 33431, USA
| | - Patrick A Grant
- Department of Biomedical Science, Charles E. Schmidt College of Medicine, Florida Atlantic University, Boca Raton, FL, 33431, USA
| | - Rashidul Haque
- Infectious Disease Division, International Centre for Diarrhoeal Disease Research, Dhaka, 1000, Bangladesh
| | - William A Petri
- Division of Infectious Diseases and International Health, University of Virginia Health System, Charlottesville, VA, 22908, USA
| | - David T Auble
- Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, VA, 22908, USA.
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43
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Deng Y, Han X, Chen H, Zhao C, Chen Y, Zhou J, de The H, Zhu J, Yuan H. Ypel5 regulates liver development and function in zebrafish. J Mol Cell Biol 2023; 15:mjad019. [PMID: 36948605 PMCID: PMC10588938 DOI: 10.1093/jmcb/mjad019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 03/16/2023] [Accepted: 03/20/2023] [Indexed: 03/24/2023] Open
Abstract
YPEL5 is a member of the Yippee-like (YPEL) gene family that is evolutionarily conserved in eukaryotic species. To date, the physiological function of YPEL5 has not been assessed due to a paucity of genetic animal models. Here, using CRISPR/Cas9-mediated genome editing, we generated a stable ypel5-/- mutant zebrafish line. Disruption of ypel5 expression leads to liver enlargement associated with hepatic cell proliferation. Meanwhile, hepatic metabolism and function are dysregulated in ypel5-/- mutant zebrafish, as revealed by metabolomic and transcriptomic analyses. Mechanistically, Hnf4a is identified as a crucial downstream mediator that is positively regulated by Ypel5. Zebrafish hnf4a overexpression could largely rescue ypel5 deficiency-induced hepatic defects. Furthermore, PPARα signaling mediates the regulation of Hnf4a by Ypel5 through directly binding to the transcriptional enhancer of the Hnf4a gene. Herein, this work demonstrates an essential role of Ypel5 in hepatocyte proliferation and function and provides the first in vivo evidence for a physiological role of the ypel5 gene in vertebrates.
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Affiliation(s)
- Yun Deng
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- CNRS-LIA Hematology and Cancer, Sino-French Research Center for Life Sciences and Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Xiao Han
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- CNRS-LIA Hematology and Cancer, Sino-French Research Center for Life Sciences and Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Huiqiao Chen
- Department of Hematology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310011, China
| | - Chaoxian Zhao
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- CNRS-LIA Hematology and Cancer, Sino-French Research Center for Life Sciences and Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Yi Chen
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Jun Zhou
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- CNRS-LIA Hematology and Cancer, Sino-French Research Center for Life Sciences and Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Hugues de The
- CNRS-LIA Hematology and Cancer, Sino-French Research Center for Life Sciences and Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- Université de Paris 7/INSERM/CNRS UMR 944/7212, Equipe Labellisée Ligue Nationale Contre le Cancer, Hôpital St. Louis, Paris 75010, France
| | - Jun Zhu
- CNRS-LIA Hematology and Cancer, Sino-French Research Center for Life Sciences and Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- Université de Paris 7/INSERM/CNRS UMR 944/7212, Equipe Labellisée Ligue Nationale Contre le Cancer, Hôpital St. Louis, Paris 75010, France
| | - Hao Yuan
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- CNRS-LIA Hematology and Cancer, Sino-French Research Center for Life Sciences and Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
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Zhang W, Qi L, Liu Z, He S, Wang C, Wu Y, Han L, Liu Z, Fu Z, Tu C, Li Z. Integrated multiomic analysis and high-throughput screening reveal potential gene targets and synergetic drug combinations for osteosarcoma therapy. MedComm (Beijing) 2023; 4:e317. [PMID: 37457661 PMCID: PMC10338795 DOI: 10.1002/mco2.317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 05/14/2023] [Accepted: 05/22/2023] [Indexed: 07/18/2023] Open
Abstract
Although great advances have been made over the past decades, therapeutics for osteosarcoma are quite limited. We performed long-read RNA sequencing and tandem mass tag (TMT)-based quantitative proteome on osteosarcoma and the adjacent normal tissues, next-generation sequencing (NGS) on paired osteosarcoma samples before and after neoadjuvant chemotherapy (NACT), and high-throughput drug combination screen on osteosarcoma cell lines. Single-cell RNA sequencing data were analyzed to reveal the heterogeneity of potential therapeutic target genes. Additionally, we clarified the synergistic mechanisms of doxorubicin (DOX) and HDACs inhibitors for osteosarcoma treatment. Consequently, we identified 2535 osteosarcoma-specific genes and several alternative splicing (AS) events with osteosarcoma specificity and/or patient heterogeneity. Hundreds of potential therapeutic targets were identified among them, which showed the core regulatory roles in osteosarcoma. We also identified 215 inhibitory drugs and 236 synergistic drug combinations for osteosarcoma treatment. More interestingly, the multiomic analysis pointed out the pivotal role of HDAC1 and TOP2A in osteosarcoma. HDAC inhibitors synergized with DOX to suppress osteosarcoma both in vitro and in vivo. Mechanistically, HDAC inhibitors synergized with DOX by downregulating SP1 to transcriptionally modulate TOP2A expression. This study provided a comprehensive view of molecular features, therapeutic targets, and synergistic drug combinations for osteosarcoma.
