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Picard M, Scott-Boyer MP, Bodein A, Leclercq M, Prunier J, Périn O, Droit A. Target repositioning using multi-layer networks and machine learning: The case of prostate cancer. Comput Struct Biotechnol J 2024; 24:464-475. [PMID: 38983753 PMCID: PMC11231507 DOI: 10.1016/j.csbj.2024.06.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 06/10/2024] [Accepted: 06/12/2024] [Indexed: 07/11/2024] Open
Abstract
The discovery of novel therapeutic targets, defined as proteins which drugs can interact with to induce therapeutic benefits, typically represent the first and most important step of drug discovery. One solution for target discovery is target repositioning, a strategy which relies on the repurposing of known targets for new diseases, leading to new treatments, less side effects and potential drug synergies. Biological networks have emerged as powerful tools for integrating heterogeneous data and facilitating the prediction of biological or therapeutic properties. Consequently, they are widely employed to predict new therapeutic targets by characterizing potential candidates, often based on their interactions within a Protein-Protein Interaction (PPI) network, and their proximity to genes associated with the disease. However, over-reliance on PPI networks and the assumption that potential targets are necessarily near known genes can introduce biases that may limit the effectiveness of these methods. This study addresses these limitations in two ways. First, by exploiting a multi-layer network which incorporates additional information such as gene regulation, metabolite interactions, metabolic pathways, and several disease signatures such as Differentially Expressed Genes, mutated genes, Copy Number Alteration, and structural variants. Second, by extracting relevant features from the network using several approaches including proximity to disease-associated genes, but also unbiased approaches such as propagation-based methods, topological metrics, and module detection algorithms. Using prostate cancer as a case study, the best features were identified and utilized to train machine learning algorithms to predict 5 novel promising therapeutic targets for prostate cancer: IGF2R, C5AR, RAB7, SETD2 and NPBWR1.
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Affiliation(s)
- Milan Picard
- Molecular Medicine Department, CHU de Québec Research Center, Université Laval, Québec, QC, Canada
| | - Marie-Pier Scott-Boyer
- Molecular Medicine Department, CHU de Québec Research Center, Université Laval, Québec, QC, Canada
| | - Antoine Bodein
- Molecular Medicine Department, CHU de Québec Research Center, Université Laval, Québec, QC, Canada
| | - Mickaël Leclercq
- Molecular Medicine Department, CHU de Québec Research Center, Université Laval, Québec, QC, Canada
| | - Julien Prunier
- Molecular Medicine Department, CHU de Québec Research Center, Université Laval, Québec, QC, Canada
| | - Olivier Périn
- Digital Transformation and Innovation Department, L'Oréal Advanced Research, Aulnay-sous-bois, France
| | - Arnaud Droit
- Molecular Medicine Department, CHU de Québec Research Center, Université Laval, Québec, QC, Canada
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2
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Chen N, Xia X, Hanif Q, Zhang F, Dang R, Huang B, Lyu Y, Luo X, Zhang H, Yan H, Wang S, Wang F, Chen J, Guan X, Liu Y, Li S, Jin L, Wang P, Sun L, Zhang J, Liu J, Qu K, Cao Y, Sun J, Liao Y, Xiao Z, Cai M, Mu L, Siddiki AZ, Asif M, Mansoor S, Babar ME, Hussain T, Silva GLLP, Gorkhali NA, Terefe E, Belay G, Tijjani A, Zegeye T, Gebre MG, Ma Y, Wang Y, Huang Y, Lan X, Chen H, Migliore NR, Colombo G, Semino O, Achilli A, Sinding MHS, Lenstra JA, Cheng H, Lu W, Hanotte O, Han J, Jiang Y, Lei C. Global genetic diversity, introgression, and evolutionary adaptation of indicine cattle revealed by whole genome sequencing. Nat Commun 2023; 14:7803. [PMID: 38016956 PMCID: PMC10684552 DOI: 10.1038/s41467-023-43626-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 11/14/2023] [Indexed: 11/30/2023] Open
Abstract
Indicine cattle, also referred to as zebu (Bos taurus indicus), play a central role in pastoral communities across a wide range of agro-ecosystems, from extremely hot semiarid regions to hot humid tropical regions. However, their adaptive genetic changes following their dispersal into East Asia from the Indian subcontinent have remained poorly documented. Here, we characterize their global genetic diversity using high-quality whole-genome sequencing data from 354 indicine cattle of 57 breeds/populations, including major indicine phylogeographic groups worldwide. We reveal their probable migration into East Asia was along a coastal route rather than inland routes and we detected introgression from other bovine species. Genomic regions carrying morphology-, immune-, and heat-tolerance-related genes underwent divergent selection according to Asian agro-ecologies. We identify distinct sets of loci that contain promising candidate variants for adaptation to hot semi-arid and hot humid tropical ecosystems. Our results indicate that the rapid and successful adaptation of East Asian indicine cattle to hot humid environments was promoted by localized introgression from banteng and/or gaur. Our findings provide insights into the history and environmental adaptation of indicine cattle.
