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Furuhashi S, Bustos MA, Mizuno S, Ryu S, Naeini Y, Bilchik AJ, Hoon DSB. Spatial profiling of cancer-associated fibroblasts of sporadic early onset colon cancer microenvironment. NPJ Precis Oncol 2023; 7:118. [PMID: 37964075 PMCID: PMC10645739 DOI: 10.1038/s41698-023-00474-w] [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: 04/30/2023] [Accepted: 10/24/2023] [Indexed: 11/16/2023] Open
Abstract
The incidence of sporadic early-onset colon cancer (EOCC) has increased worldwide. The molecular mechanisms in the tumor and the tumor microenvironment (TME) in EOCC are not fully understood. The aim of this study is to unravel unique spatial transcriptomic and proteomic profiles in tumor epithelial cells and cancer-associated fibroblasts (CAFs). Here, we divide the sporadic colon cancer tissue samples with transcriptomic data into patients diagnosed with EOCC (<50 yrs) and late-onset colon cancer (LOCC, ≥50 yrs) and then, analyze the data using CIBERSORTx deconvolution software. EOCC tumors are more enriched in CAFs with fibroblast associated protein positive expression (FAP(+)) than LOCC tumors. EOCC patients with higher FAP mRNA levels in CAFs have shorter OS (Log-rank test, p < 0.029). Spatial transcriptomic analysis of 112 areas of interest, using NanoString GeoMx digital spatial profiling, demonstrate that FAP(+) CAFs at the EOCC tumor invasive margin show a significant upregulation of WNT signaling and higher mRNA/protein levels of fibroblast growth factor 20 (FGF20). Tumor epithelial cells at tumor invasive margin of EOCC tumors neighboring FAP(+) CAFs show significantly higher mRNA/protein levels of fibroblast growth factor receptor (FGFR2) and PI3K/Akt signaling activation. NichNET analysis show a potential interaction between FGF20 and FGFFR2. The role of FGF20 in activating FGFR2/pFGFR2 and AKT/pAKT was validated in-vitro. In conclusion, we identify a unique FAP(+) CAF population that showed WNT signaling upregulation and increased FGF20 levels; while neighbor tumor cells show the upregulation/activation of FGFR2-PI3K/Akt signaling at the tumor invasive margin of EOCC tumors.
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Affiliation(s)
- Satoru Furuhashi
- Department of Translational Molecular Medicine, Saint John's Cancer Institute (SJCI), Providence Saint John's Health Center (SJHC), Santa Monica, CA, 90404, USA
| | - Matias A Bustos
- Department of Translational Molecular Medicine, Saint John's Cancer Institute (SJCI), Providence Saint John's Health Center (SJHC), Santa Monica, CA, 90404, USA
| | - Shodai Mizuno
- Department of Translational Molecular Medicine, Saint John's Cancer Institute (SJCI), Providence Saint John's Health Center (SJHC), Santa Monica, CA, 90404, USA
| | - Suyeon Ryu
- Department of Genome Sequencing Center, SJCI, Providence SJHC, Santa Monica, CA, 90404, USA
| | - Yalda Naeini
- Department of Surgical Pathology, Providence SJHC, Santa Monica, CA, 90404, USA
| | - Anton J Bilchik
- Department of Gastrointestinal and Hepatobiliary Surgery, Providence SJHC, Santa Monica, CA, 90404, USA
| | - Dave S B Hoon
- Department of Translational Molecular Medicine, Saint John's Cancer Institute (SJCI), Providence Saint John's Health Center (SJHC), Santa Monica, CA, 90404, USA.
- Department of Genome Sequencing Center, SJCI, Providence SJHC, Santa Monica, CA, 90404, USA.
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2
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Wu Y, Zhang X, Liu C, Li Z, Wen Y, Zheng R, Xu C, Tian J, Wei L, Wang J, Yan Q, Zheng X, Ma J. Epstein-Barr virus microRNA miR-BART2-5p accelerates nasopharyngeal carcinoma metastasis by suppressing RNase Ⅲ endonuclease DICER1. J Biol Chem 2023; 299:105082. [PMID: 37495108 PMCID: PMC10470218 DOI: 10.1016/j.jbc.2023.105082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 07/08/2023] [Accepted: 07/11/2023] [Indexed: 07/28/2023] Open
Abstract
The development and progression of nasopharyngeal carcinoma (NPC) is closely associated with Epstein-Barr virus (EBV) infection. NPC is usually asymptomatic until it spreads to other sites, and more than 70% of cases are classified as locally advanced disease at diagnosis. EBV-positive nasopharyngeal cancer tissues express only limited viral latent proteins, but express high levels of the EBV-encoded BamHI-A rightward transcript (BART) miRNA molecules. Here, we report that EBV-miRNA-BART2-5p (BART2-5p) promotes NPC cell invasion and metastasis in vivo and in vitro but has no effect on NPC cell proliferation and apoptosis. In addition, BART2-5p altered the mRNA and miRNA expression profiles of NPC cells. The development of human tumors has been reported to be associated with altered miRNAs expression, and overall miRNAs expression is reduced in many types of tumors. We found that BART2-5p downregulated the expression of several miRNAs that could exert oncogenic functions. Mechanistically, BART2-5p directly targets the RNase III endonuclease DICER1, inhibiting its function of cleaving double-stranded stem-loop RNA into short double-stranded RNA, which in turn causes altered expression of a series of key epithelial-mesenchymal transition molecules, and reverting DICER1 expression can rescue this phenotype. Furthermore, analysis from clinical samples showed a negative correlation between BART2-5p and DICER1 expression. According to our study, high expression of BART2-5p in tissues and plasma of patients with NPC is associated with poor prognosis. Our results suggest that, BART2-5p can accelerate NPC metastasis through modulating miRNA profiles which are mediated by DICER1, implying a novel role of EBV miRNAs in the pathogenesis of NPC.
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Affiliation(s)
- Yangge Wu
- NHC Key Laboratory of Carcinogenesis, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China; Cancer Research Institute and School of Basic Medical Science, Central South University, Changsha, China; Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Changsha, China
| | - Xiaoyue Zhang
- NHC Key Laboratory of Carcinogenesis, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China; Cancer Research Institute and School of Basic Medical Science, Central South University, Changsha, China; Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Changsha, China
| | - Can Liu
- NHC Key Laboratory of Carcinogenesis, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China; Cancer Research Institute and School of Basic Medical Science, Central South University, Changsha, China; Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Changsha, China
| | - Zhengshuo Li
- NHC Key Laboratory of Carcinogenesis, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China; Cancer Research Institute and School of Basic Medical Science, Central South University, Changsha, China; Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Changsha, China
| | - Yuqing Wen
- NHC Key Laboratory of Carcinogenesis, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China; Cancer Research Institute and School of Basic Medical Science, Central South University, Changsha, China; Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Changsha, China
| | - Run Zheng
- NHC Key Laboratory of Carcinogenesis, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China; Cancer Research Institute and School of Basic Medical Science, Central South University, Changsha, China; Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Changsha, China
| | - Chenxiao Xu
- NHC Key Laboratory of Carcinogenesis, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China; Cancer Research Institute and School of Basic Medical Science, Central South University, Changsha, China; Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Changsha, China
| | - Junrui Tian
- NHC Key Laboratory of Carcinogenesis, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China; Cancer Research Institute and School of Basic Medical Science, Central South University, Changsha, China; Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Changsha, China
| | - Lingyu Wei
- Department of Pathology and Immunology, Heping Hospital Affiliated to Changzhi Medical College, Changzhi, Shanxi, China
| | - Jia Wang
- Department of Pathology and Immunology, Heping Hospital Affiliated to Changzhi Medical College, Changzhi, Shanxi, China
| | - Qun Yan
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, China.
| | - Xiang Zheng
- Department of Pathology, Affiliated Hospital of Guilin Medical University, Guilin, Guangxi, China.
| | - Jian Ma
- NHC Key Laboratory of Carcinogenesis, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China; Cancer Research Institute and School of Basic Medical Science, Central South University, Changsha, China; Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Changsha, China.
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3
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Han T, Liu Y, Wu J, Bai Y, Zhou J, Hu C, Zhang W, Guo J, Wang Q, Hu D. An immune indicator based on BTK and DPEP2 identifies hot and cold tumors and clinical treatment outcomes in lung adenocarcinoma. Sci Rep 2023; 13:5153. [PMID: 36991102 PMCID: PMC10060209 DOI: 10.1038/s41598-023-32276-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 03/24/2023] [Indexed: 03/31/2023] Open
Abstract
In lung adenocarcinoma (LUAD), immune heterogeneity of hot and cold tumors has been recognized as one of the major factors affecting immunotherapy and other common treatments. However, there is still a lack of biomarkers that can effectively identify the immunophenotype of cold and hot tumors. First, the immune signatures were obtained based on literature mining, including macrophage/monocyte, IFN-γ response, TGF-β response, IL12 response, lymphocyte activation, and ECM/Dve/immune response. Subsequently, LUAD patients were further clustered into different immune phenotypes based on these immune signatures. Next, the key genes related to the immune phenotypes were screened by WGCNA analysis, univariate analysis, and lasso-cox analysis, and the risk signature was established via the key genes. In additional, we compared the clinicopathological characteristics, drug sensitivity, the abundance of immune infiltration, and the efficacy of immunotherapy and commonly used therapies between patients in the high- and low-risk groups in LUAD. LUAD patients were divided into immune hot phenotype and immune cold phenotype groups. The clinical presentation showed that patients with the immune hot phenotype had higher immunoactivity (including higher MHC, CYT, immune, stromal, ESTIMATE scores, higher abundance of immune cell infiltration, higher abundance of TIL, and enrichment of immune-enriched subtypes) and better survival outcomes than those with the immune cold phenotype. Subsequently, WGCNA analysis, univariate analysis, and lasso-cox analysis identified the genes highly associated with the immune phenotype: BTK and DPEP2. The risk signature, consisting of BTK and DPEP2, is highly correlated with the immune phenotype. High-risk scores were enriched in patients with immune cold phenotype and low-risk scores were enriched in patients with immune hot phenotype. Compared to the high-risk group, the low-risk group had better clinical performance, higher drug sensitivity, and a higher degree of immunoactivity, as well as better efficacy in receiving immunotherapy and common adjuvant therapy. This study developed an immune indicator consisting of BTK and DPEP2 based on the heterogeneity of hot and cold Immunophenotypes of the tumor microenvironment. This indicator has good efficacy in predicting prognosis and assessing the efficacy of immunotherapy, chemotherapy, and radiotherapy. It has the potential to facilitate personalized and precise treatment of LUAD in the future.
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Affiliation(s)
- Tao Han
- School of Medicine, Anhui University of Science and Technology, Huainan, 232001, People's Republic of China
| | - Yafeng Liu
- School of Medicine, Anhui University of Science and Technology, Huainan, 232001, People's Republic of China
- Anhui Province Engineering Laboratory of Occupational Health and Safety, Anhui University of Science and Technology, Huainan, 232001, People's Republic of China
| | - Jing Wu
- School of Medicine, Anhui University of Science and Technology, Huainan, 232001, People's Republic of China.
- Anhui Province Engineering Laboratory of Occupational Health and Safety, Anhui University of Science and Technology, Huainan, 232001, People's Republic of China.
- Key Laboratory of Industrial Dust Deep Reduction and Occupational Health and Safety of Anhui Higher Education Institutes, Anhui University of Science and Technology, Huainan, 232001, People's Republic of China.
| | - Ying Bai
- School of Medicine, Anhui University of Science and Technology, Huainan, 232001, People's Republic of China
- Anhui Province Engineering Laboratory of Occupational Health and Safety, Anhui University of Science and Technology, Huainan, 232001, People's Republic of China
| | - Jiawei Zhou
- School of Medicine, Anhui University of Science and Technology, Huainan, 232001, People's Republic of China
| | - Chunxiao Hu
- School of Medicine, Anhui University of Science and Technology, Huainan, 232001, People's Republic of China
| | - Wenting Zhang
- School of Medicine, Anhui University of Science and Technology, Huainan, 232001, People's Republic of China
| | - Jianqiang Guo
- School of Medicine, Anhui University of Science and Technology, Huainan, 232001, People's Republic of China
| | - Qingsen Wang
- School of Medicine, Anhui University of Science and Technology, Huainan, 232001, People's Republic of China
| | - Dong Hu
- School of Medicine, Anhui University of Science and Technology, Huainan, 232001, People's Republic of China.
