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Peng J, Liu X, Mao Y, Lv M, Ma T, Liu J, Zhou Q, Han Y, Li X, Wang H. Upregulation of collagen type X alpha 1 promotes the progress of triple-negative breast cancer via Wnt/β-catenin signaling. Mol Carcinog 2024. [PMID: 38780151 DOI: 10.1002/mc.23747] [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: 11/29/2023] [Revised: 04/04/2024] [Accepted: 05/07/2024] [Indexed: 05/25/2024]
Abstract
Triple-negative breast cancer (TNBC) is a malignant tumor with high degree of malignancy and lack of effective target treatment. The research aims to explore the role and mechanism of X collagen alpha-1 chain protein (COL10A1 gene) in TNBC. UALCAN and Kaplan-Meier were used to detect the expression of COL10A1 and its role in the prognosis of breast cancer patients. The cells with stably expressing high levels of COL10A1 were obtained by recombinant lentivirus infection. The expression of COL10A1 in cells was temporarily downregulated by siRNA interference fragments. Real-time quantitative polymerase chain reaction and western blot analysis were utilized to detect the changes of COL10A1 mRNA and protein expression. The biological functions of the cells were evaluated by colony formation, cell counting kit-8, cell invasion and wound healing experiments. In addition, the effect of COL10A1 on angiogenesis was investigated by tube formation assay. Xenograft tumor model was used to confirm the effect of COL10A1 on tumorigenicity in vivo and multiplex fluorescent immunohistochemistry to detect multiple proteins simultaneously. The possible molecular mechanism of the function of COL10A1 was speculated through the detection of proteins in functionally related pathways. COL10A1 is highly expressed and is significantly associated with worse overall survival (OS) and recurrence-free survival (RFS) in TNBC. Overexpression of COL10A1 increased the clone formation rate and cell migration capacity of TNBC cells. In the COL10A1 overexpression group, the clone formation rates of MD-MB-231 and BT-549 cells (21.5 ± 0.62, 27.83 ± 3.72)% were significantly higher than those in the control group(15.23 ± 2.79, 19.4 ± 1.47)%, and the relative migration ratio (47.40 ± 3.09, 41.26 ± 4.33)% were higher than those in the control group (34.48 ± 2.03, 21.80 ± 1.03)%. When the expression of COL10A1 was downregulated, the ability of clone formation and wound-healing migration capacity in TNBC cells was weakened. Upregulated COL10A1 in TNBC cells generated more junctions and longer total segments between vascular endothelial cells, and promoted angiogenesis of the cells, and thus enhanced the tumorigenesis. In TNBC, it was found that COL10A1 might affect epithelial-mesenchymal transition (EMT) of the cells through Wnt/β-catenin signaling pathway by the detection of the related pathway proteins. COL10A1 is highly expressed in TNBC, and its high expression leads to poor OS and RFS. COL10A1 may enhance TNBC cell proliferation, migration and tumor-related angiogenesis, and promote tumorigenesis in vivo via Wnt/β-catenin signaling.
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Affiliation(s)
- Jing Peng
- Breast Disease Center, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Xiangping Liu
- Medical Research Center, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Yan Mao
- Breast Disease Center, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Meng Lv
- Breast Disease Center, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Teng Ma
- Breast Disease Center, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Jiaxiu Liu
- Medical Research Center, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Quan Zhou
- Medical Research Center, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Yafei Han
- Medical Research Center, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Xin Li
- Breast Disease Center, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Haibo Wang
- Breast Disease Center, The Affiliated Hospital of Qingdao University, Qingdao, China
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Li X, Jin Y, Xue J. Unveiling Collagen's Role in Breast Cancer: Insights into Expression Patterns, Functions and Clinical Implications. Int J Gen Med 2024; 17:1773-1787. [PMID: 38711825 PMCID: PMC11073151 DOI: 10.2147/ijgm.s463649] [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: 02/12/2024] [Accepted: 04/21/2024] [Indexed: 05/08/2024] Open
Abstract
Collagen, the predominant protein constituent of the mammalian extracellular matrix (ECM), comprises a diverse family of 28 members (I-XXVIII). Beyond its structural significance, collagen is implicated in various diseases or cancers, notably breast cancer, where it influences crucial cellular processes including proliferation, metastasis, apoptosis, and drug resistance, intricately shaping cancer progression and prognosis. In breast cancer, distinct collagens exhibit differential expression profiles, with some showing heightened or diminished levels in cancerous tissues or cells compared to normal counterparts, suggesting specific and pivotal biological functions. In this review, we meticulously analyze the expression of individual collagen members in breast cancer, utilizing Transcripts Per Million (TPM) data sourced from the GEPIA2 database. Through this analysis, we identify collagens that deviate from normal expression patterns in breast cancer, providing a comprehensive overview of their expression dynamics, functional roles, and underlying mechanisms. Our findings shed light on recent advancements in understanding the intricate interplay between these aberrantly expressed collagens and breast cancer. This exploration aims to offer valuable insights for the identification of potential biomarkers and therapeutic targets, thereby advancing the prospects of more effective interventions in breast cancer treatment.
