1
|
Bao K, Ma Y, Li Y, Shen X, Zhao J, Tian S, Zhang C, Liang C, Zhao Z, Yang Y, Zhang K, Yang N, Meng FL, Hao J, Yang J, Liu T, Yao Z, Ai D, Shi L. A di-acetyl-decorated chromatin signature couples liquid condensation to suppress DNA end synapsis. Mol Cell 2024; 84:1206-1223.e15. [PMID: 38423014 DOI: 10.1016/j.molcel.2024.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 12/27/2023] [Accepted: 02/02/2024] [Indexed: 03/02/2024]
Abstract
Appropriate DNA end synapsis, regulated by core components of the synaptic complex including KU70-KU80, LIG4, XRCC4, and XLF, is central to non-homologous end joining (NHEJ) repair of chromatinized DNA double-strand breaks (DSBs). However, it remains enigmatic whether chromatin modifications can influence the formation of NHEJ synaptic complex at DNA ends, and if so, how this is achieved. Here, we report that the mitotic deacetylase complex (MiDAC) serves as a key regulator of DNA end synapsis during NHEJ repair in mammalian cells. Mechanistically, MiDAC removes combinatorial acetyl marks on histone H2A (H2AK5acK9ac) around DSB-proximal chromatin, suppressing hyperaccumulation of bromodomain-containing protein BRD4 that would otherwise undergo liquid-liquid phase separation with KU80 and prevent the proper installation of LIG4-XRCC4-XLF onto DSB ends. This study provides mechanistic insight into the control of NHEJ synaptic complex assembly by a specific chromatin signature and highlights the critical role of H2A hypoacetylation in restraining unscheduled compartmentalization of DNA repair machinery.
Collapse
Affiliation(s)
- Kaiwen Bao
- Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Yanhui Ma
- Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Yuan Li
- Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Xilin Shen
- Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Jiao Zhao
- Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Shanshan Tian
- Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Chunyong Zhang
- Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Can Liang
- Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Ziyan Zhao
- Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Ying Yang
- Core Facilities Center, Capital Medical University, Beijing, China
| | - Kai Zhang
- Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Na Yang
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Tianjin, China
| | - Fei-Long Meng
- State Key Laboratory of Molecular Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China
| | - Jihui Hao
- Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Jie Yang
- Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Tao Liu
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Molecular and Cellular Pharmacology, School of Pharmaceutical Sciences, Peking University, Beijing, China
| | - Zhi Yao
- Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Ding Ai
- Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China.
| | - Lei Shi
- Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China.
| |
Collapse
|
2
|
Balasooriya ER, Madhusanka D, López-Palacios TP, Eastmond RJ, Jayatunge D, Owen JJ, Gashler JS, Egbert CM, Bulathsinghalage C, Liu L, Piccolo SR, Andersen JL. Integrating Clinical Cancer and PTM Proteomics Data Identifies a Mechanism of ACK1 Kinase Activation. Mol Cancer Res 2024; 22:137-151. [PMID: 37847650 PMCID: PMC10831333 DOI: 10.1158/1541-7786.mcr-23-0153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 08/17/2023] [Accepted: 10/13/2023] [Indexed: 10/19/2023]
Abstract
Beyond the most common oncogenes activated by mutation (mut-drivers), there likely exists a variety of low-frequency mut-drivers, each of which is a possible frontier for targeted therapy. To identify new and understudied mut-drivers, we developed a machine learning (ML) model that integrates curated clinical cancer data and posttranslational modification (PTM) proteomics databases. We applied the approach to 62,746 patient cancers spanning 84 cancer types and predicted 3,964 oncogenic mutations across 1,148 genes, many of which disrupt PTMs of known and unknown function. The list of putative mut-drivers includes established drivers and others with poorly understood roles in cancer. This ML model is available as a web application. As a case study, we focused the approach on nonreceptor tyrosine kinases (NRTK) and found a recurrent mutation in activated CDC42 kinase-1 (ACK1) that disrupts the Mig6 homology region (MHR) and ubiquitin-association (UBA) domains on the ACK1 C-terminus. By studying these domains in cultured cells, we found that disruption of the MHR domain helps activate the kinase while disruption of the UBA increases kinase stability by blocking its lysosomal degradation. This ACK1 mutation is analogous to lymphoma-associated mutations in its sister kinase, TNK1, which also disrupt a C-terminal inhibitory motif and UBA domain. This study establishes a mut-driver discovery tool for the research community and identifies a mechanism of ACK1 hyperactivation shared among ACK family kinases. IMPLICATIONS This research identifies a potentially targetable activating mutation in ACK1 and other possible oncogenic mutations, including PTM-disrupting mutations, for further study.
