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Lin C, Sniezek C, Giglio RM, Karki R, McGann C, Garcia BA, McFaline-Figeroa JL, Schweppe DK. Lineage-specific proteome remodeling of diverse lung cancer cells by targeted epigenetic inhibitors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.23.592075. [PMID: 38853901 PMCID: PMC11160595 DOI: 10.1101/2024.05.23.592075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Epigenetic inhibitors exhibit powerful antiproliferative and anticancer activities. However, cellular responses to small-molecule epigenetic inhibition are heterogenous and dependent on factors such as the genetic background, metabolic state, and on-/off-target engagement of individual small-molecule drugs. To determine the mechanisms that drive these heterogeneous cellular responses, we quantified chromatin, proteome, and transcriptome remodeling due to histone deacetylase inhibitor (HDACi) -treated cells derived from diverse genetic backgrounds. We utilized high-throughput sample multiplexed proteomics and integrated intelligent data acquisition methods to map proteomes of cancer cell lines in response to HDACi. We determined cell type-specific and ubiquitous cellular responses based on the quantification of 10,621 total proteins. We then established how coordinated remodeling of the proteome, transcriptome and chromatin state of HDACi treated cancer cells revealed convergent (JUN, MAP2K3, CDKN1A) and divergent (CCND3, ASF1B, BRD7) molecular phenotypes. HDACi-regulated proteins differ greatly across cell lines owing to heterogeneous molecular states of these cell lines. Finally, we demonstrated that HDACi treatment drove a highly cell-type specific response that may in part be explained by cell line-specific off-target drug engagement.
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Affiliation(s)
- Chuwei Lin
- University of Washington, Seattle, WA 98105, USA
| | | | | | - Rashmi Karki
- Washington University School of Medicine, St. Louis, MO 63110, USA
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Ali A, Geetha S, Wu D, Chau K, Karam P, Khutti S, Fayyaz SS, Das K, Gimenez C, Rosca OC. TRPS1 function beyond breast: A retrospective immunohistochemical study on non-breast cytology specimens. Diagn Cytopathol 2024. [PMID: 38794964 DOI: 10.1002/dc.25359] [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: 01/25/2024] [Revised: 04/28/2024] [Accepted: 05/14/2024] [Indexed: 05/27/2024]
Abstract
INTRODUCTION Trichorhinophalangeal syndrome type 1 (TRPS1) has emerged as a reliable immunohistochemistry (IHC) marker for identifying breast origin in metastatic carcinomas. This study investigates the utility of TRPS1 IHC in non-breast cytology specimens. MATERIALS AND METHODS A retrospective search of our pathology database for the year 2021 identified fluids (pleural and peritoneal) and liver, lung and bone fine needle aspirations (FNAs) with surgical follow-up confirming non-breast metastatic carcinomas. Cell blocks from cases with sufficient neoplastic cells underwent immunostaining using a rabbit polyclonal antibody against human TRPS1. Cases lacking tumor on deeper levels after the original work-up were excluded from the study. Two pathologists independently interpreted the TRPS1 staining. RESULTS Of 136 cases assessed, 31 (22.79%) exhibited positive TRPS1 staining, while 105 (77.21%) were nonreactive. Positivity rates were observed in tumors of Mullerian cell origin, gastrointestinal tract (GIT), and lung origin at 28.85%, 25%, and 21.57%, respectively. Of the tumors of Mullerian cell origin 10 (66.67%) were serous carcinomas, 4 (26.67%) were endometrioid carcinomas, and one (6.67%) was a clear cell carcinoma. Lung tumors comprised seven (63.64%) squamous cell carcinomas and four (36.36%) adenocarcinomas, while the gastrointestinal tumors consisted of 14 (80%) adenocarcinomas and one (20%) squamous cell carcinoma. CONCLUSIONS Although recognized as a sensitive marker for mammary carcinomas, TRPS1 immunostaining was also detected in Mullerian, lung, and GIT carcinomas. This highlights the significance of being cautious when depending solely on TRPS1 immunostaining to distinguish metastatic breast tumors.
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Affiliation(s)
- Amr Ali
- Department of Pathology and Laboratory Medicine, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, New York, USA
| | - Saroja Geetha
- Department of Pathology and Laboratory Medicine, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, New York, USA
| | - Dongling Wu
- Department of Pathology and Laboratory Medicine, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, New York, USA
| | - Karen Chau
- Department of Pathology and Laboratory Medicine, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, New York, USA
| | - Priyanka Karam
- Department of Pathology and Laboratory Medicine, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, New York, USA
| | - Seema Khutti
- Department of Pathology and Laboratory Medicine, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, New York, USA
| | - Silvat-Sheik Fayyaz
- Department of Pathology and Laboratory Medicine, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, New York, USA
| | - Kasturi Das
- Department of Pathology and Laboratory Medicine, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, New York, USA
| | - Cecilia Gimenez
- Department of Pathology and Laboratory Medicine, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, New York, USA
| | - Oana C Rosca
- Department of Pathology and Laboratory Medicine, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, New York, USA
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Salem A, Wu Y, Albarracin CT, Middleton LP, Kalhor N, Peng Y, Huang X, Aung PP, Chen H, Sahin AA, Ding Q. A Comparative Evaluation of TRPS1 and GATA3 in adenoid cystic, secretory, and acinic cell carcinomas of the breast and salivary gland. Hum Pathol 2024; 145:42-47. [PMID: 38262580 DOI: 10.1016/j.humpath.2024.01.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 01/06/2024] [Accepted: 01/12/2024] [Indexed: 01/25/2024]
Abstract
GATA3 is the most used marker to determine tumors' breast origin, but its diagnostic value in triple-negative breast cancer (TNBC) is limited. The newly identified TRPS1 is highly sensitive and specific for breast carcinoma, especially TNBC. Here, we compared the utility of TRPS1 and GATA3 expression in a subset of salivary gland-type breast tumors (including adenoid cystic, acinic cell, and secretory carcinomas [AdCC, ACC, and SC, respectively]), and we compared TRPS1 and GATA3 expression of such tumors with head and neck (H&N) and AdCC of upper respiratory tumors. TRPS1 was strongly expressed in basaloid TNBC and AdCCs with solid components, including 100 % of mixed and solid breast AdCCs. However, TRPS1 was positive in only 50 % cribriform AdCCs. Expression patterns of TRPS1 in H&N and upper respiratory AdCC were similar. TRPS1 was positive in 30 % of H&N cribriform AdCCs but was strongly expressed in mixed AdCC (67 %) and solid AdCC (100 %). In the upper respiratory AdCCs, TRPS1 was positive in 58.4 % of cribriform AdCCs and positive in 100 % of AdCCs with solid components. On the contrary, GATA3 was negative in predominant AdCCs of the breast, H&N, and upper respiratory tract. These data show that GATA3 and TRPS1 expression varies AdCCs. In addition, TRPS1 and GATA3 expression patterns were similar SC and ACC of breast and H&N. Both markers were positive in SC and negative in ACC. Therefore, TRPS1 and GATA3 cannot be used to differentiate salivary gland-type carcinomas of breast origin from those of upper respiratory or H&N origin.
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Affiliation(s)
- Alireza Salem
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
| | - Yun Wu
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Constance T Albarracin
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Lavinia P Middleton
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Neda Kalhor
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yan Peng
- Department of Pathology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Xiao Huang
- Department of Pathology, The University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Phyu P Aung
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Hui Chen
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Aysegul A Sahin
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Qingqing Ding
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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Coppin E, Zhang X, Ohayon L, Johny E, Dasari A, Zheng KH, Stiekema L, Cifuentes-Pagano E, Pagano PJ, Chaparala S, Stroes ES, Dutta P. Peripheral Ischemia Imprints Epigenetic Changes in Hematopoietic Stem Cells to Propagate Inflammation and Atherosclerosis. Arterioscler Thromb Vasc Biol 2023; 43:889-906. [PMID: 36891902 PMCID: PMC10213134 DOI: 10.1161/atvbaha.123.318956] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 02/20/2023] [Indexed: 03/10/2023]
Abstract
BACKGROUND Peripheral ischemia caused by peripheral artery disease is associated with systemic inflammation, which may aggravate underlying comorbidities such as atherosclerosis and heart failure. However, the mechanisms of increased inflammation and inflammatory cell production in patients with peripheral artery disease remain poorly understood. METHODS We used peripheral blood collected from patients with peripheral artery disease and performed hind limb ischemia (HI) in Apoe-/- mice fed a Western diet and C57BL/6J mice with a standard laboratory diet. Bulk and single-cell RNA sequencing analysis, whole-mount microscopy, and flow cytometry were performed to analyze hematopoietic stem and progenitor cell (HSPC) proliferation, differentiation, and relocation. RESULTS We observed augmented numbers of leukocytes in the blood of patients with peripheral artery disease and Apoe-/- mice with HI. RNA sequencing and whole-mount imaging of the bone marrow revealed HSPC migration into the vascular niche from the osteoblastic niche and their exaggerated proliferation and differentiation. Single-cell RNA sequencing demonstrated alterations in the genes responsible for inflammation, myeloid cell mobilization, and HSPC differentiation after HI. Heightened inflammation in Apoe-/- mice after HI aggravated atherosclerosis. Surprisingly, bone marrow HSPCs expressed higher amounts of the receptors for IL (interleukin)-1 and IL-3 after HI. Concomitantly, the promoters of Il1r1 and Il3rb had augmented H3K4me3 and H3K27ac marks after HI. Genetic and pharmacological inhibition of these receptors resulted in suppressed HSPC proliferation, reduced leukocyte production, and ameliorated atherosclerosis. CONCLUSIONS Our findings demonstrate increased inflammation, HSPC abundance in the vascular niches of the bone marrow, and elevated IL-3Rb and IL-1R1 (IL-1 receptor 1) expression in HSPC following HI. Furthermore, the IL-3Rb and IL-1R1 signaling plays a pivotal role in HSPC proliferation, leukocyte abundance, and atherosclerosis aggravation after HI.
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Affiliation(s)
- Emilie Coppin
- Regeneration in Hematopoiesis, Institute for Immunology, TU Dresden, Dresden, Germany
- Immunology of Aging, Leibniz Institute on Aging – Fritz Lipmann Institute, Jena, Germany
| | - Xinyi Zhang
- Department of Cardiology, Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou 310009, China
| | - Lee Ohayon
- Pittsburgh Heart, Lung, Blood, and Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA 15213, USA
- Department of Bioengineering, Swanson School of Engineering, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Ebin Johny
- Pittsburgh Heart, Lung, Blood, and Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Ankush Dasari
- Pittsburgh Heart, Lung, Blood, and Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Kang H. Zheng
- Department of Vascular Medicine, Amsterdam Cardiovascular Sciences, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Lotte Stiekema
- Department of Vascular Medicine, Amsterdam Cardiovascular Sciences, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Eugenia Cifuentes-Pagano
- Pittsburgh Heart, Lung, Blood, and Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA 15213, USA
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Patrick J. Pagano
- Pittsburgh Heart, Lung, Blood, and Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA 15213, USA
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Srilakshmi Chaparala
- Health Sciences Library System, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Erik S. Stroes
- Department of Vascular Medicine, Amsterdam Cardiovascular Sciences, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Partha Dutta
- Pittsburgh Heart, Lung, Blood, and Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA 15213, USA
- Department of Bioengineering, Swanson School of Engineering, University of Pittsburgh, Pittsburgh, PA 15213, USA
- Division of Cardiology, Department of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
- Department of Immunology, University of Pittsburgh, Pittsburgh, PA 15213, USA
- Pittsburgh VA Medical Center-University Drive, University Drive C, Pittsburgh, PA, 15213
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A Genome-Wide Association Study Identified Novel Genetic Susceptibility Loci for Oral Cancer in Taiwan. Int J Mol Sci 2023; 24:ijms24032789. [PMID: 36769103 PMCID: PMC9917812 DOI: 10.3390/ijms24032789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 01/26/2023] [Accepted: 01/30/2023] [Indexed: 02/05/2023] Open
Abstract
Taiwan has the highest incidence rate of oral cancer in the world. Although oral cancer is mostly an environmentally induced cancer, genetic factors also play an important role in its etiology. Genome-wide association studies (GWAS) have identified nine susceptibility regions for oral cancers in populations of European descent. In this study, we performed the first GWAS of oral cancer in Taiwan with 1529 cases and 44,572 controls. We confirmed two previously reported loci on the 6p21.33 (HLA-B) and 6p21.32 (HLA-DQ gene cluster) loci, highlighting the importance of the human leukocyte antigen and, hence, the immunologic mechanisms in oral carcinogenesis. The TERT-CLMPT1L locus on 5p15.33, the 4q23 ADH1B locus, and the LAMC3 locus on 9q34.12 were also consistent in the Taiwanese. We found two new independent loci on 6p21.32, rs401775 in SKIV2L gene and rs9267798 in TNXB gene. We also found two suggestive novel Taiwanese-specific loci near the TPRS1 gene on 8q23.3 and in the TMED3 gene on 15q25.1. This study identified both common and unique oral cancer susceptibility loci in the Taiwanese as compared to populations of European descent and shed significant light on the etiology of oral cancer in Taiwan.