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Affiliation(s)
- Xia Li
- Department of Molecular Diagnosis, Northern Jiangsu People’s Hospital, Yangzhou, People’s Republic of China
| | - Yue Jin
- Department of Molecular Diagnosis, Northern Jiangsu People’s Hospital, Yangzhou, People’s Republic of China
| | - Jian Xue
- Department of Emergency Medicine, Yizheng People’s Hospital, Yangzhou, People’s Republic of China
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Wang C, Wang J, Chen S, Li K, Wan S, Yang L. COL10A1 as a Prognostic Biomarker in Association with Immune Infiltration in Prostate Cancer. Curr Cancer Drug Targets 2024; 24:340-353. [PMID: 37592784 DOI: 10.2174/1568009623666230817101809] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 03/19/2023] [Accepted: 06/06/2023] [Indexed: 08/19/2023]
Abstract
BACKGROUND The collagen type X alpha 1 (COL10A1) has recently been found to play an important role in the development and progression of cancer. However, the link between COL10A1 and the tumor immune microenvironment remains understood scantily. METHODS In the current study, the pan-cancer data of The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) were used to investigate the expression mode, the clinical prognostic and diagnostic value of COL10A1 in different tumors. We used TCGA data to assess the correlations between COL10A1 and clinical symptoms of prostate cancer. The R packages "edgR" and "clusterProfiler" were used for differential expression gene and enrichment analysis of COL10A1. Immunohistochemistry was further employed to corroborate the expression of COL10A1 gene in prostate cancer. After that, we used TIMER to evaluate the pertinence of COL10A1 expression to immune infiltration level in prostate cancer. RESULTS On the whole, COL10A1 was expressed at significantly higher levels in a variety of tumor tissues than in the corresponding normal tissues. Besides, significant correlations with tumor prognosis and relative exactitude in predicting tumors show that COL10A1 may be a probable prognostic and diagnostic biomarker of prostate cancer. In addition, the evidence indicates a significant correlation between COL10A1 and clinical symptoms of prostate cancer. Furthermore, the main molecular functions of COL10A1 included humoral immune response, complement activation, immunoglobulin, regulation of complement activation, and regulation of humoral immune response. Finally, we found that COL10A1 expression is positively correlated with enhanced macrophage and M2 macrophage infiltration in prostate cancer. CONCLUSION The study indicates that COL10A1 might participate in M2 macrophage polarization in prostate cancer. COL10A1 might be an innovative biomarker to evaluate tumor microenvironment immune cell infiltration and prognosis in prostate cancer.
