51
|
Zhang Z, Liu X, Huang R, Liu X, Liang Z, Liu T. Upregulation of nucleoprotein AHNAK is associated with poor outcome of pancreatic ductal adenocarcinoma prognosis via mediating epithelial-mesenchymal transition. J Cancer 2019; 10:3860-3870. [PMID: 31333803 PMCID: PMC6636292 DOI: 10.7150/jca.31291] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Accepted: 05/05/2019] [Indexed: 12/15/2022] Open
Abstract
The nucleoprotein AHNAK (AHNAK) is a large scaffold protein that is involved in several biological processes. Previous studies have suggested a possible relation between AHNAK and the epithelial-mesenchymal transition (EMT). However, the role of AHNAK in pancreatic ductal adenocarcinoma (PDAC) has not been unveiled. The present study focuses on identifying the potential value of the biological effects of AHNAK in PDAC, which is one of the most lethal malignancies. Bioinformatic analysis was carried for driver gene prediction, and we proved that AHNAK was a driver gene of pancreatic adenocarcinoma and a predictor of poor outcomes of PDAC by clinical characteristics analysis and in vitro experiments. High AHNAK expression was associated with short disease-free survival and poor overall survival. In vitro assays showed that AHNAK was associated with cell proliferation and migration, and a positive relation was observed between AHNAK and the EMT. In conclusion, AHNAK is a crucial biomarker that may promote cellular proliferation and migration and thus impact PDAC outcomes via the EMT, which suggests that AHANK might be a potential target for PDAC.
Collapse
Affiliation(s)
- Zhiwen Zhang
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Xiaoding Liu
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Rui Huang
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Xuguang Liu
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Zhiyong Liang
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Tonghua Liu
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| |
Collapse
|
52
|
Choi EW, Lee HW, Lee JS, Kim IY, Shin JH, Seong JK. Ahnak-knockout mice show susceptibility to Bartonella henselae infection because of CD4+ T cell inactivation and decreased cytokine secretion. BMB Rep 2019. [PMID: 30940323 PMCID: PMC6507843 DOI: 10.5483/bmbrep.2019.52.4.310] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
The present study evaluated the role of AHNAK in Bartonella henselae infection. Mice were intraperitoneally inoculated with 2 × 108 colony-forming units of B. henselae Houston-1 on day 0 and subsequently on day 10. Blood and tissue samples of the mice were collected 8 days after the final B. henselae injection. B. henselae infection in the liver of Ahnak-knockout and wild-type mice was confirmed by performing polymerase chain reaction, with Bartonella adhesion A as a marker. The proportion of B. henselae-infected cells increased in the liver of the Ahnak-knockout mice. Granulomatous lesions, inflammatory cytokine levels, and liver enzyme levels were also higher in the liver of the Ahnak-knockout mice than in the liver of the wild-type mice, indicating that Ahnak deletion accelerated B. henselae infection. The proportion of CD4+interferon-γ (IFN-γ)+ and CD4+interleukin (IL)-4+ cells was significantly lower in the B. henselae-infected Ahnak-knockout mice than in the B. henselae-infected wild-type mice. In vitro stimulation with B. henselae significantly increased IFN-γ and IL-4 secretion in the splenocytes obtained from the B. henselae-infected wild-type mice, but did not increase IFN-γ and IL-4 secretion in the splenocytes obtained from the B. henselae-infected Ahnak-KO mice. In contrast, IL-1α, IL-1β, IL-6, IL-10, RANTES, and tumor necrosis factor-α secretion was significantly elevated in the splenocytes obtained from both B. henselae-infected wild-type and Ahnak-knockout mice. These results indicate that Ahnak deletion promotes B. henselae infection. Impaired IFN-γ and IL-4 secretion in the Ahnak-knockout mice suggests the impairment of Th1 and Th2 immunity in these mice.
Collapse
Affiliation(s)
- Eun Wha Choi
- Department of Veterinary Clinical Pathology, College of Veterinary Medicine & Institute of Veterinary Science, Kangwon National University, Chuncheon 24341, Korea
- Laboratory Animal Research Center, Samsung Biomedical Research Institute, Samsung Medical Center, Seoul 06351, Korea
| | - Hee Woo Lee
- Institute of Research and Development, Chaon Corp., Seongnam 13493, Korea
| | - Jun Sik Lee
- Department of Biology, Immunology Research Lab., College of Natural Sciences, Chosun University, Gwangju 61452, Korea
| | - Il Yong Kim
- Laboratory of Developmental Biology and Genomics, BK21 Plus Program for Advanced Veterinary Science, Research Institute for Veterinary Science, College of Veterinary Medicine, and Korea Mouse Phenotyp
| | - Jae Hoon Shin
- Laboratory of Developmental Biology and Genomics, BK21 Plus Program for Advanced Veterinary Science, Research Institute for Veterinary Science, College of Veterinary Medicine, and Korea Mouse Phenotyp
| | - Je Kyung Seong
- Laboratory of Developmental Biology and Genomics, BK21 Plus Program for Advanced Veterinary Science, Research Institute for Veterinary Science, College of Veterinary Medicine, and Korea Mouse Phenotyp
- Interdiscplinary Program for Bioinformatics, Seoul National University, Seoul 08826, Korea
| |
Collapse
|
53
|
Gammerdinger WJ, Conte MA, Sandkam BA, Penman DJ, Kocher TD. Characterization of sex chromosomes in three deeply diverged species of Pseudocrenilabrinae (Teleostei: Cichlidae). HYDROBIOLOGIA 2019; 832:397-408. [PMID: 35665074 PMCID: PMC9162429 DOI: 10.1007/s10750-018-3778-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2018] [Revised: 09/17/2018] [Accepted: 09/18/2018] [Indexed: 06/15/2023]
Abstract
The African cichlid radiations have created thousands of new cichlid species with a wide diversity of trophic morphologies, behaviors, sensory systems and pigment patterns. In addition, recent research has uncovered a surprising number of young sex chromosome systems within African cichlids. Here we refine methods to describe the differentiation of young sex chromosomes from whole genome comparisons. We identified a novel XY sex chromosome system on linkage group 14 in Oreochromis mossambicus, confirmed a linkage group 1 XY system in Coptodon zillii and also defined the limits of our methodology by examining a ZW system on linkage group 3 in Pelmatolapia mariae. These data further demonstrate that cichlids are an excellent model system for understanding the early stages of sex chromosome evolution.
Collapse
|
54
|
Peng R, Zhang PF, Yang X, Wei CY, Huang XY, Cai JB, Lu JC, Gao C, Sun HX, Gao Q, Bai DS, Shi GM, Ke AW, Fan J. Overexpression of RNF38 facilitates TGF-β signaling by Ubiquitinating and degrading AHNAK in hepatocellular carcinoma. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2019; 38:113. [PMID: 30836988 PMCID: PMC6402116 DOI: 10.1186/s13046-019-1113-3] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 02/18/2019] [Indexed: 12/11/2022]
Abstract
BACKGROUND RING finger protein 38 (RNF38), a member of the RNF protein family, has just emerged as a vital driver of cancer progression. However, the oncogenic mechanisms of RNF38 remain unexplored. METHODS Using frozen tumor tissue and tissue microarray from hepatocellular carcinoma (HCC) patients, we tried to probe the expression of RNF38 in HCC and its clinical value. Then the biological functions of RNF38 were analyzed in vivo and vitro. Stable isotope labeling with amino acids (SILAC) in cell culture and co-immunoprecipitation proteomic analyses were combined to reveal the potential mechanism of RNF38 in HCC progression. RESULTS We report that RNF38 expression was markedly higher in HCC tissues than in peritumor tissues. Correspondingly, RNF38 overexpression promoted the HCC cell migration and invasion and inhibited apoptosis both in vitro and in vivo. And elevated RNF38 expression induced HCC cell epithelial-mesenchymal transition by facilitating transforming growth factor-β (TGF-β) signaling via ubiquitinating and degrading neuroblast differentiation-associated protein (AHNAK), a well-established inhibitor of TGF-β signaling. Furthermore, AHNAK interference restored the HCC cell invasion and metastasis deprived by RNF38 downregulation. Clinically, elevated RNF38 and transforming growth factor beta receptor 1 (TGFBR1) expression was related to short overall survival (OS) and high cumulative recurrence rates in HCC patients. CONCLUSIONS High levels of RNF38 promote HCC by facilitating TGF-β signaling and are a novel marker for predicting the prognosis of HCC patients and a potential therapeutic target in HCC.
Collapse
Affiliation(s)
- Rui Peng
- Liver Cancer Institute, Zhongshan Hospital, Fudan University; Key Laboratory of Carcinogenesis and Cancer Invasion (Fudan University), Ministry of Education, 180 Feng lin Road, Shanghai, 200032, People's Republic of China.,Clinical Medical College, Yangzhou University, Yangzhou, 225009, Jiangsu, China
| | - Peng-Fei Zhang
- Liver Cancer Institute, Zhongshan Hospital, Fudan University; Key Laboratory of Carcinogenesis and Cancer Invasion (Fudan University), Ministry of Education, 180 Feng lin Road, Shanghai, 200032, People's Republic of China.,Department of Oncology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, 200031, China
| | - Xuan Yang
- Liver Cancer Institute, Zhongshan Hospital, Fudan University; Key Laboratory of Carcinogenesis and Cancer Invasion (Fudan University), Ministry of Education, 180 Feng lin Road, Shanghai, 200032, People's Republic of China
| | - Chuan-Yuan Wei
- Liver Cancer Institute, Zhongshan Hospital, Fudan University; Key Laboratory of Carcinogenesis and Cancer Invasion (Fudan University), Ministry of Education, 180 Feng lin Road, Shanghai, 200032, People's Republic of China
| | - Xiao-Yong Huang
- Liver Cancer Institute, Zhongshan Hospital, Fudan University; Key Laboratory of Carcinogenesis and Cancer Invasion (Fudan University), Ministry of Education, 180 Feng lin Road, Shanghai, 200032, People's Republic of China
| | - Jia-Bin Cai
- Liver Cancer Institute, Zhongshan Hospital, Fudan University; Key Laboratory of Carcinogenesis and Cancer Invasion (Fudan University), Ministry of Education, 180 Feng lin Road, Shanghai, 200032, People's Republic of China
| | - Jia-Cheng Lu
- Liver Cancer Institute, Zhongshan Hospital, Fudan University; Key Laboratory of Carcinogenesis and Cancer Invasion (Fudan University), Ministry of Education, 180 Feng lin Road, Shanghai, 200032, People's Republic of China
| | - Chao Gao
- Liver Cancer Institute, Zhongshan Hospital, Fudan University; Key Laboratory of Carcinogenesis and Cancer Invasion (Fudan University), Ministry of Education, 180 Feng lin Road, Shanghai, 200032, People's Republic of China
| | - Hai-Xiang Sun
- Liver Cancer Institute, Zhongshan Hospital, Fudan University; Key Laboratory of Carcinogenesis and Cancer Invasion (Fudan University), Ministry of Education, 180 Feng lin Road, Shanghai, 200032, People's Republic of China
| | - Qiang Gao
- Liver Cancer Institute, Zhongshan Hospital, Fudan University; Key Laboratory of Carcinogenesis and Cancer Invasion (Fudan University), Ministry of Education, 180 Feng lin Road, Shanghai, 200032, People's Republic of China
| | - Dou-Sheng Bai
- Clinical Medical College, Yangzhou University, Yangzhou, 225009, Jiangsu, China
| | - Guo-Ming Shi
- Liver Cancer Institute, Zhongshan Hospital, Fudan University; Key Laboratory of Carcinogenesis and Cancer Invasion (Fudan University), Ministry of Education, 180 Feng lin Road, Shanghai, 200032, People's Republic of China.
| | - Ai-Wu Ke
- Liver Cancer Institute, Zhongshan Hospital, Fudan University; Key Laboratory of Carcinogenesis and Cancer Invasion (Fudan University), Ministry of Education, 180 Feng lin Road, Shanghai, 200032, People's Republic of China.
| | - Jia Fan
- Liver Cancer Institute, Zhongshan Hospital, Fudan University; Key Laboratory of Carcinogenesis and Cancer Invasion (Fudan University), Ministry of Education, 180 Feng lin Road, Shanghai, 200032, People's Republic of China. .,Cancer Center, Institutes of Biomedical Sciences, Fudan University, Shanghai, 200031, People's Republic of China.
| |
Collapse
|
55
|
Olivier M, Bouaoun L, Villar S, Robitaille A, Cahais V, Heguy A, Byrnes G, Le Calvez-Kelm F, Torres-Mejía G, Alvarado-Cabrero I, Imani-Razavi FS, Inés Sánchez G, Jaramillo R, Porras C, Rodriguez AC, Garmendia ML, Soto JL, Romieu I, Porter P, Guenthoer J, Rinaldi S. Molecular features of premenopausal breast cancers in Latin American women: Pilot results from the PRECAMA study. PLoS One 2019; 14:e0210372. [PMID: 30653559 PMCID: PMC6336331 DOI: 10.1371/journal.pone.0210372] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 12/20/2018] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND In Latin America (LA), there is a high incidence rate of breast cancer (BC) in premenopausal women, and the genomic features of these BC remain unknown. Here, we aim to characterize the molecular features of BC in young LA women within the framework of the PRECAMA study, a multicenter population-based case-control study of BC in premenopausal women. METHODS Pathological tumor tissues were collected from incident cases from four LA countries. Immunohistochemistry (IHC) was performed centrally for ER, PR, HER2, Ki67, EGFR, CK5/6, and p53 protein markers. Targeted deep sequencing was done on genomic DNA extracted from formalin-fixed, paraffin-embedded tumor tissues and their paired blood samples to screen for somatic mutations in eight genes frequently mutated in BC. A subset of samples was analyzed by exome sequencing to identify somatic mutational signatures. RESULTS The majority of cases were positive for ER or PR (168/233; 72%), and 21% were triple-negative (TN), mainly of basal type. Most tumors were positive for Ki67 (189/233; 81%). In 126 sequenced cases, TP53 and PIK3CA were the most frequently mutated genes (32.5% and 21.4%, respectively), followed by AKT1 (9.5%). TP53 mutations were more frequent in HER2-enriched and TN IHC subtypes, whereas PIK3CA/AKT1 mutations were more frequent in ER-positive tumors, as expected. Interestingly, a higher proportion of G:C>T:A mutations was observed in TP53 in PRECAMA cases compared with TCGA and METABRIC BC series (27% vs 14%). Exome-wide mutational patterns in 10 TN cases revealed alterations in signal transduction pathways and major contributions of mutational signatures caused by altered DNA repair pathways. CONCLUSIONS These pilot results on PRECAMA tumors give a preview of the molecular features of premenopausal BC in LA. Although the overall mutation burden was as expected from data in other populations, mutational patterns observed in TP53 and exome-wide suggested possible differences in mutagenic processes giving rise to these tumors compared with other populations. Further -omics analyses of a larger number of cases in the near future will enable the investigation of relationships between these molecular features and risk factors.