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Functional mechanisms of TRPS1 in disease progression and its potential role in personalized medicine. Pathol Res Pract 2022; 237:154022. [PMID: 35863130 DOI: 10.1016/j.prp.2022.154022] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 07/04/2022] [Accepted: 07/12/2022] [Indexed: 11/22/2022]
Abstract
The gene of transcriptional repressor GATA binding 1 (TRPS1), as an atypical GATA transcription factor, has received considerable attention in a plethora of physiological and pathological processes, and may become a promising biomarker for targeted therapies in diseases and tumors. However, there still lacks a comprehensive exploration of its functions and promising clinical applications. Herein, relevant researches published in English from 2000 to 2022 were retrieved from PubMed, Google Scholar and MEDLINE, concerning the roles of TRPS1 in organ differentiation and tumorigenesis. This systematic review predominantly focused on summarizing the structural characteristics and biological mechanisms of TRPS1, its involvement in tricho-rhino-phalangeal syndrome (TRPS), its participation in the development of multiple tissues, the recent advances of its vital features in metabolic disorders as well as malignant tumors, in order to prospect its potential applications in disease detection and cancer targeted therapy. From the clinical perspective, the deeply and thoroughly understanding of the complicated context-dependent and cell-lineage-specific mechanisms of TRPS1 would not only gain novel insights into the complex etiology of diseases, but also provide the fundamental basis for the development of therapeutic drugs targeting both TRPS1 and its critical cofactors, which would facilitate individualized treatment.
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Ma S, Zhao D, Liu Y, Rohr J, Zhang F, Ma Y, Gong L, Shi H, Wang Y, Fan L, Qin J, Wang Z, Guo S. Some Pleomorphic Adenomas of the Breast Share PLAG1 Rearrangements with the Analogous Tumor of the Salivary Glands. Histopathology 2021; 79:1030-1039. [PMID: 34292619 DOI: 10.1111/his.14461] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 07/13/2021] [Accepted: 07/21/2021] [Indexed: 01/04/2023]
Abstract
AIMS Pleomorphic adenoma (PA) of the breast, and especially its malignant transformation, is extremely rare and represents a diagnostic pitfall. Molecular alterations in this entity have not been investigated. We aimed to examine the clinicopathologic features of our breast PAs and perform molecular analysis. METHODS Seven cases of breast PA including two cases of carcinoma ex PA were analyzed. PLAG1 and HMGA2 gene rearrangements were assayed by FISH and RNA-Seq, respectively. RT-PCR and Sanger sequencing were used to verify RNA sequencing results. RESULTS All seven cases of breast PA occurred in women. The histological features were similar to the analogous tumor in salivary glands, including a dual epithelial-myoepithelial component and negativity of ER, PR, and HER2 by immunohistochemistry. Of the two cases with carcinoma ex PA, one demonstrated minimal invasion and one was extensively invasive. PLAG1 rearrangements were identified in two cases (28.6%), but no rearrangements of HMG2A were found. A novel fusion product in PAs, TRPS1-PLAG1, was identified in one case. No patients had recurrence or metastasis with a follow-up period of 6 to 158 months. CONCLUSIONS Breast PA is rare, but it is an important differential diagnosis of breast pathology with the potential to develop carcinoma ex PA. We reported a novel TRPS1-PLAG1 fusion gene in breast PA.
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Affiliation(s)
- Shirong Ma
- Department of Pathology, the Basic Medicine Science and the First Affiliated Hospital of the Air Force Military Medical University, Xi'an, Shaan Xi Province, 710032, China
| | - Danhui Zhao
- Department of Pathology, the Basic Medicine Science and the First Affiliated Hospital of the Air Force Military Medical University, Xi'an, Shaan Xi Province, 710032, China
| | - Yixiong Liu
- Department of Pathology, the Basic Medicine Science and the First Affiliated Hospital of the Air Force Military Medical University, Xi'an, Shaan Xi Province, 710032, China
| | - Joseph Rohr
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, 68105, NE, USA
| | - Fan Zhang
- Department of Pathology, the First Affiliated Hospital of Wannan Medical College, Anhui Province, Wuhu City, 241001, China
| | - Ying Ma
- Department of Pathology, Shengjing Hospital of China Medical University, Liao Ning Province, Shen Yang, 110004, China
| | - Li Gong
- Department of Pathology, the Second Affiliated Hospital of the Air Force Military Medical University, Xi'an, Shaan Xi Province, 710032, China
| | - Huijuan Shi
- Department of Pathology, The First Affiliated Hospital of Sun Yat-sen University, Guanggong Province, Guangzhou, 510080, China
| | - Yingmei Wang
- Department of Pathology, the Basic Medicine Science and the First Affiliated Hospital of the Air Force Military Medical University, Xi'an, Shaan Xi Province, 710032, China
| | - Linni Fan
- Department of Pathology, the Basic Medicine Science and the First Affiliated Hospital of the Air Force Military Medical University, Xi'an, Shaan Xi Province, 710032, China
| | - Junhui Qin
- Department of Pathology, the Basic Medicine Science and the First Affiliated Hospital of the Air Force Military Medical University, Xi'an, Shaan Xi Province, 710032, China
| | - Zhe Wang
- Department of Pathology, the Basic Medicine Science and the First Affiliated Hospital of the Air Force Military Medical University, Xi'an, Shaan Xi Province, 710032, China
| | - Shuangping Guo
- Department of Pathology, the Basic Medicine Science and the First Affiliated Hospital of the Air Force Military Medical University, Xi'an, Shaan Xi Province, 710032, China
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Wu H, Huang Z, Huang M, Dang Y, Lu H, Qin X, Liang L, Yang L, Ma J, Chen G, Lv Z. Clinical significance and biological function of transcriptional repressor GATA binding 1 in gastric cancer: a study based on data mining, RT-qPCR, immunochemistry, and vitro experiment. Cell Cycle 2020; 19:2866-2885. [PMID: 33044891 DOI: 10.1080/15384101.2020.1827499] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Transcriptional repressor GATA binding 1 (TRPS1) is a newly discovered transcription factor, which has been reported in many tumors, except for gastric cancer (GC). In this study, we aimed to grope for clinical significance and biological function of TRPS1 in GC. TRPS1 expression in GC and its relationship with clinicopathological features were analyzed based on public databases, and verified by immunohistochemistry and RT-qPCR. Kaplan-Meier survival curve and Cox regression model were used to estimate the influence of TRPS1 on the univariate prognosis and multivariate survival risk factors of GC. The effects of TRPS1 on malignant biological behaviors of GC cells were studied by CCK8 cell proliferation, scratch test, and Transwell assay. The function of TRPS1 was further analyzed by signaling pathway analysis. TRPS1 mRNA expression in GC tissues was up-regulated and was of great significance in some prognostic factors. Protein expression of TRPS1 in tumor tissues was significantly higher than that in paracancerous tissues. Over-expression of TRPS1 was a poor prognostic indicator for GC patients. TRPS1 knockdown could inhibit the proliferation, migration, and invasion of GC cells. The important role of TRPS1 was in the extracellular matrix, and it was involved in actin binding and proteoglycan in cancer. The hub genes of TRPS1 (FN1, ITGB1) were defined. TRPS1 may be a tumor promoter and promote the development of GC by influencing the malignant biological behaviors of GC. TRPS1 is expected to be a key diagnostic and prognostic indicator for GC patients.
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Affiliation(s)
- Hong Wu
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University , Nanning, Guangxi Zhuang Autonomous Region, P.R. China
| | - Zhiguang Huang
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University , Nanning, Guangxi Zhuang Autonomous Region, P.R. China
| | - Menglan Huang
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University , Nanning, Guangxi Zhuang Autonomous Region, P.R. China
| | - Yiwu Dang
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University , Nanning, Guangxi Zhuang Autonomous Region, P.R. China
| | - Huiping Lu
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University , Nanning, Guangxi Zhuang Autonomous Region, P.R. China
| | - Xingan Qin
- Gastrointestinal Surgery, First Affiliated Hospital of Guangxi Medical University , Nanning, Guangxi Zhuang Autonomous Region, P.R. China
| | - Liang Liang
- Gastrointestinal Surgery, First Affiliated Hospital of Guangxi Medical University , Nanning, Guangxi Zhuang Autonomous Region, P.R. China
| | - Lihua Yang
- Medical Oncology, First Affiliated Hospital of Guangxi Medical University , Nanning, Guangxi Zhuang Autonomous Region, P.R. China
| | - Jie Ma
- Medical Oncology, First Affiliated Hospital of Guangxi Medical University , Nanning, Guangxi Zhuang Autonomous Region, P.R. China
| | - Gang Chen
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University , Nanning, Guangxi Zhuang Autonomous Region, P.R. China
| | - Zili Lv
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University , Nanning, Guangxi Zhuang Autonomous Region, P.R. China
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Wang H, Huang Y, Yang Y. LncRNA PVT1 Regulates TRPS1 Expression in Breast Cancer by Sponging miR-543. Cancer Manag Res 2020; 12:7993-8004. [PMID: 32982402 PMCID: PMC7493016 DOI: 10.2147/cmar.s263383] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 08/13/2020] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Breast cancer is the most common female malignancy with high invasion and metastasis abilities. Studies have shown that long non-coding RNA (lncRNA) plasmacytoma variant translocation 1 gene (PVT1) is an oncogene and is positively correlated with progression and metastasis of breast tumors. However, the detailed mechanism of PVT1 in breast cancer tumorigenesis is not fully understood. METHODS Real-time polymerase quantitative chain reaction (RT-qPCR) was performed to identify the expression levels of PVT1, miR-543 and trichorhinophalangeal syndrome-1 gene (TRPS1) in breast cancer tissues and cells. Cell proliferation was measured by plate clone formation and 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl-2H-tetrazol-3-ium bromide (MTT) assay. Apoptosis and motility of MCF-7 and MDA-MB-436 cells were assessed with flow cytometry assay and transwell migration and invasion analyses, respectively. In addition, a model was established to probe the function of PVT1 silencing in vivo. The target relationship among PVT1, miR-543 or TRPS1 was confirmed by dual-luciferase reporter analysis, RNA immunoprecipitation (RIP) and RNA pull down assays. The protein expression level of TRPS1 was evaluated with Western blot assay. RESULTS PVT1 expression was upregulated in breast cancer tissues and cell lines. In addition, PVT1 silencing inhibited breast cancer cell growth and motility, while increased apoptosis. Meanwhile, the effects of PVT1 or miR-543 could be reversed by introducing overexpressed plasmid of miR-543 or TRPS1 in breast cancer cell lines, respectively. CONCLUSION Knockdown of PVT1 repressed breast cancer cell growth and motility, and induced apoptosis in vitro and reduced tumor volume and weight in vivo. Mechanically, the overexpression of PVT1 enhanced TRPS1 level by negatively targeted miR-543 in breast cancer.
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Affiliation(s)
- Hongtao Wang
- Department of Pharmacy, The Second Clinical Medical College, Yangtze University, Jingzhou434020, People’s Republic of China
| | - Yuanli Huang
- Department of Galactophore, The Second Clinical Medical College, Yangtze University, Jingzhou434020, People’s Republic of China
| | - Yuanrong Yang
- Department of Pharmacy, The Second Clinical Medical College, Yangtze University, Jingzhou434020, People’s Republic of China
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11
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Hu J, Zhang H, Liu L, Han B, Zhou G, Su P. TRPS1 Confers Multidrug Resistance of Breast Cancer Cells by Regulating BCRP Expression. Front Oncol 2020; 10:934. [PMID: 32695669 PMCID: PMC7338551 DOI: 10.3389/fonc.2020.00934] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2020] [Accepted: 05/12/2020] [Indexed: 11/13/2022] Open
Abstract
Multidrug resistance (MDR) is the major obstruction in the successful treatment of breast cancer (BCa). The elucidation of molecular events that confer chemoresistance of BCa is of major therapeutic importance. Several studies have elucidated the correlation of TRPS1 and BCa. Here we focused on the role of TRPS1 in acquisition of chemoresistance, and reported a unique role of TRPS1 renders BCa cells resistant to chemotherapeutic drugs via the regulation of BCRP expression. Bioinformation analysis based on publicly available BCa data suggested that TRPS1 overexpression linked to chemoresistance. Mechanistically, TRPS1 regulated BCRP expression and efflux transportation. Overexpression of TRPS1 led to upregulation of BCRP while its inhibition resulted in repression of BCRP. The correlation of TRPS1 and BCRP was further confirmed by immunohistochemistry in 180 BCa samples. MTT assay demonstrated that manipulation of TRPS1 expression affects the chemosensitivity of BCa cells. In total, high expression of TRPS1 confers MDR of BCa which is mediated by BCRP. Our data demonstrated a new insight into mechanisms and strategies to overcome chemoresistance in BCa.