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Affiliation(s)
- Ningbo Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Xiaoting Xia
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Quratulain Hanif
- National Institute for Biotechnology and Genetic Engineering, Faisalabad, 38000, Pakistan
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), 100193, Beijing, China
| | - Fengwei Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Ruihua Dang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Bizhi Huang
- Yunnan Academy of Grassland and Animal Science, Kunming, 650212, China
| | - Yang Lyu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Xiaoyu Luo
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Hucai Zhang
- Institute for Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environment Science, Yunnan University, Kunming, 650500, China
| | - Huixuan Yan
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Shikang Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Fuwen Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Jialei Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Xiwen Guan
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Yangkai Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Shuang Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Liangliang Jin
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Pengfei Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Luyang Sun
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Jicai Zhang
- Yunnan Academy of Grassland and Animal Science, Kunming, 650212, China
| | - Jianyong Liu
- Yunnan Academy of Grassland and Animal Science, Kunming, 650212, China
| | - Kaixing Qu
- Academy of Science and Technology, Chuxiong Normal University, Chuxiong, 675000, China
| | - Yanhong Cao
- Guangxi Vocational University of Agriculture, Nanning, 530007, China
| | - Junli Sun
- Guangxi Vocational University of Agriculture, Nanning, 530007, China
| | - Yuying Liao
- Guangxi Veterinary Research Institute, Guangxi Key Laboratory of Veterinary Biotechnology, Nanning, 530001, China
| | - Zhengzhong Xiao
- Guangxi Vocational University of Agriculture, Nanning, 530007, China
| | - Ming Cai
- Yunnan Academy of Grassland and Animal Science, Kunming, 650212, China
| | - Lan Mu
- College of Landscape and Horticulture, Southwest Forestry University, Kunming, 650224, China
| | - Amam Zonaed Siddiki
- Genomics Research Group, Department of Pathology and Parasitology, Faculty of Veterinary Medicine, Chattogram Veterinary and Animal Sciences University (CVASU), Chattogram, 4225, Bangladesh
| | - Muhammad Asif
- National Institute for Biotechnology and Genetic Engineering, Faisalabad, 38000, Pakistan
| | - Shahid Mansoor
- National Institute for Biotechnology and Genetic Engineering, Faisalabad, 38000, Pakistan
| | - Masroor Ellahi Babar
- The University of Agriculture, Dera Ismail Khan, Khyber Pakhtunkhwa, 29050, Pakistan
| | - Tanveer Hussain
- Department of Molecular Biology, Virtual University of Pakistan, Islamabad, 44100, Pakistan
| | | | - Neena Amatya Gorkhali
- National Animal Breeding and Genetics Centre, National Animal Science Research Institute, Nepal Agriculture Research Council, Khumaltar, Lalitpur, 45200, Nepal
| | - Endashaw Terefe
- College of Agriculture and Environmental Science, Department of Animal Science, Arsi University, Asella, Ethiopia
- International Livestock Research Institute (ILRI), P.O. Box 5689, 1000, Addis Ababa, Ethiopia
| | - Gurja Belay
- College of Natural and Computational Sciences, The School of Graduate Studies, Addis Ababa University, 1000, Addis Ababa, Ethiopia
| | - Abdulfatai Tijjani
- International Livestock Research Institute (ILRI), P.O. Box 5689, 1000, Addis Ababa, Ethiopia
- The Jackson Laboratory, Bar Harbor, ME, 04609, USA
| | - Tsadkan Zegeye
- Mekelle Agricultural Research Center, P.O. Box 258, 7000, Mekelle, Tigray, Ethiopia
| | - Mebrate Genet Gebre
- School of Animal and Rangeland Science, College of Agriculture, Haramaya University, 2040, Haramaya, Oromia, Ethiopia
| | - Yun Ma
- Key Laboratory of Ruminant Molecular and Cellular Breeding of Ningxia Hui Autonomous Region, School of Agriculture, Ningxia University, Yinchuan, 750000, China
| | - Yu Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Yongzhen Huang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Xianyong Lan
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Hong Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Nicola Rambaldi Migliore
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, 27100, Pavia, Italy
| | - Giulia Colombo
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, 27100, Pavia, Italy
| | - Ornella Semino
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, 27100, Pavia, Italy
| | - Alessandro Achilli
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, 27100, Pavia, Italy
| | - Mikkel-Holger S Sinding
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, DK-1350, Copenhagen, Denmark
| | - Johannes A Lenstra
- Faculty of Veterinary Medicine, Utrecht University, 3584 CM, Utrecht, The Netherlands
| | - Haijian Cheng
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Shandong Key Lab of Animal Disease Control and Breeding, Jinan, 250100, China
| | - Wenfa Lu
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, 130118, China
| | - Olivier Hanotte
- International Livestock Research Institute (ILRI), P.O. Box 5689, 1000, Addis Ababa, Ethiopia.
- School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK.
| | - Jianlin Han
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), 100193, Beijing, China.
- Livestock Genetics Program, International Livestock Research Institute (ILRI), 00100, Nairobi, Kenya.
- Yazhouwan National Laboratory, Sanya, 572024, China.
| | - Yu Jiang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China.
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, 712100, China.
| | - Chuzhao Lei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China.
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Combination Analysis of Ferroptosis and Immune Status Predicts Patients Survival in Breast Invasive Ductal Carcinoma. Biomolecules 2023; 13:biom13010147. [PMID: 36671532 PMCID: PMC9855618 DOI: 10.3390/biom13010147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 01/01/2023] [Accepted: 01/06/2023] [Indexed: 01/13/2023] Open
Abstract
Ferroptosis is a new form of iron-dependent cell death and plays an important role during the occurrence and development of various tumors. Increasingly, evidence shows a convincing interaction between ferroptosis and tumor immunity, which affects cancer patients' prognoses. These two processes cooperatively regulate different developmental stages of tumors and could be considered important tumor therapeutic targets. However, reliable prognostic markers screened based on the combination of ferroptosis and tumor immune status have not been well characterized. Here, we chose the ssGSEA and ESTIMATE algorithms to evaluate the ferroptosis and immune status of a TCGA breast invasive ductal carcinoma (IDC) cohort, which revealed their correlation characteristics as well as patients' prognoses. The WGCNA algorithm was used to identify genes related to both ferroptosis and immunity. Univariate COX, LASSO regression, and multivariate Cox regression models were used to screen prognostic-related genes and construct prognostic risk models. Based on the ferroptosis and immune scores, the cohort was divided into three groups: a high-ferroptosis/low-immune group, a low-ferroptosis/high-immune group, and a mixed group. These three groups exhibited distinctive survival characteristics, as well as unique clinical phenotypes, immune characteristics, and activated signaling pathways. Among them, low-ferroptosis and high-immune statuses were favorable factors for the survival rates of patients. A total of 34 differentially expressed genes related to ferroptosis-immunity were identified among the three groups. After univariate, Lasso regression, and multivariate stepwise screening, two key prognostic genes (GNAI2, PSME1) were identified. Meanwhile, a risk prognosis model was constructed, which can predict the overall survival rate in the validation set. Lastly, we verified the importance of model genes in three independent GEO cohorts. In short, we constructed a prognostic model that assists in patient risk stratification based on ferroptosis-immune-related genes in IDC. This model helps assess patients' prognoses and guide individualized treatment, which also further eelucidatesthe molecular mechanisms of IDC.
