1
|
Doi-Tanaka Y, Tamura I, Shiroshita A, Fujimura T, Shirafuta Y, Maekawa R, Taketani T, Sato S, Sugino N. Differential gene expression in decidualized human endometrial stromal cells induced by different stimuli. Sci Rep 2024; 14:7726. [PMID: 38565619 PMCID: PMC10987566 DOI: 10.1038/s41598-024-58065-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 03/25/2024] [Indexed: 04/04/2024] Open
Abstract
Decidualization can be induced by culturing human endometrial stromal cells (ESCs) with several decidualization stimuli, such as cAMP, medroxyprogesterone acetate (MPA) or Estradiol (E2). However, it has been unclear how decidualized cells induced by different stimuli are different. We compared transcriptomes and cellular functions of decidualized ESCs induced by different stimuli (MPA, E2 + MPA, cAMP, and cAMP + MPA). We also investigated which decidualization stimulus induces a closer in vivo decidualization. Differentially expressed genes (DEGs) and altered cellular functions by each decidualization stimuli were identified by RNA-sequence and gene-ontology analysis. DEGs was about two times higher for stimuli that use cAMP (cAMP and cAMP + MPA) than for stimuli that did not use cAMP (MPA and E2 + MPA). cAMP-using stimuli altered the cellular functions including angiogenesis, inflammation, immune system, and embryo implantation whereas MPA-using stimuli (MPA, E2 + MPA, and cAMP + MPA) altered the cellular functions associated with insulin signaling. A public single-cell RNA-sequence data of the human endometrium was utilized to analyze in vivo decidualization. The altered cellular functions by in vivo decidualization were close to those observed by cAMP + MPA-induced decidualization. In conclusion, decidualized cells induced by different stimuli have different transcriptome and cellular functions. cAMP + MPA may induce a decidualization most closely to in vivo decidualization.
Collapse
Affiliation(s)
- Yumiko Doi-Tanaka
- Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Minamikogushi 1-1-1, Ube, 755-8505, Japan
| | - Isao Tamura
- Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Minamikogushi 1-1-1, Ube, 755-8505, Japan.
| | - Amon Shiroshita
- Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Minamikogushi 1-1-1, Ube, 755-8505, Japan
| | - Taishi Fujimura
- Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Minamikogushi 1-1-1, Ube, 755-8505, Japan
| | - Yuichiro Shirafuta
- Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Minamikogushi 1-1-1, Ube, 755-8505, Japan
| | - Ryo Maekawa
- Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Minamikogushi 1-1-1, Ube, 755-8505, Japan
| | - Toshiaki Taketani
- Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Minamikogushi 1-1-1, Ube, 755-8505, Japan
| | - Shun Sato
- Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Minamikogushi 1-1-1, Ube, 755-8505, Japan
| | - Norihiro Sugino
- Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Minamikogushi 1-1-1, Ube, 755-8505, Japan
| |
Collapse
|
2
|
Guo Z, Chu C, Lu Y, Zhang X, Xiao Y, Wu M, Gao S, Wong CCL, Zhan X, Wang C. Structure of a SIN3-HDAC complex from budding yeast. Nat Struct Mol Biol 2023:10.1038/s41594-023-00975-z. [PMID: 37081318 DOI: 10.1038/s41594-023-00975-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 03/23/2023] [Indexed: 04/22/2023]
Abstract
SIN3-HDAC (histone deacetylases) complexes have important roles in facilitating local histone deacetylation to regulate chromatin accessibility and gene expression. Here, we present the cryo-EM structure of the budding yeast SIN3-HDAC complex Rpd3L at an average resolution of 2.6 Å. The structure reveals that two distinct arms (ARM1 and ARM2) hang on a T-shaped scaffold formed by two coiled-coil domains. In each arm, Sin3 interacts with different subunits to create a different environment for the histone deacetylase Rpd3. ARM1 is in the inhibited state with the active site of Rpd3 blocked, whereas ARM2 is in an open conformation with the active site of Rpd3 exposed to the exterior space. The observed asymmetric architecture of Rpd3L is different from those of available structures of other class I HDAC complexes. Our study reveals the organization mechanism of the SIN3-HDAC complex and provides insights into the interaction pattern by which it targets histone deacetylase to chromatin.
Collapse
Affiliation(s)
- Zhouyan Guo
- College of Life Sciences, Zhejiang University, Hangzhou, China
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, China
| | - Chen Chu
- College of Life Sciences, Zhejiang University, Hangzhou, China
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, China
| | - Yichen Lu
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, China
| | - Xiaofeng Zhang
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, China
| | - Yihang Xiao
- Department of Chemistry, School of Science, Westlake University, Hangzhou, China
| | - Mingxuan Wu
- Department of Chemistry, School of Science, Westlake University, Hangzhou, China
| | - Shuaixin Gao
- Human Nutrition Program & James Comprehensive Cancer Center, Ohio State University, Columbus, OH, USA
| | - Catherine C L Wong
- Clinical Research Institute, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
| | - Xiechao Zhan
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China.