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Affiliation(s)
- Jing Hu
- Department of Pathology, Qilu Hospital of Shandong University, Jinan, China
| | - Hui Zhang
- Department of Pathology, Qilu Hospital of Shandong University, Jinan, China
| | - Long Liu
- Department of Pathology, Qilu Hospital of Shandong University, Jinan, China
| | - Bo Han
- Department of Pathology, Qilu Hospital of Shandong University, Jinan, China
| | - Gengyin Zhou
- Department of Pathology, Qilu Hospital of Shandong University, Jinan, China
| | - Peng Su
- Department of Pathology, Qilu Hospital of Shandong University, Jinan, China
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12
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Exploring the role of post-translational modulators of transcription factors in triple-negative breast cancer gene expression. Meta Gene 2020. [DOI: 10.1016/j.mgene.2020.100681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/09/2022] Open
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13
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Nowakowski GS, Zhu J, Zhang Q, Brody J, Sun X, Maly J, Song Y, Rizvi S, Song Y, Lansigan F, Jing H, Cao J, Lue JK, Luo W, Zhang L, Li L, Han I, Sun J, Jivani M, Liu Y, Heineman T, Smith SD. ENGINE: a Phase III randomized placebo controlled study of enzastaurin/R-CHOP as frontline therapy in high-risk diffuse large B-cell lymphoma patients with the genomic biomarker DGM1. Future Oncol 2020; 16:991-999. [PMID: 32250167 DOI: 10.2217/fon-2020-0176] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
While combination of rituximab, cyclophosphamide, doxorubicin, vincristine and prednisone (R-CHOP) cures most patients with diffuse large B-cell lymphoma (DLBCL), those with high-risk international prognostic index disease have inferior survival. Enzastaurin as a potent inhibitor of PKC-β and PI3K/AKT pathway suppressor has been tested in many clinical trials including two key studies in DLBCL: Phase III maintenance study (Preventing Relapse in Lymphoma Using Daily Enzastaurin [PRELUDE]) and a first-line Phase II study (S028). DNA extracted from PRELUDE patients' blood samples was retrospectively genotyped identifying a novel genetic biomarker, DGM1 that showed high correlation with response to enzastaurin. A similar finding observed in the S028 study suggested that addition of enzastaurin to R-CHOP may significantly improve outcomes as frontline therapy for high-risk DGM1 positive DLBCL patients. ENGINE is a global, multicenter, placebo-controlled and randomized study to compare the effect of R-CHOP/enzastaurin as frontline treatment in high-risk DLBCL patients. The primary end point for this study is overall survival in patients who are DGM1 positive. Clinical Trial Registration Identifier: NCT03263026.
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MESH Headings
- Female
- Humans
- Male
- Antineoplastic Combined Chemotherapy Protocols/adverse effects
- Antineoplastic Combined Chemotherapy Protocols/therapeutic use
- Biomarkers, Tumor/genetics
- Cyclophosphamide/adverse effects
- Cyclophosphamide/therapeutic use
- Doxorubicin/adverse effects
- Doxorubicin/therapeutic use
- Genetic Association Studies
- Genetic Predisposition to Disease
- Indoles/administration & dosage
- Lymphoma, Large B-Cell, Diffuse/diagnosis
- Lymphoma, Large B-Cell, Diffuse/drug therapy
- Lymphoma, Large B-Cell, Diffuse/genetics
- Lymphoma, Large B-Cell, Diffuse/mortality
- Prednisone/adverse effects
- Prednisone/therapeutic use
- Research Design
- Rituximab/adverse effects
- Rituximab/therapeutic use
- Vincristine/adverse effects
- Vincristine/therapeutic use
- Randomized Controlled Trials as Topic
- Clinical Trials, Phase III as Topic
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Affiliation(s)
| | - Jun Zhu
- Peking University Cancer Hospital & Institute, Beijing, PR China
| | - Qingyuan Zhang
- Harbin Medical University Cancer Hospital, Harbin, PR China
| | - Joshua Brody
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Xiuhua Sun
- The Second Hospital of Dalian Medical University, Dalian, PR China
| | - Joseph Maly
- Norton Cancer Institute, Louisville, KY, USA
| | - Yuqin Song
- Peking University Cancer Hospital & Institute, Beijing, PR China
| | - Syed Rizvi
- University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Yongping Song
- Affliliated Cancer Hospital of Zhengzhou University, Zhengzhou, PR China
| | | | - Hongmei Jing
- Peking University Third Hospital, Beijing, PR China
| | - Junning Cao
- Fudan University Shanghai Cancer Center, Shanghai, PR China
| | | | - Wen Luo
- Denovo Biopharma LLC, San Diego, CA, USA
| | - Lei Zhang
- Denovo Biopharma LLC, San Diego, CA, USA
| | - Ling Li
- Denovo Biopharma LLC, San Diego, CA, USA
| | - Isabel Han
- Denovo Biopharma LLC, San Diego, CA, USA
| | - Joan Sun
- Denovo Biopharma LLC, San Diego, CA, USA
| | | | - Young Liu
- Denovo Biopharma LLC, San Diego, CA, USA
| | | | - Stephen D Smith
- University of Washington/Fred Hutchinson Cancer Center, Seattle, WA, USA
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14
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Zhang W, Zeng Y, Wang L, Liu Y, Cheng YN. An Effective Graph Clustering Method to Identify Cancer Driver Modules. Front Bioeng Biotechnol 2020; 8:271. [PMID: 32318558 PMCID: PMC7154174 DOI: 10.3389/fbioe.2020.00271] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 03/16/2020] [Indexed: 12/15/2022] Open
Abstract
Identifying the molecular modules that drive cancer progression can greatly deepen the understanding of cancer mechanisms and provide useful information for targeted therapies. Most methods currently addressing this issue primarily use mutual exclusivity without making full use of the extra layer of module property. In this paper, we propose MCLCluster to identity cancer driver modules, which use somatic mutation data, Cancer Cell Fraction (CCF) data, gene functional interaction network and protein-protein interaction (PPI) network to derive the module property on mutual exclusivity, connectivity in PPI network and functionally similarity of genes. We have taken three effective measures to ensure the effectiveness of our algorithm. First, we use CCF data to choose stronger signals and more confident mutations. Second, the weighted gene functional interaction network is used to quantify the gene functional similarity in PPI. The third, graph clustering method based on Markov is exploited to extract the candidate module. MCLCluster is tested in the two TCGA datasets (GBM and BRCA), and identifies several well-known oncogenes driver modules and some modules with functionally associated driver genes. Besides, we compare it with Multi-Dendrix, FSME Cluster and RME in simulated dataset with background noise and passenger rate, MCLCluster outperforming all of these methods.
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Affiliation(s)
- Wei Zhang
- College of Computer Engineering and Applied Mathematics, Changsha University, Changsha, China.,Hunan Province Key Laboratory of Industrial Internet Technology and Security, Changsha University, Changsha, China
| | - Yifu Zeng
- College of Computer Engineering and Applied Mathematics, Changsha University, Changsha, China.,Hunan Province Key Laboratory of Industrial Internet Technology and Security, Changsha University, Changsha, China
| | - Lei Wang
- College of Computer Engineering and Applied Mathematics, Changsha University, Changsha, China.,Key Laboratory of Hunan Province for Internet of Things and Information Security, Xiangtan University, Xiangtan, China
| | - Yue Liu
- College of Computer Science and Electronics Engineering, Hunan University, Changsha, China
| | - Yi-Nan Cheng
- College of Science, Southern University of Science and Technology, Shenzhen, China
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15
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Novel PLAG1 Gene Rearrangement Distinguishes a Subset of Uterine Myxoid Leiomyosarcoma From Other Uterine Myxoid Mesenchymal Tumors. Am J Surg Pathol 2020; 43:382-388. [PMID: 30489320 DOI: 10.1097/pas.0000000000001196] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Genetic alterations in uterine myxoid leiomyosarcoma are unknown. We investigate the clinicopathologic features of 19 uterine tumors previously diagnosed as myxoid leiomyosarcomas in which tumoral RNA was subjected to targeted RNA sequencing. PLAG1, BCOR, BCORL1, HMGA2, and ALK break-apart fluorescence in situ hybridization (FISH) and BCOR, PLAG1, and ALK immunohistochemistry were performed in cases which failed or lacked fusions by sequencing. The diagnosis of myxoid leiomyosarcoma was confirmed in 15 cases after exclusion of 4 tumors with BCOR and ALK rearrangements. These 15 patients presented at a median age of 50 years with stage I (3), II (2), III (2), and IV (1) tumors, respectively; stage was unknown in 7 cases. Tumor size ranged from 10 to 24 cm. Matrix was myxoid in all tumors and also eosinophilic in 2. Cells were spindled, epithelioid, and both in 10, 2, and 3 tumors and showed mild, moderate, and severe nuclear atypia in 3, 8, and 4 tumors, respectively. Mitotic index ranged from <1 to 14/10 HPF, while tumor necrosis was present in 6 (40%). Novel TRPS1-PLAG1 or RAD51B-PLAG1 fusions were detected by sequencing in 4 tumors, 3 of which were also confirmed by FISH. Diffuse PLAG1 expression was seen in 7 tumors, including 4 with PLAG1 rearrangement. No morphologic differences were seen among PLAG1 fusion-positive and fusion-negative tumors. No PLAG1, HMGA2, ALK, BCOR, or BCORL1 rearrangements were detected by FISH in 11 tumors. On the basis of sequencing and FISH results, PLAG1 rearrangements resulting in PLAG1 expression underpin ~25% of myxoid leiomyosarcomas and may serve as a useful diagnostic biomarker. Immunohistochemistry, targeted RNA sequencing, and/or FISH may distinguish myxoid leiomyosarcoma from its morphologic mimics.
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16
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Penolazzi L, Lambertini E, Scussel Bergamin L, Gandini C, Musio A, De Bonis P, Cavallo M, Piva R. Reciprocal Regulation of TRPS1 and miR-221 in Intervertebral Disc Cells. Cells 2019; 8:cells8101170. [PMID: 31569377 PMCID: PMC6829335 DOI: 10.3390/cells8101170] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 09/25/2019] [Accepted: 09/27/2019] [Indexed: 12/13/2022] Open
Abstract
Intervertebral disc (IVD), a moderately moving joint located between the vertebrae, has a limited capacity for self-repair, and treating injured intervertebral discs remains a major challenge. The development of innovative therapies to reverse IVD degeneration relies primarily on the discovery of key molecules that, occupying critical points of regulatory mechanisms, can be proposed as potential intradiscal injectable biological agents. This study aimed to elucidate the underlying mechanism of the reciprocal regulation of two genes differently involved in IVD homeostasis, the miR-221 microRNA and the TRPS1 transcription factor. Human lumbar IVD tissue samples and IVD primary cells were used to specifically evaluate gene expression and perform functional analysis including the luciferase gene reporter assay, chromatin immunoprecipitation, cell transfection with hTRPS1 overexpression vector and antagomiR-221. A high-level expression of TRPS1 was significantly associated with a lower pathological stage, and TRPS1 overexpression strongly decreased miR-221 expression, while increasing the chondrogenic phenotype and markers of antioxidant defense and stemness. Additionally, TRPS1 was able to repress miR-221 expression by associating with its promoter and miR-221 negatively control TRPS1 expression by targeting the TRPS1-3'UTR gene. As a whole, these results suggest that, in IVD cells, a double-negative feedback loop between a potent chondrogenic differentiation suppressor (miR-221) and a regulator of axial skeleton development (TRPS1) exists. Our hypothesis is that the hostile degenerated IVD microenvironment may be counteracted by regenerative/reparative strategies aimed at maintaining or stimulating high levels of TRPS1 expression through inhibition of one of its negative regulators such as miR-221.
