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Zhang ZY, Sun ZJ, Gao D, Hao YD, Lin H, Liu F. Excavation of gene markers associated with pancreatic ductal adenocarcinoma based on interrelationships of gene expression. IET Syst Biol 2024. [PMID: 38530028 DOI: 10.1049/syb2.12090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 02/06/2024] [Accepted: 03/10/2024] [Indexed: 03/27/2024] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) accounts for 95% of all pancreatic cancer cases, posing grave challenges to its diagnosis and treatment. Timely diagnosis is pivotal for improving patient survival, necessitating the discovery of precise biomarkers. An innovative approach was introduced to identify gene markers for precision PDAC detection. The core idea of our method is to discover gene pairs that display consistent opposite relative expression and differential co-expression patterns between PDAC and normal samples. Reversal gene pair analysis and differential partial correlation analysis were performed to determine reversal differential partial correlation (RDC) gene pairs. Using incremental feature selection, the authors refined the selected gene set and constructed a machine-learning model for PDAC recognition. As a result, the approach identified 10 RDC gene pairs. And the model could achieve a remarkable accuracy of 96.1% during cross-validation, surpassing gene expression-based models. The experiment on independent validation data confirmed the model's performance. Enrichment analysis revealed the involvement of these genes in essential biological processes and shed light on their potential roles in PDAC pathogenesis. Overall, the findings highlight the potential of these 10 RDC gene pairs as effective diagnostic markers for early PDAC detection, bringing hope for improving patient prognosis and survival.
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Affiliation(s)
- Zhao-Yue Zhang
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
- School of Healthcare Technology, Chengdu Neusoft University, Chengdu, China
| | - Zi-Jie Sun
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | - Dong Gao
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | - Yu-Duo Hao
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | - Hao Lin
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | - Fen Liu
- Department of Radiation Oncology, Peking University Cancer Hospital (Inner Mongolia Campus), Affiliated Cancer Hospital of Inner Mongolia Medical University, Inner Mongolia Cancer Hospital, Hohhot, China
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Yeyeodu S, Hanafi D, Webb K, Laurie NA, Kimbro KS. Population-enriched innate immune variants may identify candidate gene targets at the intersection of cancer and cardio-metabolic disease. Front Endocrinol (Lausanne) 2024; 14:1286979. [PMID: 38577257 PMCID: PMC10991756 DOI: 10.3389/fendo.2023.1286979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 12/07/2023] [Indexed: 04/06/2024] Open
Abstract
Both cancer and cardio-metabolic disease disparities exist among specific populations in the US. For example, African Americans experience the highest rates of breast and prostate cancer mortality and the highest incidence of obesity. Native and Hispanic Americans experience the highest rates of liver cancer mortality. At the same time, Pacific Islanders have the highest death rate attributed to type 2 diabetes (T2D), and Asian Americans experience the highest incidence of non-alcoholic fatty liver disease (NAFLD) and cancers induced by infectious agents. Notably, the pathologic progression of both cancer and cardio-metabolic diseases involves innate immunity and mechanisms of inflammation. Innate immunity in individuals is established through genetic inheritance and external stimuli to respond to environmental threats and stresses such as pathogen exposure. Further, individual genomes contain characteristic genetic markers associated with one or more geographic ancestries (ethnic groups), including protective innate immune genetic programming optimized for survival in their corresponding ancestral environment(s). This perspective explores evidence related to our working hypothesis that genetic variations in innate immune genes, particularly those that are commonly found but unevenly distributed between populations, are associated with disparities between populations in both cancer and cardio-metabolic diseases. Identifying conventional and unconventional innate immune genes that fit this profile may provide critical insights into the underlying mechanisms that connect these two families of complex diseases and offer novel targets for precision-based treatment of cancer and/or cardio-metabolic disease.
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Affiliation(s)
- Susan Yeyeodu
- Julius L Chambers Biomedical/Biotechnology Institute (JLC-BBRI), North Carolina Central University, Durham, NC, United States
- Charles River Discovery Services, Morrisville, NC, United States
| | - Donia Hanafi
- Julius L Chambers Biomedical/Biotechnology Institute (JLC-BBRI), North Carolina Central University, Durham, NC, United States
| | - Kenisha Webb
- Department of Microbiology, Biochemistry, and Immunology, Morehouse School of Medicine, Atlanta, GA, United States
| | - Nikia A. Laurie
- Julius L Chambers Biomedical/Biotechnology Institute (JLC-BBRI), North Carolina Central University, Durham, NC, United States
| | - K. Sean Kimbro
- Department of Microbiology, Biochemistry, and Immunology, Morehouse School of Medicine, Atlanta, GA, United States
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3
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Aiyappa-Maudsley R, McLoughlin LFV, Hughes TA. Semaphorins and Their Roles in Breast Cancer: Implications for Therapy Resistance. Int J Mol Sci 2023; 24:13093. [PMID: 37685898 PMCID: PMC10487980 DOI: 10.3390/ijms241713093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 08/18/2023] [Accepted: 08/21/2023] [Indexed: 09/10/2023] Open
Abstract
Breast cancer is the most common cancer worldwide and a leading cause of cancer-related deaths in women. The clinical management of breast cancer is further complicated by the heterogeneous nature of the disease, which results in varying prognoses and treatment responses in patients. The semaphorins are a family of proteins with varied roles in development and homoeostasis. They are also expressed in a wide range of human cancers and are implicated as regulators of tumour growth, angiogenesis, metastasis and immune evasion. More recently, semaphorins have been implicated in drug resistance across a range of malignancies. In breast cancer, semaphorins are associated with resistance to endocrine therapy as well as breast cancer chemotherapeutic agents such as taxanes and anthracyclines. This review will focus on the semaphorins involved in breast cancer progression and their association with drug resistance.
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Affiliation(s)
| | | | - Thomas A. Hughes
- School of Medicine, University of Leeds, Leeds LS9 7TF, UK; (R.A.-M.); (L.F.V.M.)
- School of Science, Technology and Health, York St John University, York YO31 7EX, UK
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Bica C, Tirpe A, Nutu A, Ciocan C, Chira S, Gurzau ES, Braicu C, Berindan-Neagoe I. Emerging roles and mechanisms of semaphorins activity in cancer. Life Sci 2023; 318:121499. [PMID: 36775114 DOI: 10.1016/j.lfs.2023.121499] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 02/08/2023] [Accepted: 02/08/2023] [Indexed: 02/12/2023]
Abstract
Semaphorins are regulatory molecules that are linked to the modulation of several cancer processes, such as angiogenesis, cancer cell invasiveness and metastasis, tumor growth, as well as cancer cell survival. Semaphorin (SEMA) activity depends on the cancer histotypes and their particularities. In broad terms, the effects of SEMAs result from their interaction with specific receptors/co-receptors - Plexins, Neuropilins and Integrins - and the subsequent effects upon the downstream effectors (e.g. PI3K/AKT, MAPK/ERK). The present article serves as an integrative review work, discussing the broad implications of semaphorins in cancer, focusing on cell proliferation/survival, angiogenesis, invasion, metastasis, stemness, and chemo-resistance/response whilst highlighting their heterogeneity as a family. Herein, we emphasized that semaphorins are largely implicated in cancer progression, interacting with the tumor microenvironment components. Whilst some SEMAs (e.g. SEMA3A, SEMA3B) function widely as tumor suppressors, others (e.g. SEMA3C) act as pro-tumor semaphorins. The differences observed in terms of the biological structure of SEMAs and the particularities of each cancer histotypes require that each semaphorin be viewed as a unique entity, and its roles must be researched accordingly. A more in-depth and comprehensive view of the molecular mechanisms that promote and sustain the malignant behavior of cancer cells is of utmost importance.
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Affiliation(s)
- Cecilia Bica
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca 400337, Romania.
| | - Alexandru Tirpe
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca 400337, Romania; Faculty of Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, 8 Victor Babes Street, 400012 Cluj-Napoca, Romania.
| | - Andreea Nutu
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca 400337, Romania.
| | - Cristina Ciocan
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca 400337, Romania.
| | - Sergiu Chira
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca 400337, Romania.
| | - Eugen S Gurzau
- Cluj School of Public Health, College of Political, Administrative and Communication Sciences, Babes-Bolyai University, 7 Pandurilor Street, Cluj-Napoca, Romania; Environmental Health Center, 58 Busuiocului Street, 400240 Cluj-Napoca, Romania.
| | - Cornelia Braicu
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca 400337, Romania.
| | - Ioana Berindan-Neagoe
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca 400337, Romania.