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Yu H, Liu S, Wu Z, Gao F. GNAI2 Is a Risk Factor for Gastric Cancer: Study of Tumor Microenvironment (TME) and Establishment of Immune Risk Score (IRS). OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:1254367. [PMID: 36275898 PMCID: PMC9586761 DOI: 10.1155/2022/1254367] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 08/30/2022] [Indexed: 11/18/2022]
Abstract
Purpose Although the G protein subunit α i2 (GNAI2) is upregulated in multiple cancers, its prognostic value and exact role in the development of gastric cancer (GC) remain largely unknown. Methods This study evaluated the effect of GNAI2 on the tumor microenvironment (TME) in GC, constructed an immune risk score (IRS) model based on differentially-expressed immune genes, and systematically correlated GNAI2 and epigenetic factor expression patterns with TME and IRS. Also, RT-qPCR, flow cytometry, Western blotting (WB), and transwell assays were carried out to explore the regulatory mechanism of GNAI2 in GC. Results High GNAI2 expression was associated with poor prognosis. Cytokine activation, an increase in tumor-infiltrating immune cells (TIIC), and the accumulation of regulatory T cells in the tumor immune cycle were all promoted by the TME, which was significantly associated with GNAI2 expression. Two different differentially expressed mRNA (DER) modification patterns were determined. These two DERs-clusters had significantly different TME cell infiltrations and were classified as either noninflamed or immune-inflamed phenotypes. The IRS model constructed using differentially expressed genes (DEGs) had great potential in predicting GC prognosis. The IRS model was also used in assessing clinicopathological features, such as microsatellite instability (MSI) status, epithelial-mesenchymal transition (EMT) status, clinical stages, tumor mutational burden (TMB), and tumor immune dysfunction and exclusion (TIDE) scores. Low IRS scores were associated with high immune checkpoint gene expression. Cell and animal studies confirmed that GNAI2 activated PI3K/AKT pathway and promoted the growth and migration of GC cells. Conclusion The IRS model can be used for survival prediction and GNAI2 serves as a candidate therapeutic target for GC patients.
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Affiliation(s)
- Han Yu
- Meizhou People's Hospital, Huangtang Road, Meijiang District, Meizhou, 514031 Guangdong Province, China
| | - Sha Liu
- Meizhou People's Hospital, Huangtang Road, Meijiang District, Meizhou, 514031 Guangdong Province, China
| | - ZuGuang Wu
- Meizhou People's Hospital, Huangtang Road, Meijiang District, Meizhou, 514031 Guangdong Province, China
| | - FenFei Gao
- School of Pharmacology, Shantou University, 22 Xinling Road, Shantou, 515063 Guangdong Province, China
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Gohar J, Do WL, Miller-Kleinhenz J, Conneely K, Krishnamurti U, D'Angelo O, Gogineni K, Torres M, Gabram-Mendola S, McCullough LE. Neighborhood characteristics and breast tumor methylation: using epigenomics to explore cancer outcome disparities. Breast Cancer Res Treat 2022; 191:653-663. [PMID: 34978015 DOI: 10.1007/s10549-021-06430-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 10/15/2021] [Indexed: 02/06/2023]
Abstract
BACKGROUND Social exposures may drive epigenetic alterations that affect racial disparities in breast cancer outcomes. This study examined the association between neighborhood-level factors and DNA methylation in non-Hispanic Black and White women diagnosed with breast cancer. METHODS Genome-wide DNA methylation was measured using the EPIC array in the tumor tissue of 96 women. Linear regression models were used to examine the association between nine neighborhood-level factors and methylation, regressing β values for each cytosine-phosphate guanine dinucleotide (CpG) site on neighborhood-level factors while adjusting for covariates. Neighborhood data were obtained from the Opportunity Atlas. We used a false discovery rate (FDR) threshold < 0.05, and for CpGs below this threshold, we examined interactions with race. We employed multivariable Cox proportional-hazards models to estimate whether aberrant methylation was associated with all-cause mortality. RESULTS 26 of the CpG sites were associated with job density or college education (FDR < 0.05). Further exploration of these 26 CpG sites revealed no interactions by race, but a single probe in TMEM204 was associated with all-cause mortality. CONCLUSION We identified novel associations between neighborhood-level factors and the breast tumor DNA methylome. Our data are the first to show that dysregulation in neighborhood associated CpG sites may be associated with all-cause mortality. Neighborhood-level factors may contribute to differential tumor methylation in genes related to tumor progression and metastasis. This contributes to the increasing body of evidence that area-level factors (such as neighborhood characteristics) may play an important role in cancer disparities through modulation of the breast tumor epigenome.
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Affiliation(s)
- Jazib Gohar
- Department of Epidemiology, Emory University Rollins School of Public Health, Atlanta, GA, 30322, USA
| | - Whitney L Do
- Department of Global Health, Emory University Rollins School of Public Health, Atlanta, GA, 30322, USA
| | - Jasmine Miller-Kleinhenz
- Department of Epidemiology, Emory University Rollins School of Public Health, Atlanta, GA, 30322, USA
| | - Karen Conneely
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Uma Krishnamurti
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Olivia D'Angelo
- Department of Surgery, Jackson Memorial Hospital/University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Keerthi Gogineni
- Department of Medical Oncology, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Mylin Torres
- Department of Radiation Oncology, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | | | - Lauren E McCullough
- Department of Epidemiology, Emory University Rollins School of Public Health, Atlanta, GA, 30322, USA.
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Ding S, Li H, Zhang YH, Zhou X, Feng K, Li Z, Chen L, Huang T, Cai YD. Identification of Pan-Cancer Biomarkers Based on the Gene Expression Profiles of Cancer Cell Lines. Front Cell Dev Biol 2021; 9:781285. [PMID: 34917619 PMCID: PMC8669964 DOI: 10.3389/fcell.2021.781285] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 11/16/2021] [Indexed: 12/12/2022] Open
Abstract
There are many types of cancers. Although they share some hallmarks, such as proliferation and metastasis, they are still very different from many perspectives. They grow on different organ or tissues. Does each cancer have a unique gene expression pattern that makes it different from other cancer types? After the Cancer Genome Atlas (TCGA) project, there are more and more pan-cancer studies. Researchers want to get robust gene expression signature from pan-cancer patients. But there is large variance in cancer patients due to heterogeneity. To get robust results, the sample size will be too large to recruit. In this study, we tried another approach to get robust pan-cancer biomarkers by using the cell line data to reduce the variance. We applied several advanced computational methods to analyze the Cancer Cell Line Encyclopedia (CCLE) gene expression profiles which included 988 cell lines from 20 cancer types. Two feature selection methods, including Boruta, and max-relevance and min-redundancy methods, were applied to the cell line gene expression data one by one, generating a feature list. Such list was fed into incremental feature selection method, incorporating one classification algorithm, to extract biomarkers, construct optimal classifiers and decision rules. The optimal classifiers provided good performance, which can be useful tools to identify cell lines from different cancer types, whereas the biomarkers (e.g. NCKAP1, TNFRSF12A, LAMB2, FKBP9, PFN2, TOM1L1) and rules identified in this work may provide a meaningful and precise reference for differentiating multiple types of cancer and contribute to the personalized treatment of tumors.