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Affiliation(s)
- Letizia Penolazzi
- Department of Biomedical and Specialty Surgical Sciences, University of Ferrara, 44121 Ferrara, Italy.
| | - Elisabetta Lambertini
- Department of Biomedical and Specialty Surgical Sciences, University of Ferrara, 44121 Ferrara, Italy.
| | - Leticia Scussel Bergamin
- Department of Biomedical and Specialty Surgical Sciences, University of Ferrara, 44121 Ferrara, Italy.
| | - Carlotta Gandini
- Department of Biomedical and Specialty Surgical Sciences, University of Ferrara, 44121 Ferrara, Italy.
| | - Antonio Musio
- Department of Neurosurgery, S. Anna University Hospital, 44124 Ferrara, Italy.
| | - Pasquale De Bonis
- Department of Neurosurgery, S. Anna University Hospital, 44124 Ferrara, Italy.
| | - Michele Cavallo
- Department of Neurosurgery, S. Anna University Hospital, 44124 Ferrara, Italy.
| | - Roberta Piva
- Department of Biomedical and Specialty Surgical Sciences, University of Ferrara, 44121 Ferrara, Italy.
- Center for Studies on Gender Medicine, University of Ferrara, 44121 Ferrara, Italy.
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17
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Soond SM, Kozhevnikova MV, Frolova AS, Savvateeva LV, Plotnikov EY, Townsend PA, Han YP, Zamyatnin AA. Lost or Forgotten: The nuclear cathepsin protein isoforms in cancer. Cancer Lett 2019; 462:43-50. [PMID: 31381961 DOI: 10.1016/j.canlet.2019.07.020] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 07/26/2019] [Accepted: 07/30/2019] [Indexed: 02/06/2023]
Abstract
While research into the role of cathepsins has been progressing at an exponential pace over the years, research into their respective isoform proteins has been less frenetic. In view of the functional and biological potential of such protein isoforms in model systems for cancer during their initial discovery, much later they have offered a new direction in the field of cathepsin basic and applied research. Consequently, the analysis of such isoforms has laid strong foundations in revealing other important regulatory aspects of the cathepsin proteins in general. In this review article, we address these key aspects of cathepsin isoform proteins, with particular emphasis on how they have shaped what is now known in the context of nuclear cathepsin localization and what potential these hold as nuclear-based therapeutic targets in cancer.
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Affiliation(s)
- Surinder M Soond
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, Trubetskaya str. 8-2, Moscow, 119991, Russian Federation.
| | - Maria V Kozhevnikova
- Hospital Therapy Department № 1, Sechenov First Moscow State Medical University , 6-1 Bolshaya Pirogovskaya str, Moscow, 119991, Russian Federation.
| | - Anastasia S Frolova
- Department of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119992, Russian Federation.
| | - Lyudmila V Savvateeva
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, Trubetskaya str. 8-2, Moscow, 119991, Russian Federation.
| | - Egor Y Plotnikov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russian Federation.
| | - Paul A Townsend
- Division of Cancer Sciences and Manchester Cancer Research Centre, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre; and the NIHR Manchester Biomedical Research Centre, Manchester, UK.
| | - Yuan-Ping Han
- College of Life Sciences Sichuan University, Chengdu, Sichuan, PO 6100064, People's Republic of China.
| | - Andrey A Zamyatnin
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, Trubetskaya str. 8-2, Moscow, 119991, Russian Federation; Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russian Federation.
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18
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Zhang W, Wang SL. A Novel Method for Identifying the Potential Cancer Driver Genes Based on Molecular Data Integration. Biochem Genet 2019; 58:16-39. [PMID: 31115714 DOI: 10.1007/s10528-019-09924-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2019] [Accepted: 05/02/2019] [Indexed: 12/17/2022]
Abstract
The identification of the cancer driver genes is essential for personalized therapy. The mutation frequency of most driver genes is in the middle (2-20%) or even lower range, which makes it difficult to find the driver genes with low-frequency mutations. Other forms of genomic aberrations, such as copy number variations (CNVs) and epigenetic changes, may also reflect cancer progression. In this work, a method for identifying the potential cancer driver genes (iPDG) based on molecular data integration is proposed. DNA copy number variation, somatic mutation, and gene expression data of matched cancer samples are integrated. In combination with the method of iKEEG, the "key genes" of cancer are identified, and the change in their expression levels is used for auxiliary evaluation of whether the mutated genes are potential drivers. For a mutated gene, the concept of mutational effect is defined, which takes into account the effects of copy number variation, mutation gene itself, and its neighbor genes. The method mainly includes two steps: the first step is data preprocessing. First, DNA copy number variation and somatic mutation data are integrated. Then, the integrated data are mapped to a given interaction network, and the diffusion kernel is used to form the mutation effect matrix. The second step is to obtain the key genes by using the iKGGE method, and construct the connection matrix by means of the gene expression data of the key genes and mutation impact matrix of the mutated genes. Experiments on TCGA breast cancer and Glioblastoma multiforme datasets demonstrate that iPDG is effective not only to identify the known cancer driver genes but also to discover the rare potential driver genes. When measured by functional enrichment analysis, we find that these genes are clearly associated with these two types of cancers.
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Affiliation(s)
- Wei Zhang
- College of Computer Science and Electronics Engineering, Hunan University, Changsha, 410082, Hunan, China
| | - Shu-Lin Wang
- College of Computer Science and Electronics Engineering, Hunan University, Changsha, 410082, Hunan, China.
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19
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Savini C, Yang R, Savelyeva L, Göckel-Krzikalla E, Hotz-Wagenblatt A, Westermann F, Rösl F. Folate Repletion after Deficiency Induces Irreversible Genomic and Transcriptional Changes in Human Papillomavirus Type 16 (HPV16)-Immortalized Human Keratinocytes. Int J Mol Sci 2019; 20:ijms20051100. [PMID: 30836646 PMCID: PMC6429418 DOI: 10.3390/ijms20051100] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 02/19/2019] [Accepted: 02/23/2019] [Indexed: 01/01/2023] Open
Abstract
Supplementation of micronutrients like folate is a double-edged sword in terms of their ambivalent role in cell metabolism. Although several epidemiological studies support a protective role of folate in carcinogenesis, there are also data arguing for an opposite effect. To address this issue in the context of human papillomavirus (HPV)-induced transformation, the molecular events of different folate availability on human keratinocytes immortalized by HPV16 E6 and E7 oncoproteins were examined. Several sublines were established: Control (4.5 µM folate), folate deficient (0.002 µM folate), and repleted cells (4.5 µM folate). Cells were analyzed in terms of oncogene expression, DNA damage and repair, karyotype changes, whole-genome sequencing, and transcriptomics. Here we show that folate depletion irreversibly induces DNA damage, impairment of DNA repair fidelity, and unique chromosomal alterations. Repleted cells additionally underwent growth advantage and enhanced clonogenicity, while the above mentioned impaired molecular properties became even more pronounced. Overall, it appears that a period of folate deficiency followed by repletion can shape immortalized cells toward an anomalous phenotype, thereby potentially contributing to carcinogenesis. These observations should elicit questions and inquiries for broader additional studies regarding folate fortification programs, especially in developing countries with micronutrient deficiencies and high HPV prevalence.
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Affiliation(s)
- Claudia Savini
- Division of Viral Transformation Mechanisms, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.
| | - Ruwen Yang
- Division of Viral Transformation Mechanisms, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.
| | - Larisa Savelyeva
- Division of Neuroblastoma Genomics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.
| | - Elke Göckel-Krzikalla
- Division of Viral Transformation Mechanisms, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.
| | - Agnes Hotz-Wagenblatt
- Omics IT and Data Management, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.
| | - Frank Westermann
- Division of Neuroblastoma Genomics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.
| | - Frank Rösl
- Division of Viral Transformation Mechanisms, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.
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20
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Liu Y, Xu S, Lian X, Su Y, Zhong Y, Lv R, Mo K, Zhu H, Xiaojiang W, Xu L, Wang S. Atypical GATA protein TRPS1 plays indispensable roles in mouse two-cell embryo. Cell Cycle 2019; 18:437-451. [PMID: 30712485 DOI: 10.1080/15384101.2019.1577650] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Zygotic genome activation (ZGA) is one of the most critical events at the beginning of mammalian preimplantation embryo development (PED). The mechanisms underlying mouse ZGA remain unclear although it has been widely studied. In the present study, we identified that tricho-rhino-phalangeal syndrome 1 (TRPS1), an atypical GATA family member, is an important factor for ZGA in mouse PED. We found that the Trps1 mRNA level peaked at the one-cell stage while TRPS1 protein did so at the two/four-cell stage. Knockdown of Trps1 by the microinjection of Trps1 siRNA reduced the developmental rate of mouse preimplantation embryos by approximately 30%, and increased the expression of ZGA marker genes MuERV-L and Zscan4d via suppressing the expression of major histone markers H3K4me3 and H3K27me3. Furthermore, Trps1 knockdown decreased the expression of Sox2 but increased Oct4 expression. We conclude that TRPS1 may be indispensable for zygotic genome activation during mouse PED.
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Affiliation(s)
- Yue Liu
- a Key Laboratory of Stem Cell Engineering and Regenerative Medicine , Fujian Province University
| | - Songhua Xu
- b Department of Human Anatomy, Histology and Embryology , Fujian Medical University , Fuzhou , P. R. China
| | - Xiuli Lian
- b Department of Human Anatomy, Histology and Embryology , Fujian Medical University , Fuzhou , P. R. China
| | - Yang Su
- b Department of Human Anatomy, Histology and Embryology , Fujian Medical University , Fuzhou , P. R. China
| | - Yuhuan Zhong
- b Department of Human Anatomy, Histology and Embryology , Fujian Medical University , Fuzhou , P. R. China
| | - Ruimin Lv
- b Department of Human Anatomy, Histology and Embryology , Fujian Medical University , Fuzhou , P. R. China
| | - Kaien Mo
- b Department of Human Anatomy, Histology and Embryology , Fujian Medical University , Fuzhou , P. R. China
| | - Huimin Zhu
- c Fujian Key Laboratory of Medical Bioinformatics, School of Basic Medical Sciences , Fujian Medical University , Fuzhou , P. R. China.,d Key Laboratory of Ministry of Education for Gastrointestinal Cancer, School of Basic Medical Sciences , Fujian Medical University , Fuzhou , P. R. China
| | - Wang Xiaojiang
- b Department of Human Anatomy, Histology and Embryology , Fujian Medical University , Fuzhou , P. R. China
| | - Lixuan Xu
- b Department of Human Anatomy, Histology and Embryology , Fujian Medical University , Fuzhou , P. R. China
| | - Shie Wang
- a Key Laboratory of Stem Cell Engineering and Regenerative Medicine , Fujian Province University.,b Department of Human Anatomy, Histology and Embryology , Fujian Medical University , Fuzhou , P. R. China
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21
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Atypical GATA transcription factor TRPS1 represses gene expression by recruiting CHD4/NuRD(MTA2) and suppresses cell migration and invasion by repressing TP63 expression. Oncogenesis 2018; 7:96. [PMID: 30563971 PMCID: PMC6299095 DOI: 10.1038/s41389-018-0108-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Revised: 10/30/2018] [Accepted: 11/26/2018] [Indexed: 01/10/2023] Open
Abstract
Transcriptional repressor GATA binding 1 (TRPS1), an atypical GATA transcription factor, functions as a transcriptional repressor and is also implicated in human cancers. However, the underlying mechanism of TRPS1 contributing to malignancy remains obscure. In the current study, we report that TRPS1 recognizes both gene proximal and distal transcription start site (TSS) sequences to repress gene expression. Co-IP mass spectrometry and biochemical studies showed that TRPS1 binds to CHD4/NuRD(MTA2). Genome-wide and molecular studies revealed that CHD4/NuRD(MTA2) is required for TRPS1 transcriptional repression. Mechanically, TRPS1 and CHD4/NuRD(MTA2) form precision-guided transcriptional repression machinery in which TRPS1 guides the machinery to specific target sites by recognizing GATA elements, and CHD4/NuRD(MTA2) represses the transcription of target genes. Furthermore, TP63 was identified and validated to be a direct target of TRPS1-CHD4/NuRD(MTA2) complex, which represses TP63 expression by involving decommission of TP63 enhancer in the described precision-guided manner, leading to a reduction of the ΔNp63 level and contributing to migration and invasion of cancer cells.