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China.
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, China.
| | - Chengcheng Wang
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China.
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China.
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, China.
| |
Collapse
|
3
|
Wang C, Guo Z, Chu C, Lu Y, Zhang X, Zhan X. Two assembly modes for SIN3 histone deacetylase complexes. Cell Discov 2023; 9:42. [PMID: 37076472 PMCID: PMC10115800 DOI: 10.1038/s41421-023-00539-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 03/10/2023] [Indexed: 04/21/2023] Open
Abstract
The switch-independent 3 (SIN3)/histone deacetylase (HDAC) complexes play essential roles in regulating chromatin accessibility and gene expression. There are two major types of SIN3/HDAC complexes (named SIN3L and SIN3S) targeting different chromatin regions. Here we present the cryo-electron microscopy structures of the SIN3L and SIN3S complexes from Schizosaccharomyces pombe (S. pombe), revealing two distinct assembly modes. In the structure of SIN3L, each Sin3 isoform (Pst1 and Pst3) interacts with one histone deacetylase Clr6, and one WD40-containing protein Prw1, forming two lobes. These two lobes are bridged by two vertical coiled-coil domains from Sds3/Dep1 and Rxt2/Png2, respectively. In the structure of SIN3S, there is only one lobe organized by another Sin3 isoform Pst2; each of the Cph1 and Cph2 binds to an Eaf3 molecule, providing two modules for histone recognition and binding. Notably, the Pst1 Lobe in SIN3L and the Pst2 Lobe in SIN3S adopt similar conformation with their deacetylase active sites exposed to the space; however, the Pst3 Lobe in SIN3L is in a compact state with its active center buried inside and blocked. Our work reveals two classical organization mechanisms for the SIN3/HDAC complexes to achieve specific targeting and provides a framework for studying the histone deacetylase complexes.
Collapse
Affiliation(s)
- Chengcheng Wang
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China.
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China.
- Institute of Biology, Westlake Institute for Advanced Study, Westlake University, Hangzhou, Zhejiang, China.
| | - Zhouyan Guo
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Institute of Biology, Westlake Institute for Advanced Study, Westlake University, Hangzhou, Zhejiang, China
| | - Chen Chu
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Institute of Biology, Westlake Institute for Advanced Study, Westlake University, Hangzhou, Zhejiang, China
| | - Yichen Lu
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Institute of Biology, Westlake Institute for Advanced Study, Westlake University, Hangzhou, Zhejiang, China
| | - Xiaofeng Zhang
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Institute of Biology, Westlake Institute for Advanced Study, Westlake University, Hangzhou, Zhejiang, China
| | - Xiechao Zhan
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China.
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China.
- Institute of Biology, Westlake Institute for Advanced Study, Westlake University, Hangzhou, Zhejiang, China.
| |
Collapse
|
4
|
Functional characterization and comparative analysis of gene repression-mediating domains interacting with yeast pleiotropic corepressors Sin3, Cyc8 and Tup1. Curr Genet 2023; 69:127-139. [PMID: 36854981 PMCID: PMC10163088 DOI: 10.1007/s00294-023-01262-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 02/09/2023] [Accepted: 02/12/2023] [Indexed: 03/02/2023]
Abstract
Transcriptional corepressors Sin3, Cyc8 and Tup1 are important for downregulation of gene expression by recruiting various histone deacetylases once they gain access to defined genomic locations by interaction with pathway-specific repressor proteins. In this work we systematically investigated whether 17 yeast repressor proteins (Cti6, Dal80, Fkh1, Gal80, Mig1, Mot3, Nrg1, Opi1, Rdr1, Rox1, Sko1, Ume6, Ure2, Xbp1, Yhp1, Yox1 and Whi5) representing several unrelated regulatory pathways are able to bind to Sin3, Cyc8 and Tup1. Our results show that paired amphipathic helices 1 and 2 (PAH1 and PAH2) of Sin3 are functionally redundant for some regulatory pathways. WD40 domains of Tup1 proved to be sufficient for interaction with repressor proteins. Using length variants of selected repressors, we mapped corepressor interaction domains (CIDs) in vitro and assayed gene repression in vivo. Systematic comparison of CID minimal sequences allowed us to define several related positional patterns of hydrophobic amino acids some of which could be confirmed as functionally supported by site-directed mutagenesis. Although structural predictions indicated that certain CIDs may be α-helical, most repression domains appear to be randomly structured and must be considered as intrinsically disordered regions (IDR) adopting a defined conformation only by interaction with a corepressor.