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Affiliation(s)
- Wenchao Zhang
- Department of OrthopedicsThe Second Xiangya HospitalCentral South UniversityChangshaChina
- Hunan Key Laboratory of Tumor Models and Individualized MedicineThe Second Xiangya HospitalChangshaChina
| | - Lin Qi
- Department of OrthopedicsThe Second Xiangya HospitalCentral South UniversityChangshaChina
- Hunan Key Laboratory of Tumor Models and Individualized MedicineThe Second Xiangya HospitalChangshaChina
| | - Zhongyue Liu
- Department of OrthopedicsThe Second Xiangya HospitalCentral South UniversityChangshaChina
- Hunan Key Laboratory of Tumor Models and Individualized MedicineThe Second Xiangya HospitalChangshaChina
| | - Shasha He
- Department of OncologyThe Second Xiangya HospitalCentral South UniversityChangshaChina
| | | | - Ying Wu
- MegaRobo Technologies Co., LtdSuzhouChina
| | | | | | - Zheng Fu
- MegaRobo Technologies Co., LtdSuzhouChina
| | - Chao Tu
- Department of OrthopedicsThe Second Xiangya HospitalCentral South UniversityChangshaChina
- Hunan Key Laboratory of Tumor Models and Individualized MedicineThe Second Xiangya HospitalChangshaChina
| | - Zhihong Li
- Department of OrthopedicsThe Second Xiangya HospitalCentral South UniversityChangshaChina
- Hunan Key Laboratory of Tumor Models and Individualized MedicineThe Second Xiangya HospitalChangshaChina
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Sun Y, Man Y, Cheng J, Li J, Liu Y. FAM60A promotes osteosarcoma development and progression. Cancer Med 2023; 12:17491-17503. [PMID: 37439040 PMCID: PMC10501228 DOI: 10.1002/cam4.6343] [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: 03/26/2023] [Revised: 07/02/2023] [Accepted: 07/03/2023] [Indexed: 07/14/2023] Open
Abstract
BACKGROUND Osteosarcoma (OS) is a highly malignant primary bone tumor. Family of homology 60A (FAM60A) reportedly contributes to the malignant growth of some tumors. METHODS Herein we investigated the mRNA expression level of FAM60A by combining OS and non-cancer samples from public databases. Immunohistochemistry was performed to determine protein expression levels of FAM60A in patients with OS. Further, RT-qPCR and western blotting were conducted to evaluate FAM60A expression in various OS cell lines. CCK-8 assay, colony formation assay, and flow cytometry were applied to determine the function of FAM60A. Finally, functional enrichment analysis was performed based on FAM60A co-expressed genes. RESULTS FAM60A mRNA expression level was found to be significantly upregulated (standardized mean difference = 1.27, 95% CI [0.67-1.88]). Survival analyses suggested that higher expression of FAM60A was indicative of poor prognoses. Similarly, FAM60A protein expression level was also observed to be upregulated. Knocking down FAM60A expression inhibited OS cell proliferation, increased apoptosis, and blocked cells from entering the S phase. Besides, cell cycle was the most prominently enriched pathway, and BUB1, DTL, and EXO1 were identified as hub genes. CONCLUSIONS FAM60A expression was found to be markedly upregulated in OS; furthermore, FAM60A was observed to promote OS cell proliferation, inhibit apoptosis, and participate in cell cycle regulation. Besides, FAM60A may interact with hub genes to participate in the progress of OS.