- Anhui Province Engineering Laboratory of Occupational Health and Safety, Anhui University of Science and Technology, Huainan, 232001, People's Republic of China.
- Key Laboratory of Industrial Dust Deep Reduction and Occupational Health and Safety of Anhui Higher Education Institutes, Anhui University of Science and Technology, Huainan, 232001, People's Republic of China.
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4
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Gao C, Zhou G, Shi J, Shi P, Jin L, Li Y, Wang X, Liao S, Yan H, Wu J, Lu Y, Zhai Y, Zhang J, Zhang H, Zhang H, Yang C, Cao P, Cheng S, Zhou G. The A-to-I editing of KPC1 promotes intrahepatic cholangiocarcinoma by attenuating proteasomal processing of NF-κB1 p105 to p50. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2022; 41:338. [PMID: 36476255 PMCID: PMC9730630 DOI: 10.1186/s13046-022-02549-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 11/25/2022] [Indexed: 12/12/2022]
Abstract
BACKGROUND Aberrant RNA editing of adenosine-to-inosine (A-to-I) has been linked to multiple human cancers, but its role in intrahepatic cholangiocarcinoma (iCCA) remains unknown. We conducted an exome-wide investigation to search for dysregulated RNA editing that drive iCCA pathogenesis. METHODS An integrative whole-exome and transcriptome sequencing analysis was performed to elucidate the RNA editing landscape in iCCAs. Putative RNA editing sites were validated by Sanger sequencing. In vitro and in vivo experiments were used to assess the effects of an exemplary target gene Kip1 ubiquitination-promoting complex 1 (KPC1) and its editing on iCCA cells growth and metastasis. Crosstalk between KPC1 RNA editing and NF-κB signaling was analyzed by molecular methods. RESULTS Through integrative omics analyses, we revealed an adenosine deaminases acting on RNA 1A (ADAR1)-mediated over-editing pattern in iCCAs. ADAR1 is frequently amplified and overexpressed in iCCAs and plays oncogenic roles. Notably, we identified a novel ADAR1-mediated A-to-I editing of KPC1 transcript, which results in substitution of methionine with valine at residue 8 (p.M8V). KPC1 p.M8V editing confers loss-of-function phenotypes through blunting the tumor-suppressive role of wild-type KPC1. Mechanistically, KPC1 p.M8V weakens the affinity of KPC1 to its substrate NF-κB1 p105, thereby reducing the ubiquitinating and proteasomal processing of p105 to p50, which in turn enhances the activity of oncogenic NF-κB signaling. CONCLUSIONS Our findings established that amplification-driven ADAR1 overexpression results in overediting of KPC1 p.M8V in iCCAs, leading to progression via activation of the NF-κB signaling pathway, and suggested ADAR1-KPC1-NF-κB axis as a potential therapeutic target for iCCA.
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Affiliation(s)
- Chengming Gao
- grid.506261.60000 0001 0706 7839State Key Laboratory of Proteomics, National Center for Protein Sciences at Beijing, Beijing Institute of Radiation Medicine, 27 Taiping Road, Beijing, 100850 China
| | - Guangming Zhou
- grid.506261.60000 0001 0706 7839State Key Laboratory of Proteomics, National Center for Protein Sciences at Beijing, Beijing Institute of Radiation Medicine, 27 Taiping Road, Beijing, 100850 China
| | - Jie Shi
- grid.414375.00000 0004 7588 8796Eastern Hepatobiliary Surgery Hospital, Navy Military Medical University, 225 Changhai Road, Shanghai, 200433 China
| | - Peipei Shi
- grid.256885.40000 0004 1791 4722Hebei University, Baoding City, China
| | - Liang Jin
- grid.506261.60000 0001 0706 7839State Key Laboratory of Proteomics, National Center for Protein Sciences at Beijing, Beijing Institute of Radiation Medicine, 27 Taiping Road, Beijing, 100850 China
| | - Yuanfeng Li
- grid.506261.60000 0001 0706 7839State Key Laboratory of Proteomics, National Center for Protein Sciences at Beijing, Beijing Institute of Radiation Medicine, 27 Taiping Road, Beijing, 100850 China
| | - Xiaowen Wang
- grid.419611.a0000 0004 0457 9072State Key Laboratory of Proteomics, National Center for Protein Sciences at Beijing, Beijing Institute of Lifeomics, Beijing, China
| | - Song Liao
- grid.488137.10000 0001 2267 2324Medical School of Chinese PLA, Beijing, China
| | - Han Yan
- grid.256885.40000 0004 1791 4722Hebei University, Baoding City, China
| | - Junjie Wu
- grid.186775.a0000 0000 9490 772XAnhui Medical University, Hefei City, China
| | - Yiming Lu
- grid.506261.60000 0001 0706 7839State Key Laboratory of Proteomics, National Center for Protein Sciences at Beijing, Beijing Institute of Radiation Medicine, 27 Taiping Road, Beijing, 100850 China
| | - Yun Zhai
- grid.506261.60000 0001 0706 7839State Key Laboratory of Proteomics, National Center for Protein Sciences at Beijing, Beijing Institute of Radiation Medicine, 27 Taiping Road, Beijing, 100850 China
| | - Jinxu Zhang
- grid.506261.60000 0001 0706 7839State Key Laboratory of Proteomics, National Center for Protein Sciences at Beijing, Beijing Institute of Radiation Medicine, 27 Taiping Road, Beijing, 100850 China ,grid.419611.a0000 0004 0457 9072State Key Laboratory of Proteomics, National Center for Protein Sciences at Beijing, Beijing Institute of Lifeomics, Beijing, China
| | - Haitao Zhang
- grid.506261.60000 0001 0706 7839State Key Laboratory of Proteomics, National Center for Protein Sciences at Beijing, Beijing Institute of Radiation Medicine, 27 Taiping Road, Beijing, 100850 China
| | - Hongxing Zhang
- grid.506261.60000 0001 0706 7839State Key Laboratory of Proteomics, National Center for Protein Sciences at Beijing, Beijing Institute of Radiation Medicine, 27 Taiping Road, Beijing, 100850 China ,grid.419611.a0000 0004 0457 9072State Key Laboratory of Proteomics, National Center for Protein Sciences at Beijing, Beijing Institute of Lifeomics, Beijing, China
| | - Chenning Yang
- grid.506261.60000 0001 0706 7839State Key Laboratory of Proteomics, National Center for Protein Sciences at Beijing, Beijing Institute of Radiation Medicine, 27 Taiping Road, Beijing, 100850 China
| | - Pengbo Cao
- grid.506261.60000 0001 0706 7839State Key Laboratory of Proteomics, National Center for Protein Sciences at Beijing, Beijing Institute of Radiation Medicine, 27 Taiping Road, Beijing, 100850 China
| | - Shuqun Cheng
- grid.414375.00000 0004 7588 8796Eastern Hepatobiliary Surgery Hospital, Navy Military Medical University, 225 Changhai Road, Shanghai, 200433 China
| | - Gangqiao Zhou
- grid.506261.60000 0001 0706 7839State Key Laboratory of Proteomics, National Center for Protein Sciences at Beijing, Beijing Institute of Radiation Medicine, 27 Taiping Road, Beijing, 100850 China ,grid.256885.40000 0004 1791 4722Hebei University, Baoding City, China ,grid.186775.a0000 0000 9490 772XAnhui Medical University, Hefei City, China ,grid.89957.3a0000 0000 9255 8984Collaborative Innovation Center for Personalized Cancer Medicine, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing City, China
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5
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Zhang B, Chen T, Cao M, Yuan C, Reiter RJ, Zhao Z, Zhao Y, Chen L, Fan W, Wang X, Zhou X, Li C. Gut Microbiota Dysbiosis Induced by Decreasing Endogenous Melatonin Mediates the Pathogenesis of Alzheimer's Disease and Obesity. Front Immunol 2022; 13:900132. [PMID: 35619714 PMCID: PMC9127079 DOI: 10.3389/fimmu.2022.900132] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Accepted: 04/13/2022] [Indexed: 01/15/2023] Open
Abstract
Lifestyle choices, external environment, aging, and other factors influence the synthesis of melatonin. Although the physiological functions of melatonin have been widely studied in relation to specific organs, the systemic effects of endogenous melatonin reduction has not been reported. This study evaluates the systemic changes and possible pathogenic risks in an endogenous melatonin reduction (EMR) mouse model deficient in the rate limiting enzyme in melatonin production, arylalkylamine N-acetyltransferase (Aanat) gene. Using this model, we identified a new relationship between melatonin, Alzheimer’s disease (AD), and gut microbiota. Systematic changes were evaluated using multi-omics analysis. Fecal microbiota transplantation (FMT) was performed to examine the role of gut microbiota in the pathogenic risks of EMR. EMR mice exhibited a pan-metabolic disorder, with significant transcriptome changes in 11 organs, serum metabolome alterations as well as microbiota dysbiosis. Microbiota dysbiosis was accompanied by increased gut permeability along with gut and systemic inflammation. Correlation analysis revealed that systemic inflammation may be related to the increase of Ruminiclostridium_5 relative abundance. 8-month-old EMR mice had AD-like phenotypes, including Iba-1 activation, A β protein deposition and decreased spatial memory ability. Moreover, EMR mice showed decreased anti stress ability, under high-fat diet, EMR mice had greater body weight and more obvious hepatic steatosis compared with WT group. FMT improved gut permeability, systemic inflammation, and AD-related phenotypes, while reducing obesity in EMR mice. Our findings suggest EMR causes systemic changes mediated by gut microbiota dysbiosis, which may be a pathogenic factor for AD and obesity, we further proved the gut microbiota is a potential target for the prevention and treatment of AD and obesity.
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Affiliation(s)
- Boqi Zhang
- College of Animal Sciences, Jilin University, Changchun, China
| | - Tong Chen
- College of Animal Sciences, Jilin University, Changchun, China
| | - Maosheng Cao
- College of Animal Sciences, Jilin University, Changchun, China
| | - Chenfeng Yuan
- College of Animal Sciences, Jilin University, Changchun, China
| | - Russel J Reiter
- Department of Cellular and Structural Biology, University of Texas Health Science Center, San Antonio, TX, United States
| | - Zijiao Zhao
- College of Animal Sciences, Jilin University, Changchun, China
| | - Yun Zhao
- College of Animal Sciences, Jilin University, Changchun, China
| | - Lu Chen
- College of Animal Sciences, Jilin University, Changchun, China
| | - Wenjing Fan
- College of Animal Sciences, Jilin University, Changchun, China
| | - Xin Wang
- College of Animal Sciences, Jilin University, Changchun, China
| | - Xu Zhou
- College of Animal Sciences, Jilin University, Changchun, China
| | - Chunjin Li
- College of Animal Sciences, Jilin University, Changchun, China
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6
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Su X, Li W, Lv L, Li X, Yang J, Luo XJ, Liu J. Transcriptome-Wide Association Study Provides Insights Into the Genetic Component of Gene Expression in Anxiety. Front Genet 2021; 12:740134. [PMID: 34650599 PMCID: PMC8505959 DOI: 10.3389/fgene.2021.740134] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 09/15/2021] [Indexed: 01/10/2023] Open
Abstract
Anxiety disorders are common mental disorders that often result in disability. Recently, large-scale genome-wide association studies (GWASs) have identified several novel risk variants and loci for anxiety disorders (or anxiety traits). Nevertheless, how the reported risk variants confer risk of anxiety remains unknown. To identify genes whose cis-regulated expression levels are associated with risk of anxiety traits, we conducted a transcriptome-wide association study (TWAS) by integrating genome-wide associations from a large-scale GWAS (N = 175,163) (which evaluated anxiety traits based on Generalized Anxiety Disorder 2-item scale (GAD-2) score) and brain expression quantitative trait loci (eQTL) data (from the PsychENCODE and GTEx). We identified 19 and 17 transcriptome-wide significant (TWS) genes in the PsychENCODE and GTEx, respectively. Intriguingly, 10 genes showed significant associations with anxiety in both datasets, strongly suggesting that genetic risk variants may confer risk of anxiety traits by regulating the expression of these genes. Top TWS genes included RNF123, KANSL1-AS1, GLYCTK, CRHR1, DND1P1, MAPT and ARHGAP27. Of note, 25 TWS genes were not implicated in the original GWAS. Our TWAS identified 26 risk genes whose cis-regulated expression were significantly associated with anxiety, providing important insights into the genetic component of gene expression in anxiety disorders/traits and new clues for future drug development.