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Affiliation(s)
- ShiJian Ding
- School of Life Sciences, Shanghai University, Shanghai, China
| | - Hao Li
- College of Food Engineering, Jilin Engineering Normal University, Changchun, China
| | - Yu-Hang Zhang
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, United States
| | - XianChao Zhou
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - KaiYan Feng
- Department of Computer Science, Guangdong AIB Polytechnic College, Guangzhou, China
| | - ZhanDong Li
- College of Food Engineering, Jilin Engineering Normal University, Changchun, China
| | - Lei Chen
- College of Information Engineering, Shanghai Maritime University, Shanghai, China
| | - Tao Huang
- CAS Key Laboratory of Computational Biology, Bio-Med Big Data Center, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.,CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yu-Dong Cai
- School of Life Sciences, Shanghai University, Shanghai, China
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Osan C, Chira S, Nutu AM, Braicu C, Baciut M, Korban SS, Berindan-Neagoe I. The Connection between MicroRNAs and Oral Cancer Pathogenesis: Emerging Biomarkers in Oral Cancer Management. Genes (Basel) 2021; 12:genes12121989. [PMID: 34946938 PMCID: PMC8700798 DOI: 10.3390/genes12121989] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 12/09/2021] [Accepted: 12/13/2021] [Indexed: 02/06/2023] Open
Abstract
Oral cancer is a common human malignancy that still maintains an elevated mortality rate despite scientific progress. Tumorigenesis is driven by altered gene expression patterns of proto-oncogenes and tumor-suppressor genes. MicroRNAs, a class of short non-coding RNAs involved in gene regulation, seem to play important roles in oral cancer development, progression, and tumor microenvironment modulation. As properties of microRNAs render them stable in diverse liquid biopsies, together with their differential expression signature in cancer cells, these features place microRNAs at the top of promising biomarkers for diagnostic and prognostic values. In this review, we highlight eight expression levels and functions of the most relevant microRNAs involved in oral cancer development, progression, and microenvironment sustainability. Furthermore, we emphasize the potential of using these small RNA species as non-invasive biomarkers for the early detection of oral cancerous lesions. Conclusively, we highlight the perspectives and limitations of microRNAs as novel diagnostic tools, as well as therapeutic models.
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Affiliation(s)
- Ciprian Osan
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, “Iuliu Hatieganu” University of Medicine and Pharmacy, 400337 Cluj-Napoca, Romania; (C.O.); (S.C.); (A.M.N.); (C.B.)
| | - Sergiu Chira
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, “Iuliu Hatieganu” University of Medicine and Pharmacy, 400337 Cluj-Napoca, Romania; (C.O.); (S.C.); (A.M.N.); (C.B.)
| | - Andreea Mihaela Nutu
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, “Iuliu Hatieganu” University of Medicine and Pharmacy, 400337 Cluj-Napoca, Romania; (C.O.); (S.C.); (A.M.N.); (C.B.)
| | - Cornelia Braicu
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, “Iuliu Hatieganu” University of Medicine and Pharmacy, 400337 Cluj-Napoca, Romania; (C.O.); (S.C.); (A.M.N.); (C.B.)
| | - Mihaela Baciut
- Department of Maxillofacial Surgery and Implantology, “Iuliu Hatieganu” University of Medicine and Pharmacy, 400033 Cluj-Napoca, Romania;
| | - Schuyler S. Korban
- Department of Natural Resources & Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA;
| | - Ioana Berindan-Neagoe
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, “Iuliu Hatieganu” University of Medicine and Pharmacy, 400337 Cluj-Napoca, Romania; (C.O.); (S.C.); (A.M.N.); (C.B.)
- Correspondence:
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GNAi2/gip2-Regulated Transcriptome and Its Therapeutic Significance in Ovarian Cancer. Biomolecules 2021; 11:biom11081211. [PMID: 34439877 PMCID: PMC8393559 DOI: 10.3390/biom11081211] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 08/10/2021] [Accepted: 08/11/2021] [Indexed: 12/20/2022] Open
Abstract
Increased expression of GNAi2, which encodes the α-subunit of G-protein i2, has been correlated with the late-stage progression of ovarian cancer. GNAi2, also referred to as the proto-oncogene gip2, transduces signals from lysophosphatidic acid (LPA)-activated LPA-receptors to oncogenic cellular responses in ovarian cancer cells. To identify the oncogenic program activated by gip2, we carried out micro-array-based transcriptomic and bioinformatic analyses using the ovarian cancer cell-line SKOV3, in which the expression of GNAi2/gip2 was silenced by specific shRNA. A cut-off value of 5-fold change in gene expression (p < 0.05) indicated that a total of 264 genes were dependent upon gip2-expression with 136 genes coding for functional proteins. Functional annotation of the transcriptome indicated the hitherto unknown role of gip2 in stimulating the expression of oncogenic/growth-promoting genes such as KDR/VEGFR2, CCL20, and VIP. The array results were further validated in a panel of High-Grade Serous Ovarian Carcinoma (HGSOC) cell lines that included Kuramochi, OVCAR3, and OVCAR8 cells. Gene set enrichment analyses using DAVID, STRING, and Cytoscape applications indicated the potential role of the gip2-stimulated transcriptomic network involved in the upregulation of cell proliferation, adhesion, migration, cellular metabolism, and therapy resistance. The results unravel a multi-modular network in which the hub and bottleneck nodes are defined by ACKR3/CXCR7, IL6, VEGFA, CYCS, COX5B, UQCRC1, UQCRFS1, and FYN. The identification of these genes as the critical nodes in GNAi2/gip2 orchestrated onco-transcriptome establishes their role in ovarian cancer pathophysiology. In addition, these results also point to these nodes as potential targets for novel therapeutic strategies.
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9
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Comprehensive characterization of protein-protein interactions perturbed by disease mutations. Nat Genet 2021; 53:342-353. [PMID: 33558758 DOI: 10.1038/s41588-020-00774-y] [Citation(s) in RCA: 97] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 12/22/2020] [Indexed: 02/07/2023]
Abstract
Technological and computational advances in genomics and interactomics have made it possible to identify how disease mutations perturb protein-protein interaction (PPI) networks within human cells. Here, we show that disease-associated germline variants are significantly enriched in sequences encoding PPI interfaces compared to variants identified in healthy participants from the projects 1000 Genomes and ExAC. Somatic missense mutations are also significantly enriched in PPI interfaces compared to noninterfaces in 10,861 tumor exomes. We computationally identified 470 putative oncoPPIs in a pan-cancer analysis and demonstrate that oncoPPIs are highly correlated with patient survival and drug resistance/sensitivity. We experimentally validate the network effects of 13 oncoPPIs using a systematic binary interaction assay, and also demonstrate the functional consequences of two of these on tumor cell growth. In summary, this human interactome network framework provides a powerful tool for prioritization of alleles with PPI-perturbing mutations to inform pathobiological mechanism- and genotype-based therapeutic discovery.