Collapse
|
5
|
Cifuentes-Bernal AM, Pham VVH, Li X, Liu L, Li J, Duy Le T. Dynamic cancer drivers: a causal approach for cancer driver discovery based on bio-pathological trajectories. Brief Funct Genomics 2022; 21:455-465. [PMID: 36124841 PMCID: PMC10467634 DOI: 10.1093/bfgp/elac030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 08/08/2022] [Accepted: 08/23/2022] [Indexed: 12/14/2022] Open
Abstract
The traditional way for discovering genes which drive cancer (namely cancer drivers) neglects the dynamic information of cancer development, even though it is well known that cancer progresses dynamically. To enhance cancer driver discovery, we expand cancer driver concept to dynamic cancer driver as a gene driving one or more bio-pathological transitions during cancer progression. Our method refers to the fact that cancer should not be considered as a single process but a compendium of altered biological processes causing the disease to develop over time. Reciprocally, different drivers of cancer can potentially be discovered by analysing different bio-pathological pathways. We propose a novel approach for causal inference of genes driving one or more core processes during cancer development (i.e. dynamic cancer driver). We use the concept of pseudotime for inferring the latent progression of samples along a biological transition during cancer and identifying a critical event when such a process is significantly deviated from normal to carcinogenic. We infer driver genes by assessing the causal effect they have on the process after such a critical event. We have applied our method to single-cell and bulk sequencing datasets of breast cancer. The evaluation results show that our method outperforms well-recognized cancer driver inference methods. These results suggest that including information of the underlying dynamics of cancer improves the inference process (in comparison with using static data), and allows us to discover different sets of driver genes from different processes in cancer. R scripts and datasets can be found at https://github.com/AndresMCB/DynamicCancerDriver.
Collapse
Affiliation(s)
- Andres M Cifuentes-Bernal
- UniSA STEM Unit, University of South Australia,
Mawson Lakes Blvd, 5095, South Australia , Australia
| | - Vu V H Pham
- UniSA STEM Unit, University of South Australia,
Mawson Lakes Blvd, 5095, South Australia , Australia
| | - Xiaomei Li
- UniSA STEM Unit, University of South Australia,
Mawson Lakes Blvd, 5095, South Australia , Australia
| | - Lin Liu
- UniSA STEM Unit, University of South Australia,
Mawson Lakes Blvd, 5095, South Australia , Australia
| | - Jiuyong Li
- UniSA STEM Unit, University of South Australia,
Mawson Lakes Blvd, 5095, South Australia , Australia
| | - Thuc Duy Le
- UniSA STEM Unit, University of South Australia,
Mawson Lakes Blvd, 5095, South Australia , Australia
| |
Collapse
|
6
|
Tamura I, Tamura H, Kawamoto-Jozaki M, Shirafuta Y, Fujimura T, Doi-Tanaka Y, Mihara Y, Taketani T, Sugino N. Effects of Melatonin on the Transcriptome of Human Granulosa Cells, Fertilization and Blastocyst Formation. Int J Mol Sci 2022; 23:ijms23126731. [PMID: 35743171 PMCID: PMC9223589 DOI: 10.3390/ijms23126731] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 06/14/2022] [Accepted: 06/14/2022] [Indexed: 01/25/2023] Open
Abstract
Melatonin is a promising reagent that can improve assisted reproductive technology (ART) outcomes in infertility patients. However, melatonin is not effective for all infertile patients, and it remains unclear for which patients melatonin would be effective. This study examined the effects of melatonin on ART outcomes and examined its mechanisms. Melatonin increased the fertilization rate in patients whose fertilization rates in the previous cycle were less than 50%, but not in patients whose fertilization rates were more than 50% in the previous cycle. Melatonin increased the blastocyst formation rate in patients whose embryo development rates in the previous cycle were less than 50%, but not in patients whose embryo development rates were more than 50% in the previous cycle. To clarify its mechanisms, transcriptome changes by melatonin treatment in granulosa cells (GCs) of the patients were examined by RNA-sequence. Melatonin treatment altered the transcriptomes of GCs of patients with poor ART outcomes so that they were similar to the transcriptomes of patients with good ART outcomes. The altered genes were associated with the inhibition of cell death and T-cell activity, and the activation of steroidogenesis and angiogenesis. Melatonin treatment was effective for patients with poor fertilization rates and poor embryo development rates in the previous ART cycle. Melatonin alters the GCs transcriptome and, thus, their functions, and this could improve the oocyte quality, leading to good ART outcomes.
Collapse
Affiliation(s)
| | - Hiroshi Tamura
- Correspondence: ; Tel.: +81-836-22-2288; Fax: +81-836-22-2287
| | | | | | | | | | | | | | | |
Collapse
|
7
|
Davenport ML, Davis MR, Davenport BN, Crossman DK, Hall A, Pike J, Harada S, Hurst DR, Edmonds MD. Suppression of SIN3A by miR-183 Promotes Breast Cancer Metastasis. Mol Cancer Res 2022; 20:883-894. [PMID: 35247910 PMCID: PMC9177717 DOI: 10.1158/1541-7786.mcr-21-0508] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 01/05/2022] [Accepted: 02/18/2022] [Indexed: 12/22/2022]
Abstract
Recent work has established that SWI-independent-3 (SIN3) chromatin modification complexes play key roles in cancer progression. We previously demonstrated that knockdown of SIN3A expression promotes human breast cancer cell invasion and metastasis; however, the levels of SIN3A in patient breast carcinoma are not known. We therefore examined SIN3A mRNA and protein in patient tissues and determined that SIN3A expression is lower in breast carcinoma relative to normal breast. Given the 3'-untranslated region (UTR) of SIN3A has several conserved binding sites for oncogenic miRNA, we hypothesized that SIN3A is targeted by miRNA and found that ectopic miR-183 results in decreased SIN3A in breast carcinoma cell lines. Functionally, we demonstrate that miR-183 promotes breast cancer cell migration and invasion in a SIN3A-dependent manner and ectopic miR-183 promotes metastasis in vivo. Patients with breast cancer with high levels of miR-183 and low levels of SIN3A have the shortest overall survival. Given the critical link between metastasis and survival in patients with breast cancer, it is of utmost importance to identify clinically relevant genes involved in metastasis. Here, we report for the first time the aberrant expression of the putative metastasis suppressing gene SIN3A in human breast cancers and propose a mechanism of SIN3A suppression by miR-183. IMPLICATIONS SIN3A expression is decreased in metastatic breast cancer in part due to miR-183.