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Affiliation(s)
- Xi Su
- Henan Mental Hospital, The Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, China.,Henan Key Lab of Biological Psychiatry, International Joint Research Laboratory for Psychiatry and Neuroscience of Henan, Xinxiang Medical University, Xinxiang, China
| | - Wenqiang Li
- Henan Mental Hospital, The Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, China.,Henan Key Lab of Biological Psychiatry, International Joint Research Laboratory for Psychiatry and Neuroscience of Henan, Xinxiang Medical University, Xinxiang, China
| | - Luxian Lv
- Henan Mental Hospital, The Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, China.,Henan Key Lab of Biological Psychiatry, International Joint Research Laboratory for Psychiatry and Neuroscience of Henan, Xinxiang Medical University, Xinxiang, China
| | - Xiaoyan Li
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Jinfeng Yang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Xiong-Jian Luo
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China.,KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Jiewei Liu
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
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7
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Zhang X, Bustos MA, Gross R, Ramos RI, Takeshima T, Mills GB, Yu Q, Hoon DSB. Interleukin enhancer-binding factor 2 promotes cell proliferation and DNA damage response in metastatic melanoma. Clin Transl Med 2021; 11:e608. [PMID: 34709752 PMCID: PMC8516365 DOI: 10.1002/ctm2.608] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 09/21/2021] [Accepted: 09/27/2021] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND 1q21.3 amplification, which is frequently observed in metastatic melanoma, is associated with cancer progression. Interleukin enhancer-binding factor 2 (ILF2) is located in the 1q21.3 amplified region, but its functional role or contribution to tumour aggressiveness in cutaneous melanoma is unknown. METHODS In silico analyses were performed using the TCGA SKCM dataset with clinical annotations and three melanoma microarray cohorts from the GEO datasets. RNA in situ hybridisation and immunohistochemistry were utilised to validate the gene expression in melanoma tissues. Four stable melanoma cell lines were established for in vitro ILF2 functional characterisation. RESULTS Our results showed that the ILF2 copy number variation (CNV) is positively correlated with ILF2 mRNA expression (r = 0.68, p < .0001). Additionally, ILF2 expression is significantly increased with melanoma progression (p < .0001), and significantly associated with poor overall survival for metastatic melanoma patients (p = .026). The overexpression of ILF2 (ILF2-OV) promotes proliferation in metastatic melanoma cells, whereas ILF2 knockdown decreases proliferation by blocking the cell cycle. Mechanistically, we demonstrated the interaction between ILF2 and the splicing factor U2AF2, whose knockdown reverses the proliferation effects mediated by ILF2-OV. Stage IIIB-C melanoma patients with high ILF2-U2AF2 expression showed significantly shorter overall survival (p = .024). Enhanced ILF2/U2AF2 expression promotes a more efficient DNA-damage repair by increasing RAD50 and ATM mRNA expression. Paradoxically, metastatic melanoma cells with ILF2-OV were more sensitive to ATM inhibitors. CONCLUSION Our study uncovered that ILF2 amplification of the 1q21.3 chromosome is associated with melanoma progression and triggers a functional downstream pathway in metastatic melanoma promoting drug resistance.
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Affiliation(s)
- Xiaoqing Zhang
- Department of Translational Molecular MedicineProvidence Saint John's Health CenterSaint John's Cancer InstituteSanta MonicaCalifornia
| | - Matias A. Bustos
- Department of Translational Molecular MedicineProvidence Saint John's Health CenterSaint John's Cancer InstituteSanta MonicaCalifornia
| | - Rebecca Gross
- Department of Translational Molecular MedicineProvidence Saint John's Health CenterSaint John's Cancer InstituteSanta MonicaCalifornia
| | - Romela Irene Ramos
- Department of Translational Molecular MedicineProvidence Saint John's Health CenterSaint John's Cancer InstituteSanta MonicaCalifornia
| | - Teh‐Ling Takeshima
- Department of Translational Molecular MedicineProvidence Saint John's Health CenterSaint John's Cancer InstituteSanta MonicaCalifornia
| | - Gordon B. Mills
- Department of Cell Development and Cancer BiologyKnight Cancer InstituteOregon Health and Science UniversityPortlandOregon
| | - Qiang Yu
- Agency for Science Technology and Research (A*STAR)Genome Institute of SingaporeBiopolisSingapore
| | - Dave S. B. Hoon
- Department of Translational Molecular MedicineProvidence Saint John's Health CenterSaint John's Cancer InstituteSanta MonicaCalifornia
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8
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Acetylated DNMT1 Downregulation and Related Regulatory Factors Influence Metastatic Melanoma Patients Survival. Cancers (Basel) 2021; 13:cancers13184691. [PMID: 34572918 PMCID: PMC8471314 DOI: 10.3390/cancers13184691] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Revised: 09/10/2021] [Accepted: 09/14/2021] [Indexed: 12/14/2022] Open
Abstract
Simple Summary DNA methyltransferase-1 (DNMT1) is a key epigenetic regulatory protein of gene expression in cutaneous melanoma. DNMT1 is acetylated by TIP60 promoting its degradation. This study demonstrated that DNMT1 and ac-DNMT1 protein levels were inversely correlated in stage III (n = 17) and stage IV (n = 164) metastatic melanoma tumors, and both influenced melanoma progression. Reduced TIP60 and USP7 protein expression levels were correlated with decreased ac-DNMT1 levels. Of clinical translational relevance, patients with high ac-DNMT1 protein levels, or high-acDNMT1 with concurrent low DNMT1, high TIP60, or high USP7 protein levels showed significantly better prognosis for 4-year melanoma-specific survival. These results suggested that ac-DNMT1 is a significant post-translational modification influencing advanced melanoma patient disease outcomes. Abstract The role of post-translational modifications (PTM) of the key epigenetic factor DNMT1 protein has not been well explored in cutaneous metastatic melanoma progression. The acetylated DNMT1 (ac-DNMT1) protein level was assessed using an anti-acetylated lysine antibody in a clinically annotated melanoma patient tumor specimen cohort. In this study, we showed that surgically resected tumors have significantly higher DNMT1 protein expression in metastatic melanoma (stage III metastasis n = 17, p = 0.0009; stage IV metastasis n = 164, p = 0.003) compared to normal organ tissues (n = 19). Additionally, reduced ac-DNMT1 protein levels were associated with melanoma progression. There was a significant inverse correlation between ac-DNMT1 and DNMT1 protein levels in stage IV metastatic melanoma (r = −0.18, p = 0.02, n = 164). Additionally, ac-DNMT1 protein levels were also significantly positively correlated with TIP60 (r = 0.6, p < 0.0001) and USP7 (r = 0.74, p < 0.0001) protein levels in stage IV metastatic melanoma (n = 164). Protein analysis in metastatic melanoma tumor tissues showed that with high ac-DNMT1 (p = 0.006, n = 59), or concurrent high ac-DNMT1 with low DNMT1 (p = 0.05, n = 27), or high TIP60 (p = 0.007, n = 41), or high USP7 (p = 0.01, n = 48) consistently showed better 4-year melanoma-specific survival (MSS). Multivariate Cox proportional hazard analysis showed that ac-DNMT1 level is a significant independent factor associated with MSS (HR, 0.994; 95% confidential interval (CI), 0.990–0.998; p = 0.002). These results demonstrated that low ac-DNMT1 levels may represent an important regulatory factor in controlling metastatic melanoma progression and a promising factor for stratifying aggressive stage IV metastasis.
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9
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Terranova CJ, Tang M, Maitituoheti M, Raman AT, Ghosh AK, Schulz J, Amin SB, Orouji E, Tomczak K, Sarkar S, Oba J, Creasy C, Wu CJ, Khan S, Lazcano R, Wani K, Singh A, Barrodia P, Zhao D, Chen K, Haydu LE, Wang WL, Lazar AJ, Woodman SE, Bernatchez C, Rai K. Reprogramming of bivalent chromatin states in NRAS mutant melanoma suggests PRC2 inhibition as a therapeutic strategy. Cell Rep 2021; 36:109410. [PMID: 34289358 PMCID: PMC8369408 DOI: 10.1016/j.celrep.2021.109410] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 05/13/2021] [Accepted: 06/25/2021] [Indexed: 12/27/2022] Open
Abstract
The dynamic evolution of chromatin state patterns during metastasis, their relationship with bona fide genetic drivers, and their therapeutic vulnerabilities are not completely understood. Combinatorial chromatin state profiling of 46 melanoma samples reveals an association of NRAS mutants with bivalent histone H3 lysine 27 trimethylation (H3K27me3) and Polycomb repressive complex 2. Reprogramming of bivalent domains during metastasis occurs on master transcription factors of a mesenchymal phenotype, including ZEB1, TWIST1, and CDH1. Resolution of bivalency using pharmacological inhibition of EZH2 decreases invasive capacity of melanoma cells and markedly reduces tumor burden in vivo, specifically in NRAS mutants. Coincident with bivalent reprogramming, the increased expression of pro-metastatic and melanocyte-specific cell-identity genes is associated with exceptionally wide H3K4me3 domains, suggesting a role for this epigenetic element. Overall, we demonstrate that reprogramming of bivalent and broad domains represents key epigenetic alterations in metastatic melanoma and that EZH2 plus MEK inhibition may provide a promising therapeutic strategy for NRAS mutant melanoma patients.
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Affiliation(s)
- Christopher J Terranova
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Ming Tang
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA; FAS informatics, Department of Molecular Biology, Harvard, Cambridge, MA 02138, USA
| | - Mayinuer Maitituoheti
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Ayush T Raman
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA; Epigenomics Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Graduate Program in Quantitative Sciences, Baylor College of Medicine, Houston, TX 77030, USA
| | - Archit K Ghosh
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Jonathan Schulz
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Samir B Amin
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA; The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Elias Orouji
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA; Epigenetics Initiative, Princess Margaret Genomics Centre, Toronto, ON M5G 2C1, Canada
| | - Katarzyna Tomczak
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Sharmistha Sarkar
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Junna Oba
- Department of Melanoma Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Caitlin Creasy
- Department of Melanoma Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Chang-Jiun Wu
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Samia Khan
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Rossana Lazcano
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Khalida Wani
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Anand Singh
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Praveen Barrodia
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Dongyu Zhao
- Houston Methodist Academic Institute, Methodist Hospital Research Institute, Houston, TX 77030, USA
| | - Kaifu Chen
- Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Lauren E Haydu
- Surgical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Wei-Lien Wang
- Department of Pathology, University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Alexander J Lazar
- Department of Pathology, University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Scott E Woodman
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA; Department of Melanoma Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA; Department of Systems Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Chantale Bernatchez
- Department of Melanoma Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Kunal Rai
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA.