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22
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Gong X, Liu W, Wu L, Ma Z, Wang Y, Yu S, Zhang J, Xie H, Wei G, Ma F, Lu L, Chen L. Transcriptional repressor GATA binding 1-mediated repression of SRY-box 2 expression suppresses cancer stem cell functions and tumor initiation. J Biol Chem 2018; 293:18646-18654. [PMID: 30315105 DOI: 10.1074/jbc.ra118.003983] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 10/09/2018] [Indexed: 01/22/2023] Open
Abstract
Cancer stem cells (CSCs) have been reported in a variety of cancers. SRY-box 2 (SOX2) is a member of the SOX family of transcription factors and has been shown to play a critical role in maintaining the functions of CSCs and promoting tumor initiation. However, the underlying mechanisms for the transcriptional regulation of the SOX2 gene in CSCs are unclear. In this study, using in silico and experimental approaches, we identified transcriptional repressor GATA binding 1 (TRPS1), an atypical GATA-type transcription factor, as a critical transcriptional regulator that represses SOX2 expression and thereby suppresses cancer stemness and tumorigenesis. Mechanistically, TRPS1 repressed SOX2 expression by directly targeting the consensus GATA-binding element in the SOX2 promoter as elucidated by ChIP and luciferase reporter assays. Of note, in vitro mammosphere formation assays in culture and in vivo xenograft tumor initiation experiments in mouse models revealed that TRPS1-mediated repression of SOX2 expression suppresses CSC functions and tumor initiation. Taken together, our study provides detailed mechanistic insights into CSC functions and tumor initiation by the TRPS1-SOX2 axis.
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Affiliation(s)
- Xue Gong
- From the Institute of Life Science, Southeast University, Nanjing 210096, China.,the Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Science, Nanjing Normal University, Nanjing 210023, China
| | - Weiguang Liu
- the Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Science, Nanjing Normal University, Nanjing 210023, China
| | - Lele Wu
- the Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Science, Nanjing Normal University, Nanjing 210023, China
| | - Zhifang Ma
- the Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Science, Nanjing Normal University, Nanjing 210023, China
| | - Yuzhi Wang
- From the Institute of Life Science, Southeast University, Nanjing 210096, China.,the Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Science, Nanjing Normal University, Nanjing 210023, China
| | - Shiyi Yu
- the Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Science, Nanjing Normal University, Nanjing 210023, China
| | - Jun Zhang
- the Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Science, Nanjing Normal University, Nanjing 210023, China
| | - Hao Xie
- From the Institute of Life Science, Southeast University, Nanjing 210096, China
| | - Guanyun Wei
- the Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Science, Nanjing Normal University, Nanjing 210023, China
| | - Fei Ma
- the Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Science, Nanjing Normal University, Nanjing 210023, China
| | - Ling Lu
- the Department of Otolaryngology-Head and Neck Surgery, DrumTower Clinical Medical College of Nanjing Medical University, Nanjing 210008, China, and.,the Department of Otolaryngology-Head and Neck Surgery, Nanjing Drum Tower Hospital Affiliated to Nanjing University Medical School, Nanjing, Jiangsu 210008, China
| | - Liming Chen
- From the Institute of Life Science, Southeast University, Nanjing 210096, China, .,the Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Science, Nanjing Normal University, Nanjing 210023, China
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23
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Serandour AA, Mohammed H, Miremadi A, Mulder KW, Carroll JS. TRPS1 regulates oestrogen receptor binding and histone acetylation at enhancers. Oncogene 2018; 37:5281-5291. [PMID: 29895970 PMCID: PMC6169732 DOI: 10.1038/s41388-018-0312-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 03/26/2018] [Accepted: 04/16/2018] [Indexed: 12/21/2022]
Abstract
The chromatin state is finely tuned to regulate function and specificity for transcription factors such as oestrogen receptor alpha (ER), which contributes to cell growth in breast cancer. ER transcriptional potential is mediated, in large part, by the specific associated proteins and co-factors that interact with it. Despite the identification and characterisation of several ER coregulators, a complete and systematic view of ER-regulating chromatin modifiers is lacking. By exploiting a focused siRNA screen that investigated the requirement for a library of 330 chromatin regulators in ER-mediated cell growth, we find that the NuRD and coREST histone deacetylation complexes are critical for breast cancer cell proliferation. Further, by proteomic and genomics approaches, we discover the transcription factor TRPS1 to be a key interactor of the NuRD and coREST complexes. Interestingly, TRPS1 gene amplification occurs in 28% of human breast tumours and is associated with poor prognosis. We propose that TRPS1 is required to repress spurious binding of ER, where it contributes to the removal of histone acetylation. Our data suggest that TRPS1 is an important ER-associated transcriptional repressor that regulates cell proliferation, chromatin acetylation and ER binding at the chromatin of cis-regulatory elements.
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Affiliation(s)
- A A Serandour
- Cambridge Institute, Cancer Research UK, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
- CRCINA, INSERM, CNRS, Université d'Angers, Université de Nantes; Ecole Centrale de Nantes, Nantes, France
| | - H Mohammed
- Cambridge Institute, Cancer Research UK, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
- Knight Cancer Early Detection Advanced Research Center, Oregon Health and Science University, Portland, Oregon, USA
| | - A Miremadi
- Cambridge Institute, Cancer Research UK, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
| | - K W Mulder
- Cambridge Institute, Cancer Research UK, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK.
- Faculty of Science, Radboud Institute for Molecular Life Sciences, Department of Molecular Developmental Biology, Radboud University, Nijmegen, The Netherlands.
| | - J S Carroll
- Cambridge Institute, Cancer Research UK, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK.
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24
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Wang Y, Zhang J, Wu L, Liu W, Wei G, Gong X, Liu Y, Ma Z, Ma F, Thiery JP, Chen L. Tricho-rhino-phalangeal syndrome 1 protein functions as a scaffold required for ubiquitin-specific protease 4-directed histone deacetylase 2 de-ubiquitination and tumor growth. Breast Cancer Res 2018; 20:83. [PMID: 30071870 PMCID: PMC6090974 DOI: 10.1186/s13058-018-1018-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 07/10/2018] [Indexed: 12/31/2022] Open
Abstract
Background Although numerous studies have reported that tricho-rhino-phalangeal syndrome type I (TRPS1) protein, the only reported atypical GATA transcription factor, is overexpressed in various carcinomas, the underlying mechanism(s) by which it contributes to cancer remain unknown. Methods Both overexpression and knockdown of TRPS1 assays were performed to examine the effect of TRPS1 on histone deacetylase 2 (HDAC2) protein level and luminal breast cancer cell proliferation. Also, RT-qRCR, luciferase reporter assay and RNA-sequencing were used for transcription detection. Chromatin immunoprecipitation (ChIP) using H4K16ac antibody in conjunction with qPCR was used for determining H4K16ac levels in targeted genes. Furthermore, in vitro cell proliferation assay and in vivo tumor xenografts were used to detect the effect of TRPS1 on tumor growth. Results We found that TRPS1 scaffolding recruits and enhances interaction between USP4 and HDAC2 leading to HDAC2 de-ubiquitination and H4K16 deacetylation. We detected repression of a set of cellular growth-related genes by the TRPS1-USP4-HDAC2 axis indicating it is essential in tumor growth. In vitro and in vivo experiments confirmed that silencing TRPS1 reduced tumor growth, whereas overexpression of HDAC2 restored tumor growth. Conclusion Our study deciphered the TRPS1-USP4-HDAC2 axis as a novel mechanism that contributes to tumor growth. Significantly, our results revealed the scaffolding function of TPRS1 in USP4-directed HDAC2 de-ubiquitination and provided new mechanistic insights into the crosstalk between TRPS1, ubiquitin, and histone modification systems leading to tumor growth. Electronic supplementary material The online version of this article (10.1186/s13058-018-1018-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yuzhi Wang
- The Key Laboratory of Developmental Genes and Human Disease, Ministry of Education, Institute of Life Science, Southeast University, Nanjing, 210096, People's Republic of China.,Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Science, Nanjing Normal University, Nanjing, 210023, People's Republic of China
| | - Jun Zhang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Science, Nanjing Normal University, Nanjing, 210023, People's Republic of China
| | - Lele Wu
- The Key Laboratory of Developmental Genes and Human Disease, Ministry of Education, Institute of Life Science, Southeast University, Nanjing, 210096, People's Republic of China.,Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Science, Nanjing Normal University, Nanjing, 210023, People's Republic of China
| | - Weiguang Liu
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Science, Nanjing Normal University, Nanjing, 210023, People's Republic of China
| | - Guanyun Wei
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Science, Nanjing Normal University, Nanjing, 210023, People's Republic of China
| | - Xue Gong
- The Key Laboratory of Developmental Genes and Human Disease, Ministry of Education, Institute of Life Science, Southeast University, Nanjing, 210096, People's Republic of China.,Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Science, Nanjing Normal University, Nanjing, 210023, People's Republic of China
| | - Yan Liu
- The Key Laboratory of Developmental Genes and Human Disease, Ministry of Education, Institute of Life Science, Southeast University, Nanjing, 210096, People's Republic of China.,Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Science, Nanjing Normal University, Nanjing, 210023, People's Republic of China
| | - Zhifang Ma
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Science, Nanjing Normal University, Nanjing, 210023, People's Republic of China
| | - Fei Ma
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Science, Nanjing Normal University, Nanjing, 210023, People's Republic of China
| | - Jean Paul Thiery
- Cancer Science Institute, National University of Singapore, 14 Medical Drive, Singapore, Singapore.,Institute of Molecular and Cell Biology, A*STAR, 61 Biopolis Drive, Singapore, Singapore.,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore, Singapore
| | - Liming Chen
- The Key Laboratory of Developmental Genes and Human Disease, Ministry of Education, Institute of Life Science, Southeast University, Nanjing, 210096, People's Republic of China. .,Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Science, Nanjing Normal University, Nanjing, 210023, People's Republic of China.
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25
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Browne AL, Charmsaz S, Varešlija D, Fagan A, Cosgrove N, Cocchiglia S, Purcell S, Ward E, Bane F, Hudson L, Hill AD, Carroll JS, Redmond AM, Young LS. Network analysis of SRC-1 reveals a novel transcription factor hub which regulates endocrine resistant breast cancer. Oncogene 2018; 37:2008-2021. [PMID: 29367763 PMCID: PMC5895607 DOI: 10.1038/s41388-017-0042-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Revised: 09/26/2017] [Accepted: 09/29/2017] [Indexed: 01/15/2023]
Abstract
Steroid receptor coactivator 1 (SRC-1) interacts with nuclear receptors and other transcription factors (TFs) to initiate transcriptional networks and regulate downstream genes which enable the cancer cell to evade therapy and metastasise. Here we took a top-down discovery approach to map out the SRC-1 transcriptional network in endocrine resistant breast cancer. First, rapid immunoprecipitation mass spectrometry of endogenous proteins (RIME) was employed to uncover new SRC-1 TF partners. Next, RNA sequencing (RNAseq) was undertaken to investigate SRC-1 TF target genes. Molecular and patient-derived xenograft studies confirmed STAT1 as a new SRC-1 TF partner, important in the regulation of a cadre of four SRC-1 transcription targets, NFIA, SMAD2, E2F7 and ASCL1. Extended network analysis identified a downstream 79 gene network, the clinical relevance of which was investigated in RNAseq studies from matched primary and local-recurrence tumours from endocrine resistant patients. We propose that SRC-1 can partner with STAT1 independently of the estrogen receptor to initiate a transcriptional cascade and control regulation of key endocrine resistant genes.
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Affiliation(s)
- Alacoque L Browne
- Endocrine Oncology Research Group, Department of Surgery, Royal College of Surgeons, Dublin, Ireland
| | - Sara Charmsaz
- Endocrine Oncology Research Group, Department of Surgery, Royal College of Surgeons, Dublin, Ireland
| | - Damir Varešlija
- Endocrine Oncology Research Group, Department of Surgery, Royal College of Surgeons, Dublin, Ireland
| | - Ailis Fagan
- Endocrine Oncology Research Group, Department of Surgery, Royal College of Surgeons, Dublin, Ireland
| | - Nicola Cosgrove
- Endocrine Oncology Research Group, Department of Surgery, Royal College of Surgeons, Dublin, Ireland
| | - Sinéad Cocchiglia
- Endocrine Oncology Research Group, Department of Surgery, Royal College of Surgeons, Dublin, Ireland
| | - Siobhan Purcell
- Endocrine Oncology Research Group, Department of Surgery, Royal College of Surgeons, Dublin, Ireland
| | - Elspeth Ward
- Endocrine Oncology Research Group, Department of Surgery, Royal College of Surgeons, Dublin, Ireland
| | - Fiona Bane
- Endocrine Oncology Research Group, Department of Surgery, Royal College of Surgeons, Dublin, Ireland
| | - Lance Hudson
- Endocrine Oncology Research Group, Department of Surgery, Royal College of Surgeons, Dublin, Ireland
| | - Arnold D Hill
- Endocrine Oncology Research Group, Department of Surgery, Royal College of Surgeons, Dublin, Ireland
| | - Jason S Carroll
- Cancer Research UK, Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Aisling M Redmond
- Cancer Research UK, Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Leonie S Young
- Endocrine Oncology Research Group, Department of Surgery, Royal College of Surgeons, Dublin, Ireland.