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Affiliation(s)
- Chenyang Wang
- Department of Urology, The Second Hospital of Lanzhou University, Lanzhou, China
- Gansu Province Clinical Research Center for Urology, Lanzhou, China
| | - Jirong Wang
- Department of Urology, The Second Hospital of Lanzhou University, Lanzhou, China
- Gansu Province Clinical Research Center for Urology, Lanzhou, China
| | - Siyu Chen
- Department of Urology, The Second Hospital of Lanzhou University, Lanzhou, China
- Gansu Province Clinical Research Center for Urology, Lanzhou, China
| | - Kunpeng Li
- Department of Urology, The Second Hospital of Lanzhou University, Lanzhou, China
- Gansu Province Clinical Research Center for Urology, Lanzhou, China
| | - Shun Wan
- Department of Urology, The Second Hospital of Lanzhou University, Lanzhou, China
- Gansu Province Clinical Research Center for Urology, Lanzhou, China
| | - Li Yang
- Department of Urology, The Second Hospital of Lanzhou University, Lanzhou, China
- Gansu Province Clinical Research Center for Urology, Lanzhou, China
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Lee J, Sternberg H, Bignone PA, Murai J, Malik NN, West MD, Larocca D. Clonal and Scalable Endothelial Progenitor Cell Lines from Human Pluripotent Stem Cells. Biomedicines 2023; 11:2777. [PMID: 37893151 PMCID: PMC10604251 DOI: 10.3390/biomedicines11102777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 10/02/2023] [Accepted: 10/06/2023] [Indexed: 10/29/2023] Open
Abstract
Human pluripotent stem cells (hPSCs) can be used as a renewable source of endothelial cells for treating cardiovascular disease and other ischemic conditions. Here, we present the derivation and characterization of a panel of distinct clonal embryonic endothelial progenitor cells (eEPCs) lines that were differentiated from human embryonic stem cells (hESCs). The hESC line, ESI-017, was first partially differentiated to produce candidate cultures from which eEPCs were cloned. Endothelial cell identity was assessed by transcriptomic analysis, cell surface marker expression, immunocytochemical marker analysis, and functional analysis of cells and exosomes using vascular network forming assays. The transcriptome of the eEPC lines was compared to various adult endothelial lines as well as various non-endothelial cells including both adult and embryonic origins. This resulted in a variety of distinct cell lines with functional properties of endothelial cells and strong transcriptomic similarity to adult endothelial primary cell lines. The eEPC lines, however, were distinguished from adult endothelium by their novel pattern of embryonic gene expression. We demonstrated eEPC line scalability of up to 80 population doublings (pd) and stable long-term expansion of over 50 pd with stable angiogenic properties at late passage. Taken together, these data support the finding that hESC-derived clonal eEPC lines are a potential source of scalable therapeutic cells and cell products for treating cardiovascular disease. These eEPC lines offer a highly promising resource for the development of further preclinical studies aimed at therapeutic interventions.
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Affiliation(s)
- Jieun Lee
- AgeX Therapeutics, Inc., 1101 Marina Village Parkway, Alameda, CA 94501, USA; (H.S.); (P.A.B.); (N.N.M.); (D.L.)
| | - Hal Sternberg
- AgeX Therapeutics, Inc., 1101 Marina Village Parkway, Alameda, CA 94501, USA; (H.S.); (P.A.B.); (N.N.M.); (D.L.)
| | - Paola A. Bignone
- AgeX Therapeutics, Inc., 1101 Marina Village Parkway, Alameda, CA 94501, USA; (H.S.); (P.A.B.); (N.N.M.); (D.L.)
| | - James Murai
- Advanced Cell Technology, Alameda, CA 94502, USA
| | - Nafees N. Malik
- AgeX Therapeutics, Inc., 1101 Marina Village Parkway, Alameda, CA 94501, USA; (H.S.); (P.A.B.); (N.N.M.); (D.L.)
| | | | - Dana Larocca
- AgeX Therapeutics, Inc., 1101 Marina Village Parkway, Alameda, CA 94501, USA; (H.S.); (P.A.B.); (N.N.M.); (D.L.)