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5
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Crosstalk between the peripheral nervous system and breast cancer influences tumor progression. Biochim Biophys Acta Rev Cancer 2022; 1877:188828. [DOI: 10.1016/j.bbcan.2022.188828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 10/17/2022] [Accepted: 10/19/2022] [Indexed: 11/18/2022]
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Duan J, Jin M, Qiao B. Semaphorin 6D as an independent predictor for better prognosis in clear cell renal cell carcinoma. Transl Oncol 2022; 22:101453. [PMID: 35605459 PMCID: PMC9124703 DOI: 10.1016/j.tranon.2022.101453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 04/29/2022] [Accepted: 05/10/2022] [Indexed: 11/19/2022] Open
Abstract
The role of SEMA6D in clear cell renal cell carcinoma remains unexplored. SEMA6D expression was markedly lower in ccRCC tissues compared to normal tissues. SEMA6D may serve as a diagnostic and prognostic biomarker for ccRCC.
Introduction Clear cell renal cell carcinoma (ccRCC) is the most common type of RCC and is associated with poor survival. However, the mechanisms underlying its development have not been thoroughly investigated. Semaphorin 6D (SEMA6D) is differentially expressed in various cancers, including lung adenocarcinoma and colorectal cancer. However, the role and mechanism of SEMA6D in ccRCC remain unexplored. Materials and methods We obtained 25 pairs of ccRCC tissue samples and 57 urine samples from patients with ccRCC and 52 urine samples from healthy volunteers. We performed RNA sequencing and compared the results with data from The Cancer Genome Atlas database to identify our gene of interest, SEMA6D. To verify the differential expression of SEMA6D, we used real-time quantitative polymerase chain reaction, immunohistochemistry, and enzyme-linked immunosorbent assay. Finally, we conducted in vitro proliferation, migration and invasion experiments. Results SEMA6D expression was significantly lower in ccRCC tissue compared to that in normal tissue. Comparative analysis of our results with data from online databases revealed that the expression level of SEMA6D in ccRCC tissue correlated with the clinical stage and pathological grade of ccRCC. Furthermore, higher SEMA6D expression was associated with improved quality of life of patients with ccRCC. In addition, the diagnostic value of SEMA6D was confirmed using data from two Gene Expression Omnibus ccRCC databases. The results showed that SEMA6D can be used as a predictor for ccRCC diagnosis, with an area under the curve of 0.9642. Conclusion SEMA6D may serve as a diagnostic and prognostic biomarker for ccRCC.
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Yang H, Yang Z, Yu Z, Xiong C, Zhang Y, Zhang J, Huang Y, Zhou X, Li J, Xu N. SEMA6D, Negatively Regulated by miR-7, Contributes to C28/I2 chondrocyte's Catabolic and Anabolic Activities via p38 Signaling Pathway. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:9674221. [PMID: 35757507 PMCID: PMC9225841 DOI: 10.1155/2022/9674221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 05/16/2022] [Accepted: 05/27/2022] [Indexed: 11/17/2022]
Abstract
MiR-7 has been recognized as an osteoarthritis (OA-)-promoting factor, but the specific downstream pathway of miR-7 still remains unknown. Further investigation of the molecular regulatory mechanism of miR-7 might help develop a novel therapeutic method for OA. In this study, we revealed that Semaphorin 6D (SEMA6D) was a direct target gene of miR-7 and presented a negative regulatory relation with SEMA6D in vitro and in vivo. SEMA6D could improve OA in rat OA models, as indicated by H&E and Safranin O-Fast green staining, and also μCT analysis. Further evaluation of SEMA6D suggested that SEMA6D promotes the anabolism and reduces the catabolism of C28/I2 chondrocytes via inhibiting the activation of the p38 pathway. The present research illustrated that SEMA6D is a negatively regulatory factor of miR-7 and a pivotal mediator of catabolism and anabolism in C28/I2 chondrocytes. SEMA6D exerts its function via inhibiting the activation of the p38 pathway.
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Affiliation(s)
- Haoyu Yang
- Department of Orthopedics, Wuxi 9th People's Hospital Affiliated to Soochow University, Wuxi 214000, China
| | - Zhicheng Yang
- Department of Orthopedics, The Affiliated Changzhou No.2 People's Hospital of Nanjing Medical University, Changzhou 213000, China
| | - Zhentang Yu
- Department of Orthopedics, The Affiliated Changzhou No.2 People's Hospital of Nanjing Medical University, Changzhou 213000, China
| | - Chenwei Xiong
- Department of Orthopedics, The Affiliated Changzhou No.2 People's Hospital of Nanjing Medical University, Changzhou 213000, China
| | - Yi Zhang
- Department of Orthopedics, The Affiliated Changzhou No.2 People's Hospital of Nanjing Medical University, Changzhou 213000, China
| | - Junjie Zhang
- Department of Orthopedics, The Affiliated Changzhou No.2 People's Hospital of Nanjing Medical University, Changzhou 213000, China
| | - Yong Huang
- Department of Orthopedics, The Affiliated Changzhou No.2 People's Hospital of Nanjing Medical University, Changzhou 213000, China
| | - Xindie Zhou
- Department of Orthopedics, The Affiliated Changzhou No.2 People's Hospital of Nanjing Medical University, Changzhou 213000, China
| | - Jin Li
- Department of Orthopedic Surgery, The Second Affiliated Hospital of Jiaxing University, Jiaxing 314000, China
| | - Nanwei Xu
- Department of Orthopedics, The Affiliated Changzhou No.2 People's Hospital of Nanjing Medical University, Changzhou 213000, China
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8
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Chava S, Bugide S, Zhang X, Gupta R, Wajapeyee N. Betacellulin promotes tumor development and EGFR mutant lung cancer growth by stimulating the EGFR pathway and suppressing apoptosis. iScience 2022; 25:104211. [PMID: 35494243 PMCID: PMC9048069 DOI: 10.1016/j.isci.2022.104211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 03/18/2022] [Accepted: 04/04/2022] [Indexed: 12/14/2022] Open
Abstract
Oncogenic mutations in the EGFR gene account for 15-20% of lung adenocarcinoma (LUAD) cases. However, the mechanism for EGFR driven tumor development and growth is not fully understood. Here, using an mRNA expression profiling-based approach we identified betacellulin (BTC) as one the gene upregulated by oncogenic EGFR in an MAP kinase-dependent manner. BTC protein expression was markedly increased in LUAD patient samples compared to normal lung tissue, with higher expression in EGFR-mutant LUAD. BTC was sufficient to transform immortalized mouse cells, initiate tumor development in mice, and promote the survival of immortalized human lung epithelial cells. Conversely, knockdown of BTC inhibited the growth of EGFR-mutant human LUAD cells in culture and their tumor-forming ability in mice. Mechanistically, BTC knockdown resulted in attenuated EGFR signaling and apoptosis induction. Collectively, these results demonstrate a key role of BTC in EGFR-mutant LUAD, with potential therapeutic implications in LUAD and other EGFR-mutant cancers.
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Affiliation(s)
- Suresh Chava
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35233, USA
| | - Suresh Bugide
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35233, USA
| | - Xuchen Zhang
- Department of Pathology, Yale University, New Haven, CT 06510, USA
| | - Romi Gupta
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35233, USA
- O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL 35233, USA
| | - Narendra Wajapeyee
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35233, USA
- O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL 35233, USA
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Gunyuz Z, Sahi-Ilhan E, Kucukkose C, Ipekgil D, Tok G, Mese G, Ozcivici E, Yalcin-Ozuysal O. SEMA6D Differentially Regulates Proliferation, Migration, and Invasion of Breast Cell Lines. ACS OMEGA 2022; 7:15769-15778. [PMID: 35571788 PMCID: PMC9097209 DOI: 10.1021/acsomega.2c00840] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 04/14/2022] [Indexed: 06/15/2023]
Abstract
Semaphorin 6D (SEMA6D), a member of the class 6 semaphorin family, is a membrane-associated protein that plays a key role in the development of cardiac and neural tissues. A growing body of evidence suggests that SEMA6D is also involved in tumorigenesis. In breast cancer, high SEMA6D levels are correlated with better survival rates. However, very little is known about the functional significance of SEMA6D in breast tumorigenesis. In the present study, we aimed to investigate the effects of SEMA6D expression on the normal breast cell line MCF10A and the breast cancer cell lines MCF7 and MDA MB 231. We demonstrated that SEMA6D expression increases the proliferation of MCF10A cells, whereas the opposite effect was observed in MCF7 cells. SEMA6D expression induced anchorage-independent growth in both cancer cell lines. Furthermore, migration of MCF10A and MCF7 cells and invasion of MDA MB 231 cells were elevated in response to SEMA6D overexpression. Accordingly, the genes related to epithelial-mesenchymal transition (EMT) were altered by SEMA6D expression in MCF10A and MCF7 cell lines. Finally, we provided evidence that SEMA6D levels were associated with the expression of the cell cycle, EMT, and Notch signaling pathway-related genes in breast cancer patients' data. We showed for the first time that SEMA6D overexpression has cell-specific effects on the proliferation, migration, and invasion of normal and cancer breast cell lines, which agrees with the gene expression data of clinical samples. This study lays the groundwork for future research into understanding the functional importance of SEMA6D in breast cancer.