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26
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Liu H, Liao Y, Tang M, Wu T, Tan D, Zhang S, Wang H. Trps1 is associated with the multidrug resistance of lung cancer cell by regulating MGMT gene expression. Cancer Med 2018; 7:1921-1932. [PMID: 29601666 PMCID: PMC5943538 DOI: 10.1002/cam4.1421] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 01/05/2018] [Accepted: 01/29/2018] [Indexed: 12/12/2022] Open
Abstract
Multidrug resistance (MDR) often leads to chemotherapy failure of lung cancer and has been linking to the cellular expression of several DNA transcription- and repair-related genes such as Trps1 and MGMT. However, their roles in the formation of MDR are largely unknown. In this study, overexpression/knockdown, luciferase assay and ChIP assay were performed to study the relationship between Trps1 and MGMT, as well as their roles in MDR formation. Our results demonstrated that Trps1 and MGMT expression both increased in drug-resistant lung cancer cell line (H446/CDDP). Silencing of Trps1 resulted in downregulation of MGMT expression and decrease in the multidrug sensitivity of H446/CDDP cells, while Trps1 overexpression exhibited the opposite effects in H446 cells. Ectopic expression of MGMT had no effect on Trps1 expression, but enhanced the IC50 values of H446 cells or rescued the IC50 values of Trps1-silenced H446/CDDP cells in treatment of multidrug. Our data further showed that, mechanistically, Trps1 acted as a transcription activator that directly induced MGMT transcription by binding to the MGMT promoter. Taken together, we consider that upregulation of Trps1 induces MGMT transcription contributing to the formation of MDR in lung cancer cells. Our findings proved potential targets for reversing MDR in clinical chemotherapy of lung cancer.
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Affiliation(s)
- Hongxiang Liu
- Cardiothoracic Surgery Department, Southwest Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Yi Liao
- Cardiothoracic Surgery Department, Southwest Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Meng Tang
- Cardiothoracic Surgery Department, Southwest Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Tao Wu
- Cardiothoracic Surgery Department, Southwest Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Deli Tan
- Cardiothoracic Surgery Department, Southwest Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Shixin Zhang
- Cardiothoracic Surgery Department, Southwest Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Haidong Wang
- Cardiothoracic Surgery Department, Southwest Hospital, Army Medical University (Third Military Medical University), Chongqing, China
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27
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Hu J, Su P, Jiao M, Bai X, Qi M, Liu H, Wu Z, Sun J, Zhou G, Han B. TRPS1 Suppresses Breast Cancer Epithelial-mesenchymal Transition Program as a Negative Regulator of SUZ12. Transl Oncol 2018; 11:416-425. [PMID: 29471243 PMCID: PMC5884189 DOI: 10.1016/j.tranon.2018.01.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 01/16/2018] [Accepted: 01/16/2018] [Indexed: 12/12/2022] Open
Abstract
Breast cancer (BC) is among the most common malignant diseases and metastasis is the handcuff of treatment. Cancer metastasis is a multistep process associated with the epithelial-mesenchymal transition (EMT) program. Several studies have demonstrated that transcriptional repressor GATA binding 1 (TRPS1) played important roles in development and progression of primary BC. In this study we sought to identify the mechanisms responsible for this function of TRPS1 in the continuum of the metastatic cascade. Here we described that TRPS1 was significantly associated with BC metastasis using public assessable datasets. Clinically, loss of TRPS1 expression in BC was related to higher histological grade. In vitro functional study and bioinformatics analysis revealed that TRPS1 inhibited cell migration and EMT in BC. Importantly, we identified SUZ12 as a novel target of TRPS1 related to EMT program. ChIP assay demonstrated TRPS1 directly inhibited SUZ12 transcription by binding to the SUZ12 promoter. Loss of TRPS1 resulted in increased SUZ12 binding and H3K27 tri-methylation at the CDH1 promoter and repression of E-cadherin. In all, our data indicated that TRPS1 maintained the expression of E-cadherin by inhibiting SUZ12, which might provide novel insight into how loss of TRPS1 contributed to BC progression.
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Affiliation(s)
- Jing Hu
- Department of Pathology, Shandong University, School of Basic Medicine, Jinan, 250012, China
| | - Peng Su
- Department of Pathology, Shandong University Qilu Hospital, Jinan, 250012, China
| | - Meng Jiao
- Department of Pathology, Shandong University, School of Basic Medicine, Jinan, 250012, China
| | - Xinnuo Bai
- Department of Pathology, Shandong University, School of Basic Medicine, Jinan, 250012, China
| | - Mei Qi
- Department of Pathology, Shandong University Qilu Hospital, Jinan, 250012, China
| | - Hui Liu
- Department of Pathology, Shandong University, School of Basic Medicine, Jinan, 250012, China
| | - Zhen Wu
- Department of Pathology, Shandong University, School of Basic Medicine, Jinan, 250012, China
| | - Jingtian Sun
- Department of Pathology, Shandong University, School of Basic Medicine, Jinan, 250012, China
| | - Gengyin Zhou
- Department of Pathology, Shandong University Qilu Hospital, Jinan, 250012, China
| | - Bo Han
- Department of Pathology, Shandong University, School of Basic Medicine, Jinan, 250012, China; Department of Pathology, Shandong University Qilu Hospital, Jinan, 250012, China.
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28
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Tong J, Zhan P, Wang XS, Wu Y. Quionolone carboxylic acid derivatives as HIV-1 integrase inhibitors: Docking-based HQSAR and topomer CoMFA analyses. JOURNAL OF CHEMOMETRICS 2017; 31:e2934. [PMID: 29606793 PMCID: PMC5875935 DOI: 10.1002/cem.2934] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Quionolone carboxylic acid derivatives as inhibitors of HIV-1 integrase were investigated as a potential class of drugs for the treatment of acquired immunodeficiency syndrome (AIDS). Hologram quantitative structure-activity relationships (HQSAR) and translocation comparative molecular field vector analysis (topomer CoMFA) were applied to a series of 48 quionolone carboxylic acid derivatives. The most effective HQSAR model was obtained using atoms and bonds as fragment distinctions: cross-validation q2 = 0.796, standard error of prediction SDCV = 0.36, the non-cross-validated r2 = 0.967, non-cross validated standard error SD = 0.17, the correlation coefficient of external validation Qext2 = 0.955, and the best hologram length HL = 180. topomer CoMFA models were built based on different fragment cutting models, with the most effective model of q2 = 0.775, SDCV = 0.37, r2 = 0.967, SD = 0.15, Qext2 = 0.915, and F = 163.255. These results show that the models generated form HQSAR and topomer CoMFA were able to effectively predict the inhibitory potency of this class of compounds. The molecular docking method was also used to study the interactions of these drugs by docking the ligands into the HIV-1 integrase active site, which revealed the likely bioactive conformations. This study showed that there are extensive interactions between the quionolone carboxylic acid derivatives and THR80, VAL82, GLY27, ASP29, and ARG8 residues in the active site of HIV-1 integrase. These results provide useful insights for the design of potent new inhibitors of HIV-1 integrase.
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Affiliation(s)
- Jianbo Tong
- College of Chemistry and Chemical Engineering, Shaanxi University of Science and Technology, Xi’an 710021, China
| | - Pei Zhan
- College of Chemistry and Chemical Engineering, Shaanxi University of Science and Technology, Xi’an 710021, China
| | - Xiang Simon Wang
- Department of Pharmaceutical Sciences, College of Pharmacy, Howard University, Washington, District of Columbia 20059, USA
| | - Yingji Wu
- College of Chemistry and Chemical Engineering, Shaanxi University of Science and Technology, Xi’an 710021, China
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29
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Wilke CM, Hess J, Klymenko SV, Chumak VV, Zakhartseva LM, Bakhanova EV, Feuchtinger A, Walch AK, Selmansberger M, Braselmann H, Schneider L, Pitea A, Steinhilber J, Fend F, Bösmüller HC, Zitzelsberger H, Unger K. Expression of miRNA-26b-5p and its target TRPS1 is associated with radiation exposure in post-Chernobyl breast cancer. Int J Cancer 2017; 142:573-583. [PMID: 28944451 DOI: 10.1002/ijc.31072] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 08/10/2017] [Accepted: 08/31/2017] [Indexed: 02/06/2023]
Abstract
Ionizing radiation is a well-recognized risk factor for the development of breast cancer. However, it is unknown whether radiation-specific molecular oncogenic mechanisms exist. We investigated post-Chernobyl breast cancers from radiation-exposed female clean-up workers and nonexposed controls for molecular changes. Radiation-associated alterations identified in the discovery cohort (n = 38) were subsequently validated in a second cohort (n = 39). Increased expression of hsa-miR-26b-5p was associated with radiation exposure in both of the cohorts. Moreover, downregulation of the TRPS1 protein, which is a transcriptional target of hsa-miR-26b-5p, was associated with radiation exposure. As TRPS1 overexpression is common in sporadic breast cancer, its observed downregulation in radiation-associated breast cancer warrants clarification of the specific functional role of TRPS1 in the radiation context. For this purpose, the impact of TRPS1 on the transcriptome was characterized in two radiation-transformed breast cell culture models after siRNA-knockdown. Deregulated genes upon TRPS1 knockdown were associated with DNA-repair, cell cycle, mitosis, cell migration, angiogenesis and EMT pathways. Furthermore, we identified the interaction partners of TRPS1 from the transcriptomic correlation networks derived from gene expression data on radiation-transformed breast cell culture models and sporadic breast cancer tissues provided by the TCGA database. The genes correlating with TRPS1 in the radiation-transformed breast cell lines were primarily linked to DNA damage response and chromosome segregation, while the transcriptional interaction partners in the sporadic breast cancers were mostly associated with apoptosis. Thus, upregulation of hsa-miR-26b-5p and downregulation of TRPS1 in radiation-associated breast cancer tissue samples suggests these molecules representing radiation markers in breast cancer.
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Affiliation(s)
- Christina M Wilke
- Research Unit Radiation Cytogenetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
| | - Julia Hess
- Research Unit Radiation Cytogenetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany.,Clinical Cooperation Group 'Personalized Radiotherapy in Head and Neck Cancer', Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, 85764, Germany
| | - Sergiy V Klymenko
- National Research Center for Radiation Medicine of National Academy of Medical Sciences of Ukraine, Kyiv, Ukraine
| | - Vadim V Chumak
- National Research Center for Radiation Medicine of National Academy of Medical Sciences of Ukraine, Kyiv, Ukraine
| | | | - Elena V Bakhanova
- National Research Center for Radiation Medicine of National Academy of Medical Sciences of Ukraine, Kyiv, Ukraine
| | - Annette Feuchtinger
- Research Unit Analytical Pathology, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
| | - Axel K Walch
- Research Unit Analytical Pathology, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
| | - Martin Selmansberger
- Research Unit Radiation Cytogenetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
| | - Herbert Braselmann
- Research Unit Radiation Cytogenetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany.,Clinical Cooperation Group 'Personalized Radiotherapy in Head and Neck Cancer', Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, 85764, Germany
| | - Ludmila Schneider
- Research Unit Radiation Cytogenetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany.,Clinical Cooperation Group 'Personalized Radiotherapy in Head and Neck Cancer', Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, 85764, Germany
| | - Adriana Pitea
- Research Unit Radiation Cytogenetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany.,Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
| | | | - Falko Fend
- Institute of Pathology and Neuropathology, Tübingen, Germany
| | | | - Horst Zitzelsberger
- Research Unit Radiation Cytogenetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany.,Clinical Cooperation Group 'Personalized Radiotherapy in Head and Neck Cancer', Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, 85764, Germany.,Department of Radiation Oncology, University Hospital, LMU Munich, München, Germany
| | - Kristian Unger
- Research Unit Radiation Cytogenetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany.,Clinical Cooperation Group 'Personalized Radiotherapy in Head and Neck Cancer', Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, 85764, Germany
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30
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Przytycki PF, Singh M. Differential analysis between somatic mutation and germline variation profiles reveals cancer-related genes. Genome Med 2017; 9:79. [PMID: 28841835 PMCID: PMC5574113 DOI: 10.1186/s13073-017-0465-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 08/07/2017] [Indexed: 12/30/2022] Open
Abstract
A major aim of cancer genomics is to pinpoint which somatically mutated genes are involved in tumor initiation and progression. We introduce a new framework for uncovering cancer genes, differential mutation analysis, which compares the mutational profiles of genes across cancer genomes with their natural germline variation across healthy individuals. We present DiffMut, a fast and simple approach for differential mutational analysis, and demonstrate that it is more effective in discovering cancer genes than considerably more sophisticated approaches. We conclude that germline variation across healthy human genomes provides a powerful means for characterizing somatic mutation frequency and identifying cancer driver genes. DiffMut is available at https://github.com/Singh-Lab/Differential-Mutation-Analysis.