Collapse
Affiliation(s)
- Eranga R. Balasooriya
- The Fritz B. Burns Cancer Research Laboratory, Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah
- Center for Cancer Research, Massachusetts General Hospital, Boston, Massachusetts
- Dept. of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Deshan Madhusanka
- The Fritz B. Burns Cancer Research Laboratory, Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah
- Department of Oncological Sciences and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah
| | - Tania P. López-Palacios
- The Fritz B. Burns Cancer Research Laboratory, Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah
- Department of Oncological Sciences and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah
| | - Riley J. Eastmond
- The Fritz B. Burns Cancer Research Laboratory, Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah
| | - Dasun Jayatunge
- The Fritz B. Burns Cancer Research Laboratory, Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah
- Department of Oncological Sciences and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah
| | - Jake J. Owen
- The Fritz B. Burns Cancer Research Laboratory, Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah
| | - Jack S. Gashler
- The Fritz B. Burns Cancer Research Laboratory, Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah
| | - Christina M. Egbert
- The Fritz B. Burns Cancer Research Laboratory, Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah
| | | | - Lu Liu
- Department of Computer Science, North Dakota State University, Fargo, North Dakota
| | | | - Joshua L. Andersen
- The Fritz B. Burns Cancer Research Laboratory, Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah
- Department of Oncological Sciences and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah
| |
Collapse
|
3
|
Carrasco Pro S, Hook H, Bray D, Berenzy D, Moyer D, Yin M, Labadorf AT, Tewhey R, Siggers T, Fuxman Bass JI. Widespread perturbation of ETS factor binding sites in cancer. Nat Commun 2023; 14:913. [PMID: 36808133 PMCID: PMC9938127 DOI: 10.1038/s41467-023-36535-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 02/03/2023] [Indexed: 02/19/2023] Open
Abstract
Although >90% of somatic mutations reside in non-coding regions, few have been reported as cancer drivers. To predict driver non-coding variants (NCVs), we present a transcription factor (TF)-aware burden test based on a model of coherent TF function in promoters. We apply this test to NCVs from the Pan-Cancer Analysis of Whole Genomes cohort and predict 2555 driver NCVs in the promoters of 813 genes across 20 cancer types. These genes are enriched in cancer-related gene ontologies, essential genes, and genes associated with cancer prognosis. We find that 765 candidate driver NCVs alter transcriptional activity, 510 lead to differential binding of TF-cofactor regulatory complexes, and that they primarily impact the binding of ETS factors. Finally, we show that different NCVs within a promoter often affect transcriptional activity through shared mechanisms. Our integrated computational and experimental approach shows that cancer NCVs are widespread and that ETS factors are commonly disrupted.
Collapse
Affiliation(s)
| | - Heather Hook
- Department of Biology, Boston University, Boston, MA, USA
| | - David Bray
- Bioinformatics Program, Boston University, Boston, MA, USA
| | | | - Devlin Moyer
- Bioinformatics Program, Boston University, Boston, MA, USA
| | - Meimei Yin
- Department of Biology, Boston University, Boston, MA, USA
| | - Adam Thomas Labadorf
- Bioinformatics Hub, Boston University, Boston, MA, USA
- Boston University School of Medicine, Department of Neurology, Boston, MA, USA
| | | | - Trevor Siggers
- Bioinformatics Program, Boston University, Boston, MA, USA.
- Department of Biology, Boston University, Boston, MA, USA.
- Biological Design Center, Boston University, Boston, MA, USA.
| | - Juan Ignacio Fuxman Bass
- Bioinformatics Program, Boston University, Boston, MA, USA.
- Department of Biology, Boston University, Boston, MA, USA.
| |
Collapse
|
4
|
Wang X, Rosikiewicz W, Sedkov Y, Mondal B, Martinez T, Kallappagoudar S, Tvardovskiy A, Bajpai R, Xu B, Pruett-Miller SM, Schneider R, Herz HM. The MLL3/4 complexes and MiDAC co-regulate H4K20ac to control a specific gene expression program. Life Sci Alliance 2022; 5:e202201572. [PMID: 35820704 PMCID: PMC9275676 DOI: 10.26508/lsa.202201572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 06/24/2022] [Accepted: 06/27/2022] [Indexed: 11/30/2022] Open
Abstract
The mitotic deacetylase complex MiDAC has recently been shown to play a vital physiological role in embryonic development and neurite outgrowth. However, how MiDAC functionally intersects with other chromatin-modifying regulators is poorly understood. Here, we describe a physical interaction between the histone H3K27 demethylase UTX, a complex-specific subunit of the enhancer-associated MLL3/4 complexes, and MiDAC. We demonstrate that UTX bridges the association of the MLL3/4 complexes and MiDAC by interacting with ELMSAN1, a scaffolding subunit of MiDAC. Our data suggest that MiDAC constitutes a negative genome-wide regulator of H4K20ac, an activity which is counteracted by the MLL3/4 complexes. MiDAC and the MLL3/4 complexes co-localize at many genomic regions, which are enriched for H4K20ac and the enhancer marks H3K4me1, H3K4me2, and H3K27ac. We find that MiDAC antagonizes the recruitment of UTX and MLL4 and negatively regulates H4K20ac, and to a lesser extent H3K4me2 and H3K27ac, resulting in transcriptional attenuation of associated genes. In summary, our findings provide a paradigm how the opposing roles of chromatin-modifying components, such as MiDAC and the MLL3/4 complexes, balance the transcriptional output of specific gene expression programs.
Collapse
Affiliation(s)
- Xiaokang Wang
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
- Institute of Functional Epigenetics (IFE), Helmholtz Zentrum München, Neuherberg, Germany
| | - Wojciech Rosikiewicz
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yurii Sedkov
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Baisakhi Mondal
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Tanner Martinez
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Satish Kallappagoudar
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Andrey Tvardovskiy
- Institute of Functional Epigenetics (IFE), Helmholtz Zentrum München, Neuherberg, Germany
| | - Richa Bajpai
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Beisi Xu
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Shondra M Pruett-Miller
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Robert Schneider
- Institute of Functional Epigenetics (IFE), Helmholtz Zentrum München, Neuherberg, Germany
| | - Hans-Martin Herz
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| |
Collapse
|
5
|
Mashiach D, Bacasen EM, Singh S, Kao T, Yaramada L, Mishail D, Singh S, Miller JH. Enhanced characterization of the thyA system for mutational analysis in Escherichia coli: Defining mutationally "hot" regions of the gene. Mutat Res 2021; 823:111754. [PMID: 34091127 DOI: 10.1016/j.mrfmmm.2021.111754] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 03/19/2021] [Accepted: 03/31/2021] [Indexed: 11/19/2022]
Abstract
We have extensively characterized base substitution mutations in the 795 base pair (bp) long E. coli thyA gene to define as many of the base substitution mutational sites that inactivate the gene as possible. The resulting catalog of mutational sites constitutes a system with up to 5 times as many sites for monitoring each of the six base substitution mutations as the widely used rpoB/Rifr system. We have defined 75 sites for the G:C -> A:T transition, 68 sites for the G:C -> T:A transversion, 53 sites for the G:C -> C:G transversion, 49 sites for the A:T -> G:C transition, 39 sites for the A:T -> T:A transversion, and 59 sites for the A:T -> C:G transversion. The system is thus comprised of 343 base substitution mutations at 232 different base pairs, all of which can be sequenced with a single primer pair. This allows for the examination of mutational spectra using a more detailed probe of known mutations, while still allowing one to compare the number of repeated occurrences at specific sites. We have examined several mutagens and mutators with this system, and show its utility by looking at the spectrum of cisplatin, that has a single hotspot, underscoring the value of having as large an array of sites as possible at which one can monitor repeat occurrences. To test for regions of the gene that might be hotspots for a number of mutagens, or "hot" (mutaphilic) regions, we have looked at the ratio of mutations per set of an equal number of mutational sites throughout the gene. The resulting graphs suggest that there are "hot" regions at intervals, and this may reflect aspects of secondary structures, of the higher order structure of the chromosome, or perhaps the nucleoid structure of the chromosome plus histone-like protein complexes.