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Affiliation(s)
- Zehra
Elif Gunyuz
- Department
of Molecular Biology and Genetics, Izmir
Institute of Technology, 35430 Izmir, Turkey
| | - Ece Sahi-Ilhan
- Department
of Molecular Biology and Genetics, Izmir
Institute of Technology, 35430 Izmir, Turkey
| | - Cansu Kucukkose
- Department
of Molecular Biology and Genetics, Izmir
Institute of Technology, 35430 Izmir, Turkey
| | - Dogac Ipekgil
- Department
of Molecular Biology and Genetics, Izmir
Institute of Technology, 35430 Izmir, Turkey
| | - Gunes Tok
- Department
of Molecular Biology and Genetics, Izmir
Institute of Technology, 35430 Izmir, Turkey
| | - Gulistan Mese
- Department
of Molecular Biology and Genetics, Izmir
Institute of Technology, 35430 Izmir, Turkey
| | - Engin Ozcivici
- Department
of Bioengineering, Izmir Institute of Technology, 35430 Izmir, Turkey
| | - Ozden Yalcin-Ozuysal
- Department
of Molecular Biology and Genetics, Izmir
Institute of Technology, 35430 Izmir, Turkey
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10
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In silico recognition of a prognostic signature in basal-like breast cancer patients. PLoS One 2022; 17:e0264024. [PMID: 35167614 PMCID: PMC8846521 DOI: 10.1371/journal.pone.0264024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 01/31/2022] [Indexed: 01/22/2023] Open
Abstract
Background Triple-negative breast cancers (TNBCs) display poor prognosis, have a high risk of tumour recurrence, and exhibit high resistance to drug treatments. Based on their gene expression profiles, the majority of TNBCs are classified as basal-like breast cancers. Currently, there are not available widely-accepted prognostic markers to predict outcomes in basal-like subtype, so the selection of new prognostic indicators for this BC phenotype represents an unmet clinical challenge. Results Here, we attempted to address this challenging issue by exploiting a bioinformatics pipeline able to integrate transcriptomic, genomic, epigenomic, and clinical data freely accessible from public repositories. This pipeline starts from the application of the well-established network-based SWIM methodology on the transcriptomic data to unveil important (switch) genes in relation with a complex disease of interest. Then, survival and linear regression analyses are performed to associate the gene expression profiles of the switch genes with both the patients’ clinical outcome and the disease aggressiveness. This allows us to identify a prognostic gene signature that in turn is fed to the last step of the pipeline consisting of an analysis at DNA level, to investigate whether variations in the expression of identified prognostic switch genes could be related to genetic (copy number variations) or epigenetic (DNA methylation differences) alterations in their gene loci, or to the activities of transcription factors binding to their promoter regions. Finally, changes in the protein expression levels corresponding to the so far identified prognostic switch genes are evaluated by immunohistochemical staining results taking advantage of the Human Protein Atlas. Conclusion The application of the proposed pipeline on the dataset of The Cancer Genome Atlas (TCGA)-Breast Invasive Carcinoma (BRCA) patients affected by basal-like subtype led to an in silico recognition of a basal-like specific gene signature composed of 11 potential prognostic biomarkers to be further investigated.
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Baxter DE, Allinson LM, Al Amri WS, Poulter JA, Pramanik A, Thorne JL, Verghese ET, Hughes TA. MiR-195 and Its Target SEMA6D Regulate Chemoresponse in Breast Cancer. Cancers (Basel) 2021; 13:cancers13235979. [PMID: 34885090 PMCID: PMC8656586 DOI: 10.3390/cancers13235979] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 11/23/2021] [Accepted: 11/26/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND poor prognosis primary breast cancers are typically treated with cytotoxic chemotherapy. However, recurrences remain relatively common even after this aggressive therapy. Comparison of matched tumours pre- and post-chemotherapy can allow identification of molecular characteristics of therapy resistance and thereby potentially aid discovery of novel predictive markers or targets for chemosensitisation. Through this comparison, we aimed to identify microRNAs associated with chemoresistance, define microRNA target genes, and assess targets as predictors of chemotherapy response. METHODS cancer cells were laser microdissected from matched breast cancer tissues pre- and post-chemotherapy from estrogen receptor positive/HER2 negative breast cancers showing partial responses to epirubicin/cyclophosphamide chemotherapy (n = 5). MicroRNA expression was profiled using qPCR arrays. MicroRNA/mRNA expression was manipulated in estrogen receptor positive/HER2 negative breast cancer cell lines (MCF7 and MDA-MB-175 cells) with mimics, inhibitors or siRNAs, and chemoresponse was assessed using MTT and colony forming survival assays. MicroRNA targets were identified by RNA-sequencing of microRNA mimic pull-downs, and comparison of these with mRNAs containing predicted microRNA binding sites. Survival correlations were tested using the METABRIC expression dataset (n = 1979). RESULTS miR-195 and miR-26b were consistently up-regulated after therapy, and changes in their expression in cell lines caused significant differences in chemotherapy sensitivity, in accordance with up-regulation driving resistance. SEMA6D was defined and confirmed as a target of the microRNAs. Reduced SEMA6D expression was significantly associated with chemoresistance, in accordance with SEMA6D being a down-stream effector of the microRNAs. Finally, low SEMA6D expression in breast cancers was significantly associated with poor survival after chemotherapy, but not after other therapies. CONCLUSIONS microRNAs and their targets influence chemoresponse, allowing the identification of SEMA6D as a predictive marker for chemotherapy response that could be used to direct therapy or as a target in chemosensitisation strategies.
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Affiliation(s)
- Diana E. Baxter
- School of Medicine, University of Leeds, Leeds LS9 7TF, UK; (D.E.B.); (J.A.P.); (A.P.)
- Cancer Research UK Manchester Institute, University of Manchester, Manchester SK10 4TG, UK
| | - Lisa M. Allinson
- Newcastle University Centre for Cancer, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4AD, UK;
| | - Waleed S. Al Amri
- Department of Histopathology and Cytopathology, The Royal Hospital, Muscat, Oman;
| | - James A. Poulter
- School of Medicine, University of Leeds, Leeds LS9 7TF, UK; (D.E.B.); (J.A.P.); (A.P.)
| | - Arindam Pramanik
- School of Medicine, University of Leeds, Leeds LS9 7TF, UK; (D.E.B.); (J.A.P.); (A.P.)
| | - James L. Thorne
- School of Food Science and Nutrition, University of Leeds, Leeds LS2 9JT, UK;
| | - Eldo T. Verghese
- Department of Histopathology, St. James’s University Hospital, Leeds LS9 7JX, UK;
| | - Thomas A. Hughes
- School of Medicine, University of Leeds, Leeds LS9 7TF, UK; (D.E.B.); (J.A.P.); (A.P.)
- Correspondence:
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12
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Uribe ML, Dahlhoff M, Batra RN, Nataraj NB, Haga Y, Drago-Garcia D, Marrocco I, Sekar A, Ghosh S, Vaknin I, Lebon S, Kramarski L, Tsutsumi Y, Choi I, Rueda OM, Caldas C, Yarden Y. TSHZ2 is an EGF-regulated tumor suppressor that binds to the cytokinesis regulator PRC1 and inhibits metastasis. Sci Signal 2021; 14:eabe6156. [PMID: 34158398 PMCID: PMC7614343 DOI: 10.1126/scisignal.abe6156] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Unlike early transcriptional responses to mitogens, later events are less well-characterized. Here, we identified delayed down-regulated genes (DDGs) in mammary cells after prolonged treatment with epidermal growth factor (EGF). The expression of these DDGs was low in mammary tumors and correlated with prognosis. The proteins encoded by several DDGs directly bind to and inactivate oncoproteins and might therefore act as tumor suppressors. The transcription factor teashirt zinc finger homeobox 2 (TSHZ2) is encoded by a DDG, and we found that overexpression of TSHZ2 inhibited tumor growth and metastasis and accelerated mammary gland development in mice. Although the gene TSHZ2 localizes to a locus (20q13.2) that is frequently amplified in breast cancer, we found that hypermethylation of its promoter correlated with down-regulation of TSHZ2 expression in patients. Yeast two-hybrid screens and protein-fragment complementation assays in mammalian cells indicated that TSHZ2 nucleated a multiprotein complex containing PRC1/Ase1, cyclin B1, and additional proteins that regulate cytokinesis. TSHZ2 increased the inhibitory phosphorylation of PRC1, a key driver of mitosis, mediated by cyclin-dependent kinases. Furthermore, similar to the tumor suppressive transcription factor p53, TSHZ2 inhibited transcription from the PRC1 promoter. By recognizing DDGs as a distinct group in the transcriptional response to EGF, our findings uncover a group of tumor suppressors and reveal a role for TSHZ2 in cell cycle regulation.