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10
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Wei J, Xie Q, Liu X, Wan C, Wu W, Fang K, Yao Y, Cheng P, Deng D, Liu Z. Identification the prognostic value of glutathione peroxidases expression levels in acute myeloid leukemia. ANNALS OF TRANSLATIONAL MEDICINE 2020; 8:678. [PMID: 32617298 PMCID: PMC7327321 DOI: 10.21037/atm-20-3296] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Background Glutathione peroxidases (GPXs) are an enzyme family with peroxidase activity. Abnormal GPX expression is associated with carcinogenesis. However, the potential role of the GPX gene family in acute myeloid leukemia (AML) remains to be comprehensively examined. Methods We analyzed GPX mRNA expression levels and determined the correlation between gene expression and the prognostic value via multiple universally acknowledged databases including the Oncomine, Gene Expression Profiling Interactive Analysis (GEPIA), PROGgeneV2, UALCAN, Cancer Cell Line Encyclopedia (CCLE), and The European Bioinformatics Institute (EMBL-EBI) databases. The functional network of differentially expressed GPXs was investigated via the NetworkAnalyst platform. Correlated genes as well as kinase, microRNA (miRNA), and transcription factor (TF) targets were identified using LinkedOmics. Results We observed that the transcriptional expression levels of GPX-1, -2, -4, -7, and -8 had significant difference between AML patients samples and normal samples, and that AML patients with high expression of GPX-1, -3, -4, and -7 were associated with poorer prognosis of overall survival (OS). Functional enrichment analysis showed that the differentially expressed GPXs were mainly enriched in response to oxidative stress, regulation of immune response, and inflammatory response, along with glutathione metabolism and ferroptosis. Overexpression of correlated genes, PSMB10, VPS13D, NDUFS8, ATP5D, POLR2E, and HADH were linked to adverse OS in AML. Regulatory network analysis indicated that differentially expressed GPXs regulated cell proliferation, cancer progression, apoptosis, and cell cycle signaling via pathways involving cancer-related kinases (such as DAPK1 and SRC), miRNAs (such as miR-202 and miR-181), and TFs (such as SRF and E2F1). Conclusions Our findings offer novel insights into the differential expression and prognostic potential of the GPX family in AML, and lay a foundation for subsequent research of GPX’s role in the carcinogenesis and regulatory network of AML.
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Affiliation(s)
- Jie Wei
- Department of Hematology, the First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Qiongni Xie
- Department of Hematology, the First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Xinran Liu
- Department of Hematology, the First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Chengyao Wan
- Department of Hematology, the First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Wenqi Wu
- Department of Hematology, the First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Kuiyan Fang
- Department of Hematology, the First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Yibin Yao
- Department of Hematology, the First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Peng Cheng
- Department of Hematology, the First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Donghong Deng
- Department of Hematology, the First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Zhenfang Liu
- Department of Hematology, the First Affiliated Hospital of Guangxi Medical University, Nanning, China
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11
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Tsay HC, Yuan Q, Balakrishnan A, Kaiser M, Möbus S, Kozdrowska E, Farid M, Tegtmeyer PK, Borst K, Vondran FWR, Kalinke U, Kispert A, Manns MP, Ott M, Sharma AD. Hepatocyte-specific suppression of microRNA-221-3p mitigates liver fibrosis. J Hepatol 2019; 70:722-734. [PMID: 30582979 DOI: 10.1016/j.jhep.2018.12.016] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 12/02/2018] [Accepted: 12/10/2018] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS Fibrosis, a cardinal feature of a dysfunctional liver, significantly contributes to the ever-increasing mortality due to end-stage chronic liver diseases. The crosstalk between hepatocytes and hepatic stellate cells (HSCs) plays a key role in the progression of fibrosis. Although ample efforts have been devoted to elucidate the functions of HSCs during liver fibrosis, the regulatory functions of hepatocytes remain elusive. METHODS Using an unbiased functional microRNA (miRNA) screening, we investigated the ability of hepatocytes to regulate fibrosis by fine-tuning gene expression via miRNA modulation. The in vivo functional analyses were performed by inhibiting miRNA in hepatocytes using adeno-associated virus in carbon-tetrachloride- and 3,5-di-diethoxycarbonyl-1,4-dihydrocollidine-induced liver fibrosis. RESULTS Blocking miRNA-221-3p function in hepatocytes during chronic liver injury facilitated recovery of the liver and faster resolution of the deposited extracellular matrix. Furthermore, we demonstrate that reduced secretion of C-C motif chemokine ligand 2, as a result of post-transcriptional regulation of GNAI2 (G protein alpha inhibiting activity polypeptide 2) by miRNA-221-3p, mitigates liver fibrosis. CONCLUSIONS Collectively, miRNA modulation in hepatocytes, an easy-to-target cell type in the liver, may serve as a potential therapeutic approach for liver fibrosis. LAY SUMMARY Liver fibrosis majorly contributes to mortality resulting from various liver diseases. We discovered a small RNA known as miRNA-221-3p, whose downregulation in hepatocytes results in reduced liver fibrosis. Thus, inhibition of miRNA-221-3p may serve as one of the therapeutic approaches for treatment of liver fibrosis.