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Affiliation(s)
- Pawel F Przytycki
- Department of Computer Science, Princeton University, Princeton, NJ, 08544, USA.,Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, 08544, USA
| | - Mona Singh
- Department of Computer Science, Princeton University, Princeton, NJ, 08544, USA. .,Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, 08544, USA.
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31
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Lin HY, Zeng D, Liang YK, Wei XL, Chen CF. GATA3 and TRPS1 are distinct biomarkers and prognostic factors in breast cancer: database mining for GATA family members in malignancies. Oncotarget 2017; 8:34750-34761. [PMID: 28423734 PMCID: PMC5471008 DOI: 10.18632/oncotarget.16160] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 02/13/2017] [Indexed: 02/05/2023] Open
Abstract
GATA transcription factors are zinc finger DNA binding proteins that activate transcription during development and cell differentiation. To date, 7 members of GATA family have been reported. However, the expression patterns and the exact roles of distinct GATA family members contributing to tumorigenesis and progression of breast cancer (BC) remain to be elucidated. Here, we studied the expression of GATA transcripts in a variety of tumor types compared with the normal controls using the ONCOMINE and GOBO databases, along with their corresponding expression profiles in an array of cancer cell lines through CCLE analysis. Based on Kaplan-Meier plotter, we further investigated the prognostic values of GATA members specifically high expressed in BC patients. It was found that, when compared with normal tissues, GATA3 and TRPS1 were distinctly high expressed in BC patients among all GATA members. GATA3 expression was significantly associated with ESR1, while TRPS1 was correlated with ERBB2. In survival analysis, GATA3 and TRPS1 mRNA high expressions were correlated to better survival in BC patients, and TRPS1 high expression was significantly associated with longer RFS in patients who have received chemotherapy. These results suggest that GATA3 and TRPS1 are distinct biomarkers and essential prognostic factors for breast cancer.
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Affiliation(s)
- Hao-Yu Lin
- Department of Breast and Thyroid Surgery, The First Affiliated Hospital of Shantou University Medical College, Shantou, China
| | - De Zeng
- Department of Breast Medical Oncology, Cancer Hospital of Shantou University Medical College, Shantou, China
- ChangJiang Scholar's Laboratory of Shantou University Medical College, Shantou, China
| | - Yuan-Ke Liang
- ChangJiang Scholar's Laboratory of Shantou University Medical College, Shantou, China
- Department of Medical Oncology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Xiao-Long Wei
- Department of Pathology, Cancer Hospital of SUMC, Shantou, China
| | - Chun-Fa Chen
- Department of Breast and Thyroid Surgery, The First Affiliated Hospital of Shantou University Medical College, Shantou, China
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32
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TRPS1 gene alterations in human subependymoma. J Neurooncol 2017; 134:133-138. [DOI: 10.1007/s11060-017-2496-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 05/14/2017] [Indexed: 11/25/2022]
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Do D, Bissonnette N, Lacasse P, Miglior F, Sargolzaei M, Zhao X, Ibeagha-Awemu E. Genome-wide association analysis and pathways enrichment for lactation persistency in Canadian Holstein cattle. J Dairy Sci 2017; 100:1955-1970. [DOI: 10.3168/jds.2016-11910] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 11/08/2016] [Indexed: 12/22/2022]
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Subramanian S, Chaparala S, Avali V, Ganapathiraju MK. A pilot study on the prevalence of DNA palindromes in breast cancer genomes. BMC Med Genomics 2016; 9:73. [PMID: 28117658 PMCID: PMC5260791 DOI: 10.1186/s12920-016-0232-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Background DNA palindromes are a unique pattern of repeat sequences that are present in the human genome. It consists of a sequence of nucleotides in which the second half is the complement of the first half but appearing in reverse order. These palindromic sequences may have a significant role in DNA replication, transcription and gene regulation processes. They occur frequently in human cancers by clustering at specific locations of the genome that undergo gene amplification and tumorigenesis. Moreover, some studies showed that palindromes are clustered in amplified regions of breast cancer genomes especially in chromosomes (chr) 8 and 11. With the large number of personal genomes and cancer genomes becoming available, it is now possible to study their association to diseases using computational methods. Here, we conducted a pilot study on chromosomes 8 and 11 of cancer genomes to identify computationally the differentially occurring palindromes. Methods We processed 69 breast cancer genomes from The Cancer Genome Atlas including serum-normal and tumor genomes, and 1000 Genomes to serve as control group. The Biological Language Modelling Toolkit (BLMT) computes palindromes in whole genomes. We developed a computational pipeline integrating BLMT to compute and compare prevalence of palindromes in personal genomes. Results We carried out a pilot study on chr 8 and chr 11 taking into account single nucleotide polymorphisms, insertions and deletions. Of all the palindromes that showed any variation in cancer genomes, 38% of what were near breast cancer genes happened to be the most differentiated palindromes in tumor (i.e. they ranked among the top 25% by our heuristic measure). Conclusions These results will shed light on the prevalence of palindromes in oncogenes and the mutations that are present in the palindromic regions that could contribute to genomic rearrangements, and breast cancer progression.
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Affiliation(s)
- Sandeep Subramanian
- Language Technologies Institute, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Srilakshmi Chaparala
- Department of Biomedical Informatics, University of Pittsburgh, 5607 Baum Blvd, Suite 522, Pittsburgh, PA, 15206, USA
| | - Viji Avali
- Department of Biomedical Informatics, University of Pittsburgh, 5607 Baum Blvd, Suite 522, Pittsburgh, PA, 15206, USA
| | - Madhavi K Ganapathiraju
- Department of Biomedical Informatics, University of Pittsburgh, 5607 Baum Blvd, Suite 522, Pittsburgh, PA, 15206, USA. .,Language Technologies Institute, Carnegie Mellon University, Pittsburgh, PA, 15213, USA.
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Huang R, Langdon SP, Tse M, Mullen P, Um IH, Faratian D, Harrison DJ. The role of HDAC2 in chromatin remodelling and response to chemotherapy in ovarian cancer. Oncotarget 2016; 7:4695-711. [PMID: 26683361 PMCID: PMC4826236 DOI: 10.18632/oncotarget.6618] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Accepted: 11/26/2015] [Indexed: 12/29/2022] Open
Abstract
Chromatin undergoes structural changes in response to extracellular and environmental signals. We observed changes in nuclear morphology in cancer tissue biopsied after chemotherapy and hypothesised that these DNA damage-induced changes are mediated by histone deacetylases (HDACs). Nuclear morphological changes in cell lines (PE01 and PE04 models) and a xenograft model (OV1002) were measured in response to platinum chemotherapy by image analysis of nuclear texture. HDAC2 expression increased in PEO1 cells treated with cisplatin at 24h, which was accompanied by increased expression of heterochromatin protein 1 (HP1). HDAC2 and HP1 expression were also increased after carboplatin treatment in the OV1002 carboplatin-sensitive xenograft model but not in the insensitive HOX424 model. Expression of DNA damage response pathways (pBRCA1, γH2AX, pATM, pATR) showed time-dependent changes after cisplatin treatment. HDAC2 knockdown by siRNA reduced HP1 expression, induced DNA double strand breaks (DSB) measured by γH2AX, and interfered with the activation of DNA damage response induced by cisplatin. Furthermore, HDAC2 depletion affected γH2AX foci formation, cell cycle distribution, and apoptosis triggered by cisplatin, and was additive to the inhibitory effect of cisplatin in cell lines. By inhibiting expression of HDAC2, reversible alterations in chromatin patterns during cisplatin treatment were observed. These results demonstrate quantifiable alterations in nuclear morphology after chemotherapy, and implicate HDAC2 in higher order chromatin changes and cellular DNA damage responses in ovarian cancer cells in vitro and in vivo.
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Affiliation(s)
- Rui Huang
- Division of Pathology, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Simon P Langdon
- Division of Pathology, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Matthew Tse
- Division of Pathology, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Peter Mullen
- School of Medicine, University of St Andrews, St Andrews, Fife KY16 9TF, UK
| | - In Hwa Um
- School of Medicine, University of St Andrews, St Andrews, Fife KY16 9TF, UK
| | - Dana Faratian
- Division of Pathology, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - David J Harrison
- School of Medicine, University of St Andrews, St Andrews, Fife KY16 9TF, UK
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Bach AS, Derocq D, Laurent-Matha V, Montcourrier P, Sebti S, Orsetti B, Theillet C, Gongora C, Pattingre S, Ibing E, Roger P, Linares LK, Reinheckel T, Meurice G, Kaiser FJ, Gespach C, Liaudet-Coopman E. Nuclear cathepsin D enhances TRPS1 transcriptional repressor function to regulate cell cycle progression and transformation in human breast cancer cells. Oncotarget 2016; 6:28084-103. [PMID: 26183398 PMCID: PMC4695046 DOI: 10.18632/oncotarget.4394] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Accepted: 06/15/2015] [Indexed: 11/25/2022] Open
Abstract
The lysosomal protease cathepsin D (Cath-D) is overproduced in breast cancer cells (BCC) and supports tumor growth and metastasis formation. Here, we describe the mechanism whereby Cath-D is accumulated in the nucleus of ERα-positive (ER+) BCC. We identified TRPS1 (tricho-rhino-phalangeal-syndrome 1), a repressor of GATA-mediated transcription, and BAT3 (Scythe/BAG6), a nucleo-cytoplasmic shuttling chaperone protein, as new Cath-D-interacting nuclear proteins. Cath-D binds to BAT3 in ER+ BCC and they partially co-localize at the surface of lysosomes and in the nucleus. BAT3 silencing inhibits Cath-D accumulation in the nucleus, indicating that Cath-D nuclear targeting is controlled by BAT3. Fully mature Cath-D also binds to full-length TRPS1 and they co-localize in the nucleus of ER+ BCC where they are associated with chromatin. Using the LexA-VP16 fusion co-activator reporter assay, we then show that Cath-D acts as a transcriptional repressor, independently of its catalytic activity. Moreover, microarray analysis of BCC in which Cath-D and/or TRPS1 expression were silenced indicated that Cath-D enhances TRPS1-mediated repression of several TRPS1-regulated genes implicated in carcinogenesis, including PTHrP, a canonical TRPS1 gene target. In addition, co-silencing of TRPS1 and Cath-D in BCC affects the transcription of cell cycle, proliferation and transformation genes, and impairs cell cycle progression and soft agar colony formation. These findings indicate that Cath-D acts as a nuclear transcriptional cofactor of TRPS1 to regulate ER+ BCC proliferation and transformation in a non-proteolytic manner.