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Affiliation(s)
- Mary L Uribe
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Maik Dahlhoff
- Institute of in vivo and in vitro Models, University of Veterinary Medicine Vienna, 1210 Vienna, Austria
| | - Rajbir N Batra
- Department of Oncology and Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, UK
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Nishanth B Nataraj
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Yuya Haga
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel
- Graduate School of Pharmaceutical Sciences, Osaka University, Osaka 565-0871, Japan
| | - Diana Drago-Garcia
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Ilaria Marrocco
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Arunachalam Sekar
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Soma Ghosh
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Itay Vaknin
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Sacha Lebon
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Lior Kramarski
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Yasuo Tsutsumi
- Graduate School of Pharmaceutical Sciences, Osaka University, Osaka 565-0871, Japan
- Global Center for Medical Engineering and Informatics, Osaka University, Osaka 565-0871, Japan
| | - Inpyo Choi
- Immunotherapy Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 306-809, South Korea
| | - Oscar M Rueda
- Department of Oncology and Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, UK
- MRC Biostatistics Unit, University of Cambridge, Forvie Site, Robinson Way, Cambridge CB2 0RE, UK
| | - Carlos Caldas
- Department of Oncology and Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, UK
| | - Yosef Yarden
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel.
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13
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Martin AM, Cassirer EF, Waits LP, Plowright RK, Cross PC, Andrews KR. Genomic association with pathogen carriage in bighorn sheep ( Ovis canadensis). Ecol Evol 2021; 11:2488-2502. [PMID: 33767816 PMCID: PMC7981200 DOI: 10.1002/ece3.7159] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 12/15/2020] [Accepted: 12/16/2020] [Indexed: 12/03/2022] Open
Abstract
Genetic composition can influence host susceptibility to, and transmission of, pathogens, with potential population-level consequences. In bighorn sheep (Ovis canadensis), pneumonia epidemics caused by Mycoplasma ovipneumoniae have been associated with severe population declines and limited recovery across North America. Adult survivors either clear the infection or act as carriers that continually shed M. ovipneumoniae and expose their susceptible offspring, resulting in high rates of lamb mortality for years following the outbreak event. Here, we investigated the influence of genomic composition on persistent carriage of M. ovipneumoniae in a well-studied bighorn sheep herd in the Wallowa Mountains of Oregon, USA. Using 10,605 SNPs generated using RADseq technology for 25 female bighorn sheep, we assessed genomic diversity metrics and employed family-based genome-wide association methodologies to understand variant association and genetic architecture underlying chronic carriage. We observed no differences among genome-wide diversity metrics (heterozygosity and allelic richness) between groups. However, we identified two variant loci of interest and seven associated candidate genes, which may influence carriage status. Further, we found that the SNP panel explained ~55% of the phenotypic variance (SNP-based heritability) for M. ovipneumoniae carriage, though there was considerable uncertainty in these estimates. While small sample sizes limit conclusions drawn here, our study represents one of the first to assess the genomic factors influencing chronic carriage of a pathogen in a wild population and lays a foundation for understanding genomic influence on pathogen persistence in bighorn sheep and other wildlife populations. Future research should incorporate additional individuals as well as distinct herds to further explore the genomic basis of chronic carriage.
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Affiliation(s)
- Alynn M. Martin
- United States Geological SurveyNorthern Rocky Mountain Science CenterBozemanMTUSA
| | | | | | - Raina K. Plowright
- Department of Microbiology and ImmunologyMontana State UniversityBozemanMTUSA
| | - Paul C. Cross
- United States Geological SurveyNorthern Rocky Mountain Science CenterBozemanMTUSA
| | - Kimberly R. Andrews
- Institute for Bioinformatics and Evolutionary Studies (IBEST)University of IdahoMoscowIDUSA
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14
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Wang Y, Zhang L, Chen Y, Li M, Ha M, Li S. Screening and identification of biomarkers associated with the diagnosis and prognosis of lung adenocarcinoma. J Clin Lab Anal 2020; 34:e23450. [PMID: 32672359 PMCID: PMC7595917 DOI: 10.1002/jcla.23450] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 05/26/2020] [Accepted: 05/29/2020] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND In this study, we aimed to identify the pathogenesis and prognostic biomarkers of lung adenocarcinoma (LUAD). METHODS Differentially expressed mRNAs (DEmRNAs) and single nucleotide polymorphism (SNP) mutant genes were screened. In addition, enrichment and protein-protein interaction (PPI) network analyses of the SNP-mutated genes were performed. Thereafter, the correlation between gene mutation and expression was analyzed. Finally, the mutated genes associated with LUAD prognosis were validated on the basis of The Cancer Genome Atlas (TCGA) database. RESULTS A total of 2502 DEmRNAs were initially screened in this study. We identified 756 SNP-mutated genes from more than 30 cases. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed that the mutated genes involved in LUAD were mainly associated with the ECM-receptor interaction, focal adhesion, and calcium signaling pathways. Tumor protein p53 (TP53) and neurexin 1 (NRXN1) with the higher degree were chosen as the hub genes in the PPI network. In addition, the correlation analysis revealed six genes, including assembly factor for spindle microtubules (ASPM), centromere protein F (CENPF), contactin 3 (CNTN3), catenin delta 2 (CTNND2), PKHD1 like 1 (PKHD1L1), and semaphorin 6D (SEMA6D), and three SNP mutations at ASPM rs368020495, CENPF rs762653487, and PKHD1L1 rs768349010 sites that were found to be associated with LUAD prognosis. Further validation showed that among the aforementioned six mutated genes, CENPF was upregulated and SEMA6D was downregulated. CONCLUSION CENPF, SEMA6D, TP53, and NRXN1 were found to be closely associated with the development of LUAD.
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Affiliation(s)
| | - Lin Zhang
- Department of Medical OncologyThe First Affiliated Hospital of Jinzhou Medical UniversityJinzhouChina
| | - Yitong Chen
- Department of Medical OncologyThe First Affiliated Hospital of Jinzhou Medical UniversityJinzhouChina
| | - Man Li
- Department of Radiology and Medical ImagingThe First Affiliated Hospital of Jinzhou Medical UniversityJinzhouChina
| | - Minwen Ha
- Department of Medical OncologyThe First Affiliated Hospital of Jinzhou Medical UniversityJinzhouChina
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15
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Construction of an miRNA-mRNA regulatory network in colorectal cancer with bioinformatics methods. Anticancer Drugs 2020; 30:588-595. [PMID: 30601194 DOI: 10.1097/cad.0000000000000745] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Colorectal cancer (CRC) is the third most common cancer worldwide. This study aimed to explore the regulatory mechanisms of miRNAs in CRC. Differentially expressed miRNAs (DEMs) and differentially expressed genes (DEGs) in CRC tissue samples compared with control samples in mRNA and miRNA datasets were screened. Functional and pathway enrichment analysis of the DEGs was carried out. Targets of the DEMs were identified. Overlaps between the DEGs and targets of DEMs were selected. The miRNA-mRNA regulatory network of these overlaps was constructed and visualized. The candidate genes selected were validated by quantitative real-time PCR. DEGs were identified and considered DEGs-1 and DEGs-2. A total of 584 genes in DEGs-1 and 527 genes in DEGs-2 were obtained, including 465 overlaps, and 44 DEMs were identified. The overlaps were enriched in 46 Gene Ontology terms and 19 Kyoto Encyclopedia of Genes and Genomes pathways. Moreover, 137 overlapped genes between targets of the DEMs and the 465 overlaps were obtained. The miRNA-mRNA regulating network of the 137 overlapped genes was constructed. Extracellular matrix-related proteins and pathways might play critical roles in the development of CRC. The quantitative real-time PCR results of the candidates were in agreement with the bioinformatics analysis. miR-128, miR-182, and miR-143 might be key miRNAs regulating cell proliferation and metastasis of CRC.
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16
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Ramos J, Yoo C, Felty Q, Gong Z, Liuzzi JP, Poppiti R, Thakur IS, Goel R, Vaid AK, Komotar RJ, Ehtesham NZ, Hasnain SE, Roy D. Sensitivity to differential NRF1 gene signatures contributes to breast cancer disparities. J Cancer Res Clin Oncol 2020; 146:2777-2815. [PMID: 32705365 DOI: 10.1007/s00432-020-03320-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 07/09/2020] [Indexed: 01/12/2023]
Abstract
PURPOSE Nuclear respiratory factor 1 (NRF1) drives estrogen-dependent breast tumorigenesis. Herein we examined the impact of NRF1 activity on the aggressiveness and disparate molecular signature of breast cancer in Black, White, Asian, and Hispanic women. METHODS NRF1 activity by transcription factor target enrichment analysis and causal NRF1-target gene signatures by Bayesian Network Inference with Java Objects (BANJO) and Markov Chain Monte Carlo (MCMC)-based gene order were examined in The Cancer Genome Atlas (TCGA) breast cancer cohorts. RESULTS We are the first to report increased NRF1 activity based on its differential effects on genome-wide transcription associated with luminal A and B, HER2+ and triple-negative (TN) molecular subtypes of breast cancer in women of different race/ethnicity. We observed disparate NRF1 motif-containing causal gene signatures unique to Black, White, Asian, and Hispanic women for luminal A breast cancer. Further gene order searches showed molecular heterogeneity of each subtype of breast cancer. Six different gene order sequences involving CDK1, HMMR, CCNB2, CCNB1, E2F1, CREB3L4, GTSE1, and LMNB1 with almost equal weight predicted the probability of luminal A breast cancer in whites. Three different gene order sequences consisting of CCNB1 and GTSE1, and CCNB1, LMNB1, CDK1 or CASP3 predicted almost 100% probability of luminal B breast cancer in whites; CCNB1 and LMNB1 or GTSE predicted 100% HER2+ breast cancer in whites. GTSE1 and TUBA1C combined together predicted 100% probability of developing TNBC in whites; NRF1, TUBA1B and BAX with EFNA4, and NRF1 and BTRC predicated 100% TNBC in blacks. High expressor NRF1 TN breast tumors showed unfavorable prognosis with a high risk of breast cancer death in white women. CONCLUSION Our findings showed how sensitivity to high NRF1 transcriptional activity coupled with its target gene signatures contribute to racial differences in luminal A and TN breast cancer subtypes. This knowledge may be useful in personalized intervention to prevent and treat this clinically challenging problem.