Collapse
Affiliation(s)
- Magali Olivier
- Section of Mechanisms of Carcinogenesis, International Agency for Research on Cancer, Lyon, France
| | - Liacine Bouaoun
- Section of Environment and Radiation, International Agency for Research on Cancer, Lyon, France
| | - Stephanie Villar
- Section of Mechanisms of Carcinogenesis, International Agency for Research on Cancer, Lyon, France
| | - Alexis Robitaille
- Section of Mechanisms of Carcinogenesis, International Agency for Research on Cancer, Lyon, France
| | - Vincent Cahais
- Section of Mechanisms of Carcinogenesis, International Agency for Research on Cancer, Lyon, France
| | - Adriana Heguy
- Department of Pathology and Genome Technology Center, New York University Langone Medical Center, New York, United States of America
| | - Graham Byrnes
- Section of Environment and Radiation, International Agency for Research on Cancer, Lyon, France
| | - Florence Le Calvez-Kelm
- Genetic Cancer Susceptibility Group, International Agency for Research on Cancer, Lyon, France
| | - Gabriela Torres-Mejía
- Center for Population Health Research, National Institute of Public Health, Cuernavaca, Mexico
| | - Isabel Alvarado-Cabrero
- Department of Pathology, Hospital de Oncología, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Fazlollah Shahram Imani-Razavi
- Department of Pathology, UMAE Hospital de Gineco Obstetricia No. 4 "Luis Castelazo Ayala", Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Gloria Inés Sánchez
- Group Infection and Cancer, School of Medicine, University of Antioquia, Medellín, Colombia
| | | | - Carolina Porras
- Agencia Costarricense de Investigaciones Biomédicas (ACIB)-Fundación INCIENSA, Costa Rica
| | - Ana Cecilia Rodriguez
- Agencia Costarricense de Investigaciones Biomédicas (ACIB)-Fundación INCIENSA, Costa Rica
| | | | | | - Isabelle Romieu
- Section of Nutrition and Metabolism, International Agency for Research on Cancer, Lyon, France
| | - Peggy Porter
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, United States of America
| | - Jamie Guenthoer
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, United States of America
| | - Sabina Rinaldi
- Section of Nutrition and Metabolism, International Agency for Research on Cancer, Lyon, France
| |
Collapse
|
56
|
Gu J, Mao W, Ren W, Xu F, Zhu Q, Lu C, Lin Z, Zhang Z, Chu Y, Liu R, Ge D. Ubiquitin-protein ligase E3C maintains non-small-cell lung cancer stemness by targeting AHNAK-p53 complex. Cancer Lett 2018; 443:125-134. [PMID: 30503554 DOI: 10.1016/j.canlet.2018.11.029] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 11/15/2018] [Accepted: 11/16/2018] [Indexed: 02/05/2023]
Abstract
Cancer stem-like cells (CSCs) are regarded as sources of tumorigenesis, metastasis, and drug resistance, which limits current cancer therapies. Elucidating the molecular modes governing CSC properties is necessary to optimize therapeutic approaches. In this study, we discovered that ubiquitin-protein ligase E3C (UBE3C)-mediated ubiquitination is a key posttranslational mechanism involved in maintaining CSC properties of non-small-cell lung cancer (NSCLC). UBE3C was overexpressed in stem-like NSCLC cells and acted as a stemness enhancer. Knockdown of UBE3C reduced NSCLC stemness and tumorigenesis both in vivo and in vitro. We further identified AHNAK as a novel UBE3C substrate, finding that UBE3C maintained stemness by ubiquitinating and promoting AHNAK degradation. AHNAK functioned as a cofactor assisting p53 binding to stemness-related gene promoters to inhibit transcription. Subsequent downregulation of AHNAK by UBE3C overexpression removed p53-mediated inhibition of gene expression, resulting in enhanced stemness. Clinical significance was investigated in 208 NSCLC patients and confirmed that attenuated UBE3C activity and elevated AHNAK protein levels correlated with extended survival time. Collectively, findings reveal the first global characterization of UBE3C-mediated ubiquitination as a key regulator of CSCs, with results suggesting involvement of the AHNAK-p53 complex.
Collapse
Affiliation(s)
- Jie Gu
- Department of Thoracic Surgery, The Affiliated Zhongshan Hospital, Fudan University, Shanghai, 200032, PR China; Key Laboratory of Medical Epigenetics and Metabolism, Institute of Biomedical Sciences, and Department of Immunology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, PR China
| | - Wei Mao
- Department of Thoracic Surgery, The Affiliated Zhongshan Hospital, Fudan University, Shanghai, 200032, PR China; Key Laboratory of Medical Epigenetics and Metabolism, Institute of Biomedical Sciences, and Department of Immunology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, PR China
| | - Wenjia Ren
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, PR China
| | - Fengkai Xu
- Department of Thoracic Surgery, The Affiliated Zhongshan Hospital, Fudan University, Shanghai, 200032, PR China
| | - Qiaoliang Zhu
- Department of Thoracic Surgery, The Affiliated Zhongshan Hospital, Fudan University, Shanghai, 200032, PR China
| | - Chunlai Lu
- Department of Thoracic Surgery, The Affiliated Zhongshan Hospital, Fudan University, Shanghai, 200032, PR China
| | - Zongwu Lin
- Department of Thoracic Surgery, The Affiliated Zhongshan Hospital, Fudan University, Shanghai, 200032, PR China
| | - Zhilong Zhang
- Department of Thoracic Surgery, Shanghai XuHui District Central Hospital, Shanghai, 200031, PR China
| | - Yiwei Chu
- Key Laboratory of Medical Epigenetics and Metabolism, Institute of Biomedical Sciences, and Department of Immunology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, PR China
| | - Ronghua Liu
- Key Laboratory of Medical Epigenetics and Metabolism, Institute of Biomedical Sciences, and Department of Immunology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, PR China.
| | - Di Ge
- Department of Thoracic Surgery, The Affiliated Zhongshan Hospital, Fudan University, Shanghai, 200032, PR China.
| |
Collapse
|
57
|
Wu Q, Fu C, Li M, Li J, Li Z, Qi L, Ci X, Ma G, Gao A, Fu X, A J, An N, Liu M, Li Y, King JL, Fu L, Zhang B, Dong JT. CINP is a novel cofactor of KLF5 required for its role in the promotion of cell proliferation, survival and tumor growth. Int J Cancer 2018; 144:582-594. [PMID: 30289973 DOI: 10.1002/ijc.31908] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 09/21/2018] [Indexed: 02/01/2023]
Abstract
Krüppel-like factor 5 (KLF5) both suppresses and promotes tumor growth depending on cellular context. The mechanisms underlying tumor promotion could be targetable for therapy. Although a number of transcriptional targets of KLF5 have been identified and implicated in KLF5-mediated tumor growth, how KLF5 regulates these genes remains to be addressed. Here we performed coimmunoprecipitation (co-IP) and liquid chromatography-tandem mass spectrometry (LC-MS/MS) in the TSU-Pr1 bladder cancer cell line, in which KLF5 is shown to promote tumor growth, to identify KLF5-interacting nuclear proteins that are necessary for KLF5's tumor promoting function. LC-MS/MS revealed 122 potential KLF5 binding proteins in the nuclear proteins precipitated by the KLF5 antibody, and the top nine candidates included AHNAK, TFAM, HSDL2, HNRNPC, CINP, IST1, FBL, PABPC1 and SNRNP40. SRB assays of these nine proteins indicated that silencing CINP had the most potent inhibitory effect on cell growth in KLF5-expressing cells but did not affect parental TSU-Pr1 cells. Further analyses not only confirmed the physical interaction between KLF5 and CINP, also demonstrated that knockdown of CINP attenuated the effects of KLF5 on cell cycle progression, apoptosis and tumorigenesis. Silencing CINP also attenuated the effect of KLF5 on the expression of a number of genes and signaling pathways, including cell cycle regulator Cyclin D1 and apoptosis-related Caspase 7. These results suggest that CINP is a cofactor of KLF5 that is crucial for the promotion of tumor growth, and that the KLF5-CINP interaction could be a novel therapeutic target for inhibiting KLF5-promoted tumor growth.
Collapse
Affiliation(s)
- Qiao Wu
- Department of Genetics and Cell Biology, College of Life Sciences, Nankai University, Tianjin, China
| | - Changying Fu
- Department of Genetics and Cell Biology, College of Life Sciences, Nankai University, Tianjin, China
| | - Menglin Li
- Department of Genetics and Cell Biology, College of Life Sciences, Nankai University, Tianjin, China
| | - Juan Li
- Department of Genetics and Cell Biology, College of Life Sciences, Nankai University, Tianjin, China
| | - Zhigui Li
- Department of Obstetrics, Gynecology and Reproductive Sciences, Yale University School of Medicine, New Haven, CT
| | - Leilei Qi
- Department of Genetics and Cell Biology, College of Life Sciences, Nankai University, Tianjin, China
| | - Xinpei Ci
- Department of Genetics and Cell Biology, College of Life Sciences, Nankai University, Tianjin, China
| | - Gui Ma
- Department of Genetics and Cell Biology, College of Life Sciences, Nankai University, Tianjin, China
| | - Ang Gao
- Department of Genetics and Cell Biology, College of Life Sciences, Nankai University, Tianjin, China
| | - Xing Fu
- Department of Genetics and Cell Biology, College of Life Sciences, Nankai University, Tianjin, China
| | - Jun A
- Department of Genetics and Cell Biology, College of Life Sciences, Nankai University, Tianjin, China
| | - Na An
- Department of Genetics and Cell Biology, College of Life Sciences, Nankai University, Tianjin, China
| | - Mingcheng Liu
- Department of Genetics and Cell Biology, College of Life Sciences, Nankai University, Tianjin, China
| | - Yixiang Li
- Department of Hematology and Medical Oncology, Emory Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA
| | - Jamie L King
- Department of Hematology and Medical Oncology, Emory Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA
| | - Liya Fu
- Department of Genetics and Cell Biology, College of Life Sciences, Nankai University, Tianjin, China
| | - Baotong Zhang
- Department of Hematology and Medical Oncology, Emory Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA
| | - Jin-Tang Dong
- Department of Genetics and Cell Biology, College of Life Sciences, Nankai University, Tianjin, China.,Department of Hematology and Medical Oncology, Emory Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA
| |
Collapse
|
58
|
Sundararaj S, Shishmarev D, Lin Y, Aditya S, Casarotto MG. 1H, 13C and 15N backbone NMR chemical shift assignments of the C-terminal P4 domain of Ahnak. BIOMOLECULAR NMR ASSIGNMENTS 2018; 12:253-257. [PMID: 29594929 DOI: 10.1007/s12104-018-9818-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2018] [Accepted: 03/26/2018] [Indexed: 06/08/2023]
Abstract
Ahnak is a ~ 700 kDa polypeptide that was originally identified as a tumour-related nuclear phosphoprotein, but later recognized to play a variety of diverse physiological roles related to cell architecture and migration. A critical function of Ahnak is modulation of Ca2+ signaling in cardiomyocytes by interacting with the β subunit of the L-type Ca2+ channel (CaV1.2). Previous studies have identified the C-terminal region of Ahnak, designated as P3 and P4 domains, as a key mediator of its functional activity. We report here the nearly complete 1H, 13C and 15N backbone NMR chemical shift assignments of the 11 kDa C-terminal P4 domain of Ahnak. This study lays the foundations for future investigations of functional dynamics, structure determination and interaction site mapping of the CaV1.2-Ahnak complex.
Collapse
Affiliation(s)
- Srinivasan Sundararaj
- ACRF Department of Cancer Biology and Therapeutics, The John Curtin School of Medical Research, The Australian National University, Canberra, ACT, 2601, Australia
| | - Dmitry Shishmarev
- ACRF Department of Cancer Biology and Therapeutics, The John Curtin School of Medical Research, The Australian National University, Canberra, ACT, 2601, Australia.
| | - Yiechang Lin
- ACRF Department of Cancer Biology and Therapeutics, The John Curtin School of Medical Research, The Australian National University, Canberra, ACT, 2601, Australia
| | - Shouvik Aditya
- ACRF Department of Cancer Biology and Therapeutics, The John Curtin School of Medical Research, The Australian National University, Canberra, ACT, 2601, Australia
| | - Marco G Casarotto
- ACRF Department of Cancer Biology and Therapeutics, The John Curtin School of Medical Research, The Australian National University, Canberra, ACT, 2601, Australia.
| |
Collapse
|
59
|
Sun L, Li K, Liu G, Xu Y, Zhang A, Lin D, Zhang H, Zhao X, Jin B, Li N, Zhang Y. Distinctive pattern of AHNAK methylation level in peripheral blood mononuclear cells and the association with HBV-related liver diseases. Cancer Med 2018; 7:5178-5186. [PMID: 30259695 PMCID: PMC6198198 DOI: 10.1002/cam4.1778] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 07/17/2018] [Accepted: 08/22/2018] [Indexed: 01/08/2023] Open
Abstract
The purpose of this study was to investigate the correlation between AHNAK methylation level in peripheral blood mononuclear cells (PBMC) and the progression of hepatitis B virus (HBV)‐related liver disease. Bioinformatics methods were applied to evaluate the AHNAK methylation level in PBMC and T cells at different stages of HBV related liver disease, to investigate the correlation between AHNAK methylation and clinical features, as well as to compare the methylation site of AHNAK in cancer tissues and adjacent tissues. Subsequently, the differentially expressed gene analysis technique was used to analyze the liver disease‐related genes and immune‐related pathways in hepatitis B patients with different pathological changes. Finally, promoter methylation and mRNA expression of AHNAK gene in liver cancer and adjacent tissues were determined by quantitative polymerase chain reaction (Q‐PCR), and the diagnostic value of AHNAK methylation level in hepatopathy was evaluated by receiver operating characteristic (ROC) curve. The promoter methylation level of AHNAK gene in PBMCs decreased with the progression of HBV‐related liver disease, and showed significant difference among the patients with various HBV‐related liver diseases (P = 0.0001). The AHNAK methylation level in PBMCs and T cells was negatively associated with age, white blood cell count, CREA, drinking, and positively associated with APTT and HbsAg. Higher mRNA expression of AHNAK was found in liver cancer tissues than that of adjacent tissues (P < 0.001), and the methylation level in PBMC decreased with the progression of hepatitis B‐related liver disease. The area under the ROC curve (ROC) was 0.883 (P < 0.001) in diagnosis of chronic hepatitis B (CHB), 0.885 (P < 0.001) in diagnosis of compensatory liver cirrhosis, 0.955 (P < 0.001) in diagnosis of decompensated liver cirrhosis, 0.981 (P < 0.001) in diagnosis of hepatocellular carcinoma. Our results revealed that AHNAK methylation level in peripheral blood decreases with the progression of hepatitis B‐related liver disease. This provided a potential differential diagnostic method for HBV‐related hepatopathies, and thus an early detective tool for liver cancer.
Collapse
Affiliation(s)
- Libo Sun
- Department of Hepatobiliary Surgery, Beijing You'an Hospital, Capital Medical University, Beijing, China
| | - Kang Li
- Biomedical Information Center, Beijing You'an Hospital, Capital Medical University, Beijing, China
| | - Guihai Liu
- Biomedical Information Center, Beijing You'an Hospital, Capital Medical University, Beijing, China
| | - Yuan Xu
- Department of Hepatobiliary Surgery, Beijing You'an Hospital, Capital Medical University, Beijing, China.,Department of Community Science, University of Calgary, Calgary, Alberta, Canada
| | - Aiying Zhang
- Beijing Institute of Hepatology, Beijing You'an Hospital, Capital Medical University, Beijing, China
| | - Dongdong Lin
- Department of Hepatobiliary Surgery, Beijing You'an Hospital, Capital Medical University, Beijing, China
| | - Haitao Zhang
- Department of Hepatobiliary Surgery, Beijing You'an Hospital, Capital Medical University, Beijing, China
| | - Xiaofei Zhao
- Department of Hepatobiliary Surgery, Beijing You'an Hospital, Capital Medical University, Beijing, China
| | - Boxun Jin
- Department of Hepatobiliary Surgery, Beijing You'an Hospital, Capital Medical University, Beijing, China
| | - Ning Li
- Department of Hepatobiliary Surgery, Beijing You'an Hospital, Capital Medical University, Beijing, China
| | - Yonghong Zhang
- Beijing You'an Hospital, Capital Medical University, Beijing, China
| |
Collapse
|
60
|
Sohn M, Shin S, Yoo JY, Goh Y, Lee IH, Bae YS. Ahnak promotes tumor metastasis through transforming growth factor-β-mediated epithelial-mesenchymal transition. Sci Rep 2018; 8:14379. [PMID: 30258109 PMCID: PMC6158194 DOI: 10.1038/s41598-018-32796-2] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 09/14/2018] [Indexed: 12/28/2022] Open
Abstract
Previously, we reported a molecular mechanism by which Ahnak potentiates transforming growth factor-β (TGFβ) signaling during cell growth. Here, we show that Ahnak induces epithelial-mesenchymal transition (EMT) in response to TGFβ. EMT phenotypes, including altered in cell morphology, and expression patterns of various EMT marker genes were detected in HaCaT keratinocytes transfected with Ahnak-specific siRNA. Knockdown of Ahnak expression in HaCaT keratinocytes resulted in attenuated cell migration and invasion. We found that Ahnak activates TGFβ signaling via Smad3 phosphorylation, leading to enhanced Smad3 transcriptional activity. To validate function of Ahnak in EMT of B16F10 cells having high metastatic and tumorigenic properties, we established B16F10 cells with stable knockdown of Ahnak. N-cadherin expression and Smad3 phosphorylation were significantly decreased in B16F10-shAhnak cells, compared to B16F10-shControl cells after treatment of TGFβ. Moreover, TGFβ failed to induce cell migration and cell invasion in B16F10-shAhnak cells. To determine whether Ahnak regulates the metastatic activity of B16F10 cells, we established a lung metastasis model in C57BL/6 mice via tail vein injection of B16F10-shAhnak cells. Lung metastasis was significantly suppressed in mice injected with B16F10-shAhnak cells, compared to those injected with B16F10-shControl cells. Taken together, we propose that TGFβ-Ahnak signaling axis regulates EMT during tumor metastasis.