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Affiliation(s)
- Yu Sun
- Division of Spinal SurgeryThe First Affiliated Hospital of Guangxi Medical UniversityNanningGuangxi Zhuang Autonomous RegionP.R. China
| | - Yu‐Nan Man
- Division of Spinal SurgeryThe First Affiliated Hospital of Guangxi Medical UniversityNanningGuangxi Zhuang Autonomous RegionP.R. China
| | - Jin‐hui Cheng
- Jiangxi Provincial People's HospitalThe First Affiliated Hospital of Nanchang Medical CollegeNanchangJiangxiChina
| | - Jing‐tang Li
- Jiangxi Provincial People's HospitalThe First Affiliated Hospital of Nanchang Medical CollegeNanchangJiangxiChina
| | - Ya‐yun Liu
- Jiangxi Provincial People's HospitalThe First Affiliated Hospital of Nanchang Medical CollegeNanchangJiangxiChina
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Friman ET, Flyamer IM, Marenduzzo D, Boyle S, Bickmore WA. Ultra-long-range interactions between active regulatory elements. Genome Res 2023; 33:1269-1283. [PMID: 37451823 PMCID: PMC10547262 DOI: 10.1101/gr.277567.122] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 07/07/2023] [Indexed: 07/18/2023]
Abstract
Contacts between enhancers and promoters are thought to relate to their ability to activate transcription. Investigating factors that contribute to such chromatin interactions is therefore important for understanding gene regulation. Here, we have determined contact frequencies between millions of pairs of cis-regulatory elements from chromosome conformation capture data sets and analyzed a collection of hundreds of DNA-binding factors for binding at regions of enriched contacts. This analysis revealed enriched contacts at sites bound by many factors associated with active transcription. We show that active regulatory elements, independent of cohesin and polycomb, interact with each other across distances of tens of megabases in vertebrate and invertebrate genomes and that interactions correlate and change with activity. However, these ultra-long-range interactions are not dependent on RNA polymerase II transcription or individual transcription cofactors. Using simulations, we show that a model of chromatin and multivalent binding factors can give rise to long-range interactions via bridging-induced clustering. We propose that long-range interactions between cis-regulatory elements are driven by at least three distinct processes: cohesin-mediated loop extrusion, polycomb contacts, and clustering of active regions.
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Affiliation(s)
- Elias T Friman
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom;
| | - Ilya M Flyamer
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Davide Marenduzzo
- School of Physics and Astronomy, University of Edinburgh, Edinburgh EH9 3FD, United Kingdom
| | - Shelagh Boyle
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Wendy A Bickmore
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom;
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Wang L, Wei C, Wang Y, Huang N, Zhang T, Dai Y, Xue L, Lin S, Wu ZB. Identification of the enhancer RNAs related to tumorgenesis of pituitary neuroendocrine tumors. Front Endocrinol (Lausanne) 2023; 14:1149997. [PMID: 37534217 PMCID: PMC10393250 DOI: 10.3389/fendo.2023.1149997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 06/27/2023] [Indexed: 08/04/2023] Open
Abstract
Background Pituitary neuroendocrine tumors (PitNETs), which originate from the pituitary gland, account for 10%-15% of all intracranial neoplasms. Recent studies have indicated that enhancer RNAs (eRNAs) exert regulatory effects on tumor growth. However, the mechanisms underlying the eRNA-mediated tumorigenesis of PitNETs have not been elucidated. Methods Normal pituitary and PitNETs tissues were used to identify the differentially expressed eRNAs (DEEs). Immune gene sets and hallmarks of cancer gene sets were quantified based on single sample gene set enrichment analysis (ssGSEA) algorithm using GSVA. The perspective of immune cells among all samples was calculated by the CIBERSORT algorithm. Moreover, the regulatory network composed of key DEEs, target genes of eRNAs, hallmarks of cancer gene sets, differentially expressed TF, immune cells and immune gene sets were constructed by Pearson correlation analysis. Small molecular anti-PitNETs drugs were explored by CMap analysis and the accuracy of the study was verified by in vitro and in vivo experiments, ATAC-seq and ChIP-seq. Results In this study, data of 134 PitNETs and 107 non-tumorous pituitary samples were retrieved from a public database to identify differentially expressed genes. In total, 1128 differentially expressed eRNAs (DEEs) (494 upregulated eRNAs and 634 downregulated eRNAs) were identified. Next, the correlation of DEEs with cancer-related