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10
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EpiMap: Fine-tuning integrative epigenomics maps to understand complex human regulatory genomic circuitry. Signal Transduct Target Ther 2021; 6:179. [PMID: 33966052 PMCID: PMC8106674 DOI: 10.1038/s41392-021-00620-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 04/08/2021] [Accepted: 04/21/2021] [Indexed: 11/30/2022] Open
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11
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Murakami T, Shoji Y, Nishi T, Chang SC, Jachimowicz RD, Hoshimoto S, Ono S, Shiloh Y, Takeuchi H, Kitagawa Y, Hoon DSB, Bustos MA. Regulation of MRE11A by UBQLN4 leads to cisplatin resistance in patients with esophageal squamous cell carcinoma. Mol Oncol 2021; 15:1069-1087. [PMID: 33605536 PMCID: PMC8024730 DOI: 10.1002/1878-0261.12929] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 01/20/2021] [Accepted: 02/17/2021] [Indexed: 02/06/2023] Open
Abstract
Resistance to standard cisplatin‐based chemotherapies leads to worse survival outcomes for patients with esophageal squamous cell carcinoma (ESCC). Therefore, there is an urgent need to understand the aberrant mechanisms driving resistance in ESCC tumors. We hypothesized that ubiquilin‐4 (UBQLN4), a protein that targets ubiquitinated proteins to the proteasome, regulates the expression of Meiotic Recombination 11 Homolog A (MRE11A), a critical component of the MRN complex and DNA damage repair pathways. Initially, immunohistochemistry analysis was conducted in specimens from patients with ESCC (n = 120). In endoscopic core ESCC biopsies taken from 61 patients who underwent neoadjuvant chemotherapy (NAC) (5‐fluorouracil and cisplatin), low MRE11A and high UBQLN4 protein levels were associated with reduced pathological response to NAC (P < 0.001 and P < 0.001, respectively). Multivariable analysis of surgically resected ESCC tissues from 59 patients revealed low MRE11A and high UBLQN4 expression as independent factors that can predict shorter overall survival [P = 0.01, hazard ratio (HR) = 5.11, 95% confidence interval (CI), 1.45–18.03; P = 0.02, HR = 3.74, 95% CI, 1.19–11.76, respectively]. Suppression of MRE11A expression was associated with cisplatin resistance in ESCC cell lines. Additionally, MRE11A was found to be ubiquitinated after cisplatin treatment. We observed an amplification of UBQLN4 gene copy numbers and an increase in UBQLN4 protein levels in ESCC tissues. Binding of UBQLN4 to ubiquitinated‐MRE11A increased MRE11A degradation, thereby regulating MRE11A protein levels following DNA damage and promoting cisplatin resistance. In summary, MRE11A and UBQLN4 protein levels can serve as predictors for NAC response and as prognostic markers in ESCC patients.
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Affiliation(s)
- Tomohiro Murakami
- Department of Translational Molecular Medicine, Division of Molecular Oncology, Saint John's Cancer Institute at Providence Saint John's Health Center, Santa Monica, CA, USA.,Department of Surgery, Hamamatsu University School of Medicine, Japan
| | - Yoshiaki Shoji
- Department of Translational Molecular Medicine, Division of Molecular Oncology, Saint John's Cancer Institute at Providence Saint John's Health Center, Santa Monica, CA, USA.,Department of Surgery, Keio University School of Medicine, Shinjuku-ku, Japan
| | - Tomohiko Nishi
- Department of Translational Molecular Medicine, Division of Molecular Oncology, Saint John's Cancer Institute at Providence Saint John's Health Center, Santa Monica, CA, USA.,Department of Surgery, Keio University School of Medicine, Shinjuku-ku, Japan
| | - Shu-Ching Chang
- Medical Data Research Center Providence Health and Services at Providence Saint Joseph's Health, Portland, OR, USA
| | - Ron D Jachimowicz
- Clinic I of Internal Medicine, University Hospital Cologne, Germany.,Max Planck Institute for Biology of Ageing, Cologne, Germany.,Center for Molecular Medicine Cologne, University of Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Response in Ageing-Associated Diseases, University of Cologne, Germany
| | - Sojun Hoshimoto
- Department of Translational Molecular Medicine, Division of Molecular Oncology, Saint John's Cancer Institute at Providence Saint John's Health Center, Santa Monica, CA, USA.,Department of Surgery, Keio University School of Medicine, Shinjuku-ku, Japan
| | - Shigeshi Ono
- Department of Translational Molecular Medicine, Division of Molecular Oncology, Saint John's Cancer Institute at Providence Saint John's Health Center, Santa Monica, CA, USA.,Department of Surgery, Keio University School of Medicine, Shinjuku-ku, Japan
| | - Yosef Shiloh
- David and Inez Myers Laboratory for Cancer Genetics, Sackler School of Medicine, Tel Aviv University, Israel
| | - Hiroya Takeuchi
- Department of Surgery, Hamamatsu University School of Medicine, Japan
| | - Yuko Kitagawa
- Department of Surgery, Keio University School of Medicine, Shinjuku-ku, Japan
| | - Dave S B Hoon
- Department of Translational Molecular Medicine, Division of Molecular Oncology, Saint John's Cancer Institute at Providence Saint John's Health Center, Santa Monica, CA, USA
| | - Matias A Bustos
- Department of Translational Molecular Medicine, Division of Molecular Oncology, Saint John's Cancer Institute at Providence Saint John's Health Center, Santa Monica, CA, USA
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12
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Tran KD, Gross R, Rahimzadeh N, Chenathukattil S, Hoon DSB, Bustos MA. Assessment of Cell-Free microRNA by NGS Whole-Transcriptome Analysis in Cutaneous Melanoma Patients' Blood. Methods Mol Biol 2021; 2265:475-486. [PMID: 33704735 DOI: 10.1007/978-1-0716-1205-7_34] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
MicroRNAs (miRs) are small RNA molecules (18-22 nucleotides) that regulate the transcriptome at a post-transcriptional level by affecting the expression of specific genes. This regulatory mechanism is critical to maintain cell homeostasis and specific functions. Aberrant expression of miRs have been associated with pathobiological processes including cancer. There are few technologies available that are able to profile whole-genome miR expression using minimal amounts of blood samples and without the need for time-consuming extraction steps. Here, we describe the HTG EdgeSeq miR Whole-Transcriptome Assay (WTA) in serum and plasma samples. To identify specific cell-free miR (cfmiR) patterns we have first focused on the analysis of normal donor samples and have then compared these to patients with cutaneous melanoma. The identification of specific cfmiR for melanoma patients will allow for better patient surveillance during targeted and/or checkpoint inhibitor immunotherapy (CII) treatment.
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Affiliation(s)
- Kevin D Tran
- Department of Genomic Sequencing Center, John Wayne Cancer Institute (JWCI) at Providence Saint John's Health Center, Santa Monica, CA, USA
| | - Rebecca Gross
- Department of Translational Molecular Medicine, JWCI at Providence Saint John's Health Center, Santa Monica, CA, USA
| | - Negin Rahimzadeh
- Department of Translational Molecular Medicine, JWCI at Providence Saint John's Health Center, Santa Monica, CA, USA
| | - Shanthy Chenathukattil
- Department of Translational Molecular Medicine, JWCI at Providence Saint John's Health Center, Santa Monica, CA, USA
| | - Dave S B Hoon
- Department of Genomic Sequencing Center, John Wayne Cancer Institute (JWCI) at Providence Saint John's Health Center, Santa Monica, CA, USA
- Department of Translational Molecular Medicine, JWCI at Providence Saint John's Health Center, Santa Monica, CA, USA
| | - Matias A Bustos
- Department of Translational Molecular Medicine, JWCI at Providence Saint John's Health Center, Santa Monica, CA, USA.
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13
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Li W, Liang J, Outeda P, Turner S, Wakimoto BT, Watnick T. A genetic screen in Drosophila reveals an unexpected role for the KIP1 ubiquitination-promoting complex in male fertility. PLoS Genet 2020; 16:e1009217. [PMID: 33378371 PMCID: PMC7802972 DOI: 10.1371/journal.pgen.1009217] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Revised: 01/12/2021] [Accepted: 10/19/2020] [Indexed: 12/22/2022] Open
Abstract
A unifying feature of polycystin-2 channels is their localization to both primary and motile cilia/flagella. In Drosophila melanogaster, the fly polycystin-2 homologue, Amo, is an ER protein early in sperm development but the protein must ultimately cluster at the flagellar tip in mature sperm to be fully functional. Male flies lacking appropriate Amo localization are sterile due to abnormal sperm motility and failure of sperm storage. We performed a forward genetic screen to identify additional proteins that mediate ciliary trafficking of Amo. Here we report that Drosophila homologues of KPC1 and KPC2, which comprise the mammalian KIP1 ubiquitination-promoting complex (KPC), form a conserved unit that is required for the sperm tail tip localization of Amo. Male flies lacking either KPC1 or KPC2 phenocopy amo mutants and are sterile due to a failure of sperm storage. KPC is a heterodimer composed of KPC1, an E3 ligase, and KPC2 (or UBAC1), an adaptor protein. Like their mammalian counterparts Drosophila KPC1 and KPC2 physically interact and they stabilize one another at the protein level. In flies, KPC2 is monoubiquitinated and phosphorylated and this modified form of the protein is located in mature sperm. Neither KPC1 nor KPC2 directly interact with Amo but they are detected in proximity to Amo at the tip of the sperm flagellum. In summary we have identified a new complex that is involved in male fertility in Drosophila melanogaster.
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Affiliation(s)
- Weizhe Li
- Division of Nephrology, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, United States of America
| | - Jinqing Liang
- Division of Nephrology, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, United States of America
| | - Patricia Outeda
- Division of Nephrology, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, United States of America
| | - Stacey Turner
- Division of Nephrology, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, United States of America
| | - Barbara T. Wakimoto
- Department of Biology, University of Washington Seattle, WA, United States of America
| | - Terry Watnick
- Division of Nephrology, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, United States of America
- * E-mail:
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14
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Bustos MA, Gross R, Rahimzadeh N, Cole H, Tran LT, Tran KD, Takeshima L, Stern SL, O’Day S, Hoon DSB. A Pilot Study Comparing the Efficacy of Lactate Dehydrogenase Levels Versus Circulating Cell-Free microRNAs in Monitoring Responses to Checkpoint Inhibitor Immunotherapy in Metastatic Melanoma Patients. Cancers (Basel) 2020; 12:cancers12113361. [PMID: 33202891 PMCID: PMC7696545 DOI: 10.3390/cancers12113361] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 11/09/2020] [Indexed: 12/18/2022] Open
Abstract
Simple Summary Improvement in melanoma patients with metastatic disease is needed to better assess immunotherapies. Lactate dehydrogenase (LDH) is currently an accepted biomarker for stage IV, but it has limited utility for stage III melanoma patients. Thus, finding biomarkers for metastatic melanoma is important not only to identify progressive melanoma tumors, but also to monitor patients under checkpoint inhibitor immunotherapy (CII). The aim of this pilot study was to demonstrate the utility of circulating cell-free microRNAs (cfmiRs) as potential blood biomarkers for stage III and IV melanoma patients compared to LDH. To accomplish this aim, we profiled for cfmiR the plasma of metastatic melanoma patients before and during CII treatment, and compared them to normal healthy donors’ samples. The cfmiR profiling was performed using an NGS-based miRNA assay, which requires no extraction and a small volume input. We found specific cfmiR signatures in stage III and IV metastatic melanoma patients. As a proof of concept, our results showed that certain cfmiRs are associated with CII outcomes. Abstract Serum lactate dehydrogenase (LDH) is a standard prognostic biomarker for stage IV melanoma patients. Often, LDH levels do not provide real-time information about the metastatic melanoma patients’ disease status and treatment response. Therefore, there is a need to find reliable blood biomarkers for improved monitoring of metastatic melanoma patients who are undergoing checkpoint inhibitor immunotherapy (CII). The objective in this prospective pilot study was to discover circulating cell-free microRNA (cfmiR) signatures in the plasma that could assess melanoma patients’ responses during CII. The cfmiRs were evaluated by the next-generation sequencing (NGS) HTG EdgeSeq microRNA (miR) Whole Transcriptome Assay (WTA; 2083 miRs) in 158 plasma samples obtained before and during the course of CII from 47 AJCC stage III/IV melanoma patients’ and 73 normal donors’ plasma samples. Initially, cfmiR profiles for pre- and post-treatment plasma samples of stage IV non-responder melanoma patients were compared to normal donors’ plasma samples. Using machine learning, we identified a 9 cfmiR signature that was associated with stage IV melanoma patients being non-responsive to CII. These cfmiRs were compared in pre- and post-treatment plasma samples from stage IV melanoma patients that showed good responses. Circulating miR-4649-3p, miR-615-3p, and miR-1234-3p demonstrated potential prognostic utility in assessing CII responses. Compared to LDH levels during CII, circulating miR-615-3p levels were consistently more efficient in detecting melanoma patients undergoing CII who developed progressive disease. By combining stage III/IV patients, 92 and 17 differentially expressed cfmiRs were identified in pre-treatment plasma samples from responder and non-responder patients, respectively. In conclusion, this pilot study demonstrated cfmiRs that identified treatment responses and could allow for real-time monitoring of patients receiving CII.
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Affiliation(s)
- Matias A. Bustos
- Department of Translational Molecular Medicine, John Wayne Cancer Institute (JWCI), Providence Saint John’s Health Center (SJHC), Santa Monica, CA 90404, USA; (R.G.); (N.R.); (L.T.); (D.S.B.H.)