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Affiliation(s)
- Jairo Ramos
- Department of Environmental Health Sciences, Florida International University, Miami, USA
| | - Changwon Yoo
- Department of Biostatistics, Florida International University, Miami, FL, 33199, USA
| | - Quentin Felty
- Department of Environmental Health Sciences, Florida International University, Miami, USA
| | - Zhenghua Gong
- Department of Biostatistics, Florida International University, Miami, FL, 33199, USA
| | - Juan P Liuzzi
- Department of Dietetics and Nutrition, Florida International University, Miami, FL, 33199, USA
| | - Robert Poppiti
- Department of Pathology, Florida International University, Miami, FL, USA
| | - Indu Shekhar Thakur
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Ruchika Goel
- Medanta Cancer Institute, Medanta-The Medicity, Gurugram, Haryana, 122001, India
| | - Ashok Kumar Vaid
- Medanta Cancer Institute, Medanta-The Medicity, Gurugram, Haryana, 122001, India
| | - Ricardo Jorge Komotar
- Department of Neurological Surgery, University of Miami School of Medicine, Miami, FL, USA
| | - Nasreen Z Ehtesham
- ICMR-National Institute of Pathology, Safdarjung Hospital Campus, New Delhi, India
| | - Seyed E Hasnain
- JH Institute of Molecular Medicine, Jamia Hamdard, New Delhi, India
| | - Deodutta Roy
- Department of Environmental Health Sciences, Florida International University, Miami, USA.
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miR-23a-3p is a Key Regulator of IL-17C-Induced Tumor Angiogenesis in Colorectal Cancer. Cells 2020; 9:cells9061363. [PMID: 32492770 PMCID: PMC7348989 DOI: 10.3390/cells9061363] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 05/17/2020] [Accepted: 05/26/2020] [Indexed: 12/13/2022] Open
Abstract
MicroRNAs (miRNAs) have emerged as key players in tumor angiogenesis. Interleukin-17C (IL-17C) was identified to promote colorectal cancer (CRC) progression. Therefore, we aimed to investigate the effect of IL-17C on tumor angiogenesis, the involvement of miR-23a-3p in IL-17C signaling, and the direct target gene of miR-23a-3p in CRC. In vitro and ex vivo angiogenesis, a mouse xenograft experiment, and immunostaining were performed to test the effect of IL-17C on tumor angiogenesis. ELISA, quantitative real time PCR, and gene silencing were used to uncover the underlying mechanism. IL-17C induced angiogenesis of intestinal endothelial cells, subsequently enhancing cell invasion and migration of DLD-1 cells. IL-17C-stimulated DLD-1 cells produced vascular endothelial growth factor (VEGF) to enhance angiogenesis. Moreover, IL-17C markedly accelerated xenograft tumor growth, which was manifested by substantially reduced tumor growth when treated with the VEGF receptor 2 inhibitor Ki8751. Accordingly, Ki8751 suppressed the expression of IL-17C-stimulated PECAM and VE-cadherin in xenografts. Furthermore, IL-17C activated STAT3 to increase the expression of miR-23a-3p that suppressed semaphorin 6D (SEMA6D) expression, thereby permitting VEGF production. Taken together, our study demonstrates that IL-17C promotes tumor angiogenesis through VEGF production via a STAT3/miR-23a-3p/SEMA6D axis, suggesting its potential as a novel target for anti-CRC therapy.
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Asmaa MJS, Al-Jamal HA, Hussein AR, Yahaya BH, Hassan R, Hussain FA, Shamsuddin S, Johan MF. Transcriptomic Profiles of MV4-11 and Kasumi 1 Acute Myeloid Leukemia Cell Lines Modulated by Epigenetic Modifiers Trichostatin A and 5-Azacytidine. Int J Hematol Oncol Stem Cell Res 2020; 14:72-92. [PMID: 32337016 PMCID: PMC7167603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Background: Acute myeloid leukemia (AML) is the most common form of acute leukemias in adults which is clinically and molecularly heterogeneous. Several risk and genetic factors have been widely investigated to characterize AML. However, the concomitant epigenetic factors in controlling the gene expression lead to AML transformation was not fully understood. This study was aimed to identify epigenetically regulated genes in AML cell lines induced by epigenetic modulating agents, Trichostatin A (TSA) and 5-Azacytidine (5-Aza). Materials and Methods: MV4-11 and Kasumi 1 were treated with TSA and/or 5-Aza at IC50 concentration. Gene expression profiling by microarray was utilized using SurePrint G3 Human Gene Expression v3. Gene ontology and KEGG pathway annotations were analyzed by DAVID bioinformatics software using EASE enrichment score. mRNA expression of the differentially expressed genes were verified by quantitative real time PCR. Results: Gene expression analysis revealed a significant changes in the expression of 24,822, 15,720, 15,654 genes in MV4-11 and 12,598, 8828, 18,026 genes in Kasumi 1, in response to TSA, 5-Aza and combination treatments, respectively, compared to non-treated (p<0.05). 7 genes (SOCS3, TUBA1C, CCNA1, MAP3K6, PTPRC, STAT6 and RUNX1) and 4 genes (ANGPTL4, TUBB2A, ADAM12 and PTPN6) shown to be predominantly expressed in MV4-11 and Kasumi 1, respectively (EASE<0.1). The analysis also revealed phagosome pathway commonly activated in both cell lines. Conclusion: Our data showed a distinct optimal biological characteristic and pathway in different types of leukemic cell lines. These finding may help in the identification of cell-specific epigenetic biomarker in the pathogenesis of AML.
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Affiliation(s)
| | | | | | | | - Roslin Hassan
- Department of Hematology, School of Medical Sciences, Universiti Sains Malaysia, 16150 Kubang Kerian, Kelantan, Malaysia
| | - Faezahtul Arbaeyah Hussain
- Department of Pathology, School of Medical Sciences, Universiti Sains Malaysia, 16150 Kubang Kerian, Kelantan, Malaysia
| | - Shaharum Shamsuddin
- School of Health Sciences, Universiti Sains Malaysia, 16150 Kubang Kerian, Kelantan, Malaysia,Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, 16150 Kubang Kerian, Kelantan, Malaysia
| | - Muhammad Farid Johan
- Department of Hematology, School of Medical Sciences, Universiti Sains Malaysia, 16150 Kubang Kerian, Kelantan, Malaysia
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19
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Li D, Zhong C, Cheng Y, Zhu N, Tan Y, Zhu L, Xu D, Yuan Y. A Competing Nomogram to Predict Survival Outcomes in Invasive Micropapillary Breast Cancer. J Cancer 2019; 10:6801-6812. [PMID: 31839814 PMCID: PMC6909950 DOI: 10.7150/jca.27955] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 09/14/2019] [Indexed: 12/22/2022] Open
Abstract
Background: Although it is widely accepted that invasive micropapillary carcinoma (IMPC) presents more aggressive behavior and has a higher aggressive behavior, the prognosis of IMPC compared with invasive ductal carcinoma (IDC) remains controversial. We conducted this study to explore gene expression profiles of IMPC and establish a competing nomogram that predicts the survival outcomes across these two groups of patients. Methods: Data from the Surveillance, Epidemiology, and End Results (SEER) database were reviewed. Propensity score matching (PSM) was used to adjust for potential baseline confounding between IMPC and IDC group. The Kaplan-Meier method was used to calculate the occurrence of overall mortality. The Gray method was used to estimate the rate of breast cancer specific death (BCSD). A competing regression model was used to evaluate factors associated with BCSD. A nomogram based on the competing risk regression model was established to predict individual outcomes. IMPC-specific gene expression profiles were explored using microarrays data from the Gene Expression Omnibus (GEO) database. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes pathway (KEGG) enrichment analyses were performed. Results: In this study, 330786 (99.62%) patients with IDC 1247 (0.38%) patients with IMPC were included. Patients with IMPC had more lymph node involvement and a larger tumor size compared with those with IDC. After PSM, many distributional differences were eliminated, showing that the IMPC and IDC group were more similar. Patients with IMPC had a favorable prognosis with statistical significance compared with patients with IDC (overall mortality HR = 0.68; 95%CI, 0.53-0.86; P = 0.002). Based on Gray method, patients with IMPC had a favorable prognosis with significant statistical significance compared with patients with IDC (BCSD SHR = 0.64; 95%CI, 0.47-0.88; P = 0.006). Multivariate analysis based on competing risk model demonstrated that IMPC was a favorable independent factor for BCSD. The nomogram could accurately predict BCSD with a high internal and external validated C-index (0.835, 0.818 respectively). A total of 53 upregulated differentially expressed genes (DEGs) and 40 downregulated DEGs of IMPC was identified. The GO analysis results showed that downregulated DEGs were significantly enriched in extracellular structure organization, extracellular matrix, cell-substrate adhesion junction. KEGG analysis of selective gene sets shows that downregulated DEGs significantly enriched for processes related to carbon metabolism, Rap1 signaling pathway. Conclusion: In the current study, IMPC accounted for 0.38% of the entire cohort. IMPC was found to be a favorable independent prognostic factor. The present study identified gene expression profiles and signal pathways of IMPC. The developed nomogram can help the oncologists to predict individual outcomes more accurately.