Collapse
Affiliation(s)
- Mira Sohn
- Department of Life Sciences, Ewha Womans University, Seoul, 120-750, Korea
| | - Sunmee Shin
- Department of Life Sciences, Ewha Womans University, Seoul, 120-750, Korea
| | - Jung-Yeon Yoo
- Department of Life Sciences, Ewha Womans University, Seoul, 120-750, Korea
| | - Yookyung Goh
- Department of Life Sciences, Ewha Womans University, Seoul, 120-750, Korea
| | - In Hye Lee
- Department of Life Sciences, Ewha Womans University, Seoul, 120-750, Korea.
| | - Yun Soo Bae
- Department of Life Sciences, Ewha Womans University, Seoul, 120-750, Korea.
| |
Collapse
|
61
|
Sipeky C, Gao P, Zhang Q, Wang L, Ettala O, Talala KM, Tammela TLJ, Auvinen A, Wiklund F, Wei GH, Schleutker J. Synergistic Interaction of HOXB13 and CIP2A Predisposes to Aggressive Prostate Cancer. Clin Cancer Res 2018; 24:6265-6276. [PMID: 30181389 DOI: 10.1158/1078-0432.ccr-18-0444] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 06/09/2018] [Accepted: 08/28/2018] [Indexed: 11/16/2022]
Abstract
PURPOSE Distinguishing aggressive prostate cancer from indolent disease improves personalized treatment. Although only few genetic variants are known to predispose to aggressive prostate cancer, synergistic interactions of HOXB13 G84E high-risk prostate cancer susceptibility mutation with other genetic loci remain unknown. The purpose of this study was to examine the interplay of HOXB13 rs138213197 (G84E) and CIP2A rs2278911 (R229Q) germline variants on prostate cancer risk. EXPERIMENTAL DESIGN Genotyping was done in Finnish discovery cohort (n = 2,738) and validated in Swedish (n = 3,132) and independent Finnish (n = 1,155) prostate cancer cohorts. Expression pattern analysis was followed by functional studies in prostate cancer cell models. RESULTS Interplay of HOXB13 (G84E) and CIP2A (R229Q) variants results in highest observed inherited prostate cancer risk (OR, 21.1; P = 0.000024). In addition, this synergism indicates a significant association of HOXB13 T and CIP2A T dual carriers with elevated risk for high Gleason score (OR, 2.3; P = 0.025) and worse prostate cancer-specific life expectancy (HR, 3.9; P = 0.048), and it is linked with high PSA at diagnosis (OR, 3.30; P = 0.028). Furthermore, combined high expression of HOXB13-CIP2A correlates with earlier biochemical recurrence. Finally, functional experiments showed that ectopic expression of variants stimulates prostate cancer cell growth and migration. In addition, we observed strong chromatin binding of HOXB13 at CIP2A locus and revealed that HOXB13 functionally promotes CIP2A transcription. The study is limited to retrospective Nordic cohorts. CONCLUSIONS Simultaneous presence of HOXB13 T and CIP2A T alleles confers for high prostate cancer risk and aggressiveness of disease, earlier biochemical relapse, and lower disease-specific life expectancy. HOXB13 protein binds to CIP2A gene and functionally promotes CIP2A transcription.
Collapse
Affiliation(s)
- Csilla Sipeky
- Institute of Biomedicine, University of Turku, Turku, Finland
| | - Ping Gao
- Biocenter Oulu, Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Qin Zhang
- Biocenter Oulu, Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Liang Wang
- Department of Pathology, MCW Cancer Center, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Otto Ettala
- Department of Urology, Turku University Hospital, Turku, Finland
| | - Kirsi M Talala
- Finnish Cancer Registry, Mass Screening Registry, Helsinki, Finland
| | - Teuvo L J Tammela
- Department of Urology, Tampere University Hospital and Medical School, University of Tampere, Tampere, Finland
| | - Anssi Auvinen
- Department of Epidemiology, School of Health Sciences, University of Tampere, Tampere, Finland
| | - Fredrik Wiklund
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
| | - Gong-Hong Wei
- Biocenter Oulu, Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland.
| | - Johanna Schleutker
- Institute of Biomedicine, University of Turku, Turku, Finland. .,Tyks Microbiology and Genetics, Department of Medical Genetics, Turku University Hospital, Turku, Finland
| |
Collapse
|
62
|
Lee H, Kim K, Woo J, Park J, Kim H, Lee KE, Kim H, Kim Y, Moon KC, Kim JY, Park IA, Shim BB, Moon JH, Han D, Ryu HS. Quantitative Proteomic Analysis Identifies AHNAK (Neuroblast Differentiation-associated Protein AHNAK) as a Novel Candidate Biomarker for Bladder Urothelial Carcinoma Diagnosis by Liquid-based Cytology. Mol Cell Proteomics 2018; 17:1788-1802. [PMID: 29950347 DOI: 10.1074/mcp.ra118.000562] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 06/25/2018] [Indexed: 01/04/2023] Open
Abstract
Cytological examination of urine is the most widely used noninvasive pathologic screen for bladder urothelial carcinoma (BLCA); however, inadequate diagnostic accuracy remains a major challenge. We performed mass spectrometry-based proteomic analysis of urine samples of ten patients with BLCA and ten paired patients with benign urothelial lesion (BUL) to identify ancillary proteomic markers for use in liquid-based cytology (LBC). A total of 4,839 proteins were identified and 112 proteins were confirmed as expressed at significantly different levels between the two groups. We also performed an independent proteomic profiling of tumor tissue samples where we identified 7,916 proteins of which 758 were differentially expressed. Cross-platform comparisons of these data with comparative mRNA expression profiles from The Cancer Genome Atlas identified four putative candidate proteins, AHNAK, EPPK1, MYH14 and OLFM4. To determine their immunocytochemical expression levels in LBC, we examined protein expression data from The Human Protein Atlas and in-house FFPE samples. We further investigated the expression of the four candidate proteins in urine cytology samples from two independent validation cohorts. These analyses revealed AHNAK as a unique intracellular protein differing in immunohistochemical expression and subcellular localization between tumor and non-tumor cells. In conclusion, this study identified a new biomarker, AHNAK, applicable to discrimination between BLCA and BUL by LBC. To our knowledge, the present study provides the first identification of a clinical biomarker for LBC based on in-depth proteomics.
Collapse
Affiliation(s)
- Hyebin Lee
- From the ‡Department of Radiation Oncology, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Kwangsoo Kim
- §Division of Clinical Bioinformatics, Biomedical Research Institute, Seoul National University Hospital, Seoul, South Korea
| | - Jongmin Woo
- ¶Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea
| | - Joonho Park
- ¶Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea
| | - Hyeyoon Kim
- ‖Proteomics Core Facility, Biomedical Research Institute, Seoul National University Hospital, Seoul, South Korea.,**Department of Pathology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, South Korea
| | - Kyung Eun Lee
- ‡‡Department of Statistics, Korea University, Seoul, South Korea
| | - Hyeyeon Kim
- ‖Proteomics Core Facility, Biomedical Research Institute, Seoul National University Hospital, Seoul, South Korea
| | - Youngsoo Kim
- ¶Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea
| | - Kyung Chul Moon
- **Department of Pathology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, South Korea
| | - Ji Young Kim
- **Department of Pathology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, South Korea
| | - In Ae Park
- **Department of Pathology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, South Korea
| | - Bo Bae Shim
- **Department of Pathology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, South Korea
| | - Ji Hye Moon
- **Department of Pathology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, South Korea
| | - Dohyun Han
- §Division of Clinical Bioinformatics, Biomedical Research Institute, Seoul National University Hospital, Seoul, South Korea; .,‖Proteomics Core Facility, Biomedical Research Institute, Seoul National University Hospital, Seoul, South Korea
| | - Han Suk Ryu
- **Department of Pathology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, South Korea;
| |
Collapse
|
63
|
Park JW, Kim IY, Choi JW, Lim HJ, Shin JH, Kim YN, Lee SH, Son Y, Sohn M, Woo JK, Jeong JH, Lee C, Bae YS, Seong JK. AHNAK Loss in Mice Promotes Type II Pneumocyte Hyperplasia and Lung Tumor Development. Mol Cancer Res 2018; 16:1287-1298. [PMID: 29724814 DOI: 10.1158/1541-7786.mcr-17-0726] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 01/24/2018] [Accepted: 04/19/2018] [Indexed: 11/16/2022]
Abstract
AHNAK is known to be a tumor suppressor in breast cancer due to its ability to activate the TGFβ signaling pathway. However, the role of AHNAK in lung tumor development and progression remains unknown. Here, the Ahnak gene was disrupted to determine its effect on lung tumorigenesis and the mechanism by which it triggers lung tumor development was investigated. First, AHNAK protein expression was determined to be decreased in human lung adenocarcinomas compared with matched nonneoplastic lung tissues. Then, Ahnak -/- mice were used to investigate the role of AHNAK in pulmonary tumorigenesis. Ahnak -/- mice showed increased lung volume and thicker alveolar walls with type II pneumocyte hyperplasia. Most importantly, approximately 20% of aged Ahnak -/- mice developed lung tumors, and Ahnak -/- mice were more susceptible to urethane-induced pulmonary carcinogenesis than wild-type mice. Mechanistically, Ahnak deficiency promotes the cell growth of lung epithelial cells by suppressing the TGFβ signaling pathway. In addition, increased numbers of M2-like alveolar macrophages (AM) were observed in Ahnak -/- lungs, and the depletion of AMs in Ahnak -/- lungs alleviated lung hyperplastic lesions, suggesting that M2-like AMs promoted the progression of lung hyperplastic lesions in Ahnak-null mice. Collectively, AHNAK suppresses type II pneumocyte proliferation and inhibits tumor-promoting M2 alternative activation of macrophages in mouse lung tissue. These results suggest that AHNAK functions as a novel tumor suppressor in lung cancer.Implications: The tumor suppressor function of AHNAK, in murine lungs, occurs by suppressing alveolar epithelial cell proliferation and modulating lung microenvironment. Mol Cancer Res; 16(8); 1287-98. ©2018 AACR.
Collapse
Affiliation(s)
- Jun Won Park
- Laboratory of Developmental Biology and Genomics, BK21 Program Plus for Advanced Veterinary Science, and Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul, Korea.,Korea Mouse Phenotyping Center (KMPC), Seoul, Korea
| | - Il Yong Kim
- Laboratory of Developmental Biology and Genomics, BK21 Program Plus for Advanced Veterinary Science, and Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul, Korea.,Korea Mouse Phenotyping Center (KMPC), Seoul, Korea
| | - Ji Won Choi
- Laboratory of Developmental Biology and Genomics, BK21 Program Plus for Advanced Veterinary Science, and Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul, Korea
| | - Hee Jung Lim
- Korea Mouse Phenotyping Center (KMPC), Seoul, Korea
| | - Jae Hoon Shin
- Laboratory of Developmental Biology and Genomics, BK21 Program Plus for Advanced Veterinary Science, and Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul, Korea
| | - Yo Na Kim
- Laboratory of Developmental Biology and Genomics, BK21 Program Plus for Advanced Veterinary Science, and Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul, Korea
| | - Seo Hyun Lee
- Laboratory of Developmental Biology and Genomics, BK21 Program Plus for Advanced Veterinary Science, and Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul, Korea
| | - Yeri Son
- Laboratory of Developmental Biology and Genomics, BK21 Program Plus for Advanced Veterinary Science, and Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul, Korea
| | - Mira Sohn
- Department of Life Sciences, Ewha Womans University, Seoul, Korea
| | - Jong Kyu Woo
- Laboratory of Developmental Biology and Genomics, BK21 Program Plus for Advanced Veterinary Science, and Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul, Korea.,Korea Mouse Phenotyping Center (KMPC), Seoul, Korea
| | | | - Cheolju Lee
- Center for Theragnosis, Korea Institute of Science and Technology, Seoul, Korea
| | - Yun Soo Bae
- Department of Life Sciences, Ewha Womans University, Seoul, Korea
| | - Je Kyung Seong
- Laboratory of Developmental Biology and Genomics, BK21 Program Plus for Advanced Veterinary Science, and Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul, Korea. .,Korea Mouse Phenotyping Center (KMPC), Seoul, Korea.,Interdisciplinary Program for Bioinformatics, Program for Cancer Biology and BIO-MAX/N-Bio Institute, Seoul National University, Seoul, Korea
| |
Collapse
|
64
|
Lobas AA, Pyatnitskiy MA, Chernobrovkin AL, Ilina IY, Karpov DS, Solovyeva EM, Kuznetsova KG, Ivanov MV, Lyssuk EY, Kliuchnikova AA, Voronko OE, Larin SS, Zubarev RA, Gorshkov MV, Moshkovskii SA. Proteogenomics of Malignant Melanoma Cell Lines: The Effect of Stringency of Exome Data Filtering on Variant Peptide Identification in Shotgun Proteomics. J Proteome Res 2018; 17:1801-1811. [PMID: 29619825 DOI: 10.1021/acs.jproteome.7b00841] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The identification of genetically encoded variants at the proteome level is an important problem in cancer proteogenomics. The generation of customized protein databases from DNA or RNA sequencing data is a crucial stage of the identification workflow. Genomic data filtering applied at this stage may significantly modify variant search results, yet its effect is generally left out of the scope of proteogenomic studies. In this work, we focused on this impact using data of exome sequencing and LC-MS/MS analyses of six replicates for eight melanoma cell lines processed by a proteogenomics workflow. The main objectives were identifying variant peptides and revealing the role of the genomic data filtering in the variant identification. A series of six confidence thresholds for single nucleotide polymorphisms and indels from the exome data were applied to generate customized sequence databases of different stringency. In the searches against unfiltered databases, between 100 and 160 variant peptides were identified for each of the cell lines using X!Tandem and MS-GF+ search engines. The recovery rate for variant peptides was ∼1%, which is approximately three times lower than that of the wild-type peptides. Using unfiltered genomic databases for variant searches resulted in higher sensitivity and selectivity of the proteogenomic workflow and positively affected the ability to distinguish the cell lines based on variant peptide signatures.