- Correspondence:
| | - Rebecca Gross
- Department of Translational Molecular Medicine, John Wayne Cancer Institute (JWCI), Providence Saint John’s Health Center (SJHC), Santa Monica, CA 90404, USA; (R.G.); (N.R.); (L.T.); (D.S.B.H.)
| | - Negin Rahimzadeh
- Department of Translational Molecular Medicine, John Wayne Cancer Institute (JWCI), Providence Saint John’s Health Center (SJHC), Santa Monica, CA 90404, USA; (R.G.); (N.R.); (L.T.); (D.S.B.H.)
| | - Hunter Cole
- Department of Immuno-Oncology and Clinical Research, JWCI, Providence SJHC, Santa Monica, CA 90404, USA; (H.C.); O' (S.O.)
| | - Linh T. Tran
- Department of Genomic Sequencing Center, JWCI, Providence SJHC, Santa Monica, CA 90404, USA; (L.T.T.); (K.D.T.)
| | - Kevin D. Tran
- Department of Genomic Sequencing Center, JWCI, Providence SJHC, Santa Monica, CA 90404, USA; (L.T.T.); (K.D.T.)
| | - Ling Takeshima
- Department of Translational Molecular Medicine, John Wayne Cancer Institute (JWCI), Providence Saint John’s Health Center (SJHC), Santa Monica, CA 90404, USA; (R.G.); (N.R.); (L.T.); (D.S.B.H.)
| | - Stacey L. Stern
- Department of Biostatistics, JWCI, Providence SJHC, Santa Monica, CA 90404, USA;
| | - Steven O’Day
- Department of Immuno-Oncology and Clinical Research, JWCI, Providence SJHC, Santa Monica, CA 90404, USA; (H.C.); O' (S.O.)
| | - Dave S. B. Hoon
- Department of Translational Molecular Medicine, John Wayne Cancer Institute (JWCI), Providence Saint John’s Health Center (SJHC), Santa Monica, CA 90404, USA; (R.G.); (N.R.); (L.T.); (D.S.B.H.)
- Department of Genomic Sequencing Center, JWCI, Providence SJHC, Santa Monica, CA 90404, USA; (L.T.T.); (K.D.T.)
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15
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Cao L, Zhu T, Lang X, Jia S, Yang Y, Zhu C, Wang Y, Feng S, Wang C, Zhang P, Chen J, Jiang H. Inhibiting DNA Methylation Improves Survival in Severe Sepsis by Regulating NF-κB Pathway. Front Immunol 2020; 11:1360. [PMID: 32714333 PMCID: PMC7343767 DOI: 10.3389/fimmu.2020.01360] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 05/28/2020] [Indexed: 12/17/2022] Open
Abstract
Organ dysfunction caused by sepsis is life-threatening and results in high mortality. Therapeutic options for sepsis are limited. Pathogenic factors are considered as components of environmental pressure that modify DNA methylation patterns thereby enhancing disease progression. Here, we found that sepsis patients exhibited higher levels of genomic DNA methylation patterns and hypermethylated genes associated with the NF-kB signaling pathway. Therefore, we hypothesized that a DNA methyl transferase inhibitor, Decitabine, may mitigate inflammation and improve survival by inhibiting the NF-κB signaling pathway. To test the hypothesis, mice challenged with caecal ligation and puncture (CLP) were subcutaneously injected with Decitabine solution (0.5, 1, and 1.5 mg/kg) 2 h following operation. Our results indicated that Decitabine reduces DNA methyltransferases (DNMTs), attenuates NF-κB activation, downregulates inflammatory cytokine levels, and inhibits the progression of sepsis. Thus, DNA methylation may be indispensable for sepsis and serve as a predicting factor. The use of Decitabine could represent a novel strategy in the treatment of sepsis.
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Affiliation(s)
- Luxi Cao
- Kidney Disease Center, College of Medicine, The First Affiliated Hospital, Zhejiang University, Hangzhou, China.,Key Laboratory of Nephropathy, Hangzhou, China.,Kidney Disease Immunology Laboratory, The Third-Grade Laboratory, State Administration of Traditional Chinese Medicine of China, Beijing, China.,Key Laboratory of Multiple Organ Transplantation, Ministry of Health of China, Hangzhou, China.,Institute of Nephropathy, Zhejiang University, Hangzhou, China
| | - Tingting Zhu
- Kidney Disease Center, College of Medicine, The First Affiliated Hospital, Zhejiang University, Hangzhou, China.,Key Laboratory of Nephropathy, Hangzhou, China.,Kidney Disease Immunology Laboratory, The Third-Grade Laboratory, State Administration of Traditional Chinese Medicine of China, Beijing, China.,Key Laboratory of Multiple Organ Transplantation, Ministry of Health of China, Hangzhou, China.,Institute of Nephropathy, Zhejiang University, Hangzhou, China
| | - Xiabing Lang
- Kidney Disease Center, College of Medicine, The First Affiliated Hospital, Zhejiang University, Hangzhou, China.,Key Laboratory of Nephropathy, Hangzhou, China.,Kidney Disease Immunology Laboratory, The Third-Grade Laboratory, State Administration of Traditional Chinese Medicine of China, Beijing, China.,Key Laboratory of Multiple Organ Transplantation, Ministry of Health of China, Hangzhou, China.,Institute of Nephropathy, Zhejiang University, Hangzhou, China
| | - Sha Jia
- Kidney Disease Center, College of Medicine, The First Affiliated Hospital, Zhejiang University, Hangzhou, China.,Key Laboratory of Nephropathy, Hangzhou, China.,Kidney Disease Immunology Laboratory, The Third-Grade Laboratory, State Administration of Traditional Chinese Medicine of China, Beijing, China.,Key Laboratory of Multiple Organ Transplantation, Ministry of Health of China, Hangzhou, China.,Institute of Nephropathy, Zhejiang University, Hangzhou, China
| | - Yi Yang
- Kidney Disease Center, College of Medicine, The First Affiliated Hospital, Zhejiang University, Hangzhou, China.,Key Laboratory of Nephropathy, Hangzhou, China.,Kidney Disease Immunology Laboratory, The Third-Grade Laboratory, State Administration of Traditional Chinese Medicine of China, Beijing, China.,Key Laboratory of Multiple Organ Transplantation, Ministry of Health of China, Hangzhou, China.,Institute of Nephropathy, Zhejiang University, Hangzhou, China
| | - Chaohong Zhu
- Kidney Disease Center, College of Medicine, The First Affiliated Hospital, Zhejiang University, Hangzhou, China.,Key Laboratory of Nephropathy, Hangzhou, China.,Kidney Disease Immunology Laboratory, The Third-Grade Laboratory, State Administration of Traditional Chinese Medicine of China, Beijing, China.,Key Laboratory of Multiple Organ Transplantation, Ministry of Health of China, Hangzhou, China.,Institute of Nephropathy, Zhejiang University, Hangzhou, China
| | - Yucheng Wang
- Kidney Disease Center, College of Medicine, The First Affiliated Hospital, Zhejiang University, Hangzhou, China.,Key Laboratory of Nephropathy, Hangzhou, China.,Kidney Disease Immunology Laboratory, The Third-Grade Laboratory, State Administration of Traditional Chinese Medicine of China, Beijing, China.,Key Laboratory of Multiple Organ Transplantation, Ministry of Health of China, Hangzhou, China.,Institute of Nephropathy, Zhejiang University, Hangzhou, China
| | - Shi Feng
- Kidney Disease Center, College of Medicine, The First Affiliated Hospital, Zhejiang University, Hangzhou, China.,Key Laboratory of Nephropathy, Hangzhou, China.,Kidney Disease Immunology Laboratory, The Third-Grade Laboratory, State Administration of Traditional Chinese Medicine of China, Beijing, China.,Key Laboratory of Multiple Organ Transplantation, Ministry of Health of China, Hangzhou, China.,Institute of Nephropathy, Zhejiang University, Hangzhou, China
| | - Cuili Wang
- Kidney Disease Center, College of Medicine, The First Affiliated Hospital, Zhejiang University, Hangzhou, China.,Key Laboratory of Nephropathy, Hangzhou, China.,Kidney Disease Immunology Laboratory, The Third-Grade Laboratory, State Administration of Traditional Chinese Medicine of China, Beijing, China.,Key Laboratory of Multiple Organ Transplantation, Ministry of Health of China, Hangzhou, China.,Institute of Nephropathy, Zhejiang University, Hangzhou, China
| | - Ping Zhang
- Kidney Disease Center, College of Medicine, The First Affiliated Hospital, Zhejiang University, Hangzhou, China.,Key Laboratory of Nephropathy, Hangzhou, China.,Kidney Disease Immunology Laboratory, The Third-Grade Laboratory, State Administration of Traditional Chinese Medicine of China, Beijing, China.,Key Laboratory of Multiple Organ Transplantation, Ministry of Health of China, Hangzhou, China.,Institute of Nephropathy, Zhejiang University, Hangzhou, China
| | - Jianghua Chen
- Kidney Disease Center, College of Medicine, The First Affiliated Hospital, Zhejiang University, Hangzhou, China.,Key Laboratory of Nephropathy, Hangzhou, China.,Kidney Disease Immunology Laboratory, The Third-Grade Laboratory, State Administration of Traditional Chinese Medicine of China, Beijing, China.,Key Laboratory of Multiple Organ Transplantation, Ministry of Health of China, Hangzhou, China.,Institute of Nephropathy, Zhejiang University, Hangzhou, China
| | - Hong Jiang
- Kidney Disease Center, College of Medicine, The First Affiliated Hospital, Zhejiang University, Hangzhou, China.,Key Laboratory of Nephropathy, Hangzhou, China.,Kidney Disease Immunology Laboratory, The Third-Grade Laboratory, State Administration of Traditional Chinese Medicine of China, Beijing, China.,Key Laboratory of Multiple Organ Transplantation, Ministry of Health of China, Hangzhou, China.,Institute of Nephropathy, Zhejiang University, Hangzhou, China
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16
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Bustos MA, Tran KD, Rahimzadeh N, Gross R, Lin SY, Shoji Y, Murakami T, Boley CL, Tran LT, Cole H, Kelly DF, O’Day S, Hoon DSB. Integrated Assessment of Circulating Cell-Free MicroRNA Signatures in Plasma of Patients with Melanoma Brain Metastasis. Cancers (Basel) 2020; 12:E1692. [PMID: 32630542 PMCID: PMC7352246 DOI: 10.3390/cancers12061692] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 06/23/2020] [Accepted: 06/23/2020] [Indexed: 12/11/2022] Open
Abstract
Primary cutaneous melanoma frequently metastasizes to distant organs including the brain. Identification of cell-free microRNAs (cfmiRs) found in the blood can be used as potential body fluid biomarkers for detecting and monitoring patients with melanoma brain metastasis (MBM). In this pilot study, we initially aimed to identify cfmiRs in the blood of MBM patients. Normal donors plasma (healthy, n = 48) and pre-operative MBM patients' plasma samples (n = 36) were compared for differences in >2000 microRNAs (miRs) using a next generation sequencing (NGS) probe-based assay. A 74 cfmiR signature was identified in an initial cohort of MBM plasma samples and then verified in a second cohort of MBM plasma samples (n = 24). Of these, only 58 cfmiRs were also detected in MBM tissues (n = 24). CfmiR signatures were also found in patients who have lung and breast cancer brain metastasis (n = 13) and glioblastomas (n = 36) compared to MBM plasma samples. The 74 cfmiR signature and the latter cfmiR signatures were then compared. We found a 6 cfmiR signature that was commonly upregulated in MBM plasma samples in all of the comparisons, and a 29 cfmiR signature that distinguishes MBM patients from normal donors' samples. In addition, we assessed for cfmiRs in plasma (n = 20) and urine (n = 14) samples collected from metastatic melanoma patients receiving checkpoint inhibitor immunotherapy (CII). Pre- and post-treatment samples showed consistent changes in cfmiRs. Analysis of pre- and post-treatment plasma samples showed 8 differentially expressed (DE) cfmiRs that overlapped with the 35 cfmiR signature found in MBM patients. In paired pre-treatment plasma and urine samples receiving CII 8 cfmiRs overlapped. This study identified specific cfmiRs in MBM plasma samples that may potentially allow for assessment of melanoma patients developing MBM. The cfmiR signatures identified in both blood and urine may have potential utility to assess CII responses after further validation.