and immune-related gene signatures was examined to establish a co-expression regulatory network comprising 18 DEEs, 50 potential target genes of DEEs, 5 cancer hallmark gene sets, 2 differentially expressed transcription factors, 4 immune cell types, and 4 immune gene sets. Based on this network, the following four therapeutics for PitNETs were identified using Connectivity Map analysis: ciclopirox, bepridil, clomipramine, and alexidine. The growth-inhibitory effects of these therapeutics were validated using in vitro experiments. Ciclopirox exerted potential growth-inhibitory effects on PitNETs. Among the DEEs, GNLY, HOXB7, MRPL33, PRDM16, TCF7, and ZNF26 were determined to be potential diagnostic and therapeutic biomarkers for PitNETs. Conclusion This study illustrated the significant influence of eRNAs on the occurrence and development of PitNETs. By constructing the co-expression regulation network, GNLY, HOXB6, MRPL33, PRDM16, TCF7, and ZNF26 were identified as relatively significant DEEs which were considered as the novel biomarkers of diagnosis and treatment of PitNETs. This study demonstrated the roles of eRNAs in the occurrence and development of PitNETs and revealed that ciclopirox was a potential therapeutic for pituitary adenomas.
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Affiliation(s)
- Liangbo Wang
- Department of Neurosurgery, First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
- Department of Neurosurgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chenlu Wei
- Center for Reproductive Medicine, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yu Wang
- Department of Neurosurgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Ning Huang
- Department of Neurosurgery, First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Tao Zhang
- Department of Neurosurgery, First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Yuting Dai
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Li Xue
- Department of Neurosurgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shaojian Lin
- Department of Neurosurgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhe Bao Wu
- Department of Neurosurgery, First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
- Department of Neurosurgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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Bhimsaria D, Rodríguez-Martínez JA, Mendez-Johnson JL, Ghoshdastidar D, Varadarajan A, Bansal M, Daniels DL, Ramanathan P, Ansari AZ. Hidden modes of DNA binding by human nuclear receptors. Nat Commun 2023; 14:4179. [PMID: 37443151 PMCID: PMC10345098 DOI: 10.1038/s41467-023-39577-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 06/19/2023] [Indexed: 07/15/2023] Open
Abstract
Human nuclear receptors (NRs) are a superfamily of ligand-responsive transcription factors that have central roles in cellular function. Their malfunction is linked to numerous diseases, and the ability to modulate their activity with synthetic ligands has yielded 16% of all FDA-approved drugs. NRs regulate distinct gene networks, however they often function from genomic sites that lack known binding motifs. Here, to annotate genomic binding sites of known and unexamined NRs more accurately, we use high-throughput SELEX to comprehensively map DNA binding site preferences of all full-length human NRs, in complex with their ligands. Furthermore, to identify non-obvious binding sites buried in DNA-protein interactomes, we develop MinSeq Find, a search algorithm based on the MinTerm concept from electrical engineering and digital systems design. The resulting MinTerm sequence set (MinSeqs) reveal a constellation of binding sites that more effectively annotate NR-binding profiles in cells. MinSeqs also unmask binding sites created or disrupted by 52,106 single-nucleotide polymorphisms associated with human diseases. By implicating druggable NRs as hidden drivers of multiple human diseases, our results not only reveal new biological roles of NRs, but they also provide a resource for drug-repurposing and precision medicine.
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Affiliation(s)
- Devesh Bhimsaria
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, 247667, India.
| | | | | | | | - Ashwin Varadarajan
- Department of Electrical and Computer Engineering, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Manju Bansal
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, India
| | - Danette L Daniels
- Promega Corporation, Madison, WI, 53711, USA
- Foghorn Therapeutics, Cambridge, MA, 02139, USA
| | - Parameswaran Ramanathan
- Department of Electrical and Computer Engineering, University of Wisconsin-Madison, Madison, WI, 53706, USA.
| | - Aseem Z Ansari
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA.