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Affiliation(s)
- Anne-Sophie Bach
- IRCM, Institut de Recherche en Cancérologie de Montpellier, Montpellier, France.,INSERM U1194, Montpellier, France.,Université de Montpellier, Montpellier, France.,Institut Régional du Cancer de Montpellier, Montpellier, France
| | - Danielle Derocq
- IRCM, Institut de Recherche en Cancérologie de Montpellier, Montpellier, France.,INSERM U1194, Montpellier, France.,Université de Montpellier, Montpellier, France.,Institut Régional du Cancer de Montpellier, Montpellier, France
| | - Valérie Laurent-Matha
- IRCM, Institut de Recherche en Cancérologie de Montpellier, Montpellier, France.,INSERM U1194, Montpellier, France.,Université de Montpellier, Montpellier, France.,Institut Régional du Cancer de Montpellier, Montpellier, France
| | - Philippe Montcourrier
- IRCM, Institut de Recherche en Cancérologie de Montpellier, Montpellier, France.,INSERM U1194, Montpellier, France.,Université de Montpellier, Montpellier, France.,Institut Régional du Cancer de Montpellier, Montpellier, France
| | - Salwa Sebti
- IRCM, Institut de Recherche en Cancérologie de Montpellier, Montpellier, France.,INSERM U1194, Montpellier, France.,Université de Montpellier, Montpellier, France.,Institut Régional du Cancer de Montpellier, Montpellier, France
| | - Béatrice Orsetti
- IRCM, Institut de Recherche en Cancérologie de Montpellier, Montpellier, France.,INSERM U1194, Montpellier, France.,Université de Montpellier, Montpellier, France.,Institut Régional du Cancer de Montpellier, Montpellier, France
| | - Charles Theillet
- IRCM, Institut de Recherche en Cancérologie de Montpellier, Montpellier, France.,INSERM U1194, Montpellier, France.,Université de Montpellier, Montpellier, France.,Institut Régional du Cancer de Montpellier, Montpellier, France
| | - Céline Gongora
- IRCM, Institut de Recherche en Cancérologie de Montpellier, Montpellier, France.,INSERM U1194, Montpellier, France.,Université de Montpellier, Montpellier, France.,Institut Régional du Cancer de Montpellier, Montpellier, France
| | - Sophie Pattingre
- IRCM, Institut de Recherche en Cancérologie de Montpellier, Montpellier, France.,INSERM U1194, Montpellier, France.,Université de Montpellier, Montpellier, France.,Institut Régional du Cancer de Montpellier, Montpellier, France
| | - Eva Ibing
- Universität zu Lübeck, Lübeck, Germany
| | - Pascal Roger
- Department of Pathology, CHU Nimes, Nimes, France
| | - Laetitia K Linares
- IRCM, Institut de Recherche en Cancérologie de Montpellier, Montpellier, France.,INSERM U1194, Montpellier, France.,Université de Montpellier, Montpellier, France.,Institut Régional du Cancer de Montpellier, Montpellier, France
| | - Thomas Reinheckel
- Institute of Molecular Medicine and Cell Research, Albert-Ludwigs-University, Freiburg, Germany
| | - Guillaume Meurice
- Functional Genomic Plateform, Institut Gustave Roussy, Villejuif, France
| | | | - Christian Gespach
- INSERM U938, Molecular and Clinical Oncology, Paris 6 University Pierre et Marie Curie, Hôpital Saint-Antoine, Paris, France
| | - Emmanuelle Liaudet-Coopman
- IRCM, Institut de Recherche en Cancérologie de Montpellier, Montpellier, France.,INSERM U1194, Montpellier, France.,Université de Montpellier, Montpellier, France.,Institut Régional du Cancer de Montpellier, Montpellier, France
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Ju-Rong Y, Ke-Hong C, Kun H, Bi-Qiong F, Li-Rong L, Jian-Guo Z, Kai-Long L, Ya-Ni H. Transcription Factor Trps1 Promotes Tubular Cell Proliferation after Ischemia-Reperfusion Injury through cAMP-Specific 3',5'-Cyclic Phosphodiesterase 4D and AKT. J Am Soc Nephrol 2016; 28:532-544. [PMID: 27466160 DOI: 10.1681/asn.2016010009] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 06/29/2016] [Indexed: 11/03/2022] Open
Abstract
Trichorhinophalangeal 1 (Trps1) is a transcription factor essential for epithelial cell morphogenesis during kidney development, but the role of Trps1 in AKI induced by ischemia-reperfusion (I/R) remains unclear. Our study investigated Trps1 expression during kidney repair after acute I/R in rats and explored the molecular mechanisms by which Trps1 promotes renal tubular epithelial cell proliferation. Trps1 expression positively associated with the extent of renal repair after I/R injury. Compared with wild-type rats, rats with knockdown of Trps1 exhibited significantly delayed renal repair in the moderate I/R model, with lower GFR levels and more severe morphologic injury, whereas rats overexpressing Trps1 exhibited significantly accelerated renal repair after severe I/R injury. Additionally, knockdown of Trps1 inhibited and overexpression of Trps1 enhanced the proliferation of renal tubular epithelial cells in rats. Chromatin immunoprecipitation sequencing assays and RT-PCR revealed that Trps1 regulated cAMP-specific 3',5'-cyclic phosphodiesterase 4D (Pde4d) expression. Knockdown of Trps1 decreased the renal protein expression of Pde4d and phosphorylated Akt in rats, and dual luciferase analysis showed that Trps1 directly activated Pde4d transcription. Furthermore, knockdown of Pde4d or treatment with the phosphatidylinositol 3 kinase inhibitor wortmannin significantly inhibited Trps1-induced tubular cell proliferation in vitro Trps1 may promote tubular cell proliferation through the Pde4d/phosphatidylinositol 3 kinase/AKT signaling pathway, suggesting Trps1 as a potential therapeutic target for kidney repair after I/R injury.
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Affiliation(s)
- Yang Ju-Rong
- Department of Nephrology, Daping Hospital, Third Military Medical University, Chongqing, China; and
| | - Chen Ke-Hong
- Department of Nephrology, Daping Hospital, Third Military Medical University, Chongqing, China; and
| | - Huang Kun
- Department of Nephrology, Daping Hospital, Third Military Medical University, Chongqing, China; and
| | - Fu Bi-Qiong
- Department of Nephrology, Daping Hospital, Third Military Medical University, Chongqing, China; and
| | - Lin Li-Rong
- Department of Nephrology, Daping Hospital, Third Military Medical University, Chongqing, China; and
| | - Zhang Jian-Guo
- Department of Nephrology, Daping Hospital, Third Military Medical University, Chongqing, China; and
| | - Li Kai-Long
- Department of Nephrology, Daping Hospital, Third Military Medical University, Chongqing, China; and
| | - He Ya-Ni
- Department of Nephrology, Daping Hospital, Third Military Medical University, Chongqing, China; and .,Department of Nephrology, People's Liberation Army of China General Hospital, Institute of Nephrology, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing, China
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38
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Huang JZ, Chen M, Zeng M, Xu SH, Zou FY, Chen D, Yan GR. Down-regulation of TRPS1 stimulates epithelial-mesenchymal transition and metastasis through repression ofFOXA1. J Pathol 2016; 239:186-96. [PMID: 26969828 DOI: 10.1002/path.4716] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2015] [Revised: 02/02/2016] [Accepted: 02/20/2016] [Indexed: 02/06/2023]
Affiliation(s)
- Jin-Zhou Huang
- Institutes of Life and Health Engineering, Jinan University; and Biomedicine Research Centre; Third Affiliated Hospital of Guangzhou Medical University; People's Republic of China
| | - Min Chen
- Institutes of Life and Health Engineering, Jinan University; and Biomedicine Research Centre; Third Affiliated Hospital of Guangzhou Medical University; People's Republic of China
| | - Ming Zeng
- Institutes of Life and Health Engineering, Jinan University; and Biomedicine Research Centre; Third Affiliated Hospital of Guangzhou Medical University; People's Republic of China
| | - Song-Hui Xu
- Institutes of Life and Health Engineering, Jinan University; and Biomedicine Research Centre; Third Affiliated Hospital of Guangzhou Medical University; People's Republic of China
| | - Fei-Yan Zou
- Institutes of Life and Health Engineering, Jinan University; and Biomedicine Research Centre; Third Affiliated Hospital of Guangzhou Medical University; People's Republic of China
| | - De Chen
- Biomedicine Research Centre and Department of Surgery; Third Affiliated Hospital of Guangzhou Medical University; People's Republic of China
- Key Laboratory for Major Obstetric Diseases of Guangdong Province; Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes; Guangzhou People's Republic of China
| | - Guang-Rong Yan
- Institutes of Life and Health Engineering, Jinan University; and Biomedicine Research Centre; Third Affiliated Hospital of Guangzhou Medical University; People's Republic of China
- Biomedicine Research Centre and Department of Surgery; Third Affiliated Hospital of Guangzhou Medical University; People's Republic of China
- Key Laboratory for Major Obstetric Diseases of Guangdong Province; Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes; Guangzhou People's Republic of China
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39
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Li Z, Jia M, Wu X, Cui J, Pan A, Li L. Overexpression of Trps1 contributes to tumor angiogenesis and poor prognosis of human osteosarcoma. Diagn Pathol 2015; 10:167. [PMID: 26377811 PMCID: PMC4574144 DOI: 10.1186/s13000-015-0401-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Accepted: 08/28/2015] [Indexed: 01/08/2023] Open
Abstract
Background Trichorhinophalangeal syndrome 1 (Trps1) gene is a member of GATA transcription factor family and has an important function in tumorigenesis and progression. However, there are rare studies on its roles in carcinogenesis and prognostic significance in human osteosarcoma. Methods The expression of Trps1 was detected by immunohistochemistry, and MVD was evaluated to determine the amounts of microvessels by counting CD31-positive endothelial cells. Results Of the 74 cases that underwent study, Trps1-positive cases were 24. And it was associated with MVD significantly (P = 0.008). The data also exhibited more cases of remote metastasis (P = 0.013) and higher Enneking stage (P = 0.017) in Trps1-positive group compared to Trps1-negative group. Univariate analysis revealed that distant metastasis, MVD and Trps1 expression were associated with a lower 3-year overall survival rate and disease-free survival rate (P = 0.003, and P = 0.012 respectively). Furthermore, Trps1 and distant metastasis retained their significant prognostic effects on patients survival rate by multivariate analysis (P < 0.05). Conclusions Trps1 plays a crucial role in osteosarcoma angiogenesis, metastasis and clinical surgical stage. Trps1 can be a novel promising prognostic marker and therapeutic target, and antiangiogenic therapy which targets Trps1 molecule in patients with osteosarcoma may lead to improved prognosis and longer-term survival.
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Affiliation(s)
- Zhishuang Li
- Department of Pathology, Shandong University, School of Medicine, 44 Wenhua Xi Road, Jinan, Shandong, 250012, People's Republic of China.
| | - Ming Jia
- Department of Pathology, Shandong University, School of Medicine, 44 Wenhua Xi Road, Jinan, Shandong, 250012, People's Republic of China.
| | - Xiaojuan Wu
- Department of Pathology, Shandong University, School of Medicine, 44 Wenhua Xi Road, Jinan, Shandong, 250012, People's Republic of China.
| | - Jingjing Cui
- Shandong University, School of Medicine, 44 Wenhua Xi Road, Jinan, Shandong Province, 250012, People's Republic of China.
| | - Aifeng Pan
- Department of Pathology, Shandong University, School of Medicine, 44 Wenhua Xi Road, Jinan, Shandong, 250012, People's Republic of China.
| | - Li Li
- Department of Pathology, Shandong University, School of Medicine, 44 Wenhua Xi Road, Jinan, Shandong, 250012, People's Republic of China.
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40
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Amgalan B, Lee H. DEOD: uncovering dominant effects of cancer-driver genes based on a partial covariance selection method. Bioinformatics 2015; 31:2452-60. [PMID: 25819079 DOI: 10.1093/bioinformatics/btv175] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 03/23/2015] [Indexed: 01/02/2023] Open
Abstract
MOTIVATION The generation of a large volume of cancer genomes has allowed us to identify disease-related alterations more accurately, which is expected to enhance our understanding regarding the mechanism of cancer development. With genomic alterations detected, one challenge is to pinpoint cancer-driver genes that cause functional abnormalities. RESULTS Here, we propose a method for uncovering the dominant effects of cancer-driver genes (DEOD) based on a partial covariance selection approach. Inspired by a convex optimization technique, it estimates the dominant effects of candidate cancer-driver genes on the expression level changes of their target genes. It constructs a gene network as a directed-weighted graph by integrating DNA copy numbers, single nucleotide mutations and gene expressions from matched tumor samples, and estimates partial covariances between driver genes and their target genes. Then, a scoring function to measure the cancer-driver score for each gene is applied. To test the performance of DEOD, a novel scheme is designed for simulating conditional multivariate normal variables (targets and free genes) given a group of variables (driver genes). When we applied the DEOD method to both the simulated data and breast cancer data, DEOD successfully uncovered driver variables in the simulation data, and identified well-known oncogenes in breast cancer. In addition, two highly ranked genes by DEOD were related to survival time. The copy number amplifications of MYC (8q24.21) and TRPS1 (8q23.3) were closely related to the survival time with P-values = 0.00246 and 0.00092, respectively. The results demonstrate that DEOD can efficiently uncover cancer-driver genes.
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Affiliation(s)
- Bayarbaatar Amgalan
- School of Information and Communications, Gwangju Institute of Science and Technology, Gwangju, Republic of Korea
| | - Hyunju Lee
- School of Information and Communications, Gwangju Institute of Science and Technology, Gwangju, Republic of Korea
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