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Affiliation(s)
- Matias A. Bustos
- Department of Translational Molecular Medicine, John Wayne Cancer Institute at Providence Saint John’s Health Center, Santa Monica, CA 90404, USA; (M.A.B.); (N.R.); (R.G.); (S.Y.L.); (Y.S.); (T.M.)
| | - Kevin D. Tran
- Department of Genomic Sequencing Center, John Wayne Cancer Institute at Providence Saint John’s Health Center, Santa Monica, CA 90404, USA; (K.D.T.); (L.T.T.)
| | - Negin Rahimzadeh
- Department of Translational Molecular Medicine, John Wayne Cancer Institute at Providence Saint John’s Health Center, Santa Monica, CA 90404, USA; (M.A.B.); (N.R.); (R.G.); (S.Y.L.); (Y.S.); (T.M.)
| | - Rebecca Gross
- Department of Translational Molecular Medicine, John Wayne Cancer Institute at Providence Saint John’s Health Center, Santa Monica, CA 90404, USA; (M.A.B.); (N.R.); (R.G.); (S.Y.L.); (Y.S.); (T.M.)
| | - Selena Y. Lin
- Department of Translational Molecular Medicine, John Wayne Cancer Institute at Providence Saint John’s Health Center, Santa Monica, CA 90404, USA; (M.A.B.); (N.R.); (R.G.); (S.Y.L.); (Y.S.); (T.M.)
| | - Yoshiaki Shoji
- Department of Translational Molecular Medicine, John Wayne Cancer Institute at Providence Saint John’s Health Center, Santa Monica, CA 90404, USA; (M.A.B.); (N.R.); (R.G.); (S.Y.L.); (Y.S.); (T.M.)
| | - Tomohiro Murakami
- Department of Translational Molecular Medicine, John Wayne Cancer Institute at Providence Saint John’s Health Center, Santa Monica, CA 90404, USA; (M.A.B.); (N.R.); (R.G.); (S.Y.L.); (Y.S.); (T.M.)
| | - Christine L. Boley
- Department of Immuno-Oncology and Clinical Research, John Wayne Cancer Institute, Santa Monica, CA 90404, USA; (C.L.B.); (H.C.); O’
| | - Linh T. Tran
- Department of Genomic Sequencing Center, John Wayne Cancer Institute at Providence Saint John’s Health Center, Santa Monica, CA 90404, USA; (K.D.T.); (L.T.T.)
| | - Hunter Cole
- Department of Immuno-Oncology and Clinical Research, John Wayne Cancer Institute, Santa Monica, CA 90404, USA; (C.L.B.); (H.C.); O’
| | - Daniel F. Kelly
- Pacific Neuroscience Institute, John Wayne Cancer Institute, Saint John’s Health Center, Santa Monica, CA 90404, USA;
| | - Steven O’Day
- Department of Immuno-Oncology and Clinical Research, John Wayne Cancer Institute, Santa Monica, CA 90404, USA; (C.L.B.); (H.C.); O’
| | - Dave S. B. Hoon
- Department of Translational Molecular Medicine, John Wayne Cancer Institute at Providence Saint John’s Health Center, Santa Monica, CA 90404, USA; (M.A.B.); (N.R.); (R.G.); (S.Y.L.); (Y.S.); (T.M.)
- Department of Genomic Sequencing Center, John Wayne Cancer Institute at Providence Saint John’s Health Center, Santa Monica, CA 90404, USA; (K.D.T.); (L.T.T.)
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17
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Ramos RI, Bustos MA, Wu J, Jones P, Chang SC, Kiyohara E, Tran K, Zhang X, Stern SL, Izraely S, Sagi-Assif O, Witz IP, Davies MA, Mills GB, Kelly DF, Irie RF, Hoon DSB. Upregulation of cell surface GD3 ganglioside phenotype is associated with human melanoma brain metastasis. Mol Oncol 2020; 14:1760-1778. [PMID: 32358995 PMCID: PMC7400791 DOI: 10.1002/1878-0261.12702] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 03/24/2020] [Accepted: 04/27/2020] [Indexed: 12/23/2022] Open
Abstract
Melanoma metastasis to the brain is one of the most frequent extracranial brain tumors. Cell surface gangliosides are elevated in melanoma metastasis; however, the metabolic regulatory mechanisms that govern these specific changes are poorly understood in melanoma particularly brain metastases (MBM) development. We found ganglioside GD3 levels significantly upregulated in MBM compared to lymph node metastasis (LNM) but not for other melanoma gangliosides. Moreover, we demonstrated an upregulation of ST8SIA1 (GD3 synthase) as melanoma progresses from melanocytes to MBM cells. Using RNA‐ISH on FFPE specimens, we evaluated ST8SIA1 expression in primary melanomas (PRM) (n = 23), LNM and visceral metastasis (n = 45), and MBM (n = 39). ST8SIA1 was significantly enhanced in MBM compared to all other specimens. ST8SIA1 expression was assessed in clinically well‐annotated melanoma patients from multicenters with AJCC stage III B‐D LNM (n = 58) with 14‐year follow‐up. High ST8SIA1 expression was significantly associated with poor overall survival (HR = 3.24; 95% CI, 1.19–8.86, P = 0.02). In a nude mouse human xenograft melanoma brain metastasis model, MBM variants had higher ST8SIA1 expression than their respective cutaneous melanoma variants. Elevated ST8SIA1 expression enhances levels of cell surface GD3, a phenotype that favors MBM development, hence associated with very poor prognosis. Functional assays demonstrated that ST8SIA1 overexpression enhanced cell proliferation and colony formation, whereby ST8SIA1 knockdown had opposite effects. Icaritin a plant‐derived phytoestrogen treatment significantly inhibited cell growth in high GD3‐positive MBM cells through targeting the canonical NFκB pathway. The study demonstrates GD3 phenotype associates with melanoma progression and poor outcome.
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Affiliation(s)
- Romela Irene Ramos
- Department of Translational Molecular Medicine, John Wayne Cancer Institute (JWCI), Santa Monica, CA, USA
| | - Matias A Bustos
- Department of Translational Molecular Medicine, John Wayne Cancer Institute (JWCI), Santa Monica, CA, USA
| | - Jinfeng Wu
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai, China
| | - Peter Jones
- Department of Translational Molecular Medicine, John Wayne Cancer Institute (JWCI), Santa Monica, CA, USA
| | - Shu Ching Chang
- Medical Data Research Center, Providence St. Joseph Health Center, Portland, OR, USA
| | - Eiji Kiyohara
- Department of Translational Molecular Medicine, John Wayne Cancer Institute (JWCI), Santa Monica, CA, USA
| | - Kevin Tran
- Department of Translational Molecular Medicine, John Wayne Cancer Institute (JWCI), Santa Monica, CA, USA
| | - Xiaoqing Zhang
- Department of Translational Molecular Medicine, John Wayne Cancer Institute (JWCI), Santa Monica, CA, USA
| | - Stacey L Stern
- Department of Biostatistics, JWCI, Santa Monica, CA, USA
| | - Sivan Izraely
- Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel Aviv, Israel
| | - Orit Sagi-Assif
- Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel Aviv, Israel
| | - Isaac P Witz
- Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel Aviv, Israel
| | - Michael A Davies
- Department of Melanoma Medical Oncology, Systems Biology and Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Gordon B Mills
- Department of Cell Development and Cancer Biology, Oregon Health and Science University (OHSU) Knight Cancer Institute Portland, OR, USA
| | - Daniel F Kelly
- Pacific Neuroscience Institute, JWCI, Santa Monica, CA, USA
| | - Reiko F Irie
- Department of Translational Molecular Medicine, John Wayne Cancer Institute (JWCI), Santa Monica, CA, USA
| | - Dave S B Hoon
- Department of Translational Molecular Medicine, John Wayne Cancer Institute (JWCI), Santa Monica, CA, USA
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18
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17-Aminogeldanamycin Inhibits Constitutive Nuclear Factor-Kappa B (NF-κB) Activity in Patient-Derived Melanoma Cell Lines. Int J Mol Sci 2020; 21:ijms21113749. [PMID: 32466509 PMCID: PMC7312877 DOI: 10.3390/ijms21113749] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 05/21/2020] [Accepted: 05/25/2020] [Indexed: 12/12/2022] Open
Abstract
Melanoma remains incurable skin cancer, and targeting heat shock protein 90 (HSP90) is a promising therapeutic approach. In this study, we investigate the effect of 17-aminogeldanamycin, a potent HSP90 inhibitor, on nuclear factor-kappa B (NF-κB) activity in BRAFV600E and NRASQ61R patient-derived melanoma cell lines. We performed time-lapse microscopy and flow cytometry to monitor changes in cell confluence and viability. The NF-κB activity was determined by immunodetection of phospho-p65 and assessment of expression of NF-κB-dependent genes by quantitative real-time polymerase chain reaction (qRT-PCR), Western blotting, and enzyme-linked immunosorbent assay (ELISA). Constitutive activity of p65/NF-κB was evident in all melanoma cell lines. Differences in its level might be associated with genetic alterations in CHUK, IL1B, MAP3K14, NFKBIE, RIPK1, and TLR4, while differences in transcript levels of NF-κB-inducible genes revealed by PCR array might result from the contribution of other regulatory mechanisms. 17-Aminogeldanamycin markedly diminished the level of phospho-p65, but the total p65 protein level was unaltered, indicating that 17-aminogeldanamycin inhibited activation of p65/NF-κB. This conclusion was supported by significantly reduced expression of selected NF-κB-dependent genes: cyclin D1 (CCND1), C-X-C motif chemokine ligand 8 (CXCL8), and vascular endothelial growth factor (VEGF), as shown at transcript and protein levels, as well as secretion of IL-8 and VEGF. Our study indicates that 17-aminogeldanamycin can be used for efficient inhibition of NF-κB activity and the simultaneous diminution of IL-8 and VEGF levels in the extracellular milieu of melanoma.
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19
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Wang X, Bustos MA, Zhang X, Ramos RI, Tan C, Iida Y, Chang SC, Salomon MP, Tran K, Gentry R, Kravtsova-Ivantsiv Y, Kelly DF, Mills GB, Ciechanover A, Mao Y, Hoon DS. Downregulation of the Ubiquitin-E3 Ligase RNF123 Promotes Upregulation of the NF-κB1 Target SerpinE1 in Aggressive Glioblastoma Tumors. Cancers (Basel) 2020; 12:E1081. [PMID: 32349217 PMCID: PMC7281601 DOI: 10.3390/cancers12051081] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 04/22/2020] [Accepted: 04/25/2020] [Indexed: 12/28/2022] Open
Abstract
This study examined the role of the ubiquitin E3-ligase RNF123 in modulating downstream NF-κB1 targets in glioblastoma (GB) tumor progression. Our findings revealed an oncogenic pathway (miR-155-5p-RNF123-NF-κB1-p50-SerpinE1) that may represent a new therapeutic target pathway for GB patients with isocitrate dehydrogenase 1 and 2 (IDH) WT (wild type). Mechanistically, we demonstrated that RNF123 is downregulated in IDH WT GB patients and leads to the reduction of p50 levels. RNA-sequencing, reverse-phase protein arrays, and in vitro functional assays on IDH WT GB cell lines with RNF123 overexpression showed that SerpinE1 was a downstream target that is negatively regulated by RNF123. SERPINE1 knockdown reduced the proliferation and invasion of IDH WT GB cell lines. Both SerpinE1 and miR-155-5p overexpression negatively modulated RNF123 expression. In clinical translational analysis, RNF123, SerpinE1, and miR-155-5p were all associated with poor outcomes in GB patients. Multivariable analysis in IDH WT GB patients showed that concurrent low RNF123 and high SerpinE1 was an independent prognostic factor in predicting poor overall survival (p < 0.001, hazard ratio (HR) = 2.93, 95% confidence interval (CI) 1.7-5.05), and an increased risk of recurrence (p < 0.001, relative risk (RR) = 3.56, 95% CI 1.61-7.83).