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Affiliation(s)
- Dan Li
- Department of Medical Oncology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China
| | - Chenhan Zhong
- Department of Medical Oncology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China
| | - Yi Cheng
- Department of Medical Oncology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China
| | - Ning Zhu
- Department of Medical Oncology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China
| | - Yinuo Tan
- Department of Medical Oncology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China
| | - Lizhen Zhu
- Department of Medical Oncology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China
| | - Dong Xu
- Department of Surgical Oncology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, Chinese National Ministry of Education; Key Laboratory of Molecular Biology in Medical Sciences, Zhejiang Province, China), The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China
| | - Ying Yuan
- Department of Medical Oncology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, Chinese National Ministry of Education; Key Laboratory of Molecular Biology in Medical Sciences, Zhejiang Province, China), The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China
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20
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Butti R, Kumar TV, Nimma R, Kundu GC. Impact of semaphorin expression on prognostic characteristics in breast cancer. BREAST CANCER-TARGETS AND THERAPY 2018; 10:79-88. [PMID: 29910635 PMCID: PMC5987790 DOI: 10.2147/bctt.s135753] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Breast cancer is one of the major causes of cancer-related deaths among women worldwide. Aberrant regulation of various growth factors, cytokines, and other proteins and their receptors in cancer cells drives the activation of various oncogenic signaling pathways that lead to cancer progression. Semaphorins are a class of proteins which are differentially expressed in various types of cancer including breast cancer. Earlier, these proteins were known to have a major function in the nerve cell adhesion, migration, and development of the central nervous system. However, their role in the regulation of several aspects of tumor progression has eventually emerged. There are over 30 genes encoding the semaphorins, which are divided into eight subclasses. It has been reported that some members of semaphorin classes are antiangiogenic and antimetastatic in nature, whereas others act as proangiogenic and prometastatic genes. Because of their differential expression and role in angiogenesis and metastasis, semaphorins emerged as one of the important prognostic factors for appraising breast cancer progression.
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Affiliation(s)
- Ramesh Butti
- Laboratory of Tumor Biology, Angiogenesis and Nanomedicine Research, National Centre for Cell Science, Savitribai Phule Pune University, Pune, India
| | - Totakura Vs Kumar
- Laboratory of Tumor Biology, Angiogenesis and Nanomedicine Research, National Centre for Cell Science, Savitribai Phule Pune University, Pune, India
| | - Ramakrishna Nimma
- Laboratory of Tumor Biology, Angiogenesis and Nanomedicine Research, National Centre for Cell Science, Savitribai Phule Pune University, Pune, India
| | - Gopal C Kundu
- Laboratory of Tumor Biology, Angiogenesis and Nanomedicine Research, National Centre for Cell Science, Savitribai Phule Pune University, Pune, India
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21
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Encinas G, Sabelnykova VY, de Lyra EC, Hirata Katayama ML, Maistro S, de Vasconcellos Valle PWM, de Lima Pereira GF, Rodrigues LM, de Menezes Pacheco Serio PA, de Gouvêa ACRC, Geyer FC, Basso RA, Pasini FS, del Pilar Esteves Diz M, Brentani MM, Guedes Sampaio Góes JC, Chammas R, Boutros PC, Koike Folgueira MAA. Somatic mutations in early onset luminal breast cancer. Oncotarget 2018; 9:22460-22479. [PMID: 29854292 PMCID: PMC5976478 DOI: 10.18632/oncotarget.25123] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 03/06/2018] [Indexed: 12/20/2022] Open
Abstract
Breast cancer arising in very young patients may be biologically distinct; however, these tumors have been less well studied. We characterized a group of very young patients (≤ 35 years) for BRCA germline mutation and for somatic mutations in luminal (HER2 negative) breast cancer. Thirteen of 79 unselected very young patients were BRCA1/2 germline mutation carriers. Of the non-BRCA tumors, eight with luminal subtype (HER2 negative) were submitted for whole exome sequencing and integrated with 29 luminal samples from the COSMIC database or previous literature for analysis. We identified C to T single nucleotide variants (SNVs) as the most common base-change. A median of six candidate driver genes was mutated by SNVs in each sample and the most frequently mutated genes were PIK3CA, GATA3, TP53 and MAP2K4. Potential cancer drivers affected in the present non-BRCA tumors include GRHL2, PIK3AP1, CACNA1E, SEMA6D, SMURF2, RSBN1 and MTHFD2. Sixteen out of 37 luminal tumors (43%) harbored SNVs in DNA repair genes, such as ATR, BAP1, ERCC6, FANCD2, FANCL, MLH1, MUTYH, PALB2, POLD1, POLE, RAD9A, RAD51 and TP53, and 54% presented pathogenic mutations (frameshift or nonsense) in at least one gene involved in gene transcription. The differential biology of luminal early-age onset breast cancer needs a deeper genomic investigation.
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Affiliation(s)
- Giselly Encinas
- Instituto do Cancer do Estado de Sao Paulo, Departamento de Radiologia e Oncologia, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, SP, Brazil
| | | | | | - Maria Lucia Hirata Katayama
- Instituto do Cancer do Estado de Sao Paulo, Departamento de Radiologia e Oncologia, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, SP, Brazil
| | - Simone Maistro
- Instituto do Cancer do Estado de Sao Paulo, Departamento de Radiologia e Oncologia, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, SP, Brazil
| | | | - Gláucia Fernanda de Lima Pereira
- Instituto do Cancer do Estado de Sao Paulo, Departamento de Radiologia e Oncologia, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, SP, Brazil
| | - Lívia Munhoz Rodrigues
- Instituto do Cancer do Estado de Sao Paulo, Departamento de Radiologia e Oncologia, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, SP, Brazil
| | - Pedro Adolpho de Menezes Pacheco Serio
- Instituto do Cancer do Estado de Sao Paulo, Departamento de Radiologia e Oncologia, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, SP, Brazil
| | - Ana Carolina Ribeiro Chaves de Gouvêa
- Instituto do Cancer do Estado de Sao Paulo, Departamento de Radiologia e Oncologia, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, SP, Brazil
| | - Felipe Correa Geyer
- Instituto do Cancer do Estado de Sao Paulo, Departamento de Radiologia e Oncologia, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, SP, Brazil
| | | | - Fátima Solange Pasini
- Instituto do Cancer do Estado de Sao Paulo, Departamento de Radiologia e Oncologia, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, SP, Brazil
| | - Maria del Pilar Esteves Diz
- Instituto do Cancer do Estado de Sao Paulo, Departamento de Radiologia e Oncologia, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, SP, Brazil
| | - Maria Mitzi Brentani
- Instituto do Cancer do Estado de Sao Paulo, Departamento de Radiologia e Oncologia, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, SP, Brazil
| | | | - Roger Chammas
- Instituto do Cancer do Estado de Sao Paulo, Departamento de Radiologia e Oncologia, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, SP, Brazil
| | - Paul C. Boutros
- Ontario Institute for Cancer Research, Toronto, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, Canada
| | - Maria Aparecida Azevedo Koike Folgueira
- Instituto do Cancer do Estado de Sao Paulo, Departamento de Radiologia e Oncologia, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, SP, Brazil
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22
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Gao S, Wang Y, Wang M, Li Z, Zhao Z, Wang RX, Wu R, Yuan Z, Cui R, Jiao K, Wang L, Ouyang L, Liu R. MicroRNA-155, induced by FOXP3 through transcriptional repression of BRCA1, is associated with tumor initiation in human breast cancer. Oncotarget 2018; 8:41451-41464. [PMID: 28562349 PMCID: PMC5522316 DOI: 10.18632/oncotarget.17816] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2016] [Accepted: 04/11/2017] [Indexed: 12/12/2022] Open
Abstract
MicroRNA (miR)-155 is upregulated in breast cancer cells and in sera of patients with breast cancer, but its clinical relevance remains uncertain. The objective of the present effort was to address the transcriptional regulation of miR-155. A bioinformatics analysis of public datasets validated upregulation of miR-155 in tumor cells of patients with breast cancer, particularly those who were at early stages and had triple-negative cancers. The expression profiling and clinical relevance of miR-155 in tumor cells and blood cells were characterized by TaqMan miR assays and, in plasma and exosomes, by nest-quantitative PCR analysis. There was a positive correlation between expression of FOXP3 and miR-155 in breast cancer cell lines and primary breast cancers. In breast cancer cells, FOXP3 induced miR-155 through transcriptional repression of BRCA1. Furthermore, in an Alabama cohort, blood and plasma samples were collected from 259 participants, including patients with breast cancer or benign breast tumors, members of breast cancer families, and matched healthy female controls. For patients with early stage or localized breast cancer, there were high levels of miR-155 in both plasma and blood cells. In cultured breast cancer cells, expression of miR-155 was induced by FOXP3 but was not significantly changed in culture medium or exosomes, suggesting that circulating miR-155 originated from blood cells. These findings reveal a transcriptional axis of FOXP3-BRCA1-miR-155 in breast cancer cells and show that plasma miR-155 may serve as a non-invasive biomarker for detection of early stage breast cancer.