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Affiliation(s)
- Hsin-Chieh Tsay
- Research Group MicroRNA in Liver Regeneration, Cluster of Excellence REBIRTH, Hannover Medical School, Hannover, Germany; Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover, Germany; TWINCORE, Centre for Experimental and Clinical Infection Research, Hannover, Germany
| | - Qinggong Yuan
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover, Germany; TWINCORE, Centre for Experimental and Clinical Infection Research, Hannover, Germany
| | - Asha Balakrishnan
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover, Germany; TWINCORE, Centre for Experimental and Clinical Infection Research, Hannover, Germany
| | - Marina Kaiser
- Institute for Molecular Biology, Hannover Medical School, Hannover, Germany
| | - Selina Möbus
- Research Group MicroRNA in Liver Regeneration, Cluster of Excellence REBIRTH, Hannover Medical School, Hannover, Germany; Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover, Germany
| | - Emilia Kozdrowska
- Research Group MicroRNA in Liver Regeneration, Cluster of Excellence REBIRTH, Hannover Medical School, Hannover, Germany; Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover, Germany
| | - Marwa Farid
- Research Group MicroRNA in Liver Regeneration, Cluster of Excellence REBIRTH, Hannover Medical School, Hannover, Germany; Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover, Germany; TWINCORE, Centre for Experimental and Clinical Infection Research, Hannover, Germany; Human Cytogenetics Department, Human Genetics and Genome Research Division, National Research Centre, Cairo, Egypt
| | - Pia-Katharina Tegtmeyer
- TWINCORE, Centre for Experimental and Clinical Infection Research, Hannover, Germany; Institute for Experimental Infection Research, TWINCORE, Centre for Experimental and Clinical Infection Research, A joint venture between the Helmholtz Centre for Infection Research and the Hannover Medical School, Hannover, Germany
| | - Katharina Borst
- TWINCORE, Centre for Experimental and Clinical Infection Research, Hannover, Germany; Institute for Experimental Infection Research, TWINCORE, Centre for Experimental and Clinical Infection Research, A joint venture between the Helmholtz Centre for Infection Research and the Hannover Medical School, Hannover, Germany
| | - Florian W R Vondran
- Regenerative Medicine and Experimental Surgery (RedMediES), Department of General, Visceral and Transplant Surgery, Hannover Medical School, Hannover, Germany; German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Hannover, Germany
| | - Ulrich Kalinke
- TWINCORE, Centre for Experimental and Clinical Infection Research, Hannover, Germany; Institute for Experimental Infection Research, TWINCORE, Centre for Experimental and Clinical Infection Research, A joint venture between the Helmholtz Centre for Infection Research and the Hannover Medical School, Hannover, Germany
| | - Andreas Kispert
- Institute for Molecular Biology, Hannover Medical School, Hannover, Germany
| | - Michael P Manns
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover, Germany
| | - Michael Ott
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover, Germany; TWINCORE, Centre for Experimental and Clinical Infection Research, Hannover, Germany.
| | - Amar Deep Sharma
- Research Group MicroRNA in Liver Regeneration, Cluster of Excellence REBIRTH, Hannover Medical School, Hannover, Germany; Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover, Germany.
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12
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Ha JH, Ward JD, Radhakrishnan R, Jayaraman M, Song YS, Dhanasekaran DN. Lysophosphatidic acid stimulates epithelial to mesenchymal transition marker Slug/Snail2 in ovarian cancer cells via Gαi2, Src, and HIF1α signaling nexus. Oncotarget 2018; 7:37664-37679. [PMID: 27166196 PMCID: PMC5122340 DOI: 10.18632/oncotarget.9224] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Accepted: 04/19/2016] [Indexed: 12/18/2022] Open
Abstract
Recent studies have identified a critical role for lysophosphatidic acid (LPA) in the progression of ovarian cancer. Using a transcription factor activation reporter array, which analyzes 45 distinct transcription factors, it has been observed that LPA observed robustly activates the transcription factor hypoxia-induced factor-1α (HIF1α) in SKOV3.ip ovarian cancer cells. HIF1α showed 150-fold increase in its activation profile compared to the untreated control. Validation of the array analysis indicated that LPA stimulates a rapid increase in the levels of HIF1α in ovarian cancer cells, with an observed maximum level of HIF1α-induction by 4 hours. Our report demonstrates that LPA stimulates the increase in HIF1α levels via Gαi2. Consistent with the role of HIF1α in epithelial to mesenchymal transition (EMT) of cancer cells, LPA stimulates EMT and associated invasive cell migration along with an increase in the expression levels N-cadherin and Slug/Snail2. Using the expression of Slug/Snail2 as a marker for EMT, we demonstrate that the inhibition of Gαi2, HIF1α or Src attenuates this response. In line with the established role of EMT in promoting invasive cell migration, our data demonstrates that the inhibition of HIF1α with the clinically used HIF1α inhibitor, PX-478, drastically attenuates LPA-stimulates invasive migration of SKOV3.ip cells. Thus, our present study demonstrates that LPA utilizes a Gαi2-mediated signaling pathway via Src kinase to stimulate an increase in HIF1α levels and downstream EMT-specific factors such as Slug, leading to invasive migration of ovarian cancer cells.
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Affiliation(s)
- Ji Hee Ha
- Stephenson Cancer Center, The University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA.,Department of Cell Biology, The University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - Jeremy D Ward
- Department of Cell Biology, The University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | | | - Muralidharan Jayaraman
- Stephenson Cancer Center, The University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA.,Department of Cell Biology, The University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - Yong Sang Song
- Cancer Research Institute, Seoul National University, Seoul, Korea
| | - Danny N Dhanasekaran
- Stephenson Cancer Center, The University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA.,Department of Cell Biology, The University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
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13
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Palaniappan A, Ramar K, Ramalingam S. Computational Identification of Novel Stage-Specific Biomarkers in Colorectal Cancer Progression. PLoS One 2016; 11:e0156665. [PMID: 27243824 PMCID: PMC4887059 DOI: 10.1371/journal.pone.0156665] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Accepted: 05/17/2016] [Indexed: 12/19/2022] Open
Abstract
It is well-known that the conversion of normal colon epithelium to adenoma and then to carcinoma stems from acquired molecular changes in the genome. The genetic basis of colorectal cancer has been elucidated to a certain extent, and much remains to be known about the identity of specific cancer genes that are associated with the advancement of colorectal cancer from one stage to the next. Here in this study we attempted to identify novel cancer genes that could underlie the stage-specific progression and metastasis of colorectal cancer. We conducted a stage-based meta-analysis of the voluminous tumor genome-sequencing data and mined using multiple approaches for novel genes driving the progression to stage-II, stage-III and stage-IV colorectal cancer. The consensus of these driver genes seeded the construction of stage-specific networks, which were then analyzed for the centrality of genes, clustering of subnetworks, and enrichment of gene-ontology processes. Our study identified three novel driver genes as hubs for stage-II progression: DYNC1H1, GRIN2A, GRM1. Four novel driver genes were identified as hubs for stage-III progression: IGF1R, CPS1, SPTA1, DSP. Three novel driver genes were identified as hubs for stage-IV progression: GSK3B, GGT1, EIF2B5. We also identified several non-driver genes that appeared to underscore the progression of colorectal cancer. Our study yielded potential diagnostic biomarkers for colorectal cancer as well as novel stage-specific drug targets for rational intervention. Our methodology is extendable to the analysis of other types of cancer to fill the gaps in our knowledge.