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Affiliation(s)
- Xiaowen Wang
- Department of Translational Molecular Medicine, John Wayne Cancer Institute (JWCI) at Providence Saint John’s Health Center, Santa Monica, CA 90404, USA; (X.W.); (M.A.B.); (X.Z.); (R.I.R.); (Y.I.); (M.P.S.); (K.T.); (R.G.); (Y.M.)
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Matias A. Bustos
- Department of Translational Molecular Medicine, John Wayne Cancer Institute (JWCI) at Providence Saint John’s Health Center, Santa Monica, CA 90404, USA; (X.W.); (M.A.B.); (X.Z.); (R.I.R.); (Y.I.); (M.P.S.); (K.T.); (R.G.); (Y.M.)
| | - Xiaoqing Zhang
- Department of Translational Molecular Medicine, John Wayne Cancer Institute (JWCI) at Providence Saint John’s Health Center, Santa Monica, CA 90404, USA; (X.W.); (M.A.B.); (X.Z.); (R.I.R.); (Y.I.); (M.P.S.); (K.T.); (R.G.); (Y.M.)
| | - Romela Irene Ramos
- Department of Translational Molecular Medicine, John Wayne Cancer Institute (JWCI) at Providence Saint John’s Health Center, Santa Monica, CA 90404, USA; (X.W.); (M.A.B.); (X.Z.); (R.I.R.); (Y.I.); (M.P.S.); (K.T.); (R.G.); (Y.M.)
| | - Cong Tan
- Department of Pathology, Cancer Hospital, Fudan University, Shanghai 200032, China;
| | - Yuuki Iida
- Department of Translational Molecular Medicine, John Wayne Cancer Institute (JWCI) at Providence Saint John’s Health Center, Santa Monica, CA 90404, USA; (X.W.); (M.A.B.); (X.Z.); (R.I.R.); (Y.I.); (M.P.S.); (K.T.); (R.G.); (Y.M.)
| | - Shu-Ching Chang
- Medical Data Research Center, Providence Saint Joseph’s Health, Portland, OR 97225, USA;
| | - Matthew P. Salomon
- Department of Translational Molecular Medicine, John Wayne Cancer Institute (JWCI) at Providence Saint John’s Health Center, Santa Monica, CA 90404, USA; (X.W.); (M.A.B.); (X.Z.); (R.I.R.); (Y.I.); (M.P.S.); (K.T.); (R.G.); (Y.M.)
| | - Kevin Tran
- Department of Translational Molecular Medicine, John Wayne Cancer Institute (JWCI) at Providence Saint John’s Health Center, Santa Monica, CA 90404, USA; (X.W.); (M.A.B.); (X.Z.); (R.I.R.); (Y.I.); (M.P.S.); (K.T.); (R.G.); (Y.M.)
| | - Rebecca Gentry
- Department of Translational Molecular Medicine, John Wayne Cancer Institute (JWCI) at Providence Saint John’s Health Center, Santa Monica, CA 90404, USA; (X.W.); (M.A.B.); (X.Z.); (R.I.R.); (Y.I.); (M.P.S.); (K.T.); (R.G.); (Y.M.)
| | - Yelena Kravtsova-Ivantsiv
- The David and Janet Polak Cancer and Vascular Biology Research Center, The Rappaport Faculty of Medicine and Research Institute, Technion-Israel Institute of Technology, Efron Street, Bat-Galim, Haifa 31096, Israel; (Y.K.-I.); (A.C.)
| | - Daniel F. Kelly
- Pacific Neuroscience Institute, JWCI, Santa Monica, CA 90404, USA;
| | - Gordon B. Mills
- Department of Cell Development and Cancer Biology, Knight Cancer Institute, Portland, OR 97239, USA;
| | - Aaron Ciechanover
- The David and Janet Polak Cancer and Vascular Biology Research Center, The Rappaport Faculty of Medicine and Research Institute, Technion-Israel Institute of Technology, Efron Street, Bat-Galim, Haifa 31096, Israel; (Y.K.-I.); (A.C.)
| | - Ying Mao
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai 200040, China
- The Collaborative Innovation Center for Brain Science, Fudan University, Shanghai 200032, China
| | - Dave S.B. Hoon
- Department of Translational Molecular Medicine, John Wayne Cancer Institute (JWCI) at Providence Saint John’s Health Center, Santa Monica, CA 90404, USA; (X.W.); (M.A.B.); (X.Z.); (R.I.R.); (Y.I.); (M.P.S.); (K.T.); (R.G.); (Y.M.)
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20
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Lin SY, Chang SC, Lam S, Ramos RI, Tran K, Ohe S, Salomon MP, Bhagat AAS, Lim CT, Fischer TD, Foshag LJ, Boley CL, O’Day SJ, Hoon DS. Prospective Molecular Profiling of Circulating Tumor Cells from Patients with Melanoma Receiving Combinatorial Immunotherapy. Clin Chem 2020; 66:169-177. [PMID: 31672856 PMCID: PMC7193771 DOI: 10.1373/clinchem.2019.307140] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 08/23/2019] [Indexed: 12/12/2022]
Abstract
BACKGROUND Blood molecular profiling of circulating tumor cells (CTCs) can enable monitoring of patients with metastatic melanoma during checkpoint inhibitor immunotherapy (CII) and in combination with targeted therapies. We developed a microfluidics-based CTC platform to explore CTC profiling utility in CII-treated patients with melanoma using a melanoma messenger RNA (mRNA)/DNA biomarker panel. METHODS Blood samples (n = 213) were collected prospectively from 75 American Joint Committee on Cancer-staged III/IV melanoma patients during CII treatment and those enriched for CTCs. CTC profiling was performed using 5 known melanoma mRNA biomarkers and BRAF V600E DNA mutation. CTC biomarker status associations with clinical outcomes were assessed. RESULTS CTCs were detected in 88% of blood samples from patients with melanoma. CTC-derived biomarkers and clinical variables analyzed using classification and regression tree analysis revealed that a combination of lactate dehydrogenase, CTC-mRNA biomarkers, and tumor BRAF-mutation status was indicative of clinical outcomes for patients with stage IV melanoma (n = 52). The panel stratified low-risk and high-risk patients, whereby the latter had poor disease-free (P = 0.03) and overall survival (P = 0.02). Incorporation of a DNA biomarker with mRNA profiling increased overall CTC-detection capability by 57% compared to mRNA profiling only. RNA sequencing of isolated CTCs identified significant catenin beta 1 (CTNNB1) overexpression (P <0.01) compared to nondisease donor blood. CTC-CTNNB1 was associated with progressive disease/stable disease compared to complete-responder patient status (P = 0.02). Serial CTC profiling identified subclinical disease in patients who developed progressive disease during treatment/follow-up. CONCLUSIONS CTC-derived mRNA/DNA biomarkers have utility for monitoring CII, targeted, and combinatorial therapies in metastatic melanoma patients.
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Affiliation(s)
- Selena Y. Lin
- Department of Translational Molecular Medicine, John Wayne
Cancer Institute, Saint John’s Health Center, PHS, Santa Monica, CA
| | - Shu-Ching Chang
- Medical Data Research Center, Providence Saint Joseph
Health, Portland, OR
| | - Stella Lam
- Department of Translational Molecular Medicine, John Wayne
Cancer Institute, Saint John’s Health Center, PHS, Santa Monica, CA
| | - Romela Irene Ramos
- Department of Translational Molecular Medicine, John Wayne
Cancer Institute, Saint John’s Health Center, PHS, Santa Monica, CA
| | - Kevin Tran
- Department of Translational Molecular Medicine, John Wayne
Cancer Institute, Saint John’s Health Center, PHS, Santa Monica, CA
| | - Shuichi Ohe
- Department of Translational Molecular Medicine, John Wayne
Cancer Institute, Saint John’s Health Center, PHS, Santa Monica, CA
| | - Matthew P. Salomon
- Department of Translational Molecular Medicine, John Wayne
Cancer Institute, Saint John’s Health Center, PHS, Santa Monica, CA
| | - Ali Asgar S. Bhagat
- Department of Biomedical Engineering and Department of
Mechanical Engineering, National University of Singapore, Singapore
| | - Chwee Teck Lim
- Department of Biomedical Engineering and Department of
Mechanical Engineering, National University of Singapore, Singapore
| | - Trevan D. Fischer
- Department of Surgical Oncology, John Wayne Cancer
Institute, PHS, Santa Monica, CA
| | - Leland J. Foshag
- Department of Surgical Oncology, John Wayne Cancer
Institute, PHS, Santa Monica, CA
| | - Christine L. Boley
- Department of Immuno-Oncology and Clinical Research, John
Wayne Cancer Institute, PHS, Santa Monica, CA
| | - Steven J. O’Day
- Department of Immuno-Oncology and Clinical Research, John
Wayne Cancer Institute, PHS, Santa Monica, CA
| | - Dave S.B. Hoon
- Department of Translational Molecular Medicine, John Wayne
Cancer Institute, Saint John’s Health Center, PHS, Santa Monica, CA
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21
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B7H3 regulates differentiation and serves as a potential biomarker and theranostic target for human glioblastoma. J Transl Med 2019; 99:1117-1129. [PMID: 30914782 DOI: 10.1038/s41374-019-0238-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 02/09/2019] [Accepted: 02/18/2019] [Indexed: 12/27/2022] Open
Abstract
B7H3 (CD276), a co-stimulator molecule of the cell surface B7 protein superfamily, is expressed on glioblastomas (GBM). Recently, B7H3 functions beyond immune costimulation have been demonstrated. However, the mechanisms underlying B7H3 function are diverse and not well understood. GBM tumors contain undifferentiated self-renewing cells, which confound therapeutic attempts. We investigated the role of B7H3 in the regulation of GBM cell differentiation and the regulatory pathways involved. Analysis of public databases (TCGA, Rembrandt, and GEO NCBI) and RNA sequencing were performed to explore the role of B7H3 in GBM. Knockdown and overexpression of B7H3, were used to verify the downstream pathway in vitro. Further studies in vivo were performed to support the new finding. Bioinformatics analysis identified a correlation between the expression of B7H3, the expression of glioma self-renewing cell (GSC)-related genes, and MYC expression. These observations were verified by RNA-sequencing analyses in primary GBM cell lines. In vitro knockdown of B7H3-induced differentiation, associated with downregulation of SMAD6 (a TGF-β pathway inhibitor) and enhancement of SMAD1 phosphorylation-induced SMAD4 expression. Importantly, activation of the TGF-β pathway resulted in downregulation of MYC expression. In vivo assays conducted in a human GBM cell line xenograft mouse model demonstrated that B7H3 knockdown decreased MYC expression and inhibited tumor growth. B7H3 knockdown could regulate GBM differentiation by modulating MYC expression. So, B7H3 could serve as a potential theranostic target for the treatment of patients with GBM.
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Kitanaka N, Nakano R, Kitanaka T, Namba S, Konno T, Nakayama T, Sugiya H. NF-κB p65 and p105 implicate in interleukin 1β-mediated COX-2 expression in melanoma cells. PLoS One 2018; 13:e0208955. [PMID: 30562372 PMCID: PMC6298655 DOI: 10.1371/journal.pone.0208955] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 11/27/2018] [Indexed: 12/11/2022] Open
Abstract
Inflammatory and microenvironmental factors produced by cancer cells are thought to directly or indirectly promote cancer cell growth. Prostaglandins, including prostaglandin E2, have key roles as a microenvironment factor in influencing the development of tumors, and are produced by the rate limiting enzyme cyclooxygenase 2 (COX-2). In this study, we used canine melanoma cells treated with the proinflammatory cytokine interleukin 1β (IL-1β) and investigated the transcriptional factor nuclear factor-κB (NF-κB) signaling in IL-1β-induced COX-2 expression. IL-1β induced prostaglandin E2 release and COX-2 mRNA expression in a time- and dose-dependent manner. In the cells treated with the NF-κB inhibitors BAY11-7082 and TPC-1, IL-1β-mediated prostaglandin E2 release and COX-2 mRNA expression were inhibited. IL-1β also provoked phosphorylation of p65/RelA and p105/NF-κB1, which are members of the NF-κB families. The IL-1β-induced phosphorylation of p65 and p105 was attenuated in the presence of both NF-κB inhibitors. In melanoma cells transfected with siRNA of p65 or p105, IL-1β-mediated COX-2 mRNA expression was inhibited. These findings suggest that canonical activation of NF-κB signaling plays a crucial role for inflammatory states in melanoma cells.