Collapse
Affiliation(s)
- Anna A Lobas
- Moscow Institute of Physics and Technology (State University) , Dolgoprudny 141700 , Moscow Region , Russia.,V.L. Talrose Institute for Energy Problems of Chemical Physics , Russian Academy of Sciences , Moscow 119334 , Russia
| | - Mikhail A Pyatnitskiy
- Institute of Biomedical Chemistry , Moscow 119121 , Russia.,Higher School of Economics , Moscow 101000 , Russia
| | | | - Irina Y Ilina
- Institute of Biomedical Chemistry , Moscow 119121 , Russia
| | - Dmitry S Karpov
- Institute of Biomedical Chemistry , Moscow 119121 , Russia.,Engelhardt Institute of Molecular Biology , Russian Academy of Sciences , Moscow 119991 , Russia
| | - Elizaveta M Solovyeva
- V.L. Talrose Institute for Energy Problems of Chemical Physics , Russian Academy of Sciences , Moscow 119334 , Russia
| | | | - Mark V Ivanov
- V.L. Talrose Institute for Energy Problems of Chemical Physics , Russian Academy of Sciences , Moscow 119334 , Russia
| | - Elena Y Lyssuk
- Institute of Gene Biology , Russian Academy of Sciences , Moscow 119334 , Russia
| | - Anna A Kliuchnikova
- Institute of Biomedical Chemistry , Moscow 119121 , Russia.,Pirogov Russian National Research Medical University , Moscow 117997 , Russia
| | - Olga E Voronko
- Institute of Biomedical Chemistry , Moscow 119121 , Russia
| | - Sergey S Larin
- Institute of Gene Biology , Russian Academy of Sciences , Moscow 119334 , Russia
| | | | - Mikhail V Gorshkov
- V.L. Talrose Institute for Energy Problems of Chemical Physics , Russian Academy of Sciences , Moscow 119334 , Russia
| | - Sergei A Moshkovskii
- Institute of Biomedical Chemistry , Moscow 119121 , Russia.,Pirogov Russian National Research Medical University , Moscow 117997 , Russia
| |
Collapse
|
65
|
Ritchie C, Mack A, Harper L, Alfadhli A, Stork PJS, Nan X, Barklis E. Analysis of K-Ras Interactions by Biotin Ligase Tagging. Cancer Genomics Proteomics 2018. [PMID: 28647697 DOI: 10.21873/cgp.20034] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Mutations of the human K-Ras 4B (K-Ras) G protein are associated with a significant proportion of all human cancers. Despite this fact, a comprehensive analysis of K-Ras interactions is lacking. Our investigations focus on characterization of the K-Ras interaction network. MATERIALS AND METHODS We employed a biotin ligase-tagging approach, in which tagged K-Ras proteins biotinylate neighbor proteins in a proximity-dependent fashion, and proteins are identified via mass spectrometry (MS) sequencing. RESULTS In transfected cells, a total of 748 biotinylated proteins were identified from cells expressing biotin ligase-tagged K-Ras variants. Significant differences were observed between membrane-associated variants and a farnesylation-defective mutant. In pancreatic cancer cells, 56 K-Ras interaction partners were identified. Most of these were cytoskeletal or plasma membrane proteins, and many have been identified previously as potential cancer biomarkers. CONCLUSION Biotin ligase tagging offers a rapid and convenient approach to the characterization of K-Ras interaction networks.
Collapse
Affiliation(s)
- Christopher Ritchie
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, OR, U.S.A
| | - Andrew Mack
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, OR, U.S.A
| | - Logan Harper
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, OR, U.S.A
| | - Ayna Alfadhli
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, OR, U.S.A
| | - Philip J S Stork
- Department of Vollum Institute, Oregon Health & Science University, Portland, OR, U.S.A
| | - Xiaolin Nan
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR, U.S.A
| | - Eric Barklis
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, OR, U.S.A.
| |
Collapse
|
66
|
The Effects of Smad3 on Adrenocorticotropic Hormone-Secreting Pituitary Adenoma Development, Cell Proliferation, Apoptosis, and Hormone Secretion. World Neurosurg 2018. [PMID: 29524699 DOI: 10.1016/j.wneu.2018.02.181] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
OBJECTIVE Down-regulation of mothers against decapentaplegic homolog 3 (Smad3) results in the formation of tumors both in vivo and in vitro. However, little is known about the effect of Smad3 on adrenocorticotropic hormone-secreting pituitary adenomas (ACTH-PAs). Our objective was to study the expression and effect of Smad3 in ACTH-PAs and its possible mechanisms. METHODS Smad3, COOH-terminally phosphorylated mothers against decapentaplegic homolog 3 (pSmad3), and mothers against decapentaplegic homolog 2 proteins (Smad2) were detected in samples from 5 normal anterior pituitaries and 18 ACTH-PAs by Western blot and immunohistochemical analysis. Then, Smad3 expression was up-regulated by Smad3-CMV plasmid or down-regulated by small interfering RNA in ACTH tumor cells (AtT-20) in vitro. Cell proliferation, apoptosis, ACTH level, and pSmad3, B-cell lymphoma/lewkmia-2 (BCL-2), and pro-opiomelanocortin (POMC) protein expression in the AtT-20 cells were measured to investigate the antitumor effects of Smad3. RESULTS Reduced expression of Smad3 and pSmad3 but unchanged Smad2 levels were found in ACTH-PAs compared with normal pituitaries. In vitro, the overexpression of Smad3 inhibited cell proliferation, promoted cell apoptosis, and decreased ACTH secretion; in contrast, Smad3 knockdown increased cell proliferation and decreased cell apoptosis but had no significant effect on ACTH secretion. At the same time, overexpression of Smad3 increased pSmad3 but inhibited BCL-2 and POMC protein expression. On the contrary, underexpression of Smad3 inhibited pSmad3 but promoted BCL-2 and POMC protein expression. CONCLUSIONS Smad3 is underexpressed in ACTH-PAs. Reversing the expression of Smad3 in AtT-20 cells could suppress cell growth, promote tumor apoptosis, and decrease ACTH secretion. Tumor suppression was possibly mediated by the promotion of pSmad3 and the reduction of BCL-2 and POMC expression.
Collapse
|
67
|
Cao Y, Zhou W, Li L, Wang J, Gao Z, Jiang Y, Jiang X, Shan A, Bailey MH, Huang KL, Sun SQ, McLellan MD, Niu B, Wang W, Ding L, Ning G. Pan-cancer analysis of somatic mutations across 21 neuroendocrine tumor types. Cell Res 2018; 28:601-604. [PMID: 29507395 DOI: 10.1038/s41422-018-0019-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 01/07/2018] [Accepted: 01/26/2018] [Indexed: 11/09/2022] Open
Affiliation(s)
- Yanan Cao
- Shanghai Clinical Center for Endocrine and Metabolic Diseases, Shanghai Key Laboratory for Endocrine Tumors, Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China. .,Laboratory of Endocrinology and Metabolism, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.
| | - Weiwei Zhou
- Shanghai Clinical Center for Endocrine and Metabolic Diseases, Shanghai Key Laboratory for Endocrine Tumors, Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lin Li
- Shanghai Clinical Center for Endocrine and Metabolic Diseases, Shanghai Key Laboratory for Endocrine Tumors, Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | | | | | - Yiran Jiang
- Shanghai Clinical Center for Endocrine and Metabolic Diseases, Shanghai Key Laboratory for Endocrine Tumors, Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiuli Jiang
- Shanghai Clinical Center for Endocrine and Metabolic Diseases, Shanghai Key Laboratory for Endocrine Tumors, Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Aijing Shan
- Shanghai Clinical Center for Endocrine and Metabolic Diseases, Shanghai Key Laboratory for Endocrine Tumors, Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Matthew H Bailey
- McDonnell Genome Institute, Washington University, St. Louis, MO, USA.,Department of Medicine, Division of Oncology, Washington University, St. Louis, MO, USA
| | - Kuan-Lin Huang
- McDonnell Genome Institute, Washington University, St. Louis, MO, USA.,Department of Medicine, Division of Oncology, Washington University, St. Louis, MO, USA
| | - Sam Q Sun
- McDonnell Genome Institute, Washington University, St. Louis, MO, USA.,Department of Medicine, Division of Oncology, Washington University, St. Louis, MO, USA
| | | | - Beifang Niu
- McDonnell Genome Institute, Washington University, St. Louis, MO, USA.,Department of High-Performance Computing Technology and Application Development, Computer Network Information Center, Chinese Academy of Sciences, Beijing, China
| | - Weiqing Wang
- Shanghai Clinical Center for Endocrine and Metabolic Diseases, Shanghai Key Laboratory for Endocrine Tumors, Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Li Ding
- McDonnell Genome Institute, Washington University, St. Louis, MO, USA. .,Department of Medicine, Division of Oncology, Washington University, St. Louis, MO, USA. .,Siteman Cancer Center, Washington University, St. Louis, MO, USA.
| | - Guang Ning
- Shanghai Clinical Center for Endocrine and Metabolic Diseases, Shanghai Key Laboratory for Endocrine Tumors, Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China. .,Laboratory of Endocrinology and Metabolism, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.
| |
Collapse
|
68
|
Wei S, Li Q, Li Z, Wang L, Zhang L, Xu Z. miR-424-5p promotes proliferation of gastric cancer by targeting Smad3 through TGF-β signaling pathway. Oncotarget 2018; 7:75185-75196. [PMID: 27655675 PMCID: PMC5342733 DOI: 10.18632/oncotarget.12092] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Accepted: 09/10/2016] [Indexed: 02/07/2023] Open
Abstract
MiRNAs have been reported to regulate gene expression and be associated with cancer progression. Recently, miR-424-5p was reported to play important role in a variety of tumors. However, the role and molecular mechanisms of miR-424-5p in GC (gastric cancer) remains largely unknown. In this study, we aimed to explore the role of miR-424-5p in GC. QRT-PCR was used to determine the expression levels of miR-424-5p and Smad3. CCK8 assay, plate clone assay and cell cycle assay were used to measure the effects of miR-424-5p on GC cell proliferation. Luciferase reporter assay and western blotting were used to prove that Smad3 was one of the direct targets of miR-424-5p. Tumorigenesis assay was used to investigate the role of miR-424-5p in tumor growth of GC cells in vivo. We found that miR-424-5p was up-regulated in GC tissues and cells. Over-expression of miR-424-5p could promote the proliferation of GC cells. In addition, luciferase reporter assay and western blotting assay revealed that Smad3 was a direct target of miR-424-5p. Over-expression of Smad3 could partially reverse the effects of miR-424-5p on GC cell proliferation. Our study further revealed that miR-424-5p could inhibit TGF-β signaling pathway by Smad3.
Collapse
Affiliation(s)
- Song Wei
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Qing Li
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Zheng Li
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Linjun Wang
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Lei Zhang
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Zekuan Xu
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| |
Collapse
|
69
|
Davis T, van Niekerk G, Peres J, Prince S, Loos B, Engelbrecht AM. Doxorubicin resistance in breast cancer: A novel role for the human protein AHNAK. Biochem Pharmacol 2018; 148:174-183. [DOI: 10.1016/j.bcp.2018.01.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 01/03/2018] [Indexed: 12/24/2022]
|
70
|
McKuen MJ, Mueller KE, Bae YS, Fields KA. Fluorescence-Reported Allelic Exchange Mutagenesis Reveals a Role for Chlamydia trachomatis TmeA in Invasion That Is Independent of Host AHNAK. Infect Immun 2017; 85:e00640-17. [PMID: 28970272 PMCID: PMC5695130 DOI: 10.1128/iai.00640-17] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 09/21/2017] [Indexed: 01/05/2023] Open
Abstract
Development of approaches to genetically manipulate Chlamydia is fostering important advances in understanding pathogenesis. Fluorescence-reported allelic exchange mutagenesis (FRAEM) now enables the complete deletion of specific genes in C. trachomatis L2. We have leveraged this technology to delete the coding sequences for a known type III effector. The evidence provided here indicates that CT694/CTL0063 is a virulence protein involved in chlamydial invasion. Based on our findings, we designate the gene product corresponding to ct694-ctl0063translocated membrane-associated effector A (TmeA). Deletion of tmeA did not impact development of intracellular chlamydiae. However, the absence of TmeA manifested as a decrease in infectivity in both tissue culture and murine infection models. The in vitro defect was reflected by impaired invasion of host cells. TmeA binds human AHNAK, and we demonstrate here that AHNAK is transiently recruited by invading chlamydiae. TmeA, however, is not required for endogenous AHNAK recruitment. TmeA also impairs AHNAK-dependent actin bundling activity. This TmeA-mediated effect likely does not explain impaired invasion displayed by the tmeA strain of Chlamydia, since AHNAK-deficient cells revealed no invasion phenotype. Overall, our data indicate the efficacy of FRAEM and reveal a role of TmeA during chlamydial invasion that manifests independently of effects on AHNAK.
Collapse
Affiliation(s)
- M J McKuen
- Department of Microbiology and Immunology, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - K E Mueller
- Department of Microbiology, Immunology & Molecular Genetics, University of Kentucky College of Medicine, Lexington, Kentucky, USA
| | - Y S Bae
- Department of Life Science, Ewha Womans University, Seoul, South Korea
| | - K A Fields
- Department of Microbiology, Immunology & Molecular Genetics, University of Kentucky College of Medicine, Lexington, Kentucky, USA
| |
Collapse
|
71
|
Neelamraju Y, Gonzalez-Perez A, Bhat-Nakshatri P, Nakshatri H, Janga SC. Mutational landscape of RNA-binding proteins in human cancers. RNA Biol 2017; 15:115-129. [PMID: 29023197 PMCID: PMC5786023 DOI: 10.1080/15476286.2017.1391436] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
RNA Binding Proteins (RBPs) are a class of post-transcriptional regulatory molecules which are increasingly documented to be dysfunctional in cancer genomes. However, our current understanding of these alterations is limited. Here, we delineate the mutational landscape of ∼1300 RBPs in ∼6000 cancer genomes. Our analysis revealed that RBPs have an average of ∼3 mutations per Mb across 26 cancer types. We identified 281 RBPs to be enriched for mutations (GEMs) in at least one cancer type. GEM RBPs were found to undergo frequent frameshift and inframe deletions as well as missense, nonsense and silent mutations when compared to those that are not enriched for mutations. Functional analysis of these RBPs revealed the enrichment of pathways associated with apoptosis, splicing and translation. Using the OncodriveFM framework, we also identified more than 200 candidate driver RBPs that were found to accumulate functionally impactful mutations in at least one cancer. Expression levels of 15% of these driver RBPs exhibited significant difference, when transcriptome groups with and without deleterious mutations were compared. Functional interaction network of the driver RBPs revealed the enrichment of spliceosomal machinery, suggesting a plausible mechanism for tumorogenesis while network analysis of the protein interactions between RBPs unambiguously revealed the higher degree, betweenness and closeness centrality for driver RBPs compared to non-drivers. Analysis to reveal cancer-specific Ribonucleoprotein (RNP) mutational hotspots showed extensive rewiring even among common drivers between cancer types. Knockdown experiments on pan-cancer drivers such as SF3B1 and PRPF8 in breast cancer cell lines, revealed cancer subtype specific functions like selective stem cell features, indicating a plausible means for RBPs to mediate cancer-specific phenotypes. Hence, this study would form a foundation to uncover the contribution of the mutational spectrum of RBPs in dysregulating the post-transcriptional regulatory networks in different cancer types.