Collapse
Affiliation(s)
- Daniel Mashiach
- Department of Microbiology, Immunology, and Molecular Genetics, and The Molecular Biology Institute, University of California, and the David Geffen School of Medicine, Los Angeles, CA 90095, United States
| | - Erin Mae Bacasen
- Department of Microbiology, Immunology, and Molecular Genetics, and The Molecular Biology Institute, University of California, and the David Geffen School of Medicine, Los Angeles, CA 90095, United States
| | - Sunjum Singh
- Department of Microbiology, Immunology, and Molecular Genetics, and The Molecular Biology Institute, University of California, and the David Geffen School of Medicine, Los Angeles, CA 90095, United States
| | - Timothy Kao
- Department of Microbiology, Immunology, and Molecular Genetics, and The Molecular Biology Institute, University of California, and the David Geffen School of Medicine, Los Angeles, CA 90095, United States
| | - Lekha Yaramada
- Department of Microbiology, Immunology, and Molecular Genetics, and The Molecular Biology Institute, University of California, and the David Geffen School of Medicine, Los Angeles, CA 90095, United States
| | - Daniel Mishail
- Department of Microbiology, Immunology, and Molecular Genetics, and The Molecular Biology Institute, University of California, and the David Geffen School of Medicine, Los Angeles, CA 90095, United States
| | - Summer Singh
- Department of Microbiology, Immunology, and Molecular Genetics, and The Molecular Biology Institute, University of California, and the David Geffen School of Medicine, Los Angeles, CA 90095, United States
| | - Jeffrey H Miller
- Department of Microbiology, Immunology, and Molecular Genetics, and The Molecular Biology Institute, University of California, and the David Geffen School of Medicine, Los Angeles, CA 90095, United States.
| |
Collapse
|
6
|
Cheng Z, Vermeulen M, Rollins-Green M, DeVeale B, Babak T. Cis-regulatory mutations with driver hallmarks in major cancers. iScience 2021; 24:102144. [PMID: 33665563 PMCID: PMC7903341 DOI: 10.1016/j.isci.2021.102144] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 09/02/2020] [Accepted: 01/25/2021] [Indexed: 12/05/2022] Open
Abstract
Despite the recent availability of complete genome sequences of tumors from thousands of patients, isolating disease-causing (driver) non-coding mutations from the plethora of somatic variants remains challenging, and only a handful of validated examples exist. By integrating whole-genome sequencing, genetic data, and allele-specific gene expression from TCGA, we identified 320 somatic non-coding mutations that affect gene expression in cis (FDR<0.25). These mutations cluster into 47 cis-regulatory elements that modulate expression of their subject genes through diverse molecular mechanisms. We further show that these mutations have hallmark features of non-coding drivers; namely, that they preferentially disrupt transcription factor binding motifs, are associated with a selective advantage, increased oncogene expression and decreased tumor suppressor expression. Enrichment of functional non-coding somatic mutations predicts drivers Elevated variant allele frequencies are consistent with roles in tumorigenesis Putative non-coding drivers disrupt transcription factor binding motifs Predicted drivers associate with increased oncogene and decreased TSG expression
Collapse
Affiliation(s)
- Zhongshan Cheng
- Department of Biology, Queen's University, Kingston, ON K7L 3N6, Canada
| | - Michael Vermeulen
- Department of Biology, Queen's University, Kingston, ON K7L 3N6, Canada
| | | | - Brian DeVeale
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Tomas Babak
- Department of Biology, Queen's University, Kingston, ON K7L 3N6, Canada
| |
Collapse
|
7
|
Sun W, Jiang C, Ji Y, Xiao C, Song H. Long Noncoding RNAs: New Regulators of Resistance to Systemic Therapies for Gastric Cancer. BIOMED RESEARCH INTERNATIONAL 2021; 2021:8853269. [PMID: 33506041 PMCID: PMC7808844 DOI: 10.1155/2021/8853269] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 12/07/2020] [Accepted: 12/19/2020] [Indexed: 02/07/2023]
Abstract
Gastric cancer (GC) is the second leading cause of cancer mortality and the fourth most commonly diagnosed malignant disease, with approximately 951,000 new cases diagnosed and approximately 723,000 cases of mortality each year. The highest mortality rate of GC is in East Asia, and the lowest is in North America. A large number of studies have demonstrated that GC patients are characterized by higher morbidity, metastasis rates, and mortality and lower early diagnosis rates, radical resection rates, and 5-year survival rates. All cases of GC can be divided into two important stages, namely, early- and advanced-stage GC, and the stage mainly determines the treatment strategy for and the therapeutic effect in GC patients. Patients with early-stage GC undergo radical surgery followed by chemotherapy, and the 5-year survival rate can be as high as 90%. However, patients with advanced-stage GC cannot undergo radical surgery because they are at risk for metastasis; therefore, they can choose only radiotherapy or chemotherapy and have a poor prognosis. Based on the lack of specific clinical manifestations and detection methods, most GC patients (>70%) are diagnosed in the advanced stage; therefore, continued efforts toward developing treatments have been focused on advanced-stage GC patients and include molecular targeted therapy, immunotherapy, and small molecular therapy. Nevertheless, in recent years, accumulating evidence has indicated that small molecules, especially long noncoding RNAs (lncRNAs), are involved in the occurrence, development, and progression of GC, and their abundantly dysregulated expression has been identified in GC tissues and cell lines. Therefore, lncRNAs are considered easily detectable molecules and ideal biomarkers or target-specific agents for the future diagnosis or treatment of GC. In this review, we primarily discuss the status of GC, the role of lncRNAs in GC, and the emerging systemic treatments for GC.