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Affiliation(s)
- Song Gao
- The Second Department of Clinical Oncology, Shengjing Hospital of China Medical University, Shenyang, China.,Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Yicun Wang
- Provincial Key Laboratory on Molecular and Chemical Genetic, Second Hospital of Jilin University, Changchun, China
| | - Meng Wang
- Department of Oncology, Cancer Hospital of Harbin Medical University, Harbin, China
| | - Zhi Li
- Department of General Surgery, Henan Cancer Hospital, Zhengzhou, China
| | - Zhiying Zhao
- School of Computer Science and Engineering, Northeastern University, Shenyang, China
| | - Raymond X Wang
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Rong Wu
- The Second Department of Clinical Oncology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Zhengwei Yuan
- The Second Department of Clinical Oncology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Ranji Cui
- Provincial Key Laboratory on Molecular and Chemical Genetic, Second Hospital of Jilin University, Changchun, China
| | - Kai Jiao
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA.,Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Lizhong Wang
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA.,Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Ling Ouyang
- Department of Gynecology and Obstetrics, Shengjing Hospital of China Medical University, Shenyang, China
| | - Runhua Liu
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA.,Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, Alabama, USA
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23
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Abstract
Several neuronal guidance proteins, known as semaphorin molecules, function in the immune system. This dual tissue performance has led to them being defined as "neuroimmune semaphorins". They have been shown to regulate T cell activation by serving as costimulatory molecules. Similar to classical costimulatory molecules, neuroimmune semaphorins are either constitutively or inducibly expressed on immune cells. In contrast to the classical costimulatory molecule function, the action of neuroimmune semaphorins requires the presence of two signals, the first one provided by TCR/MHC engagement, and the second one provided by B7/CD28 interaction. Thus, neuroimmune semaphorins serve as a "signal three" for immune cell activation and regulate the overall intensity of immune response. The current knowledge on their structures, multiple receptors, specific cell/tissue/organ expression, and distinct functions in different diseases are summarized and discussed in this review.
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Affiliation(s)
- Svetlana P Chapoval
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA.
- Center for Vascular and Inflammatory Diseases, University of Maryland School of Medicine, Baltimore, MD, USA.
- Program in Oncology at the Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore, MD, USA.
- SemaPlex LLC, Ellicott City, MD, USA.
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24
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Minicã CC, Mbarek H, Pool R, Dolan CV, Boomsma DI, Vink JM. Pathways to smoking behaviours: biological insights from the Tobacco and Genetics Consortium meta-analysis. Mol Psychiatry 2017; 22:82-88. [PMID: 27021816 PMCID: PMC5777181 DOI: 10.1038/mp.2016.20] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Revised: 02/04/2016] [Accepted: 02/05/2016] [Indexed: 01/19/2023]
Abstract
By running gene and pathway analyses for several smoking behaviours in the Tobacco and Genetics Consortium (TAG) sample of 74 053 individuals, 21 genes and several chains of biological pathways were implicated. Analyses were carried out using the HYbrid Set-based Test (HYST) as implemented in the Knowledge-based mining system for Genome-wide Genetic studies software. Fifteen genes are novel and were not detected with the single nucleotide polymorphism-based approach in the original TAG analysis. For quantity smoked, 14 genes passed the false discovery rate of 0.05 (corrected for multiple testing), with the top association signal located at the IREB2 gene (P=1.57E-37). Three genomic loci were significantly associated with ever smoked. The top signal is located at the noncoding antisense RNA transcript BDNF-AS (P=6.25E-07) on 11p14. The SLC25A21 gene (P=2.09E-08) yielded the top association signal in the analysis of smoking cessation. The 19q13 noncoding RNA locus exceeded the genome-wide significance in the analysis of age at initiation (P=1.33E-06). Pathways belonging to the Neuronal system pathways, harbouring the nicotinic acetylcholine receptor genes expressing the α (CHRNA 1-9), β (CHRNB 1-4), γ, δ and ɛ subunits, yielded the smallest P-values in the pathway analysis of the quantity smoked (lowest P=4.90E-42). Additionally, pathways belonging to 'a subway map of cancer pathways' regulating the cell cycle, mitotic DNA replication, axon growth and synaptic plasticity were found significantly enriched for genetic variants in ever smokers relative to never smokers (lowest P=1.61E-07). In addition, these pathways were also significantly associated with the quantity smoked (lowest P=4.28E-17). Our results shed light on one of the world's leading causes of preventable death and open a path to potential therapeutic targets. These results are informative in decoding the biological bases of other disease traits, such as depression and cancers, with which smoking shares genetic vulnerabilities.
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Affiliation(s)
- Camelia C. Minicã
- Department of Biological Psychology, Vrije Universiteit, Amsterdam, The Netherlands
| | - Hamdi Mbarek
- Department of Biological Psychology, Vrije Universiteit, Amsterdam, The Netherlands
| | - René Pool
- Department of Biological Psychology, Vrije Universiteit, Amsterdam, The Netherlands
| | - Conor V. Dolan
- Department of Biological Psychology, Vrije Universiteit, Amsterdam, The Netherlands
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25
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Novel insight into triple-negative breast cancers, the emerging role of angiogenesis, and antiangiogenic therapy. Expert Rev Mol Med 2016; 18:e18. [DOI: 10.1017/erm.2016.17] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Triple-negative breast cancer (TNBC) is a heterogeneous group of tumours characterised by lack of expression of oestrogen-, progesterone- and human epidermal growth factor receptors. TNBC, which represents approximately 15% of all mammary tumours, has a poor prognosis because of an aggressive behaviour and the lack of specific treatment. Accordingly, TNBC has become a major focus of research into breast cancer and is now classified into several molecular subtypes, each with a different prognosis. Pathological angiogenesis occurs at a late stage in the proliferation of TNBC and is associated with invasion and metastasis; there is an association with metabolic syndrome. Semaphorins are a versatile family of proteins with multiple roles in angiogenesis, tumour growth and metastasis and may represent a clinically useful focus for therapeutic targeting in this type of breast cancer. Another important field of investigation into the control of pathological angiogenesis is related to the expression of noncoding RNA (ncRNA) – these molecules can be considered as a therapeutic target or as a biomarker. Several molecular agents for intervening in the activity of different signalling pathways are being explored in TNBC, but none has so far proved effective in clinical trials and the disease continues to pose a defining challenge for clinical management as well as innovative cancer research.
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26
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Neufeld G, Mumblat Y, Smolkin T, Toledano S, Nir-Zvi I, Ziv K, Kessler O. The role of the semaphorins in cancer. Cell Adh Migr 2016; 10:652-674. [PMID: 27533782 PMCID: PMC5160032 DOI: 10.1080/19336918.2016.1197478] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2016] [Revised: 05/19/2016] [Accepted: 05/30/2016] [Indexed: 12/16/2022] Open
Abstract
The semaphorins were initially characterized as axon guidance factors, but have subsequently been implicated also in the regulation of immune responses, angiogenesis, organ formation, and a variety of additional physiological and developmental functions. The semaphorin family contains more then 20 genes divided into 7 subfamilies, all of which contain the signature sema domain. The semaphorins transduce signals by binding to receptors belonging to the neuropilin or plexin families. Additional receptors which form complexes with these primary semaphorin receptors are also frequently involved in semaphorin signaling. Recent evidence suggests that semaphorins also fulfill important roles in the etiology of multiple forms of cancer. Some semaphorins have been found to function as bona-fide tumor suppressors and to inhibit tumor progression by various mechanisms while other semaphorins function as inducers and promoters of tumor progression.