Collapse
Affiliation(s)
| | - Mara R. Davis
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Baylea N. Davenport
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - David K. Crossman
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | | | | | - Shuko Harada
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Douglas R. Hurst
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Mick D. Edmonds
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, USA
| |
Collapse
|
8
|
Takagi H, Tamura I, Fujimura T, Doi-Tanaka Y, Shirafuta Y, Mihara Y, Maekawa R, Taketani T, Sato S, Tamura H, Sugino N. Transcriptional coactivator PGC-1α contributes to decidualization by forming a histone-modifying complex with C/EBPβ and p300. J Biol Chem 2022; 298:101874. [PMID: 35358514 PMCID: PMC9048111 DOI: 10.1016/j.jbc.2022.101874] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 03/17/2022] [Accepted: 03/18/2022] [Indexed: 12/17/2022] Open
Abstract
We previously reported that CCAAT/enhancer-binding protein beta (C/EBPβ) is the pioneer factor inducing transcription enhancer mark H3K27 acetylation (H3K27ac) in the promoter and enhancer regions of genes encoding insulin-like growth factor–binding protein-1 (IGFBP-1) and prolactin (PRL) and that this contributes to decidualization of human endometrial stromal cells (ESCs). Peroxisome proliferator–activated receptor gamma coactivator 1-alpha (PGC-1α; PPARGC1A) is a transcriptional coactivator known to regulate H3K27ac. However, although PGC-1α is expressed in ESCs, the potential role of PGC-1α in mediating decidualization is unclear. Here, we investigated the involvement of PGC-1α in the regulation of decidualization. We incubated ESCs with cAMP to induce decidualization and knocked down PPARGC1A to inhibit cAMP-induced expression of IGFBP-1 and PRL. We found cAMP increased the recruitment of PGC-1α and p300 to C/EBPβ-binding sites in the promoter and enhancer regions of IGFBP-1 and PRL, corresponding with increases in H3K27ac. Moreover, PGC-1α knockdown inhibited these increases, suggesting PGC-1α forms a histone-modifying complex with C/EBPβ and p300 at these regions. To further investigate the regulation of PGC-1α, we focused on C/EBPβ upstream of PGC-1α. We found cAMP increased C/EBPβ recruitment to the novel enhancer regions of PPARGC1A. Deletion of these enhancers decreased PGC-1α expression, indicating that C/EBPβ upregulates PGC-1α expression by binding to novel enhancer regions. In conclusion, PGC-1α is upregulated by C/EBPβ recruitment to novel enhancers and contributes to decidualization by forming a histone-modifying complex with C/EBPβ and p300, thereby inducing epigenomic changes in the promoters and enhancers of IGFBP-1 and PRL.
Collapse
Affiliation(s)
- Haruka Takagi
- Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Ube, Japan
| | - Isao Tamura
- Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Ube, Japan.
| | - Taishi Fujimura
- Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Ube, Japan
| | - Yumiko Doi-Tanaka
- Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Ube, Japan
| | - Yuichiro Shirafuta
- Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Ube, Japan
| | - Yumiko Mihara
- Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Ube, Japan
| | - Ryo Maekawa
- Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Ube, Japan
| | - Toshiaki Taketani
- Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Ube, Japan
| | - Shun Sato
- Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Ube, Japan
| | - Hiroshi Tamura
- Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Ube, Japan
| | - Norihiro Sugino
- Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Ube, Japan
| |
Collapse
|
9
|
Nan S, Zhang S, Jin R, Wang J. LINC00665 up-regulates SIN3A expression to modulate the progression of colorectal cancer via sponging miR-138-5p. Cancer Cell Int 2022; 22:51. [PMID: 35101035 PMCID: PMC8802510 DOI: 10.1186/s12935-021-02176-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 08/24/2021] [Indexed: 12/13/2022] Open
Abstract
Background Colorectal cancer (CRC) is a malignant tumor affecting people worldwide. Long noncoding RNAs (lncRNAs) is a crucial factor modulating various cancer progression, including CRC. Long intergenic non-protein coding RNA 665 (LINC00665) has been proven as an oncogene in several cancers, but its function in CRC is still unclear. Methods QRT-PCR was performed for RNA quantification. Functional assays were designed and carried to test cell phenotype while mechanism experiments were adopted for detecting the interaction of LINC00665, microRNA-138-5p (miR-138-5p) and SIN3 transcription regulator family member A (SIN3A). In vivo experiments were conducted to test LINC00665 function on modulating CRC tumor progression. Results LINC00665 displayed high expression in CRC tissues and cells, and promoted tumor progression in vivo. MiR-138-5p displayed abnormally low expression in CRC, and was verified to be sponged by LINC00665. Furthermore, SIN3A, as the downstream mRNA of miR-138-5p, exerted promoting impacts on CRC cells. Rescue experiments certified that overexpressed SIN3A or silenced miR-138-5p could offset the repressed function of LINC00665 knockdown on CRC progression. Conclusions LINC00665 could sponge miR-138-5p to up-regulate SIN3A expression, thus accelerating CRC progression. Graphic abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s12935-021-02176-4.