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Affiliation(s)
- Ashok Palaniappan
- Faculty of Allied Health Sciences, Chettinad Academy of Research and Education, Kelambakkam, Tamil Nadu 603103, India
- * E-mail:
| | - Karthick Ramar
- Faculty of Allied Health Sciences, Chettinad Academy of Research and Education, Kelambakkam, Tamil Nadu 603103, India
| | - Satish Ramalingam
- Faculty of Allied Health Sciences, Chettinad Academy of Research and Education, Kelambakkam, Tamil Nadu 603103, India
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14
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van Unen J, Stumpf AD, Schmid B, Reinhard NR, Hordijk PL, Hoffmann C, Gadella TWJ, Goedhart J. A New Generation of FRET Sensors for Robust Measurement of Gαi1, Gαi2 and Gαi3 Activation Kinetics in Single Cells. PLoS One 2016; 11:e0146789. [PMID: 26799488 PMCID: PMC4723041 DOI: 10.1371/journal.pone.0146789] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Accepted: 12/22/2015] [Indexed: 01/14/2023] Open
Abstract
G-protein coupled receptors (GPCRs) can activate a heterotrimeric G-protein complex with subsecond kinetics. Genetically encoded biosensors based on Förster resonance energy transfer (FRET) are ideally suited for the study of such fast signaling events in single living cells. Here we report on the construction and characterization of three FRET biosensors for the measurement of Gαi1, Gαi2 and Gαi3 activation. To enable quantitative long-term imaging of FRET biosensors with high dynamic range, fluorescent proteins with enhanced photophysical properties are required. Therefore, we use the currently brightest and most photostable CFP variant, mTurquoise2, as donor fused to Gαi subunit, and cp173Venus fused to the Gγ2 subunit as acceptor. The Gαi FRET biosensors constructs are expressed together with Gβ1 from a single plasmid, providing preferred relative expression levels with reduced variation in mammalian cells. The Gαi FRET sensors showed a robust response to activation of endogenous or over-expressed alpha-2A-adrenergic receptors, which was inhibited by pertussis toxin. Moreover, we observed activation of the Gαi FRET sensor in single cells upon stimulation of several GPCRs, including the LPA2, M3 and BK2 receptor. Furthermore, we show that the sensors are well suited to extract kinetic parameters from fast measurements in the millisecond time range. This new generation of FRET biosensors for Gαi1, Gαi2 and Gαi3 activation will be valuable for live-cell measurements that probe Gαi activation.
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Affiliation(s)
- Jakobus van Unen
- Swammerdam Institute for Life Sciences, Section of Molecular Cytology, van Leeuwenhoek Centre for Advanced Microscopy, University of Amsterdam, P.O. Box 94215, NL-1090 GE, Amsterdam, The Netherlands
| | - Anette D Stumpf
- Bio-Imaging-Center/Rudolf-Virchow-Zentrum and Department of Pharmacology and Toxicology, University of Wuerzburg, Versbacher Strasse 9, 97078, Wuerzburg, Germany
| | - Benedikt Schmid
- Bio-Imaging-Center/Rudolf-Virchow-Zentrum and Department of Pharmacology and Toxicology, University of Wuerzburg, Versbacher Strasse 9, 97078, Wuerzburg, Germany
| | - Nathalie R Reinhard
- Swammerdam Institute for Life Sciences, Section of Molecular Cytology, van Leeuwenhoek Centre for Advanced Microscopy, University of Amsterdam, P.O. Box 94215, NL-1090 GE, Amsterdam, The Netherlands.,Department of Molecular Cell Biology, Sanquin Research and Landsteiner Laboratory, Academic Medical Center, University of Amsterdam, NL-1066 CX, Amsterdam, the Netherlands
| | - Peter L Hordijk
- Swammerdam Institute for Life Sciences, Section of Molecular Cytology, van Leeuwenhoek Centre for Advanced Microscopy, University of Amsterdam, P.O. Box 94215, NL-1090 GE, Amsterdam, The Netherlands.,Department of Molecular Cell Biology, Sanquin Research and Landsteiner Laboratory, Academic Medical Center, University of Amsterdam, NL-1066 CX, Amsterdam, the Netherlands
| | - Carsten Hoffmann
- Bio-Imaging-Center/Rudolf-Virchow-Zentrum and Department of Pharmacology and Toxicology, University of Wuerzburg, Versbacher Strasse 9, 97078, Wuerzburg, Germany
| | - Theodorus W J Gadella
- Swammerdam Institute for Life Sciences, Section of Molecular Cytology, van Leeuwenhoek Centre for Advanced Microscopy, University of Amsterdam, P.O. Box 94215, NL-1090 GE, Amsterdam, The Netherlands
| | - Joachim Goedhart
- Swammerdam Institute for Life Sciences, Section of Molecular Cytology, van Leeuwenhoek Centre for Advanced Microscopy, University of Amsterdam, P.O. Box 94215, NL-1090 GE, Amsterdam, The Netherlands
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15
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Arendt ML, Melin M, Tonomura N, Koltookian M, Courtay-Cahen C, Flindall N, Bass J, Boerkamp K, Megquir K, Youell L, Murphy S, McCarthy C, London C, Rutteman GR, Starkey M, Lindblad-Toh K. Genome-Wide Association Study of Golden Retrievers Identifies Germ-Line Risk Factors Predisposing to Mast Cell Tumours. PLoS Genet 2015; 11:e1005647. [PMID: 26588071 PMCID: PMC4654484 DOI: 10.1371/journal.pgen.1005647] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Accepted: 10/14/2015] [Indexed: 02/07/2023] Open
Abstract
Canine mast cell tumours (CMCT) are one of the most common skin tumours in dogs with a major impact on canine health. Certain breeds have a higher risk of developing mast cell tumours, suggesting that underlying predisposing germ-line genetic factors play a role in the development of this disease. The genetic risk factors are largely unknown, although somatic mutations in the oncogene C-KIT have been detected in a proportion of CMCT, making CMCT a comparative model for mastocytosis in humans where C-KIT mutations are frequent. We have performed a genome wide association study in golden retrievers from two continents and identified separate regions in the genome associated with risk of CMCT in the two populations. Sequence capture of associated regions and subsequent fine mapping in a larger cohort of dogs identified a SNP associated with development of CMCT in the GNAI2 gene (p = 2.2x10-16), introducing an alternative splice form of this gene resulting in a truncated protein. In addition, disease associated haplotypes harbouring the hyaluronidase genes HYAL1, HYAL2 and HYAL3 on cfa20 and HYAL4, SPAM1 and HYALP1 on cfa14 were identified as separate risk factors in European and US golden retrievers, respectively, suggesting that turnover of hyaluronan plays an important role in the development of CMCT.