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Ali R, Sultan A, Ishrat R, Haque S, Khan NJ, Prieto MA. Identification of New Key Genes and Their Association with Breast Cancer Occurrence and Poor Survival Using In Silico and In Vitro Methods. Biomedicines 2023; 11:biomedicines11051271. [PMID: 37238942 DOI: 10.3390/biomedicines11051271] [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: 01/31/2023] [Revised: 02/20/2023] [Accepted: 03/07/2023] [Indexed: 05/28/2023] Open
Abstract
Breast cancer is one of the most prevalent types of cancer diagnosed globally and continues to have a significant impact on the global number of cancer deaths. Despite all efforts of epidemiological and experimental research, therapeutic concepts in cancer are still unsatisfactory. Gene expression datasets are widely used to discover the new biomarkers and molecular therapeutic targets in diseases. In the present study, we analyzed four datasets using R packages with accession number GSE29044, GSE42568, GSE89116, and GSE109169 retrieved from NCBI-GEO and differential expressed genes (DEGs) were identified. Protein-protein interaction (PPI) network was constructed to screen the key genes. Subsequently, the GO function and KEGG pathways were analyzed to determine the biological function of key genes. Expression profile of key genes was validated in MCF-7 and MDA-MB-231 human breast cancer cell lines using qRT-PCR. Overall expression level and stage wise expression pattern of key genes was determined by GEPIA. The bc-GenExMiner was used to compare expression level of genes among groups of patients with respect to age factor. OncoLnc was used to analyze the effect of expression levels of LAMA2, TIMP4, and TMTC1 on the survival of breast cancer patients. We identified nine key genes, of which COL11A1, MMP11, and COL10A1 were found up-regulated and PCOLCE2, LAMA2, TMTC1, ADAMTS5, TIMP4, and RSPO3 were found down-regulated. Similar expression pattern of seven among nine genes (except ADAMTS5 and RSPO3) was observed in MCF-7 and MDA-MB-231 cells. Further, we found that LAMA2, TMTC1, and TIMP4 were significantly expressed among different age groups of patients. LAMA2 and TIMP4 were found significantly associated and TMTC1 was found less correlated with breast cancer occurrence. We found that the expression level of LAMA2, TIMP4, and TMTC1 was abnormal in all TCGA tumors and significantly associated with poor survival.
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Affiliation(s)
- Rafat Ali
- Department of Biosciences, Jamia Millia Islamia (A Central University), New Delhi 110025, India
| | - Armiya Sultan
- Department of Biosciences, Jamia Millia Islamia (A Central University), New Delhi 110025, India
| | - Romana Ishrat
- Center for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia (A Central University), New Delhi 110025, India
| | - Shafiul Haque
- Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan 45142, Saudi Arabia
- Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Beirut P.O. Box 36, Lebanon
- Centre of Medical and Bio-Allied Health Sciences Research, Ajman University, Ajman P.O. Box 346, United Arab Emirates
| | - Nida Jamil Khan
- Department of Biosciences, Jamia Millia Islamia (A Central University), New Delhi 110025, India
| | - Miguel Angel Prieto
- Nutrition and Bromatology Group, Department of Analytical Chemistry and Food Science, Faculty of Science, Universidade de Vigo, E32004 Ourense, Spain
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Wang X, Bai Y, Zhang F, Li D, Chen K, Wu R, Tang Y, Wei X, Han P. Prognostic value of COL10A1 and its correlation with tumor-infiltrating immune cells in urothelial bladder cancer: A comprehensive study based on bioinformatics and clinical analysis validation. Front Immunol 2023; 14:955949. [PMID: 37006317 PMCID: PMC10063846 DOI: 10.3389/fimmu.2023.955949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Accepted: 02/22/2023] [Indexed: 03/19/2023] Open
Abstract
IntroductionBladder cancer (BLCA) is one of the most lethal diseases. COL10A1 is secreted small-chain collagen in the extracellular matrix associated with various tumors, including gastric, colon, breast, and lung cancer. However, the role of COL10A1 in BLCA remains unclear. This is the first research focusing on the prognostic value of COL10A1 in BLCA. In this research, we aimed to uncover the association between COL10A1 and the prognosis, as well as other clinicopathological parameters in BLCA.MethodsWe obtained gene expression profiles of BLCA and normal tissues from the TCGA, GEO, and ArrayExpress databases. Immunohistochemistry staining was performed to investigate the protein expression and prognostic value of COL10A1 in BLCA patients. GO and KEGG enrichment along with GSEA analyses were performed to reveal the biological functions and potential regulatory mechanisms of COL10A1 based on the gene co-expression network. We used the “maftools” R package to display the mutation profiles between the high and low COL10A1 groups. GIPIA2, TIMER, and CIBERSORT algorithms were utilized to explore the effect of COL10A1 on the tumor immune microenvironment.ResultsWe found that COL10A1 was upregulated in the BLCA samples, and increased COL10A1 expression was related to poor overall survival. Functional annotation of 200 co-expressed genes positively correlated with COL10A1 expression, including GO, KEGG, and GSEA enrichment analyses, indicated that COL10A1 was basically involved in the extracellular matrix, protein modification, molecular binding, ECM-receptor interaction, protein digestion and absorption, focal adhesion, and PI3K-Akt signaling pathway. The most commonly mutated genes of BLCA were different between high and low COL10A1 groups. Tumor immune infiltrating analyses showed that COL10A1 might have an essential role in recruiting infiltrating immune cells and regulating immunity in BLCA, thus affecting prognosis. Finally, external datasets and biospecimens were used, and the results further validated the aberrant expression of COL10A1 in BLCA samples.ConclusionsIn conclusion, our study demonstrates that COL10A1 is an underlying prognostic and predictive biomarker in BLCA.