Collapse
Affiliation(s)
- Shoushan Nan
- Department of Gastroenterology, Tianjin Fifth Center Hospital, No. 41 Zhejiang Road, Binhai New District, Tianjin, 300450, China.
| | - Shuangxia Zhang
- Department of Gastroenterology, Tianjin First Center Hospital, Tianjin, 300384, China
| | - Rong Jin
- Department of Gynaecology and Obstetrics, Tianjin Fifth Center Hospital, Tianjin, 300450, China
| | - Juelei Wang
- Department of Gastroenterology, Tianjin Fifth Center Hospital, No. 41 Zhejiang Road, Binhai New District, Tianjin, 300450, China
| |
Collapse
|
10
|
Ibrahim IH, Abd El-Aziz HG, Amer NNL, Abd El-Sameea HS. Mutational pattern of PIK3CA exon 20 in circulating DNA in breast cancer. Saudi J Biol Sci 2022; 29:2828-2835. [PMID: 35531214 PMCID: PMC9073026 DOI: 10.1016/j.sjbs.2022.01.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 12/28/2021] [Accepted: 01/02/2022] [Indexed: 02/06/2023] Open
Abstract
Breast cancer (BC) is one of the most common cancers with diverse mutations, etiology and causes. Mutational signature of the driver genes could allow for better understanding disease etiology and progression. This study aims to assess PIK3CA Exon 20 somatic mutational signature in relation to potential underlying etiology. Circulating DNA of 71 Egyptian BC patients was isolated, amplified for PIK3CA Exon 20, and sequenced. Mutational signature was determined according to COSMIC v2 signature. Public BC dataset was analysed to assess PIK3CA mutations effect on the transcriptomic profile. Somatic mutations of PIK3CA exon 20 were found in 66.2% of the study cohort. Nucleotide substitution patterns were similar to general nucleotide substitution patterns in BC. Signature 3 and 9 were the most common signatures in the studied BC patients. Signature of Aristolochic acid exposure was found in some cases. The most common nucleotide substitution was T > A transversion, but substitutions T > G and T > C were correlated to each other and to the total mutation number. PIK3CA mutations were found to disrupt several pathways including RAC1, PDGF, Wnt, and integrin signalling. PIK3CA exon 20 mutational signatures in Egyptian BC patients could suggest a disease etiology involving homologous recombination deficiency (HRD) and polymerase eta (Pol η). Nucleotide substitution patterns could indicate the role of exposure to oxidative stress and some carcinogens such as 4-aminobiphenyl and Aristolochic acid.
Collapse
|
11
|
Adedokun B, Du Z, Gao G, Ahearn TU, Lunetta KL, Zirpoli G, Figueroa J, John EM, Bernstein L, Zheng W, Hu JJ, Ziegler RG, Nyante S, Bandera EV, Ingles SA, Press MF, Deming-Halverson SL, Rodriguez-Gil JL, Yao S, Ogundiran TO, Ojengbede O, Blot W, Troester MA, Nathanson KL, Hennis A, Nemesure B, Ambs S, Fiorica PN, Sucheston-Campbell LE, Bensen JT, Kushi LH, Torres-Mejia G, Hu D, Fejerman L, Bolla MK, Dennis J, Dunning AM, Easton DF, Michailidou K, Pharoah PDP, Wang Q, Sandler DP, Taylor JA, O'Brien KM, Kitahara CM, Falusi AG, Babalola C, Yarney J, Awuah B, Addai-Wiafe B, Chanock SJ, Olshan AF, Ambrosone CB, Conti DV, Ziv E, Olopade OI, Garcia-Closas M, Palmer JR, Haiman CA, Huo D. Cross-ancestry GWAS meta-analysis identifies six breast cancer loci in African and European ancestry women. Nat Commun 2021; 12:4198. [PMID: 34234117 PMCID: PMC8263739 DOI: 10.1038/s41467-021-24327-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 06/02/2021] [Indexed: 02/06/2023] Open
Abstract
Our study describes breast cancer risk loci using a cross-ancestry GWAS approach. We first identify variants that are associated with breast cancer at P < 0.05 from African ancestry GWAS meta-analysis (9241 cases and 10193 controls), then meta-analyze with European ancestry GWAS data (122977 cases and 105974 controls) from the Breast Cancer Association Consortium. The approach identifies four loci for overall breast cancer risk [1p13.3, 5q31.1, 15q24 (two independent signals), and 15q26.3] and two loci for estrogen receptor-negative disease (1q41 and 7q11.23) at genome-wide significance. Four of the index single nucleotide polymorphisms (SNPs) lie within introns of genes (KCNK2, C5orf56, SCAMP2, and SIN3A) and the other index SNPs are located close to GSTM4, AMPD2, CASTOR2, and RP11-168G16.2. Here we present risk loci with consistent direction of associations in African and European descendants. The study suggests that replication across multiple ancestry populations can help improve the understanding of breast cancer genetics and identify causal variants.