Collapse
Affiliation(s)
- Yaseswini Neelamraju
- a Department of Bio Health Informatics, School of Informatics and Computing , Indiana University Purdue University , Indianapolis , Indiana , USA
| | - Abel Gonzalez-Perez
- b Research Unit on Biomedical Informatics, Department of Experimental and Health Sciences , Universitat Pompeu Fabra , Barcelona , Spain
| | - Poornima Bhat-Nakshatri
- c Department of Surgery , Indiana University School of Medicine , Indianapolis , Indiana , USA
| | - Harikrishna Nakshatri
- c Department of Surgery , Indiana University School of Medicine , Indianapolis , Indiana , USA.,d Department of Biochemistry & Molecular Biology , Indiana University School of Medicine , Indianapolis , Indiana , USA.,e VA Roudebush Medical Center , Indianapolis , Indiana , USA
| | - Sarath Chandra Janga
- a Department of Bio Health Informatics, School of Informatics and Computing , Indiana University Purdue University , Indianapolis , Indiana , USA.,f Centre for Computational Biology and Bioinformatics , Indiana University School of Medicine , 5021 Health Information and Translational Sciences (HITS), Indianapolis , Indiana , USA.,g Department of Medical and Molecular Genetics , Indiana University School of Medicine , Medical Research and Library Building, Indianapolis , Indiana , USA
| |
Collapse
|
72
|
Ogburn RN, Jin L, Meng H, Fitzgerald MC. Discovery of Tamoxifen and N-Desmethyl Tamoxifen Protein Targets in MCF-7 Cells Using Large-Scale Protein Folding and Stability Measurements. J Proteome Res 2017; 16:4073-4085. [PMID: 28927269 DOI: 10.1021/acs.jproteome.7b00442] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The proteins in an MCF-7 cell line were probed for tamoxifen (TAM) and n-desmethyl tamoxifen (NDT) induced stability changes using the Stability of Proteins from Rates of Oxidation (SPROX) technique in combination with two different quantitative proteomics strategies, including one based on SILAC and one based on isobaric mass tags. Over 1000 proteins were assayed for TAM- and NDT-induced protein stability changes, and a total of 163 and 200 protein hits were identified in the TAM and NDT studies, respectively. A subset of 27 high-confidence protein hits were reproducibly identified with both proteomics strategies and/or with multiple peptide probes. One-third of the high-confidence hits have previously established experimental links to the estrogen receptor, and nearly all of the high-confidence hits have established links to breast cancer. One high-confidence protein hit that has known estrogen receptor binding properties, Y-box binding protein 1 (YBX1), was further validated as a direct binding target of TAM using both the SPROX and pulse proteolysis techniques. Proteins with TAM- and/or NDT-induced expression level changes were also identified in the SILAC-SPROX experiments. These proteins with expression level changes included only a small fraction of those with TAM- and/or NDT-induced stability changes.
Collapse
Affiliation(s)
- Ryenne N Ogburn
- Department of Chemistry, Duke University , Durham, North Carolina 27708, United States
| | - Lorrain Jin
- Department of Chemistry, Duke University , Durham, North Carolina 27708, United States
| | - He Meng
- Department of Chemistry, Duke University , Durham, North Carolina 27708, United States
| | - Michael C Fitzgerald
- Department of Chemistry, Duke University , Durham, North Carolina 27708, United States
| |
Collapse
|
73
|
Mao XY, Lee MJ, Zhu J, Zhu C, Law SM, Snijders AM. Genome-wide screen identifies a novel prognostic signature for breast cancer survival. Oncotarget 2017; 8:14003-14016. [PMID: 28122328 PMCID: PMC5355157 DOI: 10.18632/oncotarget.14776] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 12/31/2016] [Indexed: 12/17/2022] Open
Abstract
Large genomic datasets in combination with clinical data can be used as an unbiased tool to identify genes important in patient survival and discover potential therapeutic targets. We used a genome-wide screen to identify 587 genes significantly and robustly deregulated across four independent breast cancer (BC) datasets compared to normal breast tissue. Gene expression of 381 genes was significantly associated with relapse-free survival (RFS) in BC patients. We used a gene co-expression network approach to visualize the genetic architecture in normal breast and BCs. In normal breast tissue, co-expression cliques were identified enriched for cell cycle, gene transcription, cell adhesion, cytoskeletal organization and metabolism. In contrast, in BC, only two major co-expression cliques were identified enriched for cell cycle-related processes or blood vessel development, cell adhesion and mammary gland development processes. Interestingly, gene expression levels of 7 genes were found to be negatively correlated with many cell cycle related genes, highlighting these genes as potential tumor suppressors and novel therapeutic targets. A forward-conditional Cox regression analysis was used to identify a 12-gene signature associated with RFS. A prognostic scoring system was created based on the 12-gene signature. This scoring system robustly predicted BC patient RFS in 60 sampling test sets and was further validated in TCGA and METABRIC BC data. Our integrated study identified a 12-gene prognostic signature that could guide adjuvant therapy for BC patients and includes novel potential molecular targets for therapy.
Collapse
Affiliation(s)
- Xuan Y Mao
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Matthew J Lee
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Jeffrey Zhu
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Carissa Zhu
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Sindy M Law
- Department of Psychiatry, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, California, USA
| | - Antoine M Snijders
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| |
Collapse
|
74
|
Wilking-Busch MJ, Ndiaye MA, Liu X, Ahmad N. RNA interference-mediated knockdown of SIRT1 and/or SIRT2 in melanoma: Identification of downstream targets by large-scale proteomics analysis. J Proteomics 2017; 170:99-109. [PMID: 28882678 DOI: 10.1016/j.jprot.2017.09.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Revised: 08/14/2017] [Accepted: 09/03/2017] [Indexed: 02/07/2023]
Abstract
Melanoma is the most notorious and fatal of all skin cancers and the existing treatment options have not been proven to effectively manage this neoplasm, especially the metastatic disease. Sirtuin (SIRT) proteins have been shown to be differentially expressed in melanoma. We have shown that SIRTs 1 and 2 were overexpressed in melanoma and inhibition of SIRT1 imparts anti-proliferative responses in human melanoma cells. To elucidate the impact of SIRT 1 and/or 2 in melanoma, we created stable knockdowns of SIRTs 1, 2, and their combination using shRNA mediated RNA interference in A375 human melanoma cells. We found that SIRT1 and SIRT1&2 combination knockdown caused a decreased cellular proliferation in melanoma cells. Further, the knockdown of SIRT 1 and/or 2 resulted in a decreased colony formation in melanoma cells. To explore the downstream targets of SIRTs 1 and/or 2, we employed a label-free quantitative nano-LC-MS/MS proteomics analysis using the stable lines. We found aberrant levels of proteins involved in many vital cellular processes, including cytoskeletal organization, ribosomal activity, oxidative stress response, and angiogenesis. These findings provide clear evidence of cellular systems undergoing alterations in response to sirtuin inhibition, and have unveiled several excellent candidates for future study. SIGNIFICANCE Melanoma is the deadliest form of skin cancer, due to its aggressive nature, metastatic potential, and a lack of sufficient treatment options for advanced disease. Therefore, detailed investigations into the molecular mechanisms of melanoma growth and progression are needed. In the search for candidate genes to serve as therapeutic targets, the sirtuins show promise as they have been found to be upregulated in melanoma and they regulate a large number of proteins involved in cellular processes known to affect tumor growth, such as DNA damage repair, cell cycle arrest, and apoptosis. In this study, we used a large-scale label-free comparative proteomics system to identify novel protein targets that are affected following knockdown of SIRT1 and/or 2 in A375 metastatic melanoma cell line. Our study offers important insight into the potential downstream targets of SIRTs 1 and/or 2. This may unravel new potential areas of exploration in melanoma research.
Collapse
Affiliation(s)
- Melissa J Wilking-Busch
- Department of Dermatology, University of Wisconsin, 1300 University Avenue, Madison, WI 53706, USA
| | - Mary A Ndiaye
- Department of Dermatology, University of Wisconsin, 1300 University Avenue, Madison, WI 53706, USA
| | - Xiaoqi Liu
- Department of Biochemistry, Purdue University, 175 S. University Street, West Lafayette, IN, USA
| | - Nihal Ahmad
- Department of Dermatology, University of Wisconsin, 1300 University Avenue, Madison, WI 53706, USA; William S. Middleton VA Medical Center, 2500 Overlook Terrace, Madison, WI 53705, USA.
| |
Collapse
|
75
|
Zhao Z, Xiao S, Yuan X, Yuan J, Zhang C, Li H, Su J, Wang X, Liu Q. AHNAK as a Prognosis Factor Suppresses the Tumor Progression in Glioma. J Cancer 2017; 8:2924-2932. [PMID: 28928883 PMCID: PMC5604443 DOI: 10.7150/jca.20277] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 07/07/2017] [Indexed: 12/25/2022] Open
Abstract
PURPOSE AHNAK is originally identified as a giant protein based on the estimated size of approximately 700 kDa. The aim of this study is to identify the role of AHNAK in the pathogenesis of glioma. METHODS We tested AHNAK mRNA level in a panel of six human glioma cell lines, and in 30 cases of normal brain tissues and 73 cases of glioma tissue samples using a qRT-PCR method. Further, we analyzed the relationship of AHNAK expression with clinicopathological characteristics in glioma patients. Meanwhile, we analyzed the relationship of expression of AHNAK and survival of glioma patients in survival analyses. Then, in vitro, we analyzed the biological effects of AHNAK in glioma cell lines (U87 and U251) including proliferation assay, cell transwell assay, and apoptosis. And in vivo, we examined the effects of AHNAK on tumor growth using xenograft model of human glioma cells in nude mice. Then we examined the expression of Ki-67-positive cells in these tumors. RESULTS We found that the mRNA levels of AHNAK were down-regulated in 4 of 6 human glioma cell lines, especially in U87 and U251 cell lines. Meanwhile, in glioma patients, a negative correlation was found between the expression of AHNAK and the glioma histopathology. And a low expression of AHNAK was a significant and independent prognostic factor for poor survival of glioma patients. Through over expression of AHNAK in both of U87 and U251, we demonstrated that overexpression of AHNAK could inhibit glioma cell proliferation and invasion, induce apoptosis, and inhibit in vivo glioma tumor growth and ki-67 expression. CONCLUSIONS The AHNAK acts as a potential tumor suppressor. Our study provides a preclinical basis for developing AHNAK as a reliable clinical prognostic indicator for glioma patients, and a new biomarker for treatment response, and a potentially therapeutic target in glioma management options.
Collapse
Affiliation(s)
- Zijin Zhao
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Institute of Skull Base Surgery and Neuro-oncology at Hunan, Changsha, China
| | - Songhua Xiao
- Department of Neurology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guanzhou, Guangdong, China
| | - Xianrui Yuan
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Institute of Skull Base Surgery and Neuro-oncology at Hunan, Changsha, China
| | - Jian Yuan
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Institute of Skull Base Surgery and Neuro-oncology at Hunan, Changsha, China
| | - Chi Zhang
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Institute of Skull Base Surgery and Neuro-oncology at Hunan, Changsha, China
| | - Haoyu Li
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Institute of Skull Base Surgery and Neuro-oncology at Hunan, Changsha, China
| | - Jun Su
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Xiangyu Wang
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Qing Liu
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Institute of Skull Base Surgery and Neuro-oncology at Hunan, Changsha, China
| |
Collapse
|
76
|
Porcine familial adenomatous polyposis model enables systematic analysis of early events in adenoma progression. Sci Rep 2017; 7:6613. [PMID: 28747659 PMCID: PMC5529429 DOI: 10.1038/s41598-017-06741-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 06/16/2017] [Indexed: 12/30/2022] Open
Abstract
We compared gene expression in low and high-grade intraepithelial dysplastic polyps from pigs carrying an APC1311 truncating mutation orthologous to human APC1309, analysing whole samples and microdissected dysplastic epithelium. Gene set enrichment analysis revealed differential expression of gene sets similar to human normal mucosa versus T1 stage polyps. Transcriptome analysis of whole samples revealed many differentially-expressed genes reflecting immune infiltration. Analysis of microdissected dysplastic epithelium was markedly different and showed increased expression in high-grade intraepithelial neoplasia of several genes known to be involved in human CRC; and revealed possible new roles for GBP6 and PLXND1. The pig model thus facilitates analysis of CRC pathogenesis.
Collapse
|
77
|
Díaz-Díaz A, Casas-Pais A, Calamia V, Castosa R, Martinez-Iglesias O, Roca-Lema D, Santamarina I, Valladares-Ayerbes M, Calvo L, Chantada V, Figueroa A. Proteomic Analysis of the E3 Ubiquitin-Ligase Hakai Highlights a Role in Plasticity of the Cytoskeleton Dynamics and in the Proteasome System. J Proteome Res 2017; 16:2773-2788. [PMID: 28675930 DOI: 10.1021/acs.jproteome.7b00046] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Carcinoma, the most common type of cancer, arises from epithelial cells. The transition from adenoma to carcinoma is associated with the loss of E-cadherin and, in consequence, the disruption of cell-cell contacts. E-cadherin is a tumor suppressor, and it is down-regulated during epithelial-to-mesenchymal transition (EMT); indeed, its loss is a predictor of poor prognosis. Hakai is an E3 ubiquitin-ligase protein that mediates E-cadherin ubiquitination, endocytosis and finally degradation, leading the alterations of cell-cell contacts. Although E-cadherin is the most established substrate for Hakai activity, other regulated molecular targets for Hakai may be involved in cancer cell plasticity during tumor progression. In this work we employed an iTRAQ approach to explore novel molecular pathways involved in Hakai-driven EMT during tumor progression. Our results show that Hakai may have an important influence on cytoskeleton-related proteins, extracellular exosome-associated proteins, RNA-related proteins and proteins involved in metabolism. Moreover, a profound decreased expression in several proteasome subunits during Hakai-driven EMT was highlighted. Since proteasome inhibitors are becoming increasingly used in cancer treatment, our findings suggest that the E3 ubiquitin-ligase, such as Hakai, may be a better target than proteasome for using novel specific inhibitors in tumor subtypes that follow EMT.
Collapse
Affiliation(s)
- Andrea Díaz-Díaz
- Epithelial Plasticity and Metastasis Group, Instituto de Investigación Biomédica de A Coruña (INIBIC), Complexo Hospitalario Universitario de A Coruña (CHUAC), Sergas, Universidade da Coruña (UDC) , 15006 A Coruña, Spain
| | - Alba Casas-Pais
- Epithelial Plasticity and Metastasis Group, Instituto de Investigación Biomédica de A Coruña (INIBIC), Complexo Hospitalario Universitario de A Coruña (CHUAC), Sergas, Universidade da Coruña (UDC) , 15006 A Coruña, Spain
| | - Valentina Calamia
- Proteomics Group-ProteoRed PRB2/ISCIII, INIBIC-CHUAC, UDC , 15006 A Coruña, Spain
| | - Raquel Castosa
- Epithelial Plasticity and Metastasis Group, Instituto de Investigación Biomédica de A Coruña (INIBIC), Complexo Hospitalario Universitario de A Coruña (CHUAC), Sergas, Universidade da Coruña (UDC) , 15006 A Coruña, Spain
| | - Olaia Martinez-Iglesias
- Epithelial Plasticity and Metastasis Group, Instituto de Investigación Biomédica de A Coruña (INIBIC), Complexo Hospitalario Universitario de A Coruña (CHUAC), Sergas, Universidade da Coruña (UDC) , 15006 A Coruña, Spain
| | - Daniel Roca-Lema
- Epithelial Plasticity and Metastasis Group, Instituto de Investigación Biomédica de A Coruña (INIBIC), Complexo Hospitalario Universitario de A Coruña (CHUAC), Sergas, Universidade da Coruña (UDC) , 15006 A Coruña, Spain
| | - Isabel Santamarina
- Epithelial Plasticity and Metastasis Group, Instituto de Investigación Biomédica de A Coruña (INIBIC), Complexo Hospitalario Universitario de A Coruña (CHUAC), Sergas, Universidade da Coruña (UDC) , 15006 A Coruña, Spain
| | - Manuel Valladares-Ayerbes
- Clinical and Translational Oncology Group, Hospital Universitario Virgen del Rocio, Instituto de Investigación Biomédica de Sevilla (IBIS) , 41013 Sevilla, Spain
| | - Lourdes Calvo
- Clinical and Translational Oncology Group, Complexo Hospitalario Universitario de A Coruña (CHUAC), Sergas , 15006 A Coruña, Spain
| | - Venancio Chantada
- Epithelial Plasticity and Metastasis Group, Instituto de Investigación Biomédica de A Coruña (INIBIC), Complexo Hospitalario Universitario de A Coruña (CHUAC), Sergas, Universidade da Coruña (UDC) , 15006 A Coruña, Spain
| | - Angélica Figueroa
- Epithelial Plasticity and Metastasis Group, Instituto de Investigación Biomédica de A Coruña (INIBIC), Complexo Hospitalario Universitario de A Coruña (CHUAC), Sergas, Universidade da Coruña (UDC) , 15006 A Coruña, Spain
| |
Collapse
|
78
|
Chen B, Wang J, Dai D, Zhou Q, Guo X, Tian Z, Huang X, Yang L, Tang H, Xie X. AHNAK suppresses tumour proliferation and invasion by targeting multiple pathways in triple-negative breast cancer. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2017; 36:65. [PMID: 28494797 PMCID: PMC5427595 DOI: 10.1186/s13046-017-0522-4] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 03/31/2017] [Indexed: 12/18/2022]
Abstract
Background AHNAK, also known as desmoyokin, is a giant protein with the molecular size of approximately 700 kDa and exerts diverse functions in different types of cancer. Results In the present study, we demonstrated that AHNAK mRNA levels were down-regulated in 7 out of 8 human breast cancer cell lines, especially in triple - negative breast cancer (TNBC) cell lines. Moreover, in patients with TNBC, the expression of AHNAK gene was inversely correlated with the tumor status (P = 0.015), lymph node status (P < 0.001), lymph node (LN) infiltration (P < 0.001) and TNM stage (P < 0.001). Moreover, down-regulated AHNAK expression was considered an independent prognostic factor associated with the poor survival of patients with TNBC. Overexpression of AHNAK in two TNBC cell lines, MDA-MB-231 and BT549, suppressed the in vitro TNBC cell proliferation and colony formation, and inhibited the in vivo TNBC xenograft growth and lung metastasis. The tumor suppressing effect of AHNAK in TNBC was associated with the AKT/MAPK signaling pathway and Wnt/β-catenin pathway. Consistent results were observed when AHNAK was knockdown in BT20 and MDA-MB-435 cells. Conclusions Taken together, our results suggest that AHNAK acts as a tumor suppressor that negatively regulates TNBC cell proliferation, TNBC xenograft growth and metastasis via different signaling pathways. Electronic supplementary material The online version of this article (doi:10.1186/s13046-017-0522-4) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Bo Chen
- Department of Breast Oncology, Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, 651 East Dongfeng Road, Guangzhou, 510060, People's Republic of China
| | - Jin Wang
- Department of Breast Oncology, Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, 651 East Dongfeng Road, Guangzhou, 510060, People's Republic of China
| | - Danian Dai
- Department of Breast Oncology, Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, 651 East Dongfeng Road, Guangzhou, 510060, People's Republic of China
| | - Qingyu Zhou
- College of Pharmacy, University of South Florida, 12901 Bruce B Downs Blvd, MD30, Tampa, FL, 33612-4749, USA
| | - Xiaofang Guo
- College of Pharmacy, University of South Florida, 12901 Bruce B Downs Blvd, MD30, Tampa, FL, 33612-4749, USA
| | - Zhi Tian
- College of Pharmacy, University of South Florida, 12901 Bruce B Downs Blvd, MD30, Tampa, FL, 33612-4749, USA
| | - Xiaojia Huang
- Department of Breast Oncology, Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, 651 East Dongfeng Road, Guangzhou, 510060, People's Republic of China
| | - Lu Yang
- Department of Breast Oncology, Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, 651 East Dongfeng Road, Guangzhou, 510060, People's Republic of China
| | - Hailin Tang
- Department of Breast Oncology, Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, 651 East Dongfeng Road, Guangzhou, 510060, People's Republic of China.