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Laub V, Devraj K, Elias L, Schulte D. Bioinformatics for wet-lab scientists: practical application in sequencing analysis. BMC Genomics 2023; 24:382. [PMID: 37420172 DOI: 10.1186/s12864-023-09454-7] [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: 03/23/2023] [Accepted: 06/15/2023] [Indexed: 07/09/2023] Open
Abstract
BACKGROUND Genomics data is available to the scientific community after publication of research projects and can be investigated for a multitude of research questions. However, in many cases deposited data is only assessed and used for the initial publication, resulting in valuable resources not being exploited to their full depth. MAIN: A likely reason for this is that many wetlab-based researchers are not formally trained to apply bioinformatic tools and may therefore assume that they lack the necessary experience to do so themselves. In this article, we present a series of freely available, predominantly web-based platforms and bioinformatic tools that can be combined in analysis pipelines to interrogate different types of next-generation sequencing data. Additionally to the presented exemplary route, we also list a number of alternative tools that can be combined in a mix-and-match fashion. We place special emphasis on tools that can be followed and used correctly without extensive prior knowledge in programming. Such analysis pipelines can be applied to existing data downloaded from the public domain or be compared to the results of own experiments. CONCLUSION Integrating transcription factor binding to chromatin (ChIP-seq) with transcriptional output (RNA-seq) and chromatin accessibility (ATAC-seq) can not only assist to form a deeper understanding of the molecular interactions underlying transcriptional regulation but will also help establishing new hypotheses and pre-testing them in silico.
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Affiliation(s)
- Vera Laub
- Neurological Institute (Edinger Institute), University Hospital Frankfurt, Goethe University, Frankfurt, Germany.
| | - Kavi Devraj
- Neurological Institute (Edinger Institute), University Hospital Frankfurt, Goethe University, Frankfurt, Germany
- Department of Biological Sciences, Birla Institute of Technology and Science Pilani, Hyderabad Campus, Hyderabad, Telangana, India
| | - Lena Elias
- Neurological Institute (Edinger Institute), University Hospital Frankfurt, Goethe University, Frankfurt, Germany
| | - Dorothea Schulte
- Neurological Institute (Edinger Institute), University Hospital Frankfurt, Goethe University, Frankfurt, Germany
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50
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Gu JJ, Deng CC, Feng QL, Liu J, Zhu DH, Cheng Q, Rong Z, Yang B. Relief of Extracellular Matrix Deposition Repression by Downregulation of IRF1-Mediated TWEAK/Fn14 Signaling in Keloids. J Invest Dermatol 2023; 143:1208-1219.e6. [PMID: 36716919 DOI: 10.1016/j.jid.2023.01.008] [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: 11/03/2021] [Revised: 01/04/2023] [Accepted: 01/07/2023] [Indexed: 01/29/2023]
Abstract
Keloids represent a fibrotic disorder characterized by the excessive deposition of extracellular matrix (ECM). However, the mechanisms through which ECM deposition in keloids is regulated remain elusive. In this study, we found that the expression of both TWEAK and its cognate receptor Fn14 was significantly downregulated in keloids and that TWEAK/Fn14 signaling repressed the expression of ECM-related genes in keloid fibroblasts. The IRF1 gene was essential for this repression, and the TWEAK/Fn14 downstream transcription factor p65 directly bound to the promoter of the IRF1 gene and induced its expression. Furthermore, in patients with keloid, the expression of TWEAK and Fn14 was negatively correlated with that of ECM genes and positively correlated with that of IRF1. These observations indicate that relief of TWEAK/Fn14/IRF1-mediated ECM deposition repression contributes to keloid pathogenesis, and the identified mechanism and related molecules provide potential targets for keloid treatment in the future.
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Affiliation(s)
- Jing-Jing Gu
- Dermatology Hospital, Southern Medical University, Guangzhou, China
| | - Cheng-Cheng Deng
- Dermatology Hospital, Southern Medical University, Guangzhou, China
| | - Qing-Lan Feng
- Dermatology Hospital, Southern Medical University, Guangzhou, China
| | - Jun Liu
- Dermatology Hospital, Southern Medical University, Guangzhou, China
| | - Ding-Heng Zhu
- Dermatology Hospital, Southern Medical University, Guangzhou, China
| | - Qing Cheng
- Dermatology Hospital, Southern Medical University, Guangzhou, China
| | - Zhili Rong
- Dermatology Hospital, Southern Medical University, Guangzhou, China; Cancer Research Institute, School of Basic Medical Sciences, State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Key Laboratory of Organ Failure Research (Ministry of Education), Southern Medical University, Guangzhou, China
| | - Bin Yang
- Dermatology Hospital, Southern Medical University, Guangzhou, China.
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