Collapse
Affiliation(s)
- Babatunde Adedokun
- Center for Clinical Cancer Genetics and Global Health, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Zhaohui Du
- Department of Preventative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Guimin Gao
- Department of Public Health Sciences, University of Chicago, Chicago, IL, USA
| | - Thomas U Ahearn
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Kathryn L Lunetta
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Gary Zirpoli
- Slone Epidemiology Center, Boston University, Boston, MA, USA
| | - Jonine Figueroa
- Usher Institute and CRUK Edinburgh Centre, University of Edinburgh, Edinburgh, UK
| | - Esther M John
- Departments of Epidemiology & Population Health and of Medicine (Oncology) and Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Leslie Bernstein
- Biomarkers of Early Detection and Prevention, Department of Population Sciences, Beckman Research Institute, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, TN, USA
| | - Jennifer J Hu
- Department of Public Health Sciences, University of Miami, Miami, FL, USA
| | - Regina G Ziegler
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Sarah Nyante
- Department of Radiology, University of North Carolina, Chapel Hill, NC, USA
| | - Elisa V Bandera
- Cancer Prevention and Control Program, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
| | - Sue A Ingles
- Department of Preventative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Michael F Press
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Sandra L Deming-Halverson
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, TN, USA
| | - Jorge L Rodriguez-Gil
- Genomics, Development and Disease Section, Genetic Disease Research Branch, National Human Genome Research Institute, NIH, Bethesda, MD, USA
| | - Song Yao
- Department of Cancer Prevention and Control, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Temidayo O Ogundiran
- Department of Surgery, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Oladosu Ojengbede
- Center for Population and Reproductive Health, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - William Blot
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, TN, USA
| | - Melissa A Troester
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
| | - Katherine L Nathanson
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Anselm Hennis
- University of the West Indies, Bridgetown, Barbados
- Department of Family, Population and Preventive Medicine, Stony Brook University, Stony Brook, NY, USA
| | - Barbara Nemesure
- Department of Family, Population and Preventive Medicine, Stony Brook University, Stony Brook, NY, USA
| | - Stefan Ambs
- Laboratory of Human Carcinogenesis, National Cancer Institute, Bethesda, MD, USA
| | - Peter N Fiorica
- Department of Public Health Sciences, University of Chicago, Chicago, IL, USA
| | - Lara E Sucheston-Campbell
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, OH, USA
| | - Jeannette T Bensen
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
| | - Lawrence H Kushi
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Gabriela Torres-Mejia
- Center for Population Health Research, Instituto Nacional de Salud Publica, Cuernavaca, Mexico
| | - Donglei Hu
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Laura Fejerman
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Manjeet K Bolla
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Joe Dennis
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Alison M Dunning
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Douglas F Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Kyriaki Michailidou
- Biostatistics Unit, The Cyprus Institute of Neurology & Genetics, Nicosia, Cyprus
| | - Paul D P Pharoah
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Qin Wang
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Dale P Sandler
- Epidemiology Branch, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA
| | - Jack A Taylor
- Epidemiology Branch, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA
| | - Katie M O'Brien
- Epidemiology Branch, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA
| | - Cari M Kitahara
- Radiation Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Adeyinka G Falusi
- Institute for Advanced Medical Research and Training, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria
| | - Chinedum Babalola
- Department of Pharmaceutical Chemistry, University of Ibadan, Ibadan, Oyo, Nigeria
| | | | | | | | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Andrew F Olshan
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
| | - Christine B Ambrosone
- Department of Cancer Prevention and Control, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - David V Conti
- Department of Preventative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Elad Ziv
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Olufunmilayo I Olopade
- Center for Clinical Cancer Genetics and Global Health, Department of Medicine, University of Chicago, Chicago, IL, USA
| | | | - Julie R Palmer
- Slone Epidemiology Center, Boston University, Boston, MA, USA
| | - Christopher A Haiman
- Department of Preventative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
| | - Dezheng Huo
- Center for Clinical Cancer Genetics and Global Health, Department of Medicine, University of Chicago, Chicago, IL, USA.