| | - Xiaoming Xie
- Department of Breast Oncology, Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, 651 East Dongfeng Road, Guangzhou, 510060, People's Republic of China.
| |
Collapse
|
79
|
Lu D, Wang J, Shi X, Yue B, Hao J. AHNAK2 is a potential prognostic biomarker in patients with PDAC. Oncotarget 2017; 8:31775-31784. [PMID: 28423668 PMCID: PMC5458247 DOI: 10.18632/oncotarget.15990] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2016] [Accepted: 02/21/2017] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND AHNAK nucleoprotein 2 (AHNAK2) belongs to the AHNAK protein family. The studies of AHNAK2 are limited. A recent study reported that AHNAK2 might be a biomarker for pancreatic ductal adenocarcinoma (PDAC); however, tissue-based experiments have not been conducted. The aim of this study was to determine the tissue expression of AHNAK2 and to find the correlation between AHNAK2 and overall survival rate in PDAC. RESULTS AHNAK2 is highly expressed in PDAC (n=79) compared with adjacent normal tissues (n=64, P<0.001). Overexpression of AHNAK2 showed a significant relationship with a lower overall survival rate (P=0.033) in PDAC patients. The predictive value of increased expression of AHNAK2 remains relevant in patients with AJCC grade above II (n=43, P=0.006) or lymph node metastasis (n=32, P=0.004). Cox regression analysis showed that AHNAK2 expression (P=0.003) and pathology grade (P<0.001) are independent prognostic factors for PDAC. The nomogram model was performed to predict the 1- and 3-year survival rates based on Cox regression. The C-index was 0.61. The calibration curves were also made to show the association between the observed and predicted probability of the overall survival rates. MATERIALS AND METHODS AHNAK2 expression was performed in tissue microarrays by immunohistochemistry. The overall survival rate analysis was performed using the Kaplan-Meier method, Cox proportional hazards regression, and a nomogram model. CONCLUSIONS AHNAK2 is overexpressed in PDAC tissues and is an independent prognostic factor in patients with PDAC.
Collapse
Affiliation(s)
- Di Lu
- Department of Gastroenterology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing 100020, China
| | - Junxiong Wang
- Department of Gastroenterology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing 100020, China
| | - Xiaoyan Shi
- Department of Pathology, Beijing Friendship Hospital, Capital Medical University, Beijing 100050, China
| | - Bing Yue
- Department of Pathology, Beijing Friendship Hospital, Capital Medical University, Beijing 100050, China
| | - Jianyu Hao
- Department of Gastroenterology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing 100020, China
| |
Collapse
|
80
|
Zhao J, Cheng F, Zhao Z. Tissue-Specific Signaling Networks Rewired by Major Somatic Mutations in Human Cancer Revealed by Proteome-Wide Discovery. Cancer Res 2017; 77:2810-2821. [PMID: 28364002 DOI: 10.1158/0008-5472.can-16-2460] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Revised: 10/17/2016] [Accepted: 03/27/2017] [Indexed: 01/06/2023]
Abstract
Massive somatic mutations discovered by large cancer genome sequencing projects provide unprecedented opportunities in the development of precision oncology. However, deep understanding of functional consequences of somatic mutations and identifying actionable mutations and the related drug responses currently remain formidable challenges. Dysfunction of protein posttranslational modification plays critical roles in tumorigenesis and drug responses. In this study, we proposed a novel computational oncoproteomics approach, named kinome-wide network module for cancer pharmacogenomics (KNMPx), for identifying actionable mutations that rewired signaling networks and further characterized tumorigenesis and anticancer drug responses. Specifically, we integrated 746,631 missense mutations in 4,997 tumor samples across 16 major cancer types/subtypes from The Cancer Genome Atlas into over 170,000 carefully curated nonredundant phosphorylation sites covering 18,610 proteins. We found 47 mutated proteins (e.g., ERBB2, TP53, and CTNNB1) that had enriched missense mutations at their phosphorylation sites in pan-cancer analysis. In addition, tissue-specific kinase-substrate interaction modules altered by somatic mutations identified by KNMPx were significantly associated with patient survival. We further reported a kinome-wide landscape of pharmacogenomic interactions by incorporating somatic mutation-rewired signaling networks in 1,001 cancer cell lines via KNMPx. Interestingly, we found that cell lines could highly reproduce oncogenic phosphorylation site mutations identified in primary tumors, supporting the confidence in their associations with sensitivity/resistance of inhibitors targeting EGF, MAPK, PI3K, mTOR, and Wnt signaling pathways. In summary, our KNMPx approach is powerful for identifying oncogenic alterations via rewiring phosphorylation-related signaling networks and drug sensitivity/resistance in the era of precision oncology. Cancer Res; 77(11); 2810-21. ©2017 AACR.
Collapse
Affiliation(s)
- Junfei Zhao
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, Texas
| | - Feixiong Cheng
- Center for Cancer Systems Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts.,Center for Complex Networks Research, Northeastern University, Boston, Massachusetts
| | - Zhongming Zhao
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, Texas. .,Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, Texas
| |
Collapse
|
81
|
Bhargava S, Patil V, Mahalingam K, Somasundaram K. Elucidation of the genetic and epigenetic landscape alterations in RNA binding proteins in glioblastoma. Oncotarget 2017; 8:16650-16668. [PMID: 28035070 PMCID: PMC5369992 DOI: 10.18632/oncotarget.14287] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 11/30/2016] [Indexed: 01/03/2023] Open
Abstract
RNA binding proteins (RBPs) have been implicated in cancer development. An integrated bioinformatics analysis of RBPs (n = 1756) in various datasets (n = 11) revealed several genetic and epigenetically altered events among RBPs in glioblastoma (GBM). We identified 13 mutated and 472 differentially regulated RBPs in GBM samples. Mutations in AHNAK predicted poor prognosis. Copy number variation (CNV), DNA methylation and miRNA targeting contributed to RBP differential regulation. Two sets of differentially regulated RBPs that may be implicated in initial astrocytic transformation and glioma progression were identified. We have also identified a four RBP (NOL3, SUCLG1, HERC5 and AFF3) signature, having a unique expression pattern in glioma stem-like cells (GSCs), to be an independent poor prognostic indicator in GBM. RBP risk score derived from the signature also stratified GBM into low-risk and high-risk groups with significant survival difference. Silencing NOL3, SUCLG1 and HERC5 inhibited GSC maintenance. Gene set enrichment analysis of differentially regulated genes between high-risk and low-risk underscored the importance of inflammation, EMT and hypoxia in high-risk GBM. Thus, we provide a comprehensive overview of genetic and epigenetic regulation of RBPs in glioma development and progression.
Collapse
Affiliation(s)
- Shruti Bhargava
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore-560012, India
| | - Vikas Patil
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore-560012, India
- Department of Bio-Medical Sciences, School of Biosciences and Technology, VIT University, Vellore-632014, India
| | - Kulandaivelu Mahalingam
- Department of Bio-Medical Sciences, School of Biosciences and Technology, VIT University, Vellore-632014, India
| | - Kumaravel Somasundaram
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore-560012, India
| |
Collapse
|
82
|
Yu L, Di Y, Xin L, Ren Y, Liu X, Sun X, Zhang W, Yao Z, Yang J. SND1 acts as a novel gene transcription activator recognizing the conserved Motif domains of Smad promoters, inducing TGFβ1 response and breast cancer metastasis. Oncogene 2017; 36:3903-3914. [DOI: 10.1038/onc.2017.30] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Revised: 12/29/2016] [Accepted: 12/30/2016] [Indexed: 02/06/2023]
|
83
|
Wang M, Li X, Zhang J, Yang Q, Chen W, Jin W, Huang YR, Yang R, Gao WQ. AHNAK2 is a Novel Prognostic Marker and Oncogenic Protein for Clear Cell Renal Cell Carcinoma. Am J Cancer Res 2017; 7:1100-1113. [PMID: 28435451 PMCID: PMC5399579 DOI: 10.7150/thno.18198] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 12/17/2016] [Indexed: 11/25/2022] Open
Abstract
Integrative database analysis was performed to identify novel candidate oncogene AHNAK2 overexpressed in clear cell renal cell carcinoma (ccRCC). However, the function of AHNAK2 in cancer cells is currently unknown. In this study, we first confirmed the upregulation of AHNAK2 in ccRCC tissues compared with adjacent normal tissues in 15 pairs of samples. Then we analyzed AHNAK2 expression in a large cohort of ccRCC patient samples (n = 355), and found that up-regulation of AHNAK2 was positively correlated with tumor progression and poor survival (p = 0.032). Knockdown of AHNAK2 inhibited cancer cell proliferation, colony formation and migration in vitro and tumorigenic ability in vivo. Meanwhile, knockdown of AHNAK2 impaired the cell oncologic-metabolism by inhibiting lipid synthesis. Moreover, we observed that expression of AHNAK2 was greatly upregulated, at least in part, by hypoxia in cancer cells. By using chromatin immune-precipitation (CHIP) and promoter-luciferase reporter assays, we identified that upregulation of AHNAK2 induced by hypoxia was hypoxia-inducible factor-1α (HIF1α)-dependent. Knockdown of AHNAK2 impaired hypoxia-induced epithelial-mesenchymal transition (EMT) and stem cell-like properties. Considered together, we reveal that AHNAK2 is upregulated in cancer cells and hypoxic upregulation of AHNAK2 can drive tumorigenesis and progression by supporting EMT and cancer cell stemness. Thus, AHNAK2 is a novel prognostic marker and an oncogenic protein for ccRCC.
Collapse
|
84
|
Duffy DJ, Krstic A, Halasz M, Schwarzl T, Konietzny A, Iljin K, Higgins DG, Kolch W. Retinoic acid and TGF-β signalling cooperate to overcome MYCN-induced retinoid resistance. Genome Med 2017; 9:15. [PMID: 28187790 PMCID: PMC5303304 DOI: 10.1186/s13073-017-0407-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 01/20/2017] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Retinoid therapy is widely employed in clinical oncology to differentiate malignant cells into their more benign counterparts. However, certain high-risk cohorts, such as patients with MYCN-amplified neuroblastoma, are innately resistant to retinoid therapy. Therefore, we employed a precision medicine approach to globally profile the retinoid signalling response and to determine how an excess of cellular MYCN antagonises these signalling events to prevent differentiation and confer resistance. METHODS We applied RNA sequencing (RNA-seq) and interaction proteomics coupled with network-based systems level analysis to identify targetable vulnerabilities of MYCN-mediated retinoid resistance. We altered MYCN expression levels in a MYCN-inducible neuroblastoma cell line to facilitate or block retinoic acid (RA)-mediated neuronal differentiation. The relevance of differentially expressed genes and transcriptional regulators for neuroblastoma outcome were then confirmed using existing patient microarray datasets. RESULTS We determined the signalling networks through which RA mediates neuroblastoma differentiation and the inhibitory perturbations to these networks upon MYCN overexpression. We revealed opposing regulation of RA and MYCN on a number of differentiation-relevant genes, including LMO4, CYP26A1, ASCL1, RET, FZD7 and DKK1. Furthermore, we revealed a broad network of transcriptional regulators involved in regulating retinoid responsiveness, such as Neurotrophin, PI3K, Wnt and MAPK, and epigenetic signalling. Of these regulators, we functionally confirmed that MYCN-driven inhibition of transforming growth factor beta (TGF-β) signalling is a vulnerable node of the MYCN network and that multiple levels of cross-talk exist between MYCN and TGF-β. Co-targeting of the retinoic acid and TGF-β pathways, through RA and kartogenin (KGN; a TGF-β signalling activating small molecule) combination treatment, induced the loss of viability of MYCN-amplified retinoid-resistant neuroblastoma cells. CONCLUSIONS Our approach provides a powerful precision oncology tool for identifying the driving signalling networks for malignancies not primarily driven by somatic mutations, such as paediatric cancers. By applying global omics approaches to the signalling networks regulating neuroblastoma differentiation and stemness, we have determined the pathways involved in the MYCN-mediated retinoid resistance, with TGF-β signalling being a key regulator. These findings revealed a number of combination treatments likely to improve clinical response to retinoid therapy, including co-treatment with retinoids and KGN, which may prove valuable in the treatment of high-risk MYCN-amplified neuroblastoma.
Collapse
Affiliation(s)
- David J Duffy
- Systems Biology Ireland, University College Dublin, Belfield, Dublin 4, Ireland.
- Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland.
- School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland.