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Affiliation(s)
- Nanako Kitanaka
- Laboratories of Veterinary Biochemistry, Nihon University College of Bioresource Sciences, Kameino, Fujisawa, Kanagawa, Japan
| | - Rei Nakano
- Laboratories of Veterinary Biochemistry, Nihon University College of Bioresource Sciences, Kameino, Fujisawa, Kanagawa, Japan
- Laboratory for Cellular Function Conversion Technology, RIKEN Center for Integrative Medical Sciences, Suehiro-cho, Tsurumi, Yokohama, Kanagawa, Japan
| | - Taku Kitanaka
- Laboratories of Veterinary Biochemistry, Nihon University College of Bioresource Sciences, Kameino, Fujisawa, Kanagawa, Japan
| | - Shinichi Namba
- Laboratories of Veterinary Biochemistry, Nihon University College of Bioresource Sciences, Kameino, Fujisawa, Kanagawa, Japan
| | - Tadayoshi Konno
- Laboratories of Veterinary Biochemistry, Nihon University College of Bioresource Sciences, Kameino, Fujisawa, Kanagawa, Japan
| | - Tomohiro Nakayama
- Veterinary Radiotherapy, Nihon University College of Bioresource Sciences, Kameino, Fujisawa, Kanagawa, Japan
| | - Hiroshi Sugiya
- Laboratories of Veterinary Biochemistry, Nihon University College of Bioresource Sciences, Kameino, Fujisawa, Kanagawa, Japan
- * E-mail:
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23
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Salomon MP, Wang X, Marzese DM, Hsu SC, Nelson N, Zhang X, Matsuba C, Takasumi Y, Ballesteros-Merino C, Fox BA, Barkhoudarian G, Kelly DF, Hoon DSB. The Epigenomic Landscape of Pituitary Adenomas Reveals Specific Alterations and Differentiates Among Acromegaly, Cushing's Disease and Endocrine-Inactive Subtypes. Clin Cancer Res 2018; 24:4126-4136. [PMID: 30084836 DOI: 10.1158/1078-0432.ccr-17-2206] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 12/19/2017] [Accepted: 05/15/2018] [Indexed: 11/16/2022]
Abstract
Purpose: Pituitary adenomas are one of the most common benign neoplasms of the central nervous system. Although emerging evidence suggests roles for both genetic and epigenetic factors in tumorigenesis, the degree to which these factors contribute to disease remains poorly understood.Experimental Design: A multiplatform analysis was performed to identify the genomic and epigenomic underpinnings of disease among the three major subtypes of surgically resected pituitary adenomas in 48 patients: growth hormone (GH)-secreting (n = 17), adrenocorticotropic hormone (ACTH)-secreting (n = 13, including 3 silent-ACTH adenomas), and endocrine-inactive (n = 18). Whole-exome sequencing was used to profile the somatic mutational landscape, whole-transcriptome sequencing was used to identify disease-specific patterns of gene expression, and array-based DNA methylation profiling was used to examine genome-wide patterns of DNA methylation.Results: Recurrent single-nucleotide and small indel somatic mutations were infrequent among the three adenoma subtypes. However, somatic copy-number alterations (SCNA) were identified in all three pituitary adenoma subtypes. Methylation analysis revealed adenoma subtype-specific DNA methylation profiles, with GH-secreting adenomas being dominated by hypomethylated sites. Likewise, gene-expression patterns revealed adenoma subtype-specific profiles. Integrating DNA methylation and gene-expression data revealed that hypomethylation of promoter regions are related with increased expression of GH1 and SSTR5 genes in GH-secreting adenomas and POMC gene in ACTH-secreting adenomas. Finally, multispectral IHC staining of immune-related proteins showed abundant expression of PD-L1 among all three adenoma subtypes.Conclusions: Taken together, these data stress the contribution of epigenomic alterations to disease-specific etiology among adenoma subtypes and highlight potential targets for future immunotherapy-based treatments. This article reveals novel insights into the epigenomics underlying pituitary adenomas and highlights how differences in epigenomic states are related to important transcriptome alterations that define adenoma subtypes. Clin Cancer Res; 24(17); 4126-36. ©2018 AACR.
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Affiliation(s)
- Matthew P Salomon
- Department of Translational Molecular Medicine, John Wayne Cancer Institute at Saint John's Health Center, Providence Health System, Santa Monica, California
| | - Xiaowen Wang
- Department of Translational Molecular Medicine, John Wayne Cancer Institute at Saint John's Health Center, Providence Health System, Santa Monica, California
| | - Diego M Marzese
- Department of Translational Molecular Medicine, John Wayne Cancer Institute at Saint John's Health Center, Providence Health System, Santa Monica, California
| | - Sandy C Hsu
- Sequencing Center, John Wayne Cancer Institute at Saint John's Health Center, Providence Health and Service (PHS), Santa Monica, California
| | - Nellie Nelson
- Sequencing Center, John Wayne Cancer Institute at Saint John's Health Center, Providence Health and Service (PHS), Santa Monica, California
| | - Xin Zhang
- Department of Translational Molecular Medicine, John Wayne Cancer Institute at Saint John's Health Center, Providence Health System, Santa Monica, California
| | - Chikako Matsuba
- Department of Translational Molecular Medicine, John Wayne Cancer Institute at Saint John's Health Center, Providence Health System, Santa Monica, California
| | - Yuki Takasumi
- Department of Pathology, Saint John's Health Center, PHS, Santa Monica, California
| | | | - Bernard A Fox
- Earle A. Chiles Research Institute, Providence Cancer Center, PHS, Portland, Oregon
| | - Garni Barkhoudarian
- Pacific Neuroscience Institute, PHS, Santa Monica, California.,John Wayne Cancer Institute Brain Tumor Center, Saint John's Health Center, Providence Health System, Santa Monica, California
| | - Daniel F Kelly
- Pacific Neuroscience Institute, PHS, Santa Monica, California.,John Wayne Cancer Institute Brain Tumor Center, Saint John's Health Center, Providence Health System, Santa Monica, California
| | - Dave S B Hoon
- Department of Translational Molecular Medicine, John Wayne Cancer Institute at Saint John's Health Center, Providence Health System, Santa Monica, California. .,Sequencing Center, John Wayne Cancer Institute at Saint John's Health Center, Providence Health and Service (PHS), Santa Monica, California.,Pacific Neuroscience Institute, PHS, Santa Monica, California
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24
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Graff-Baker AN, Orozco JIJ, Marzese DM, Salomon MP, Hoon DSB, Goldfarb M. Epigenomic and Transcriptomic Characterization of Secondary Breast Cancers. Ann Surg Oncol 2018; 25:3082-3087. [PMID: 29956094 DOI: 10.1245/s10434-018-6582-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Indexed: 12/12/2022]
Abstract
BACKGROUND Molecular alterations impact tumor prognosis and response to treatment. This study was designed to identify transcriptomic and epigenomic signatures of breast cancer (BC) tumors from patients with any prior malignancy. METHODS RNA-sequencing and genome-wide DNA methylation profiles from BCs were generated in the Cancer Genome Atlas project. Patients with secondary breast cancer (SBC) were separated by histological subtype and matched to primary breast cancer controls to create two independent cohorts of invasive ductal (IDC, n = 36) and invasive lobular (ILC, n = 40) carcinoma. Differentially expressed genes, as well as differentially methylated genomic regions, were integrated to identify epigenetically regulated abnormal gene pathways in SBCs. RESULTS Differentially expressed genes were identified in IDC SBCs (n = 727) and in ILC SBCs (n = 261; Wilcoxon's test; P < 0.05). In IDC SBCs, 105 genes were upregulated and hypomethylated, including an estrogen receptor gene, and 73 genes were downregulated and hypermethylated, including genes involved in antigen presentation and interferon response pathways (HLA-E, IRF8, and RELA). In ILC SBCs, however, only 17 genes were synchronously hypomethylated and upregulated, whereas 46 genes hypermethylated and downregulated. Interestingly, the SBC gene expression signatures closely corresponded with each histological subtype with only 1.51% of genes overlapping between the two histological subtypes. CONCLUSIONS Differential gene expression and DNA methylation signatures are seen in both IDC and ILC SBCs, including genes that are relevant to tumor growth and proliferation. Differences in gene expression signatures corresponding with each histological subtype emphasize the importance of disease subtype-specific evaluations of molecular alterations.
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Affiliation(s)
- Amanda N Graff-Baker
- Center for Endocrine Tumors and Disorders, John Wayne Cancer Institute at Providence Saint John's Health Center, Santa Monica, CA, USA
| | - Javier I J Orozco
- Center for Endocrine Tumors and Disorders, John Wayne Cancer Institute at Providence Saint John's Health Center, Santa Monica, CA, USA
| | - Diego M Marzese
- Center for Endocrine Tumors and Disorders, John Wayne Cancer Institute at Providence Saint John's Health Center, Santa Monica, CA, USA
| | - Matthew P Salomon
- Center for Endocrine Tumors and Disorders, John Wayne Cancer Institute at Providence Saint John's Health Center, Santa Monica, CA, USA
| | - Dave S B Hoon
- Center for Endocrine Tumors and Disorders, John Wayne Cancer Institute at Providence Saint John's Health Center, Santa Monica, CA, USA
| | - Melanie Goldfarb
- Center for Endocrine Tumors and Disorders, John Wayne Cancer Institute at Providence Saint John's Health Center, Santa Monica, CA, USA.
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Zheng L, Wong YS, Shao M, Huang S, Wang F, Chen J. Apoptosis induced by 9,11‑dehydroergosterol peroxide from Ganoderma Lucidum mycelium in human malignant melanoma cells is Mcl‑1 dependent. Mol Med Rep 2018; 18:938-944. [PMID: 29845223 PMCID: PMC6059726 DOI: 10.3892/mmr.2018.9035] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 05/11/2018] [Indexed: 12/11/2022] Open
Abstract
9,11-Dehydroergosterol peroxide [9(11)-DHEP] is an important steroid from medicinal mushroom, which has been reported to exert antitumor activity in several tumor types. However, the role of 9(11)-DHEP toward the malignant melanoma cells has not been investigated. In the present study, the steroid from Ganoderma lucidum was purified on a submerged culture, and its antitumor mechanisms on A375 human malignant melanoma cells was investigated by MTT, flow cytometry and western blotting. The studies demonstrated that apoptotic mechanisms of the steroid were caspase-dependent and mediated via the mitochondrial pathway. The steroid did not cause significant changes in the expression levels of B-cell lymphoma 2 (Bcl-2) family proteins, Bcl-2-like protein 11, p53 upregulated modulator of apoptosis, Bcl-2-associated X protein, BH3 interacting-domain death agonist, Bcl-2-associated death promoter and Bcl-2, but it significantly downregulated induced myeloid leukemia cell differentiation protein Mcl-1 (Mcl-1) in melanoma cells, suggesting the key role of Mcl-1 in regulating apoptosis of melanoma cells induced by the steroid. These properties of 9(11)-DHEP advocate its usage as supplements in human malignant melanoma chemoprevention. The present study also suggests that mycelium of G. lucidum has a potential for producing bioactive substances and extracts with applications in medicine.
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Affiliation(s)
- Lin Zheng
- Shenzhen Key Laboratory of Hospital Chinese Medicine Preparation, Shenzhen Traditional Chinese Medicine Hospital, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, Guangdong 518033, P.R. China
| | - Yum-Shing Wong
- Food and Nutritional Sciences Programme, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, SAR, P.R. China
| | - Mumin Shao
- Department of Pathology, Shenzhen Traditional Chinese Medicine Hospital, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, Guangdong 518033, P.R. China
| | - Shiying Huang
- Shenzhen Key Laboratory of Hospital Chinese Medicine Preparation, Shenzhen Traditional Chinese Medicine Hospital, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, Guangdong 518033, P.R. China
| | - Fochang Wang
- Shenzhen Key Laboratory of Hospital Chinese Medicine Preparation, Shenzhen Traditional Chinese Medicine Hospital, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, Guangdong 518033, P.R. China
| | - Jianping Chen
- Shenzhen Key Laboratory of Hospital Chinese Medicine Preparation, Shenzhen Traditional Chinese Medicine Hospital, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, Guangdong 518033, P.R. China
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