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Affiliation(s)
- Gera Neufeld
- Cancer Research and Vascular Biology Center, The Bruce Rappaport Faculty of Medicine, Technion, Israel Institute of Technology, Haifa, Israel
| | - Yelena Mumblat
- Cancer Research and Vascular Biology Center, The Bruce Rappaport Faculty of Medicine, Technion, Israel Institute of Technology, Haifa, Israel
| | - Tatyana Smolkin
- Cancer Research and Vascular Biology Center, The Bruce Rappaport Faculty of Medicine, Technion, Israel Institute of Technology, Haifa, Israel
| | - Shira Toledano
- Cancer Research and Vascular Biology Center, The Bruce Rappaport Faculty of Medicine, Technion, Israel Institute of Technology, Haifa, Israel
| | - Inbal Nir-Zvi
- Cancer Research and Vascular Biology Center, The Bruce Rappaport Faculty of Medicine, Technion, Israel Institute of Technology, Haifa, Israel
| | - Keren Ziv
- Cancer Research and Vascular Biology Center, The Bruce Rappaport Faculty of Medicine, Technion, Israel Institute of Technology, Haifa, Israel
| | - Ofra Kessler
- Cancer Research and Vascular Biology Center, The Bruce Rappaport Faculty of Medicine, Technion, Israel Institute of Technology, Haifa, Israel
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27
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Neufeld G, Mumblat Y, Smolkin T, Toledano S, Nir-Zvi I, Ziv K, Kessler O. The semaphorins and their receptors as modulators of tumor progression. Drug Resist Updat 2016; 29:1-12. [DOI: 10.1016/j.drup.2016.08.001] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2016] [Revised: 07/31/2016] [Accepted: 08/23/2016] [Indexed: 12/16/2022]
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28
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Array-CGH diagnosis in ovarian failure: identification of new molecular actors for ovarian physiology. J Ovarian Res 2016; 9:63. [PMID: 27716277 PMCID: PMC5048446 DOI: 10.1186/s13048-016-0272-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 09/23/2016] [Indexed: 11/13/2022] Open
Abstract
Background Ovarian failure (OF) is considered premature if it occurs before the age of 40. This study investigates the genetic aetiology underlying OF in women under the age of 40 years. Methods We conducted an experimental prospective study performing all genome microarrays in 60 patients younger than 40 years presenting an OF revealed by a decrease of circulating Anti-Müllerian Hormone (AMH) and leading to an oocyte donation program. Results We identified nine significant copy number variations (CNVs) including candidate genes potentially implicated in reproductive function. These genes are principally involved in cell division and chromosome segregation (SYCE1, CLASP1, CENP-A, CDC16), in ciliary development and/or function (RSPH1, KIF24), are linked with known gonadal genes or expressed in female genital tract (CSMD1, SEMA6D, KIAA1324). Conclusions Our data strengthen the idea that microarrays should be used in combination with karyotype for aetiological assessment of patients with OF. This analysis may have a therapeutic impact as the identification of new molecular actors for gonadal development or ovarian physiology is useful for the prediction of an ovarian reserve decline and makes possible preventive fertility preservation.
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29
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Gurrapu S, Tamagnone L. Transmembrane semaphorins: Multimodal signaling cues in development and cancer. Cell Adh Migr 2016; 10:675-691. [PMID: 27295627 DOI: 10.1080/19336918.2016.1197479] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Semaphorins constitute a large family of membrane-bound and secreted proteins that provide guidance cues for axon pathfinding and cell migration. Although initially discovered as repelling cues for axons in nervous system, they have been found to regulate cell adhesion and motility, angiogenesis, immune function and tumor progression. Notably, semaphorins are bifunctional cues and for instance can mediate both repulsive and attractive functions in different contexts. While many studies focused so far on the function of secreted family members, class 1 semaphorins in invertebrates and class 4, 5 and 6 in vertebrate species comprise around 14 transmembrane semaphorin molecules with emerging functional relevance. These can signal in juxtacrine, paracrine and autocrine fashion, hence mediating long and short range repulsive and attractive guidance cues which have a profound impact on cellular morphology and functions. Importantly, transmembrane semaphorins are capable of bidirectional signaling, acting both in "forward" mode via plexins (sometimes in association with receptor tyrosine kinases), and in "reverse" manner through their cytoplasmic domains. In this review, we will survey known molecular mechanisms underlying the functions of transmembrane semaphorins in development and cancer.
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Affiliation(s)
- Sreeharsha Gurrapu
- a Department of Oncology , University of Torino c/o IRCCS , Candiolo ( TO ), Italy.,b Candiolo Cancer Institute, IRCCS-FPO , Candiolo ( TO ), Italy
| | - Luca Tamagnone
- a Department of Oncology , University of Torino c/o IRCCS , Candiolo ( TO ), Italy.,b Candiolo Cancer Institute, IRCCS-FPO , Candiolo ( TO ), Italy
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30
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Schulten HJ, Hussein D, Al-Adwani F, Karim S, Al-Maghrabi J, Al-Sharif M, Jamal A, Al-Ghamdi F, Baeesa SS, Bangash M, Chaudhary A, Al-Qahtani M. Microarray Expression Data Identify DCC as a Candidate Gene for Early Meningioma Progression. PLoS One 2016; 11:e0153681. [PMID: 27096627 PMCID: PMC4838307 DOI: 10.1371/journal.pone.0153681] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2016] [Accepted: 04/01/2016] [Indexed: 12/23/2022] Open
Abstract
Meningiomas are the most common primary brain tumors bearing in a minority of cases an aggressive phenotype. Although meningiomas are stratified according to their histology and clinical behavior, the underlying molecular genetics predicting aggressiveness are not thoroughly understood. We performed whole transcript expression profiling in 10 grade I and four grade II meningiomas, three of which invaded the brain. Microarray expression analysis identified deleted in colorectal cancer (DCC) as a differentially expressed gene (DEG) enabling us to cluster meningiomas into DCC low expression (3 grade I and 3 grade II tumors), DCC medium expression (2 grade I and 1 grade II tumors), and DCC high expression (5 grade I tumors) groups. Comparison between the DCC low expression and DCC high expression groups resulted in 416 DEGs (p-value < 0.05; fold change > 2). The most significantly downregulated genes in the DCC low expression group comprised DCC, phosphodiesterase 1C (PDE1C), calmodulin-dependent 70kDa olfactomedin 2 (OLFM2), glutathione S-transferase mu 5 (GSTM5), phosphotyrosine interaction domain containing 1 (PID1), sema domain, transmembrane domain (TM) and cytoplasmic domain, (semaphorin) 6D (SEMA6D), and indolethylamine N-methyltransferase (INMT). The most significantly upregulated genes comprised chromosome 5 open reading frame 63 (C5orf63), homeodomain interacting protein kinase 2 (HIPK2), and basic helix-loop-helix family, member e40 (BHLHE40). Biofunctional analysis identified as predicted top upstream regulators beta-estradiol, TGFB1, Tgf beta complex, LY294002, and dexamethasone and as predicted top regulator effectors NFkB, PIK3R1, and CREBBP. The microarray expression data served also for a comparison between meningiomas from female and male patients and for a comparison between brain invasive and non-invasive meningiomas resulting in a number of significant DEGs and related biofunctions. In conclusion, based on its expression levels, DCC may constitute a valid biomarker to identify those benign meningiomas at risk for progression.
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Affiliation(s)
- Hans-Juergen Schulten
- Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia
- KACST Technology Innovation Center in Personalized Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
- * E-mail:
| | - Deema Hussein
- King Fahad Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Fatima Al-Adwani
- Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Biology, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Sajjad Karim
- Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia
- KACST Technology Innovation Center in Personalized Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Jaudah Al-Maghrabi
- Department of Pathology, Faculty of Medicine, King Abdulaziz University Hospital, Jeddah, Saudi Arabia
- Department of Pathology, King Faisal Specialist Hospital and Research Center, Jeddah, Saudi Arabia
| | - Mona Al-Sharif
- Department of Biology, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Awatif Jamal
- Department of Pathology, Faculty of Medicine, King Abdulaziz University Hospital, Jeddah, Saudi Arabia
| | - Fahad Al-Ghamdi
- Department of Pathology, Faculty of Medicine, King Abdulaziz University Hospital, Jeddah, Saudi Arabia
| | - Saleh S. Baeesa
- Division of Neurosurgery, Department of Surgery, King Abdulaziz University Hospital, Jeddah, Saudi Arabia
| | - Mohammed Bangash
- Division of Neurosurgery, Department of Surgery, King Abdulaziz University Hospital, Jeddah, Saudi Arabia
| | - Adeel Chaudhary
- Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia
- KACST Technology Innovation Center in Personalized Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mohammed Al-Qahtani
- Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia
- KACST Technology Innovation Center in Personalized Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
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