- The Whitney Laboratory for Marine Bioscience and Sea Turtle Hospital, University of Florida, St. Augustine, Florida, 32080, USA.
| | - Aleksandar Krstic
- Systems Biology Ireland, University College Dublin, Belfield, Dublin 4, Ireland
- Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland
- School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland
| | - Melinda Halasz
- Systems Biology Ireland, University College Dublin, Belfield, Dublin 4, Ireland
- Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland
- School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland
| | - Thomas Schwarzl
- Systems Biology Ireland, University College Dublin, Belfield, Dublin 4, Ireland
- European Molecular Biology Laboratory (EMBL), Meyerhofstraße 1, 69117, Heidelberg, Germany
| | - Anja Konietzny
- Systems Biology Ireland, University College Dublin, Belfield, Dublin 4, Ireland
- Present address: Department of Biology, University of Konstanz, Konstanz, Germany
| | - Kristiina Iljin
- VTT Technical Research Centre of Finland, Tietotie 2, FI-02044 VTT, Espoo, Finland
| | - Desmond G Higgins
- Systems Biology Ireland, University College Dublin, Belfield, Dublin 4, Ireland
- Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland
- School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland
| | - Walter Kolch
- Systems Biology Ireland, University College Dublin, Belfield, Dublin 4, Ireland
- Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland
- School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland
| |
Collapse
|
85
|
Cantelli G, Crosas-Molist E, Georgouli M, Sanz-Moreno V. TGFΒ-induced transcription in cancer. Semin Cancer Biol 2017; 42:60-69. [PMID: 27586372 PMCID: PMC6137079 DOI: 10.1016/j.semcancer.2016.08.009] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 08/19/2016] [Indexed: 12/15/2022]
Abstract
The Transforming Growth Factor-beta (TGFβ) pathway mediates a broad spectrum of cellular processes and is involved in several diseases, including cancer. TGFβ has a dual role in tumours, acting as a tumour suppressor in the early phase of tumorigenesis and as a tumour promoter in more advanced stages. In this review, we discuss the effects of TGFβ-driven transcription on all stages of tumour progression, with special focus on lung cancer. Since some TGFβ target genes are specifically involved in promoting metastasis, we speculate that these genes might be good targets to block tumour progression without compromising the tumour suppressor effects of the TGFβ pathway.
Collapse
Affiliation(s)
- Gaia Cantelli
- Tumour Plasticity Laboratory, Randall Division of Cell and Molecular Biophysics, New Hunt's House, Guy's Campus, King's College London, London SE1 1UL, UK
| | - Eva Crosas-Molist
- Tumour Plasticity Laboratory, Randall Division of Cell and Molecular Biophysics, New Hunt's House, Guy's Campus, King's College London, London SE1 1UL, UK
| | - Mirella Georgouli
- Tumour Plasticity Laboratory, Randall Division of Cell and Molecular Biophysics, New Hunt's House, Guy's Campus, King's College London, London SE1 1UL, UK
| | - Victoria Sanz-Moreno
- Tumour Plasticity Laboratory, Randall Division of Cell and Molecular Biophysics, New Hunt's House, Guy's Campus, King's College London, London SE1 1UL, UK.
| |
Collapse
|
86
|
Yokobori T, Nishiyama M. TGF-β Signaling in Gastrointestinal Cancers: Progress in Basic and Clinical Research. J Clin Med 2017; 6:jcm6010011. [PMID: 28106769 PMCID: PMC5294964 DOI: 10.3390/jcm6010011] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 12/31/2016] [Accepted: 01/16/2017] [Indexed: 12/18/2022] Open
Abstract
Transforming growth factor (TGF)-β superfamily proteins have many important biological functions, including regulation of tissue differentiation, cell proliferation, and migration in both normal and cancer cells. Many studies have reported that TGF-β signaling is associated with disease progression and therapeutic resistance in several cancers. Similarly, TGF-β-induced protein (TGFBI)—a downstream component of the TGF-β signaling pathway—has been shown to promote and/or inhibit cancer. Here, we review the state of basic and clinical research on the roles of TGF-β and TGFBI in gastrointestinal cancers.
Collapse
Affiliation(s)
- Takehiko Yokobori
- Research Program for Omics-based Medical Science, Division of Integrated Oncology Research, Gunma University Initiative for Advanced Research, 3-39-22 Showa-machi, Maebashi, Gunma 371-8511, Japan.
| | - Masahiko Nishiyama
- Research Program for Omics-based Medical Science, Division of Integrated Oncology Research, Gunma University Initiative for Advanced Research, 3-39-22 Showa-machi, Maebashi, Gunma 371-8511, Japan.
- Department of Molecular Pharmacology and Oncology, Gunma University Graduate School of Medicine, 3-39-22 Showa-machi, Maebashi, Gunma 371-8511, Japan.
| |
Collapse
|
87
|
AHNAK is downregulated in melanoma, predicts poor outcome, and may be required for the expression of functional cadherin-1. Melanoma Res 2017; 26:108-16. [PMID: 26672724 PMCID: PMC4777222 DOI: 10.1097/cmr.0000000000000228] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The aim of this study was to further our understanding of the transformation process by identifying differentially expressed proteins in melanocytes compared with melanoma cell lines. Tandem mass spectrometry incorporating iTRAQ reagents was used as a screen to identify and comparatively quantify the expression of proteins in membrane-enriched samples isolated from primary human melanocytes or three melanoma cells lines. Real-time PCR was used to validate significant hits. Immunohistochemistry was used to validate the expression of proteins of interest in melanocytes in human skin and in melanoma-infiltrated lymph nodes. Publically available databases were examined to assess mRNA expression and correlation to patient outcome in a larger cohort of samples. Finally, preliminary functional studies were carried out using siRNAs to reduce the expression of a protein of interest in primary melanocytes and in a keratinocyte cell line. Two proteins, AHNAK and ANXA2, were significantly downregulated in the melanoma cell lines compared with melanocytes. Downregulation was confirmed in tumor cells in a subset of human melanoma-infiltrated human lymph nodes compared with melanocytes in human skin. Examination of Gene Expression Omnibus database data sets suggests that downregulation of AHNAK mRNA and mutation of the AHNAK gene are common in metastatic melanoma and correlates to a poor outcome. Knockdown of AHNAK in primary melanocytes and in a keratinocyte cell line led to a reduction in detectable cadherin-1. This is the first report that we are aware of which correlates a loss of AHNAK with melanoma and poor patient outcome. We hypothesize that AHNAK is required for the expression of functional cadherin-1.
Collapse
|
88
|
Abstract
Based on the histological features and outcome, the current WHO classification separates thymomas into A, AB, B1, B2 and B3 subtypes. It is hypothesized that the type A thymomas are derived from the thymic medulla while the type B thymomas are derived from the cortex. Due to occasional histological overlap between the tumor subtypes creating difficulties in their separation, the aim of this study was to provide their proteomic characterization and identify potential immunohistochemical markers aiding in tissue diagnosis. Pair-wise comparison of neoplastic and normal thymus by liquid chromatography tandem mass spectrometry (LC-MS/MS) of formalin fixed paraffin embedded tissue revealed 61 proteins differentially expressed in thymomas compared to normal tissue. Hierarchical clustering showed distinct segregation of subtypes AB, B1 and B2 from that of A and B3. Most notably, desmoyokin, a protein that is encoded by the AHNAK gene, was associated with type A thymomas and medulla of normal thymus, by LC-MS/MS and immunohistochemistry. In this global proteomic characterization of the thymoma, several proteins unique to different thymic compartments and thymoma subtypes were identified. Among differentially expressed proteins, desmoyokin is a marker specific for thymic medulla and is potentially promising immunohistochemical marker in separation of type A and B3 thymomas.
Collapse
|
89
|
Seno A, Kasai T, Ikeda M, Vaidyanath A, Masuda J, Mizutani A, Murakami H, Ishikawa T, Seno M. Characterization of Gene Expression Patterns among Artificially Developed Cancer Stem Cells Using Spherical Self-Organizing Map. Cancer Inform 2016; 15:163-78. [PMID: 27559294 PMCID: PMC4988459 DOI: 10.4137/cin.s39839] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Revised: 05/15/2016] [Accepted: 05/30/2016] [Indexed: 12/20/2022] Open
Abstract
We performed gene expression microarray analysis coupled with spherical self-organizing map (sSOM) for artificially developed cancer stem cells (CSCs). The CSCs were developed from human induced pluripotent stem cells (hiPSCs) with the conditioned media of cancer cell lines, whereas the CSCs were induced from primary cell culture of human cancer tissues with defined factors (OCT3/4, SOX2, and KLF4). These cells commonly expressed human embryonic stem cell (hESC)/hiPSC-specific genes (POU5F1, SOX2, NANOG, LIN28, and SALL4) at a level equivalent to those of control hiPSC 201B7. The sSOM with unsupervised method demonstrated that the CSCs could be divided into three groups based on their culture conditions and original cancer tissues. Furthermore, with supervised method, sSOM nominated TMED9, RNASE1, NGFR, ST3GAL1, TNS4, BTG2, SLC16A3, CD177, CES1, GDF15, STMN2, FAM20A, NPPB, CD99, MYL7, PRSS23, AHNAK, and LOC152573 genes commonly upregulating among the CSCs compared to hiPSC, suggesting the gene signature of the CSCs.
Collapse
Affiliation(s)
- Akimasa Seno
- Laboratory of Nano-Biotechnology, Department of Medical Bioengineering Science, Graduate School of Natural Science and Technology, Okayama University, Kita-ku, Okayama, Japan
| | - Tomonari Kasai
- Laboratory of Nano-Biotechnology, Department of Medical Bioengineering Science, Graduate School of Natural Science and Technology, Okayama University, Kita-ku, Okayama, Japan
| | - Masashi Ikeda
- Laboratory of Nano-Biotechnology, Department of Medical Bioengineering Science, Graduate School of Natural Science and Technology, Okayama University, Kita-ku, Okayama, Japan
| | - Arun Vaidyanath
- Laboratory of Nano-Biotechnology, Department of Medical Bioengineering Science, Graduate School of Natural Science and Technology, Okayama University, Kita-ku, Okayama, Japan
| | - Junko Masuda
- Laboratory of Nano-Biotechnology, Department of Medical Bioengineering Science, Graduate School of Natural Science and Technology, Okayama University, Kita-ku, Okayama, Japan
| | - Akifumi Mizutani
- Laboratory of Nano-Biotechnology, Department of Medical Bioengineering Science, Graduate School of Natural Science and Technology, Okayama University, Kita-ku, Okayama, Japan
| | - Hiroshi Murakami
- Laboratory of Nano-Biotechnology, Department of Medical Bioengineering Science, Graduate School of Natural Science and Technology, Okayama University, Kita-ku, Okayama, Japan
| | - Tetsuya Ishikawa
- Cell Biology, Core Facilities for Research and Innovative Medicine, National Cancer Center Research Institute, Chuo-ku, Tokyo, Japan.; Central Animal Division, Fundamental Innovative Oncology Core Center, National Cancer Center Research Institute, Chuo-ku, Tokyo, Japan
| | - Masaharu Seno
- Laboratory of Nano-Biotechnology, Department of Medical Bioengineering Science, Graduate School of Natural Science and Technology, Okayama University, Kita-ku, Okayama, Japan
| |
Collapse
|
90
|
Icay K, Chen P, Cervera A, Rantanen V, Lehtonen R, Hautaniemi S. SePIA: RNA and small RNA sequence processing, integration, and analysis. BioData Min 2016; 9:20. [PMID: 27213017 PMCID: PMC4875694 DOI: 10.1186/s13040-016-0099-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Accepted: 05/08/2016] [Indexed: 02/07/2023] Open
Abstract
Background Large-scale sequencing experiments are complex and require a wide spectrum of computational tools to extract and interpret relevant biological information. This is especially true in projects where individual processing and integrated analysis of both small RNA and complementary RNA data is needed. Such studies would benefit from a computational workflow that is easy to implement and standardizes the processing and analysis of both sequenced data types. Results We developed SePIA (Sequence Processing, Integration, and Analysis), a comprehensive small RNA and RNA workflow. It provides ready execution for over 20 commonly known RNA-seq tools on top of an established workflow engine and provides dynamic pipeline architecture to manage, individually analyze, and integrate both small RNA and RNA data. Implementation with Docker makes SePIA portable and easy to run. We demonstrate the workflow’s extensive utility with two case studies involving three breast cancer datasets. SePIA is straightforward to configure and organizes results into a perusable HTML report. Furthermore, the underlying pipeline engine supports computational resource management for optimal performance. Conclusion SePIA is an open-source workflow introducing standardized processing and analysis of RNA and small RNA data. SePIA’s modular design enables robust customization to a given experiment while maintaining overall workflow structure. It is available at http://anduril.org/sepia. Electronic supplementary material The online version of this article (doi:10.1186/s13040-016-0099-z) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Katherine Icay
- Research Programs Unit, Genome-Scale Biology, Medicum and Department of Biochemistry and Developmental Biology, Faculty of Medicine, University of Helsinki, POB 63, Helsinki, 00014 Finland
| | - Ping Chen
- Research Programs Unit, Genome-Scale Biology, Medicum and Department of Biochemistry and Developmental Biology, Faculty of Medicine, University of Helsinki, POB 63, Helsinki, 00014 Finland
| | - Alejandra Cervera
- Research Programs Unit, Genome-Scale Biology, Medicum and Department of Biochemistry and Developmental Biology, Faculty of Medicine, University of Helsinki, POB 63, Helsinki, 00014 Finland
| | - Ville Rantanen
- Research Programs Unit, Genome-Scale Biology, Medicum and Department of Biochemistry and Developmental Biology, Faculty of Medicine, University of Helsinki, POB 63, Helsinki, 00014 Finland
| | - Rainer Lehtonen
- Research Programs Unit, Genome-Scale Biology, Medicum and Department of Biochemistry and Developmental Biology, Faculty of Medicine, University of Helsinki, POB 63, Helsinki, 00014 Finland
| | - Sampsa Hautaniemi
- Research Programs Unit, Genome-Scale Biology, Medicum and Department of Biochemistry and Developmental Biology, Faculty of Medicine, University of Helsinki, POB 63, Helsinki, 00014 Finland
| |
Collapse
|
91
|
Xu Y, Guo W, Li P, Zhang Y, Zhao M, Fan Z, Zhao Z, Yan J. Long-Range Chromosome Interactions Mediated by Cohesin Shape Circadian Gene Expression. PLoS Genet 2016; 12:e1005992. [PMID: 27135601 PMCID: PMC4852938 DOI: 10.1371/journal.pgen.1005992] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2015] [Accepted: 03/27/2016] [Indexed: 01/08/2023] Open
Abstract
Mammalian circadian rhythm is established by the negative feedback loops consisting of a set of clock genes, which lead to the circadian expression of thousands of downstream genes in vivo. As genome-wide transcription is organized under the high-order chromosome structure, it is largely uncharted how circadian gene expression is influenced by chromosome architecture. We focus on the function of chromatin structure proteins cohesin as well as CTCF (CCCTC-binding factor) in circadian rhythm. Using circular chromosome conformation capture sequencing, we systematically examined the interacting loci of a Bmal1-bound super-enhancer upstream of a clock gene Nr1d1 in mouse liver. These interactions are largely stable in the circadian cycle and cohesin binding sites are enriched in the interactome. Global analysis showed that cohesin-CTCF co-binding sites tend to insulate the phases of circadian oscillating genes while cohesin-non-CTCF sites are associated with high circadian rhythmicity of transcription. A model integrating the effects of cohesin and CTCF markedly improved the mechanistic understanding of circadian gene expression. Further experiments in cohesin knockout cells demonstrated that cohesin is required at least in part for driving the circadian gene expression by facilitating the enhancer-promoter looping. This study provided a novel insight into the relationship between circadian transcriptome and the high-order chromosome structure.