Collapse
Affiliation(s)
- Weihong Sun
- Department of Internal Medicine-Oncology Affiliated Qingdao Central Hospital, Qingdao University, 127 Siliu South Road, Qingdao 266042, China
- Department of Internal Medicine-Oncology Qingdao Tumor Hospital, 127 Siliu South Road, Qingdao 266042, China
| | - Changqing Jiang
- Department of Pathology Qingdao Municipal Hospital, Donghai Middle Road, Qingdao 266071, China
| | - Ying Ji
- Department of Internal Medicine-Oncology Affiliated Qingdao Central Hospital, Qingdao University, 127 Siliu South Road, Qingdao 266042, China
- Department of Internal Medicine-Oncology Qingdao Tumor Hospital, 127 Siliu South Road, Qingdao 266042, China
| | - Chao Xiao
- Department of Internal Medicine-Oncology Affiliated Qingdao Central Hospital, Qingdao University, 127 Siliu South Road, Qingdao 266042, China
- Department of Internal Medicine-Oncology Qingdao Tumor Hospital, 127 Siliu South Road, Qingdao 266042, China
| | - Haiping Song
- Department of Internal Medicine-Oncology Affiliated Qingdao Central Hospital, Qingdao University, 127 Siliu South Road, Qingdao 266042, China
- Department of Internal Medicine-Oncology Qingdao Tumor Hospital, 127 Siliu South Road, Qingdao 266042, China
| |
Collapse
|
8
|
Martinez-Ledesma E, Flores D, Trevino V. Computational methods for detecting cancer hotspots. Comput Struct Biotechnol J 2020; 18:3567-3576. [PMID: 33304455 PMCID: PMC7711189 DOI: 10.1016/j.csbj.2020.11.020] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 11/12/2020] [Accepted: 11/13/2020] [Indexed: 12/14/2022] Open
Abstract
Cancer mutations that are recurrently observed among patients are known as hotspots. Hotspots are highly relevant because they are, presumably, likely functional. Known hotspots in BRAF, PIK3CA, TP53, KRAS, IDH1 support this idea. However, hundreds of hotspots have never been validated experimentally. The detection of hotspots nevertheless is challenging because background mutations obscure their statistical and computational identification. Although several algorithms have been applied to identify hotspots, they have not been reviewed before. Thus, in this mini-review, we summarize more than 40 computational methods applied to detect cancer hotspots in coding and non-coding DNA. We first organize the methods in cluster-based, 3D, position-specific, and miscellaneous to provide a general overview. Then, we describe their embed procedures, implementations, variations, and differences. Finally, we discuss some advantages, provide some ideas for future developments, and mention opportunities such as application to viral integrations, translocations, and epigenetics.
Collapse
Affiliation(s)
- Emmanuel Martinez-Ledesma
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Bioinformática y Diagnóstico Clínico, Monterrey, Nuevo León, Mexico
| | - David Flores
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Bioinformática y Diagnóstico Clínico, Monterrey, Nuevo León, Mexico
- Universidad del Caribe, Departamento de Ciencias Básicas e Ingenierías, Cancún, Quintana Roo, Mexico
| | - Victor Trevino
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Bioinformática y Diagnóstico Clínico, Monterrey, Nuevo León, Mexico
| |
Collapse
|
9
|
Genomic Instability Signature of Palindromic Non-Coding Somatic Mutations in Bladder Cancer. Cancers (Basel) 2020; 12:cancers12102882. [PMID: 33049910 PMCID: PMC7650671 DOI: 10.3390/cancers12102882] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 10/01/2020] [Accepted: 10/03/2020] [Indexed: 02/07/2023] Open
Abstract
Numerous pan-genomic studies identified alterations in protein-coding genes and signaling pathways involved in bladder carcinogenesis, while non-coding somatic alterations remain weakly explored. The goal of this study was to identify clinical biomarkers in non-coding regions for bladder cancer patients. We have previously identified in bladder tumors two non-coding mutational hotspots occurring at high frequencies (≥30%). These mutations are located close to the GPR126 and PLEKHS1 genes, at the guanine or the cytosine of a TGAACA core motif flanked, on both sides, by a stretch of palindromic sequences. Here, we hypothesize that such a pattern of recurrent non-coding mutations could be a signature of somatic genomic instability specifically involved in bladder cancer. We analyzed 26 additional mutable non-coding sites with the same core motif in a cohort of 103 bladder cancers composed of 44 NMIBC cases and 59 MIBC cases using high-resolution melting (HRM) and Sanger sequencing. Five bladder cancers were additionally analyzed for protein-coding gene mutations using a targeted NGS panel composed of 571 genes. Expression levels of three members of the APOBEC3 family genes were assessed using real-time quantitative RT-PCR. Non-coding somatic mutations were observed for at least one TGAACA core motif locus in 62.1% (64/103) of bladder tumor samples. These non-coding mutations co-occurred in the bladder tumors but were absent in prostate tumor, HPV-positive Head and Neck Squamous Cell Carcinoma, and high microsatellite instability (MSI-H) colorectal tumor series. This signature of palindromic non-coding somatic mutations, specific to bladder tumors, was not associated with patients' outcome and was more frequent in females. Interestingly, this signature was associated with high tumor mutational burden (TMB) and high expression levels of APOBEC3B and interferon inducible genes. We identified a new type of somatic genomic instability targeting the TGAACA core motif loci flanked by palindromic sequences in bladder cancer. This mutational signature is a promising candidate clinical biomarker for the early detection of relapse and a major low-cost alternative to the TMB to monitor the response to immunotherapy for bladder cancer patients.