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Sorvina A, Antoniou M, Esmaeili Z, Kochetkova M. Unusual Suspects: Bone and Cartilage ECM Proteins as Carcinoma Facilitators. Cancers (Basel) 2023; 15:cancers15030791. [PMID: 36765749 PMCID: PMC9913341 DOI: 10.3390/cancers15030791] [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: 12/31/2022] [Revised: 01/25/2023] [Accepted: 01/25/2023] [Indexed: 01/31/2023] Open
Abstract
The extracellular matrix (ECM) is the complex three-dimensional network of fibrous proteins and proteoglycans that constitutes an essential part of every tissue to provide support for normal tissue homeostasis. Tissue specificity of the ECM in its topology and structure supports unique biochemical and mechanical properties of each organ. Cancers, like normal tissues, require the ECM to maintain multiple processes governing tumor development, progression and spread. A large body of experimental and clinical evidence has now accumulated to demonstrate essential roles of numerous ECM components in all cancer types. Latest findings also suggest that multiple tumor types express, and use to their advantage, atypical ECM components that are not found in the cancer tissue of origin. However, the understanding of cancer-specific expression patterns of these ECM proteins and their exact roles in selected tumor types is still sketchy. In this review, we summarize the latest data on the aberrant expression of bone and cartilage ECM proteins in epithelial cancers and their specific functions in the pathogenesis of carcinomas and discuss future directions in exploring the utility of this selective group of ECM components as future drug targets.
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Wen Z, Sun J, Luo J, Fu Y, Qiu Y, Li Y, Xu Y, Wu H, Zhang Q. COL10A1-DDR2 axis promotes the progression of pancreatic cancer by regulating MEK/ERK signal transduction. Front Oncol 2022; 12:1049345. [PMID: 36530986 PMCID: PMC9750160 DOI: 10.3389/fonc.2022.1049345] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 11/10/2022] [Indexed: 09/16/2023] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal malignant tumors with a poor prognosis. Type X collagen α 1 chain (COL10A1), a member of the collagen family, is a gene associated with the progression of a variety of human tumors, but the specific function and molecular mechanism of COL10A1 in pancreatic cancer remain unclear. Our study found that COL10A1 is highly expressed in pancreatic cancer cells and tissues, and its high expression is related to poor prognosis and some clinicopathological features, such as tumor size and differentiation. Biological functional experiments showed that overexpression of COL10A1 enhanced the proliferation and migration of PDAC cells. Interestingly, discoid protein domain receptor 2 (DDR2), the receptor of COL10A1, is regulated by COL10A1. We found that the COL10A1-DDR2 axis activates the mitogen-activated protein kinase (MEK)/extracellular signal-regulated kinase (ERK) pathway, which leads to epithelial-mesenchymal transformation (EMT) and accelerates the progression of pancreatic cancer. In summary, COL10A1 regulates PDAC cell proliferation and MEK/ERK signaling pathways by binding to DDR2 to promote migration, invasion and EMT. Our study suggested that COL10A1 might be a critical factor in promoting PDAC progression. More research is needed to confirm COL10A1 as a potential biomarker and therapeutic target for PDAC.