- Department of Public Health Sciences, University of Chicago, Chicago, IL, USA.
| |
Collapse
|
12
|
Yang Z, Shen Z, Jin D, Zhang N, Wang Y, Lei W, Zhang Z, Chen H, Naz F, Xu L, Wang L, Wang S, Su X, Yu C, Li C. Mutations of METTL3 predict response to neoadjuvant chemotherapy in muscle-invasive bladder cancer. J Clin Transl Res 2021; 7:386-413. [PMID: 34239995 PMCID: PMC8259609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 01/27/2021] [Accepted: 05/10/2021] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND AND AIM Neoadjuvant chemotherapy (NAC) followed by radical cystectomy is the current gold standard treatment for muscle-invasive urothelial bladder cancer (MIBC). Nonetheless, some MIBC patients showed limited pathological response after NAC. Herein, we used whole-exome sequencing (WES) to identify genetic mutations in MIBC that can predict NAC response. METHODS Forty MIBC patients were enrolled in this study, in which 33 were successfully examined by WES and Sanger sequencing in the discovery cohort (n=13) and the validation cohort (n=20), respectively. ANNOVAR software was used to identify the potential mutations based on the data of WES. In addition, tumor-specific somatic mutations including single nucleotide variants and indels were called with the muTECT and Strelka software. The mutational analysis of specific genes was carried out based on the data from cBioPortal for Cancer Genomics. RESULTS In the discovery cohort, the mutation frequencies of TP53, MED16, DRC7, CEND1, ATAD5, SETD8, and PIK3CA were significantly higher in 13 MIBC patients. Specifically, the presence of somatic mutations of APC, ATM, CDH9, CTNNB1, METTL3, NBEAL1, PTPRH, RNASEL, and FBXW7 in NAC responder signifies that these mutations were potential predictors of pathological response to NAC. Furthermore, somatic mutations of CCDC141, PIK3CA, CHD5, GPR149, MUC20, TSC1, and USP54 were exclusively identified in NAC nonresponders, suggesting that these mutations may participate in the process of NAC resistance. In the validation cohort, the somatic mutations of CDH9, METTL3, and PTPRH were significantly enriched in NAC responders while the somatic mutation of CCDC141 was significantly enriched in NAC nonresponders. Furthermore, survival analysis revealed that the patients expressing mutated METTL3 have a longer overall survival and disease- or progression-free survival than the patients acquiring wild-type METTL3. CONCLUSION The somatic mutation of METTL3 can be a potential predictive biomarker of NAC response in MIBC patients. RELEVANCE FOR PATIENTS MIBC patients bearing mutated METTL3 display a pathological response to NAC and have a significantly longer overall survival or disease/progression-free survival as compared to the patients bearing wild-type METTL3. Thus, the somatic mutation of METTL3 is a potential biomarker for predicting response to NAC in MIBC patients, assisting doctors in making the clinical decision.
Collapse
Affiliation(s)
- Zhao Yang
- 1College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China,2College of Life Science, Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin of Xinjiang Production and Construction Corps, Tarim University, Alar 843300, Xinjiang, China,Corresponding authors: Zhao Yang College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China. E-mail:
| | - Zongyi Shen
- 1College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Di Jin
- 3Department of Urology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Nan Zhang
- 1College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Yue Wang
- 4Department of Cancer Research, Novogene Bioinformatics Institute, Beijing 100016, China
| | - Wanjun Lei
- 4Department of Cancer Research, Novogene Bioinformatics Institute, Beijing 100016, China
| | - Zhiming Zhang
- 4Department of Cancer Research, Novogene Bioinformatics Institute, Beijing 100016, China
| | - Haige Chen
- 3Department of Urology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Faiza Naz
- 1College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Lida Xu
- 1College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Lei Wang
- 1College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Shihui Wang
- 1College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Xin Su
- 1College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Changyuan Yu
- 1College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China,
Changyuan Yu College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China. E-mail:
| | - Chong Li
- 5Core Facility for Protein Research, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China,6Zhongke Jianlan Medical Research Institute, Beijing 101400, China,
Chong Li Core Facility for Protein Research, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China. E-mail:
| |
Collapse
|
13
|
Isayama K, Watanabe K, Okamoto M, Murata T, Mizukami Y. Standardization of an LNA-based TaqMan assay qPCR analysis for Aspiculuris tetraptera DNA in mouse faeces. BMC Microbiol 2020; 20:371. [PMID: 33287731 PMCID: PMC7720592 DOI: 10.1186/s12866-020-02053-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 11/26/2020] [Indexed: 11/24/2022] Open
Abstract
Background Aspiculuris tetraptera, as a parasitic pinworm, is most frequently detected in laboratory mice, and transmission is mediated by the eggs contained in the faeces of infected mice. A highly sensitive and quantitative faeces-based diagnostic tool would be useful for the early detection of A. tetraptera to inhibit the expansion of infection. In this study, we developed a quantitative assay that exhibits high sensitivity in detecting A. tetraptera in faeces using PCR techniques. Results Endpoint PCR demonstrated the detection of A. tetraptera DNA in 0.5 ng genomic DNA extracted from the faeces of infected mice. To quantitatively detect the small amount of A. tetraptera DNA, locked nucleic acid (LNA)-based primers and LNA-based TaqMan probes were used for the quantitative PCR assay (qPCR). The combination of LNA-based DNA increased detection sensitivity by more than 100-fold compared to using normal oligo DNAs. The copy number of the A. tetraptera DNA detected was positively related to the infected faeces-derived genomic DNA with a simple linearity regression in the range of 20 pg to 15 ng of the genomic DNA. To more conveniently detect infection using faeces, the LNA-based TaqMan assay was applied to the crude fraction of the faeces without DNA purification. An assay using ethanol precipitation of the faeces yielded results consistent with those of direct microscopic observation. Conclusion The LNA-TaqMan assay developed in this study quantitatively detects A. tetraptera infection in mouse faeces. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-020-02053-6.