Collapse
|
10
|
Turnbull RE, Fairall L, Saleh A, Kelsall E, Morris KL, Ragan TJ, Savva CG, Chandru A, Millard CJ, Makarova OV, Smith CJ, Roseman AM, Fry AM, Cowley SM, Schwabe JWR. The MiDAC histone deacetylase complex is essential for embryonic development and has a unique multivalent structure. Nat Commun 2020; 11:3252. [PMID: 32591534 PMCID: PMC7319964 DOI: 10.1038/s41467-020-17078-8] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 06/05/2020] [Indexed: 12/31/2022] Open
Abstract
MiDAC is one of seven distinct, large multi-protein complexes that recruit class I histone deacetylases to the genome to regulate gene expression. Despite implications of involvement in cell cycle regulation and in several cancers, surprisingly little is known about the function or structure of MiDAC. Here we show that MiDAC is important for chromosome alignment during mitosis in cancer cell lines. Mice lacking the MiDAC proteins, DNTTIP1 or MIDEAS, die with identical phenotypes during late embryogenesis due to perturbations in gene expression that result in heart malformation and haematopoietic failure. This suggests that MiDAC has an essential and unique function that cannot be compensated by other HDAC complexes. Consistent with this, the cryoEM structure of MiDAC reveals a unique and distinctive mode of assembly. Four copies of HDAC1 are positioned at the periphery with outward-facing active sites suggesting that the complex may target multiple nucleosomes implying a processive deacetylase function.
Collapse
Affiliation(s)
- Robert E Turnbull
- Leicester Institute of Structural and Chemical Biology, University of Leicester, Leicester, LE1 7RH, UK
- Department of Molecular and Cell Biology, University of Leicester, Leicester, LE1 7RH, UK
| | - Louise Fairall
- Leicester Institute of Structural and Chemical Biology, University of Leicester, Leicester, LE1 7RH, UK
- Department of Molecular and Cell Biology, University of Leicester, Leicester, LE1 7RH, UK
| | - Almutasem Saleh
- Leicester Institute of Structural and Chemical Biology, University of Leicester, Leicester, LE1 7RH, UK
- Department of Molecular and Cell Biology, University of Leicester, Leicester, LE1 7RH, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College, Hammersmith Hospital Campus, Du Cane Road, London, W12 0HS, UK
| | - Emma Kelsall
- Department of Molecular and Cell Biology, University of Leicester, Leicester, LE1 7RH, UK
- AstraZeneca, Milstein Building, Granta Park, Cambridge, CB21 6GH, UK
| | - Kyle L Morris
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
- MRC London Institute of Medical Sciences, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - T J Ragan
- Leicester Institute of Structural and Chemical Biology, University of Leicester, Leicester, LE1 7RH, UK
| | - Christos G Savva
- Leicester Institute of Structural and Chemical Biology, University of Leicester, Leicester, LE1 7RH, UK
| | - Aditya Chandru
- Department of Molecular and Cell Biology, University of Leicester, Leicester, LE1 7RH, UK
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK
| | - Christopher J Millard
- Leicester Institute of Structural and Chemical Biology, University of Leicester, Leicester, LE1 7RH, UK
- Department of Molecular and Cell Biology, University of Leicester, Leicester, LE1 7RH, UK
| | - Olga V Makarova
- Department of Molecular and Cell Biology, University of Leicester, Leicester, LE1 7RH, UK
| | - Corinne J Smith
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Alan M Roseman
- Division of Molecular and Cellular Function, University of Manchester, Manchester, M13 9PL, UK
| | - Andrew M Fry
- Department of Molecular and Cell Biology, University of Leicester, Leicester, LE1 7RH, UK
| | - Shaun M Cowley
- Department of Molecular and Cell Biology, University of Leicester, Leicester, LE1 7RH, UK.
| | - John W R Schwabe
- Leicester Institute of Structural and Chemical Biology, University of Leicester, Leicester, LE1 7RH, UK.
- Department of Molecular and Cell Biology, University of Leicester, Leicester, LE1 7RH, UK.
| |
Collapse
|
11
|
Fernandez K, D'Souza S, Ahn JJ, Singh S, Bacasen EM, Mashiach D, Mishail D, Kao T, Thai J, Hwang S, Yaramada L, Miller JH. Mutations induced by Bleomycin, 4-nitroquinoline-1-oxide, and hydrogen peroxide in the rpoB gene of Escherichia coli: Perspective on Mutational Hotspots. Mutat Res 2020; 821:111702. [PMID: 32422468 DOI: 10.1016/j.mrfmmm.2020.111702] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 02/05/2020] [Accepted: 03/11/2020] [Indexed: 06/11/2023]
Abstract
We report the mutational spectra in a segment of the E. coli rpoB gene of bleomycin (BLEO), 4-nitroquinoline-1-oxide (NQO), and hydrogen peroxide (H2O2). We compare these spectra with those of other mutagens and repair deficient strains in the same rpoB system, and review the key elements determining mutational hotspots and outline the questions that remain unanswered. We consider three tiers of hotspots that derive from 1) the nature of the sequence change at a specific base, 2) the direct nearest neighbors and 3) some aspect of the larger sequence context or the local 3D-structure of segments of DNA. This latter tier can have a profound effect on mutation frequencies, even among sites with identical nearest neighbor sequences. BLEO is dependent on the SOS-induced translesion Pol V for mutagenesis, and has a dramatic hotspot at a single mutational site in rpoB. NQO is not dependent on any of the translesion polymerases, in contrast to findings with plasmids treated in vitro and transformed into E. coli. The rpoB system allows one to monitor both G:C -> A:T transitions and G:C -> T:A transversions at the same site in 11 cases, each site having the identical sequence context for each of the two mutations. The combined preference for G:C -> A:T transitions at these sites is 20-fold. Several of the favored sites for hydrogen peroxide mutagenesis are not seen in the spectra of BLEO and NQO mutations, indicating that mutagenesis from reactive oxygen species is not a major cause of BLEO or NQO mutagenesis, but rather specific adducts. The variance in mutation rates at sites with identical nearest neighbors suggests that the local structure of different DNA segments is an important factor in mutational hotspots.