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Affiliation(s)
- Zhihui Wen
- Department of Pathology, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jingbo Sun
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China
| | - Junjie Luo
- Department of General Surgery, The Third Affiliated Hospital of Southern Medical University, Guangzhou, Guangdong, China
| | - Yun Fu
- Department of Pathology, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Yue Qiu
- Department of Pathology, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Yanyan Li
- Department of Pathology, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Yangwei Xu
- Department of Pathology, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Hongmei Wu
- Department of Pathology, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Qingling Zhang
- Department of Pathology, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China
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Kahlert UD, Shi W, Strecker M, Scherpinski LA, Wartmann T, Dölling M, Perrakis A, Relja B, Mengoni M, Braun A, Croner RS. COL10A1 allows stratification of invasiveness of colon cancer and associates to extracellular matrix and immune cell enrichment in the tumor parenchyma. Front Oncol 2022; 12:1007514. [PMID: 36267978 PMCID: PMC9577326 DOI: 10.3389/fonc.2022.1007514] [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: 07/30/2022] [Accepted: 09/06/2022] [Indexed: 11/25/2022] Open
Abstract
Background Treatment options for metastatic colorectal cancer (CRC) are mostly ineffective. We present new evidence that tumor tissue collagen type X alpha 1 (COL10A1) is a relevant candidate biomarker to improve this dilemma. Methods Several public databases had been screened to observe COL10A1 expression in transcriptome levels with cell lines and tissues. Protein interactions and alignment to changes in clinical parameters and immune cell invasion were performed, too. We also used algorithms to build a novel COL10A1-related immunomodulator signature. Various wet-lab experiments were conducted to quantify COL10A1 protein and transcript expression levels in disease and control cell models. Results COL10A1 mRNA levels in tumor material is clinical and molecular prognostic, featuring upregulation compared to non-cancer tissue, increase with histomorphological malignancy grading of the tumor, elevation in tumors that invade perineural areas, or lymph node invasion. Transcriptomic alignment noted a strong positive correlation of COL10A1 with transcriptomic signature of cancer-associated fibroblasts (CAFs) and populations of the immune compartment, namely, B cells and macrophages. We verified those findings in functional assays showing that COL10A1 are decreased in CRC cells compared to fibroblasts, with strongest signal in the cell supernatant of the cells. Conclusion COL10A1 abundance in CRC tissue predicts metastatic and immunogenic properties of the disease. COL10A1 transcription may mediate tumor cell interaction with its stromal microenvironment.
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Affiliation(s)
- Ulf D. Kahlert
- University Clinic for General, Visceral, Vascular and Transplantation Surgery, Faculty of Medicine, Otto-von-Guericke-University, Magdeburg, Germany
| | - Wenjie Shi
- University Clinic for General, Visceral, Vascular and Transplantation Surgery, Faculty of Medicine, Otto-von-Guericke-University, Magdeburg, Germany
- University Hospital for Gynecology, Pius-Hospital, University Medicine Oldenburg, Oldenburg, Germany
| | - Marco Strecker
- University Clinic for General, Visceral, Vascular and Transplantation Surgery, Faculty of Medicine, Otto-von-Guericke-University, Magdeburg, Germany
| | - Lorenz A. Scherpinski
- University Clinic for General, Visceral, Vascular and Transplantation Surgery, Faculty of Medicine, Otto-von-Guericke-University, Magdeburg, Germany
| | - Thomas Wartmann
- University Clinic for General, Visceral, Vascular and Transplantation Surgery, Faculty of Medicine, Otto-von-Guericke-University, Magdeburg, Germany
| | - Maximilian Dölling
- University Clinic for General, Visceral, Vascular and Transplantation Surgery, Faculty of Medicine, Otto-von-Guericke-University, Magdeburg, Germany
| | - Aristotelis Perrakis
- University Clinic for General, Visceral, Vascular and Transplantation Surgery, Faculty of Medicine, Otto-von-Guericke-University, Magdeburg, Germany
| | - Borna Relja
- Experimental Radiology, University Clinic of Radiology and Nuclear Medicine, Faculty of Medicine, Otto-von-Guericke-University, Magdeburg, Germany
| | - Miriam Mengoni
- University Clinic for Dermatology, Faculty of Medicine, Otto-von-Guericke-University, Magdeburg, Germany
| | - Andreas Braun