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Affiliation(s)
- Maja L. Arendt
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
- * E-mail: (MLA); (KLT)
| | - Malin Melin
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Noriko Tonomura
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Department of Clinical Sciences, Cummings School of Veterinary Medicine at Tufts University, North Grafton, Massachusetts, United States of America
| | - Michele Koltookian
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | | | | | - Joyce Bass
- Animal Health Trust, Newmarket, United Kingdom
| | - Kim Boerkamp
- Department of Clinical Sciences of Companion Animals, Utrecht University, Utrecht, The Netherlands
| | - Katherine Megquir
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Department of Clinical Sciences, Cummings School of Veterinary Medicine at Tufts University, North Grafton, Massachusetts, United States of America
| | - Lisa Youell
- Animal Health Trust, Newmarket, United Kingdom
| | - Sue Murphy
- Animal Health Trust, Newmarket, United Kingdom
| | - Colleen McCarthy
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Cheryl London
- Department of Veterinary Clinical Sciences Ohio State University, Columbus, Ohio, United States of America
| | - Gerard R. Rutteman
- Department of Clinical Sciences of Companion Animals, Utrecht University, Utrecht, The Netherlands
- Veterinary Specialist Center De Wagenrenk, Wageningen, The Netherlands
| | | | - Kerstin Lindblad-Toh
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- * E-mail: (MLA); (KLT)
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16
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Ziegler YS, Moresco JJ, Tu PG, Yates JR, Nardulli AM. Plasma membrane proteomics of human breast cancer cell lines identifies potential targets for breast cancer diagnosis and treatment. PLoS One 2014; 9:e102341. [PMID: 25029196 PMCID: PMC4100819 DOI: 10.1371/journal.pone.0102341] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Accepted: 06/16/2014] [Indexed: 01/06/2023] Open
Abstract
The use of broad spectrum chemotherapeutic agents to treat breast cancer results in substantial and debilitating side effects, necessitating the development of targeted therapies to limit tumor proliferation and prevent metastasis. In recent years, the list of approved targeted therapies has expanded, and it includes both monoclonal antibodies and small molecule inhibitors that interfere with key proteins involved in the uncontrolled growth and migration of cancer cells. The targeting of plasma membrane proteins has been most successful to date, and this is reflected in the large representation of these proteins as targets of newer therapies. In view of these facts, experiments were designed to investigate the plasma membrane proteome of a variety of human breast cancer cell lines representing hormone-responsive, ErbB2 over-expressing and triple negative cell types, as well as a benign control. Plasma membranes were isolated by using an aqueous two-phase system, and the resulting proteins were subjected to mass spectrometry analysis. Overall, each of the cell lines expressed some unique proteins, and a number of proteins were expressed in multiple cell lines, but in patterns that did not always follow traditional clinical definitions of breast cancer type. From our data, it can be deduced that most cancer cells possess multiple strategies to promote uncontrolled growth, reflected in aberrant expression of tyrosine kinases, cellular adhesion molecules, and structural proteins. Our data set provides a very rich and complex picture of plasma membrane proteins present on breast cancer cells, and the sorting and categorizing of this data provides interesting insights into the biology, classification, and potential treatment of this prevalent and debilitating disease.
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Affiliation(s)
- Yvonne S. Ziegler
- Department of Molecular and Integrative Physiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - James J. Moresco
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Patricia G. Tu
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California, United States of America
| | - John R. Yates
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Ann M. Nardulli
- Department of Molecular and Integrative Physiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
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17
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Appleton KM, Bigham KJ, Lindsey CC, Hazard S, Lirjoni J, Parnham S, Hennig M, Peterson YK. Development of inhibitors of heterotrimeric Gαi subunits. Bioorg Med Chem 2014; 22:3423-34. [PMID: 24818958 DOI: 10.1016/j.bmc.2014.04.035] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Revised: 04/10/2014] [Accepted: 04/20/2014] [Indexed: 10/25/2022]
Abstract
Heterotrimeric G-proteins are the immediate downstream effectors of G-protein coupled receptors (GPCRs). Endogenous protein guanine nucleotide dissociation inhibitors (GDIs) like AGS3/4 and RGS12/14 function through GPR/Goloco GDI domains. Extensive characterization of GPR domain peptides indicate they function as selective GDIs for Gαi by competing for the GPCR and Gβγ and preventing GDP release. We modified a GPR consensus peptide by testing FGF and TAT leader sequences to make the peptide cell permeable. FGF modification inhibited GDI activity while TAT preserved GDI activity. TAT-GPR suppresses G-protein coupling to the receptor and completely blocked α2-adrenoceptor (α2AR) mediated decreases in cAMP in HEK293 cells at 100nM. We then sought to discover selective small molecule inhibitors for Gαi. Molecular docking was used to identify potential molecules that bind to and stabilize the Gαi-GDP complex by directly interacting with both Gαi and GDP. Gαi-GTP and Gαq-GDP were used as a computational counter screen and Gαq-GDP was used as a biological counter screen. Thirty-seven molecules were tested using nucleotide exchange. STD NMR assays with compound 0990, a quinazoline derivative, showed direct interaction with Gαi. Several compounds showed Gαi specific inhibition and were able to block α2AR mediated regulation of cAMP. In addition to being a pharmacologic tool, GDI inhibition of Gα subunits has the advantage of circumventing the upstream component of GPCR-related signaling in cases of overstimulation by agonists, mutations, polymorphisms, and expression-related defects often seen in disease.
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Affiliation(s)
- Kathryn M Appleton
- Department of Drug Discovery and Biomedical Sciences, Medical University of South Carolina, Charleston, SC 29425, United States
| | - Kevin J Bigham
- Department of Drug Discovery and Biomedical Sciences, Medical University of South Carolina, Charleston, SC 29425, United States
| | - Christopher C Lindsey
- Department of Drug Discovery and Biomedical Sciences, Medical University of South Carolina, Charleston, SC 29425, United States
| | - Starr Hazard
- Department of Pharmacology, Medical University of South Carolina, Charleston, SC 29425, United States
| | - Jonel Lirjoni
- Department of Drug Discovery and Biomedical Sciences, Medical University of South Carolina, Charleston, SC 29425, United States
| | - Stuart Parnham
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, United States
| | - Mirko Hennig
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, United States
| | - Yuri K Peterson
- Department of Drug Discovery and Biomedical Sciences, Medical University of South Carolina, Charleston, SC 29425, United States.
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