Collapse
Affiliation(s)
- Kristen Fernandez
- Department of Microbiology, Immunology, and Molecular Genetics, and the Molecular Biology Institute, University of California, and the David Geffen School of Medicine, Los Angeles, CA 90095, United States
| | - Sara D'Souza
- Department of Microbiology, Immunology, and Molecular Genetics, and the Molecular Biology Institute, University of California, and the David Geffen School of Medicine, Los Angeles, CA 90095, United States
| | - Jenny J Ahn
- Department of Microbiology, Immunology, and Molecular Genetics, and the Molecular Biology Institute, University of California, and the David Geffen School of Medicine, Los Angeles, CA 90095, United States
| | - Summer Singh
- Department of Microbiology, Immunology, and Molecular Genetics, and the Molecular Biology Institute, University of California, and the David Geffen School of Medicine, Los Angeles, CA 90095, United States
| | - Erin Mae Bacasen
- Department of Microbiology, Immunology, and Molecular Genetics, and the Molecular Biology Institute, University of California, and the David Geffen School of Medicine, Los Angeles, CA 90095, United States
| | - Daniel Mashiach
- Department of Microbiology, Immunology, and Molecular Genetics, and the Molecular Biology Institute, University of California, and the David Geffen School of Medicine, Los Angeles, CA 90095, United States
| | - Daniel Mishail
- Department of Microbiology, Immunology, and Molecular Genetics, and the Molecular Biology Institute, University of California, and the David Geffen School of Medicine, Los Angeles, CA 90095, United States
| | - Timothy Kao
- Department of Microbiology, Immunology, and Molecular Genetics, and the Molecular Biology Institute, University of California, and the David Geffen School of Medicine, Los Angeles, CA 90095, United States
| | - Jasmine Thai
- Department of Microbiology, Immunology, and Molecular Genetics, and the Molecular Biology Institute, University of California, and the David Geffen School of Medicine, Los Angeles, CA 90095, United States
| | - Spring Hwang
- Department of Microbiology, Immunology, and Molecular Genetics, and the Molecular Biology Institute, University of California, and the David Geffen School of Medicine, Los Angeles, CA 90095, United States
| | - Lekha Yaramada
- Department of Microbiology, Immunology, and Molecular Genetics, and the Molecular Biology Institute, University of California, and the David Geffen School of Medicine, Los Angeles, CA 90095, United States
| | - Jeffrey H Miller
- Department of Microbiology, Immunology, and Molecular Genetics, and the Molecular Biology Institute, University of California, and the David Geffen School of Medicine, Los Angeles, CA 90095, United States.
| |
Collapse
|
12
|
Corona RI, Seo JH, Lin X, Hazelett DJ, Reddy J, Fonseca MAS, Abassi F, Lin YG, Mhawech-Fauceglia PY, Shah SP, Huntsman DG, Gusev A, Karlan BY, Berman BP, Freedman ML, Gayther SA, Lawrenson K. Non-coding somatic mutations converge on the PAX8 pathway in ovarian cancer. Nat Commun 2020; 11:2020. [PMID: 32332753 PMCID: PMC7181647 DOI: 10.1038/s41467-020-15951-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 03/31/2020] [Indexed: 02/07/2023] Open
Abstract
The functional consequences of somatic non-coding mutations in ovarian cancer (OC) are unknown. To identify regulatory elements (RE) and genes perturbed by acquired non-coding variants, here we establish epigenomic and transcriptomic landscapes of primary OCs using H3K27ac ChIP-seq and RNA-seq, and then integrate these with whole genome sequencing data from 232 OCs. We identify 25 frequently mutated regulatory elements, including an enhancer at 6p22.1 which associates with differential expression of ZSCAN16 (P = 6.6 × 10-4) and ZSCAN12 (P = 0.02). CRISPR/Cas9 knockout of this enhancer induces downregulation of both genes. Globally, there is an enrichment of single nucleotide variants in active binding sites for TEAD4 (P = 6 × 10-11) and its binding partner PAX8 (P = 2×10-10), a known lineage-specific transcription factor in OC. In addition, the collection of cis REs associated with PAX8 comprise the most frequently mutated set of enhancers in OC (P = 0.003). These data indicate that non-coding somatic mutations disrupt the PAX8 transcriptional network during OC development.