Collapse
Affiliation(s)
- Keishiro Isayama
- Institute of Laboratory Animals, Yamaguchi University Science Research Center, Yamaguchi, 755-8505, Japan
| | - Kenji Watanabe
- Institute of Gene Research, Yamaguchi University Science Research Center, Yamaguchi, 755-8505, Japan
| | - Mariko Okamoto
- Laboratory of Veterinary Immunology, School of Veterinary Medicine, Azabu University, Sagamihara, 252-5201, Japan
| | - Tomoaki Murata
- Institute of Laboratory Animals, Yamaguchi University Science Research Center, Yamaguchi, 755-8505, Japan
| | - Yoichi Mizukami
- Institute of Gene Research, Yamaguchi University Science Research Center, Yamaguchi, 755-8505, Japan.
| |
Collapse
|
14
|
Adams MK, Banks CAS, Thornton JL, Kempf CG, Zhang Y, Miah S, Hao Y, Sardiu ME, Killer M, Hattem GL, Murray A, Katt ML, Florens L, Washburn MP. Differential Complex Formation via Paralogs in the Human Sin3 Protein Interaction Network. Mol Cell Proteomics 2020; 19:1468-1484. [PMID: 32467258 PMCID: PMC8143632 DOI: 10.1074/mcp.ra120.002078] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Indexed: 01/09/2023] Open
Abstract
Despite the continued analysis of HDAC inhibitors in clinical trials, the heterogeneous nature of the protein complexes they target limits our understanding of the beneficial and off-target effects associated with their application. Among the many HDAC protein complexes found within the cell, Sin3 complexes are conserved from yeast to humans and likely play important roles as regulators of transcriptional activity. The presence of two Sin3 paralogs in humans, SIN3A and SIN3B, may result in a heterogeneous population of Sin3 complexes and contributes to our poor understanding of the functional attributes of these complexes. Here, we profile the interaction networks of SIN3A and SIN3B to gain insight into complex composition and organization. In accordance with existing data, we show that Sin3 paralog identity influences complex composition. Additionally, chemical cross-linking MS identifies domains that mediate interactions between Sin3 proteins and binding partners. The characterization of rare SIN3B proteoforms provides additional evidence for the existence of conserved and divergent elements within human Sin3 proteins. Together, these findings shed light on both the shared and divergent properties of human Sin3 proteins and highlight the heterogeneous nature of the complexes they organize.
Collapse
Affiliation(s)
- Mark K Adams
- Stowers Institute for Medical Research, Kansas City, Missouri, USA
| | | | - Janet L Thornton
- Stowers Institute for Medical Research, Kansas City, Missouri, USA
| | | | - Ying Zhang
- Stowers Institute for Medical Research, Kansas City, Missouri, USA
| | - Sayem Miah
- Stowers Institute for Medical Research, Kansas City, Missouri, USA
| | - Yan Hao
- Stowers Institute for Medical Research, Kansas City, Missouri, USA
| | - Mihaela E Sardiu
- Stowers Institute for Medical Research, Kansas City, Missouri, USA
| | - Maxime Killer
- Stowers Institute for Medical Research, Kansas City, Missouri, USA
| | - Gaye L Hattem
- Stowers Institute for Medical Research, Kansas City, Missouri, USA
| | - Alexis Murray
- Stowers Institute for Medical Research, Kansas City, Missouri, USA
| | - Maria L Katt
- Stowers Institute for Medical Research, Kansas City, Missouri, USA
| | - Laurence Florens
- Stowers Institute for Medical Research, Kansas City, Missouri, USA
| | - Michael P Washburn
- Stowers Institute for Medical Research, Kansas City, Missouri, USA; Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, Kansas, USA.
| |
Collapse
|
15
|
Tang X, Xiao Q, Yu K. Breast Cancer Candidate Gene Detection Through Integration of Subcellular Localization Data With Protein–Protein Interaction Networks. IEEE Trans Nanobioscience 2020; 19:556-561. [DOI: 10.1109/tnb.2020.2990178] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
|