- University Clinic for Dermatology, Faculty of Medicine, Otto-von-Guericke-University, Magdeburg, Germany
| | - Roland S. Croner
- University Clinic for General, Visceral, Vascular and Transplantation Surgery, Faculty of Medicine, Otto-von-Guericke-University, Magdeburg, Germany
- *Correspondence: Roland S. Croner,
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Bioinformatics-Based Analysis: Noncoding RNA-Mediated COL10A1 Is Associated with Poor Prognosis and Immune Cell Infiltration in Pancreatic Cancer. JOURNAL OF HEALTHCARE ENGINEERING 2022; 2022:7904982. [PMID: 36105715 PMCID: PMC9467764 DOI: 10.1155/2022/7904982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 07/26/2022] [Accepted: 07/28/2022] [Indexed: 11/17/2022]
Abstract
Background. Collagen type X alpha 1 (COL10A1) is a structural component of the extracellular matrix that is aberrantly expressed in a variety of cancer tissues. However, its role in pancreatic cancer progression is not well understood. Methods. The Cancer Genome Atlas (TCGA), Gene Expression Omnibus (GEO), and Gene Expression Profiling Interaction Analysis (GEPIA) data were employed to explore the expression of COL10A1 in normal and tumor tissues and its prognostic value in pancreatic adenocarcinoma. The clinical data of pancreatic cancer in TCGA were used to explore the relationship between COL10A1 and clinical features. Genes coexpressed with COL10A1 were explored using multiple databases and analyzed for functional enrichment. In addition, the lncRNA/miRNA/COL10A1 axis that may be involved in COL10A1 regulation in pancreatic cancer was explored by constructing a competitive endogenous RNA (ceRNA) regulatory axis. Finally, COL10A1 was analyzed for correlation with immune cell infiltration and various immune checkpoint molecules in pancreatic cancer. Results. It was found that the expression of COL10A1 was significantly increased in pancreatic cancer tissues. High expression of COL10A1 was related to the clinicopathological characteristics and the worse prognosis of pancreatic cancer patients. The TUG1/miR-144-3p/COL10A1 axis was identified as the most likely upstream noncoding RNA pathway for COL10A1 in pancreatic cancer. Besides, in pancreatic adenocarcinoma, the expression level of COL10A1 showed a significant positive correlation with tumor immune cell infiltration, biomarkers of immune cells, and expression of immune checkpoint molecules. Conclusion. COL10A1 is an early diagnostic marker, and its high expression correlates with immune infiltration in pancreatic cancer. The TUG1/miR-144-3p/COL10A1 axis was identified as the most likely upstream noncoding RNA pathway for COL10A1 in pancreatic cancer.
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Wu H, Gao S, Xia L, Li P. Evolutionary rates of body-size-related genes and ecological factors involved in driving body size evolution of squamates. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.1007409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Body size is one of the most important traits of an organism. Among reptiles, both lizards and snakes show body size differences that span a similar six orders of magnitude variation. However, the molecular mechanisms underlying body size variation in squamates remain obscure. Here, we performed comparative genomic analyses of 101 body-size-related genes from 28 reptilian genomes. Phylogenetic analysis by maximum likelihood (PAML) revealed that snakes showed higher evolutionary rates in body-size-related genes, and had an almost two-fold increase in the number of positively selected genes (∼20.3%) compared with lizards (∼8.9%). The high similarities in dN/dS values were obtained between the branches of large-bodied lizards and large-bodied snakes by Spearman correlation analysis. Combining the results from site model, branch-site model and clade model analyses, we found some key genes regulating the evolution of body size in squamates, such as COL10A1, GHR, NPC1, GALNS, CDKN2C, FBN1, and LCORL. Phylogenetic generalized least squares (PGLS) indicated that AKT1, BMP1, IGF1, SOX5, SOX7 in lizards and BMP5, BMP7, GPC6, SH2B3, SOX17 in snakes were significantly correlated with body length and body mass. Furthermore, ecological factors had varying degrees of impact on body size and the evolutionary rate of body-size-related genes in squamates. Intriguingly, climate had little effect on body size of lizards and snakes, but the contribution of climate-related factors to the variation in evolutionary rate of body-size-related genes were relatively higher. Our study lays a foundation for a comprehensive understanding of genetic mechanisms of body size evolution in squamates during the process of adapting to terrestrial life.