Collapse
Affiliation(s)
- Rosario I Corona
- Cedars-Sinai Women's Cancer Program at the Samuel Oschin Cancer Center, Los Angeles, CA, USA
- Center for Bioinformatics and Functional Genomics, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Ji-Heui Seo
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Xianzhi Lin
- Cedars-Sinai Women's Cancer Program at the Samuel Oschin Cancer Center, Los Angeles, CA, USA
| | - Dennis J Hazelett
- Center for Bioinformatics and Functional Genomics, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Jessica Reddy
- Cedars-Sinai Women's Cancer Program at the Samuel Oschin Cancer Center, Los Angeles, CA, USA
| | - Marcos A S Fonseca
- Cedars-Sinai Women's Cancer Program at the Samuel Oschin Cancer Center, Los Angeles, CA, USA
| | - Forough Abassi
- Cedars-Sinai Women's Cancer Program at the Samuel Oschin Cancer Center, Los Angeles, CA, USA
| | - Yvonne G Lin
- Department of Obstetrics and Gynecology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | | | - Sohrab P Shah
- Department of Computer Science, University of British Columbia, Vancouver, BC, Canada
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - David G Huntsman
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
- Department of Gynecology and Obstetrics, University of British Columbia, Vancouver, BC, Canada
| | - Alexander Gusev
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- McGraw/Patterson Center for Population Sciences, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Beth Y Karlan
- Cedars-Sinai Women's Cancer Program at the Samuel Oschin Cancer Center, Los Angeles, CA, USA
| | - Benjamin P Berman
- Center for Bioinformatics and Functional Genomics, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Matthew L Freedman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA.
- The Eli and Edythe L. Broad Institute, Cambridge, MA, USA.
| | - Simon A Gayther
- Cedars-Sinai Women's Cancer Program at the Samuel Oschin Cancer Center, Los Angeles, CA, USA.
- Center for Bioinformatics and Functional Genomics, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
| | - Kate Lawrenson
- Cedars-Sinai Women's Cancer Program at the Samuel Oschin Cancer Center, Los Angeles, CA, USA.
- Center for Bioinformatics and Functional Genomics, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
| |
Collapse
|
13
|
Structural basis for adhesion G protein-coupled receptor Gpr126 function. Nat Commun 2020; 11:194. [PMID: 31924782 PMCID: PMC6954182 DOI: 10.1038/s41467-019-14040-1] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 12/11/2019] [Indexed: 12/11/2022] Open
Abstract
Many drugs target the extracellular regions (ECRs) of cell-surface receptors. The large and alternatively-spliced ECRs of adhesion G protein-coupled receptors (aGPCRs) have key functions in diverse biological processes including neurodevelopment, embryogenesis, and tumorigenesis. However, their structures and mechanisms of action remain unclear, hampering drug development. The aGPCR Gpr126/Adgrg6 regulates Schwann cell myelination, ear canal formation, and heart development; and GPR126 mutations cause myelination defects in human. Here, we determine the structure of the complete zebrafish Gpr126 ECR and reveal five domains including a previously unknown domain. Strikingly, the Gpr126 ECR adopts a closed conformation that is stabilized by an alternatively spliced linker and a conserved calcium-binding site. Alternative splicing regulates ECR conformation and receptor signaling, while mutagenesis of the calcium-binding site abolishes Gpr126 function in vivo. These results demonstrate that Gpr126 ECR utilizes a multi-faceted dynamic approach to regulate receptor function and provide relevant insights for ECR-targeted drug design. The extracellular regions (ECRs) of adhesion GPCRs have diverse biological functions, but their structures and mechanisms of action remain unclear. Here, the authors solve the ECR structure of the Gpr126 receptor and show that ECR conformation and signaling functions are regulated by alternative splicing.
Collapse
|
14
|
Cesar ASM, Regitano LCA, Reecy JM, Poleti MD, Oliveira PSN, de Oliveira GB, Moreira GCM, Mudadu MA, Tizioto PC, Koltes JE, Fritz-Waters E, Kramer L, Garrick D, Beiki H, Geistlinger L, Mourão GB, Zerlotini A, Coutinho LL. Identification of putative regulatory regions and transcription factors associated with intramuscular fat content traits. BMC Genomics 2018; 19:499. [PMID: 29945546 PMCID: PMC6020320 DOI: 10.1186/s12864-018-4871-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 06/14/2018] [Indexed: 12/21/2022] Open
Abstract
Background Integration of high throughput DNA genotyping and RNA-sequencing data allows for the identification of genomic regions that control gene expression, known as expression quantitative trait loci (eQTL), on a whole genome scale. Intramuscular fat (IMF) content and carcass composition play important roles in metabolic and physiological processes in mammals because they influence insulin sensitivity and consequently prevalence of metabolic diseases such as obesity and type 2 diabetes. However, limited information is available on the genetic variants and mechanisms associated with IMF deposition in mammals. Thus, our hypothesis was that eQTL analyses could identify putative regulatory regions and transcription factors (TFs) associated with intramuscular fat (IMF) content traits. Results We performed an integrative eQTL study in skeletal muscle to identify putative regulatory regions and factors associated with intramuscular fat content traits. Data obtained from skeletal muscle samples of 192 animals was used for association analysis between 461,466 SNPs and the transcription level of 11,808 genes. This yielded 1268 cis- and 10,334 trans-eQTLs, among which we identified nine hotspot regions that each affected the expression of > 119 genes. These putative regulatory regions overlapped with previously identified QTLs for IMF content. Three of the hotspots respectively harbored the transcription factors USF1, EGR4 and RUNX1T1, which are known to play important roles in lipid metabolism. From co-expression network analysis, we further identified modules significantly correlated with IMF content and associated with relevant processes such as fatty acid metabolism, carbohydrate metabolism and lipid metabolism. Conclusion This study provides novel insights into the link between genotype and IMF content as evident from the expression level. It thereby identifies genomic regions of particular importance and associated regulatory factors. These new findings provide new knowledge about the biological processes associated with genetic variants and mechanisms associated with IMF deposition in mammals. Electronic supplementary material The online version of this article (10.1186/s12864-018-4871-y) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Aline S M Cesar
- Department of Animal Science, University of São Paulo, Piracicaba, SP, 13418-900, Brazil.,Department of Animal Science, Iowa State University, Ames, IA, 50011, USA
| | | | - James M Reecy
- Department of Animal Science, Iowa State University, Ames, IA, 50011, USA
| | - Mirele D Poleti
- Department of Animal Science, University of São Paulo, Piracicaba, SP, 13418-900, Brazil
| | | | | | - Gabriel C M Moreira
- Department of Animal Science, University of São Paulo, Piracicaba, SP, 13418-900, Brazil
| | | | - Polyana C Tizioto
- Department of Animal Science, University of São Paulo, Piracicaba, SP, 13418-900, Brazil
| | - James E Koltes
- Department of Animal Science, Iowa State University, Ames, IA, 50011, USA
| | - Elyn Fritz-Waters
- Department of Animal Science, Iowa State University, Ames, IA, 50011, USA
| | - Luke Kramer
- Department of Animal Science, Iowa State University, Ames, IA, 50011, USA
| | - Dorian Garrick
- School of Agriculture, Massey University, Ruakura, Hamilton, New Zealand
| | - Hamid Beiki
- Department of Animal Science, Iowa State University, Ames, IA, 50011, USA
| | | | - Gerson B Mourão
- Department of Animal Science, University of São Paulo, Piracicaba, SP, 13418-900, Brazil
| | | | - Luiz L Coutinho
- Department of Animal Science, University of São Paulo, Piracicaba, SP, 13418-900, Brazil.