Collapse
Affiliation(s)
- Yichi Xu
- CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Shanghai, China
| | - Weimin Guo
- CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Ping Li
- Beijing Institute of Biotechnology, Beijing, China
| | - Yan Zhang
- Beijing Institute of Biotechnology, Beijing, China
| | - Meng Zhao
- CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Zenghua Fan
- CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Shanghai, China
| | - Zhihu Zhao
- Beijing Institute of Biotechnology, Beijing, China
| | - Jun Yan
- CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| |
Collapse
|
92
|
Seo J, Lee EW, Sung H, Seong D, Dondelinger Y, Shin J, Jeong M, Lee HK, Kim JH, Han SY, Lee C, Seong JK, Vandenabeele P, Song J. CHIP controls necroptosis through ubiquitylation- and lysosome-dependent degradation of RIPK3. Nat Cell Biol 2016; 18:291-302. [DOI: 10.1038/ncb3314] [Citation(s) in RCA: 105] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 01/18/2016] [Indexed: 12/16/2022]
|
93
|
Shin S, Seong JK, Bae YS. Ahnak stimulates BMP2-mediated adipocyte differentiation through Smad1 activation. Obesity (Silver Spring) 2016; 24:398-407. [PMID: 26813528 DOI: 10.1002/oby.21367] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Accepted: 09/09/2015] [Indexed: 01/18/2023]
Abstract
OBJECTIVE Previous reports have indicated that Ahnak-deficient mice were protected from high-fat diet-induced obesity. However, the molecular mechanism in which Ahnak mediates adipocyte differentiation and high-fat diet-induced obesity is unclear. METHODS Adipocytes from Ahnak knockout (Ahnak(-/-) ) mice and knockdown of Ahnak in C3H10T1/2 were used to investigate the function of Ahnak in adipocyte differentiation. Ahnak-induced adipocyte differentiation was analyzed by Oil Red O staining. RESULTS Adipocytes from Ahnak(-/-) mice were smaller than those from wild-type mice. Silencing of Ahnak in C3H10T1/2 and adipose tissue-derived mesenchymal stem cells (ADSCs) from Ahnak(-/-) mice showed severely impaired adipocyte differentiation. Down-regulation of Ahnak in C3H10T1/2 cells and ADSCs from Ahnak(-/-) mice attenuated the phosphorylation and nuclear localization of Smad1 in response to BMP2, whereas Ahnak overexpression in 3T3-L1 cells significantly increased Smad1 activation. Because PPARγ is a well-known transcriptional factor in adipocyte differentiation, the PPARγ expression in Ahnak-mediated adipocyte differentiation was investigated. Transfection of C3H10T1/2 cells with Ahnak siRNA resulted in reduced PPARγ expression apparently through inhibited binding of Smad1 to the Smad1-binding site in the PPARγ promoter. These results suggest that Ahnak regulates adipogenesis by regulating Smad1-dependent PPARγ expression. CONCLUSIONS A molecular mechanism was proposed in which Ahnak regulates adipocyte differentiation through Smad1 activation.
Collapse
Affiliation(s)
- Sunmee Shin
- Department of Life Science, Ewha Womans University, Seoul, Korea
| | - Je Kyung Seong
- Laboratory of Developmental Biology and Genomics, College of Veterinary Medicine, and BK21 Program for Veterinary Science, Seoul National University, Daehak-Dong, Gwanak-Gu, Seoul, Korea
| | - Yun Soo Bae
- Department of Life Science, Ewha Womans University, Seoul, Korea
| |
Collapse
|
94
|
Olsen JB, Cao XJ, Han B, Chen LH, Horvath A, Richardson TI, Campbell RM, Garcia BA, Nguyen H. Quantitative Profiling of the Activity of Protein Lysine Methyltransferase SMYD2 Using SILAC-Based Proteomics. Mol Cell Proteomics 2016; 15:892-905. [PMID: 26750096 DOI: 10.1074/mcp.m115.053280] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Indexed: 12/13/2022] Open
Abstract
The significance of non-histone lysine methylation in cell biology and human disease is an emerging area of research exploration. The development of small molecule inhibitors that selectively and potently target enzymes that catalyze the addition of methyl-groups to lysine residues, such as the protein lysine mono-methyltransferase SMYD2, is an active area of drug discovery. Critical to the accurate assessment of biological function is the ability to identify target enzyme substrates and to define enzyme substrate specificity within the context of the cell. Here, using stable isotopic labeling with amino acids in cell culture (SILAC) coupled with immunoaffinity enrichment of mono-methyl-lysine (Kme1) peptides and mass spectrometry, we report a comprehensive, large-scale proteomic study of lysine mono-methylation, comprising a total of 1032 Kme1 sites in esophageal squamous cell carcinoma (ESCC) cells and 1861 Kme1 sites in ESCC cells overexpressing SMYD2. Among these Kme1 sites is a subset of 35 found to be potently down-regulated by both shRNA-mediated knockdown of SMYD2 and LLY-507, a selective small molecule inhibitor of SMYD2. In addition, we report specific protein sequence motifs enriched in Kme1 sites that are directly regulated by endogenous SMYD2 activity, revealing that SMYD2 substrate specificity is more diverse than expected. We further show direct activity of SMYD2 toward BTF3-K2, PDAP1-K126 as well as numerous sites within the repetitive units of two unique and exceptionally large proteins, AHNAK and AHNAK2. Collectively, our findings provide quantitative insights into the cellular activity and substrate recognition of SMYD2 as well as the global landscape and regulation of protein mono-methylation.
Collapse
Affiliation(s)
- Jonathan B Olsen
- From the ‡Lilly USA, Lilly Research Laboratories, Indianapolis, Indiana 46285
| | - Xing-Jun Cao
- §Epigenetics Program, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania Philadelphia, Pennsylvania 19104
| | - Bomie Han
- From the ‡Lilly USA, Lilly Research Laboratories, Indianapolis, Indiana 46285
| | - Lisa Hong Chen
- From the ‡Lilly USA, Lilly Research Laboratories, Indianapolis, Indiana 46285
| | | | | | - Robert M Campbell
- From the ‡Lilly USA, Lilly Research Laboratories, Indianapolis, Indiana 46285
| | - Benjamin A Garcia
- §Epigenetics Program, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania Philadelphia, Pennsylvania 19104;
| | - Hannah Nguyen
- From the ‡Lilly USA, Lilly Research Laboratories, Indianapolis, Indiana 46285;
| |
Collapse
|
95
|
Zhang S, Yuan H, Zhao B, Zhou Y, Jiang H, Zhang L, Liang Z, Zhang Y. Integrated platform with a combination of online digestion and (18)O labeling for proteome quantification via an immobilized trypsin microreactor. Analyst 2016; 140:5227-34. [PMID: 26063120 DOI: 10.1039/c5an00887e] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
A novel automated integrated platform for quantitative proteome analysis was established with a combination of online digestion of proteins and in situ(18)O labeling by an immobilized enzyme reactor (IMER); digests were captured and desalted by a C18 trap column, and peptides were analyzed by nanoRPLC-ESI-MS/MS. Bovine serum albumin (BSA) was used to evaluate the performance of the developed platform. Compared with traditional offline methods, not only the digestion and labeling time was shortened from 36 h to just 1 h, but also the labeling efficiency was improved from 95% to 99%. Furthermore, the back-exchange from (18)O to (16)O could also be efficiently avoided by the use of IMER. The platform was further evaluated by the quantitative analysis of 100 ng (18)O and (16)O online labeled yeast sample with a mixing ratio of 1 : 1, and the results showed significantly improved sensitivity and reproducibility, as well as improved quantitative accuracy than offline method. With these advantages, the integrated platform was finally applied to the quantitative profiling of 100 ng proteins extracted from two mouse hepatocarcinoma ascites syngeneic cell lines with high and low lymph node metastases rates, and ten differentially expressed proteins were successfully found, most of which were related to tumorigenesis and tumor metastasis. All these results demonstrate that the developed integrated platform can provide a new way for high efficiency (18)O labeling and the quantitative analysis of trace amounts of sample with high accuracy and high reproducibility.
Collapse
Affiliation(s)
- Shen Zhang
- National Chromatographic Research and Analysis Center, Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, 116023, China.
| | | | | | | | | | | | | | | |
Collapse
|
96
|
Lim HJ, Kim J, Park CH, Lee SA, Lee MR, Kim KS, Kim J, Bae YS. Regulation of c-Myc Expression by Ahnak Promotes Induced Pluripotent Stem Cell Generation. J Biol Chem 2015; 291:752-61. [PMID: 26598518 DOI: 10.1074/jbc.m115.659276] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Indexed: 01/01/2023] Open
Abstract
We have previously reported that Ahnak-mediated TGFβ signaling leads to down-regulation of c-Myc expression. Here, we show that inhibition of Ahnak can promote generation of induced pluripotent stem cells (iPSC) via up-regulation of endogenous c-Myc. Consistent with the c-Myc inhibitory role of Ahnak, mouse embryonic fibroblasts from Ahnak-deficient mouse (Ahnak(-/-) MEF) show an increased level of c-Myc expression compared with wild type MEF. Generation of iPSC with just three of the four Yamanaka factors, Oct4, Sox2, and Klf4 (hereafter 3F), was significantly enhanced in Ahnak(-/-) MEF. Similar results were obtained when Ahnak-specific shRNA was applied to wild type MEF. Of note, expressionof Ahnak was significantly induced during the formation of embryoid bodies from embryonic stem cells, suggesting that Ahnak-mediated c-Myc inhibition is involved in embryoid body formation and the initial differentiation of pluripotent stem cells. The iPSC from 3F-infected Ahnak(-/-) MEF cells (Ahnak(-/-)-iPSC-3F) showed expression of all stem cell markers examined and the capability to form three primary germ layers. Moreover, injection of Ahnak(-/-)-iPSC-3F into athymic nude mice led to development of teratoma containing tissues from all three primary germ layers, indicating that iPSC from Ahnak(-/-) MEF are bona fide pluripotent stem cells. Taken together, these data provide evidence for a new role for Ahnak in cell fate determination during development and suggest that manipulation of Ahnak and the associated signaling pathway may provide a means to regulate iPSC generation.
Collapse
Affiliation(s)
- Hee Jung Lim
- From the Department of Life Sciences, Ewha Womans University, Seoul 120-750, Korea
| | - Jusong Kim
- From the Department of Life Sciences, Ewha Womans University, Seoul 120-750, Korea
| | - Chang-Hwan Park
- the Graduate School of Biomedical Science and Engineering, Department of Biomedical Science, Hanyang University, Seoul 133-791, Korea, and
| | - Sang A Lee
- the Soonchunhyang Institute of Medi-bioscience, Soon Chun Hyang University, Cheonan 31538, Korea
| | - Man Ryul Lee
- the Soonchunhyang Institute of Medi-bioscience, Soon Chun Hyang University, Cheonan 31538, Korea
| | - Kye-Seong Kim
- the Graduate School of Biomedical Science and Engineering, Department of Biomedical Science, Hanyang University, Seoul 133-791, Korea, and
| | - Jaesang Kim
- From the Department of Life Sciences, Ewha Womans University, Seoul 120-750, Korea,
| | - Yun Soo Bae
- From the Department of Life Sciences, Ewha Womans University, Seoul 120-750, Korea,
| |
Collapse
|
97
|
Shin JH, Kim IY, Kim YN, Shin SM, Roh KJ, Lee SH, Sohn M, Cho SY, Lee SH, Ko CY, Kim HS, Choi CS, Bae YS, Seong JK. Obesity Resistance and Enhanced Insulin Sensitivity in Ahnak-/- Mice Fed a High Fat Diet Are Related to Impaired Adipogenesis and Increased Energy Expenditure. PLoS One 2015; 10:e0139720. [PMID: 26466345 PMCID: PMC4605776 DOI: 10.1371/journal.pone.0139720] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 09/16/2015] [Indexed: 11/18/2022] Open
Abstract
Objective Recent evidence has suggested that AHNAK expression is altered in obesity, although its role in adipose tissue development remains unclear. The objective of this study was to determine the molecular mechanism by which Ahnak influences adipogenesis and glucose homeostasis. Design We investigated the in vitro role of AHNAK in adipogenesis using adipose-derived mesenchymal stem cells (ADSCs) and C3H10T1/2 cells. AHNAK-KO male mice were fed a high-fat diet (HFD; 60% calories from fat) and examined for glucose and insulin tolerances, for body fat compositions, and by hyperinsulinemic-euglycemic clamping. Energy expenditures were assessed using metabolic cages and by measuring the expression levels of genes involved in thermogenesis in white or brown adipose tissues. Results Adipogenesis in ADSCs was impaired in AHNAK-KO mice. The loss of AHNAK led to decreased BMP4/SMAD1 signaling, resulting in the downregulation of key regulators of adipocyte differentiation (P<0.05). AHNAK directly interacted with SMAD1 on the Pparγ2 promoter. Concomitantly, HFD-fed AHNAK-KO mice displayed reduced hepatosteatosis and improved metabolic profiles, including improved glucose tolerance (P<0.001), enhanced insulin sensitivity (P<0.001), and increased energy expenditure (P<0.05), without undergoing alterations in food intake and physical activity. Conclusion AHNAK plays a crucial role in body fat accumulation by regulating adipose tissue development via interaction with the SMAD1 protein and can be involved in metabolic homeostasis.
Collapse
Affiliation(s)
- Jae Hoon Shin
- Laboratory of Developmental Biology and Genomics, College of Veterinary Medicine, and BK21 Program for Veterinary Science, Seoul National University, Seoul, South Korea
- Korea Mouse Phenotyping Center (KMPC), Seoul National University, Seoul, South Korea
| | - Il Yong Kim
- Laboratory of Developmental Biology and Genomics, College of Veterinary Medicine, and BK21 Program for Veterinary Science, Seoul National University, Seoul, South Korea
- Korea Mouse Phenotyping Center (KMPC), Seoul National University, Seoul, South Korea
| | - Yo Na Kim
- Laboratory of Developmental Biology and Genomics, College of Veterinary Medicine, and BK21 Program for Veterinary Science, Seoul National University, Seoul, South Korea
- Korea Mouse Phenotyping Center (KMPC), Seoul National University, Seoul, South Korea
| | - Sun Mee Shin
- Division of Life Sciences, Ewha Womans University, Seoul, South Korea
| | - Kyung Jin Roh
- Lee Gil Ya Cancer and Diabetes Institute and Division of Endocrinology Gil Medical Center, Gachon University of Medicine and Science, Incheon, South Korea
| | - Seo Hyun Lee
- Laboratory of Developmental Biology and Genomics, College of Veterinary Medicine, and BK21 Program for Veterinary Science, Seoul National University, Seoul, South Korea
- Korea Mouse Phenotyping Center (KMPC), Seoul National University, Seoul, South Korea
| | - Mira Sohn
- Division of Life Sciences, Ewha Womans University, Seoul, South Korea
| | - Soo Young Cho
- Laboratory of Developmental Biology and Genomics, College of Veterinary Medicine, and BK21 Program for Veterinary Science, Seoul National University, Seoul, South Korea
- Korea Mouse Phenotyping Center (KMPC), Seoul National University, Seoul, South Korea
| | - Sang Hyuk Lee
- Ewha Research Center for Systems Biology, Ewha Womans University, Seoul, South Korea
| | - Chang-Yong Ko
- Department of Biomedical Engineering, College of Health Science, Institute of Medical Engineering, Yonsei University, Wonju, South Korea
| | - Han-Sung Kim
- Laboratory of Developmental Biology and Genomics, College of Veterinary Medicine, and BK21 Program for Veterinary Science, Seoul National University, Seoul, South Korea
- Korea Mouse Phenotyping Center (KMPC), Seoul National University, Seoul, South Korea
| | - Cheol Soo Choi
- Lee Gil Ya Cancer and Diabetes Institute and Division of Endocrinology Gil Medical Center, Gachon University of Medicine and Science, Incheon, South Korea
| | - Yun Soo Bae
- Division of Life Sciences, Ewha Womans University, Seoul, South Korea
- * E-mail: (JKS); (YSB)
| | - Je Kyung Seong
- Laboratory of Developmental Biology and Genomics, College of Veterinary Medicine, and BK21 Program for Veterinary Science, Seoul National University, Seoul, South Korea
- Korea Mouse Phenotyping Center (KMPC), Seoul National University, Seoul, South Korea
- Interdisciplinary Program for Bioinformatics, Program for Cancer Biology and BIO-MAX Institute, Seoul National University, Seoul, South Korea
- * E-mail: (JKS); (YSB)
| |
Collapse
|
98
|
Shin JH, Kim YN, Kim IY, Choi DH, Yi SS, Seong JK. Increased Cell Proliferations and Neurogenesis in the Hippocampal Dentate Gyrus of Ahnak Deficient Mice. Neurochem Res 2015; 40:1457-62. [DOI: 10.1007/s11064-015-1615-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Revised: 05/06/2015] [Accepted: 05/12/2015] [Indexed: 10/23/2022]
|