| |
Collapse
|
15
|
Chakravorty S, Hegde M. Inferring the effect of genomic variation in the new era of genomics. Hum Mutat 2018; 39:756-773. [PMID: 29633501 DOI: 10.1002/humu.23427] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 03/20/2018] [Accepted: 03/28/2018] [Indexed: 12/11/2022]
Abstract
Accurate and detailed understanding of the effects of variants in the coding and noncoding regions of the genome is the next big challenge in the new genomic era of personalized medicine, especially to tackle newer findings of genetic and phenotypic heterogeneity of diseases. This is necessary to resolve the gene-variant-disease relationship, the pathogenic variant spectrum of genes, pathogenic variants with variable clinical consequences, and multiloci diseases. In turn, this will facilitate patient recruitment for relevant clinical trials. In this review, we describe the trends in research at the intersection of basic and clinical genomics aiming to (a) overcome molecular diagnostic challenges and increase the clinical utility of next-generation sequencing (NGS) platforms, (b) elucidate variants associated with disease, (c) determine overall genomic complexity including epistasis, complex inheritance patterns such as "synergistic heterozygosity," digenic/multigenic inheritance, modifier effect, and rare variant load. We describe the newly emerging field of integrated functional genomics, in vivo or in vitro large-scale functional approaches, statistical bioinformatics algorithms that support NGS genomics data to interpret variants for timely clinical diagnostics and disease management. Thus, facilitating the discovery of new therapeutic or biomarker options, and their roles in the future of personalized medicine.
Collapse
Affiliation(s)
- Samya Chakravorty
- Department of Human Genetics, Emory University School of Medicine, Whitehead Biomedical Research Building Suite 301, Atlanta, Georgia
| | - Madhuri Hegde
- Department of Human Genetics, Emory University School of Medicine, Whitehead Biomedical Research Building Suite 301, Atlanta, Georgia
| |
Collapse
|
16
|
Singh B, Trincado JL, Tatlow PJ, Piccolo SR, Eyras E. Genome Sequencing and RNA-Motif Analysis Reveal Novel Damaging Noncoding Mutations in Human Tumors. Mol Cancer Res 2018; 16:1112-1124. [DOI: 10.1158/1541-7786.mcr-17-0601] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 01/26/2018] [Accepted: 03/16/2018] [Indexed: 11/16/2022]
|
17
|
Gan KA, Carrasco Pro S, Sewell JA, Fuxman Bass JI. Identification of Single Nucleotide Non-coding Driver Mutations in Cancer. Front Genet 2018; 9:16. [PMID: 29456552 PMCID: PMC5801294 DOI: 10.3389/fgene.2018.00016] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 01/12/2018] [Indexed: 12/14/2022] Open
Abstract
Recent whole-genome sequencing studies have identified millions of somatic variants present in tumor samples. Most of these variants reside in non-coding regions of the genome potentially affecting transcriptional and post-transcriptional gene regulation. Although a few hallmark examples of driver mutations in non-coding regions have been reported, the functional role of the vast majority of somatic non-coding variants remains to be determined. This is because the few driver variants in each sample must be distinguished from the thousands of passenger variants and because the logic of regulatory element function has not yet been fully elucidated. Thus, variants prioritized based on mutational burden and location within regulatory elements need to be validated experimentally. This is generally achieved by combining assays that measure physical binding, such as chromatin immunoprecipitation, with those that determine regulatory activity, such as luciferase reporter assays. Here, we present an overview of in silico approaches used to prioritize somatic non-coding variants and the experimental methods used for functional validation and characterization.
Collapse
Affiliation(s)
- Kok A Gan
- Department of Biology, Boston University, Boston, MA, United States
| | | | - Jared A Sewell
- Department of Biology, Boston University, Boston, MA, United States
| | | |
Collapse
|
18
|
Abstract
microRNAs (miRNAs) are a small RNA species without protein-coding potential. However, they are key modulators of protein translation. Many studies have linked miRNAs with cancer initiation, progression, diagnosis, and prognosis, and recent studies have also linked them with cancer etiology and susceptibility, especially through single-nucleotide polymorphisms (SNPs). This review discusses some of the recent advances in miRNA-SNP literature-including SNPs in miRNA genes, miRNA target sites, and the processing machinery. In addition, we highlight some emerging areas of interest, including isomiRs and non-3'UTR focused miRNA-binding mechanisms that could provide further novel insight into the relationship between miR-SNPs and cancer. Finally, we note that additional epidemiological and experimental research is needed to close the gap in our understanding of the genotype-phenotype relationship between miRNA-SNPs and cancer.
Collapse
Affiliation(s)
- Bríd M Ryan
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, United States.
| |
Collapse
|