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Zhang M, Jin M, Gao Z, Yu W, Zhang W. High COL10A1 expression potentially contributes to poor outcomes in gastric cancer with the help of LEF1 and Wnt2. J Clin Lab Anal 2022; 36:e24612. [PMID: 35929139 PMCID: PMC9459277 DOI: 10.1002/jcla.24612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 05/15/2022] [Accepted: 06/13/2022] [Indexed: 11/14/2022] Open
Abstract
Background COL10A1 is a secreted, short‐chain collagen found in several types of cancer. Studies have shown that COL10A1 aberrant expression is considered an oncogenic factor. However, its underlying mechanisms and regulation of gastric cancer remain undefined. Methods The data on the expression of COL10A1, clinicopathological characteristics, and outcome of patients with GC were obtained from The Cancer Genome Atlas. The ALGGEN‐PROMO database defined the related transcription factors. Quantitative real‐time reverse transcription‐polymerase chain reaction and western blotting analysis were used to identify the differential expression levels of COL10A1 and related transcription factors. Results We found that high COL10A1 expression is an independent risk factor for gastric cancer. Upregulation of LEF1 and Wnt2 was also observed in gastric cancer, suggesting a potential correlation between LEF1/COL10A1 regulation in the Wnt2 signaling pathway. Conclusion High COL10A1 expression may contribute to poor outcomes via upregulation of LEF1 and Wnt2 in gastric cancer.
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Affiliation(s)
- Miaozun Zhang
- Department of Gastrointestinal Surgery, The Affiliated Lihuili Hospital, Ningbo University, Ningbo, China
| | - Ming Jin
- Department of Radiation Oncology, The Affiliated Lihuili Hospital, Ningbo University, Ningbo, China
| | - Zhiqiang Gao
- Department of Gastroenterology, The Affiliated Lihuili Hospital, Ningbo University, Ningbo, China
| | - Weiming Yu
- Department of Gastrointestinal Surgery, The Affiliated Lihuili Hospital, Ningbo University, Ningbo, China
| | - Wei Zhang
- Department of Gastroenterology, The HwaMei Hospital, University of Chinese Academy of Sciences, Ningbo, China
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13
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Lv D, Chen D, Wang Z, Cui Z, Ma JH, Ji S, Chen J, Tang S. COL10A1 is a novel factor in the development of choroidal neovascularization. Microvasc Res 2022; 139:104239. [PMID: 34520774 DOI: 10.1016/j.mvr.2021.104239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 08/16/2021] [Accepted: 08/31/2021] [Indexed: 11/29/2022]
Abstract
With the dramatic rise in the aging population, researching age-related macular degeneration (AMD), especially the severe form neovascular AMD (nAMD), has become more important than ever. In this study, we found that collagen type X was increased in retina-choroid tissue of mice with laser-induced choroidal neovascularization (CNV) based on immunohistofluorescence. RNA sequencing and bioinformatic analyses were performed to compare the retina-choroid tissue complex of the CNV mouse model to normal controls. Collagen type X alpha 1 chain (Col10a1) was among the most significantly upregulated genes, and the results were validated with an animal model at the mRNA and protein levels by quantitative real-time polymerase chain reaction (qPCR) and western blotting, respectively. COL10A1 was also upregulated in human retinal microvascular endothelial cells (HRMECs), human umbilical vein endothelial cells (HUVECs), RPE19 cells and RF/6A cells under hypoxic conditions. Next, in vitro and in vivo experiments were performed to study the effect of COL10A1 on neovascularization. siRNA knockdown of COL10A1 suppressed the proliferation and tube formation ability of HRMECs under hypoxic conditions. Snail family transcriptional repressor 1 (SNAIL1) and angiopoietin-2 (ANGPT2) were downregulated in COL10A1 knockdown HRMECs under hypoxic conditions and thus were potential downstream genes. Significant decreases in CNV leakage and CNV lesion area, as assessed by fundus fluorescein angiography (FFA) and immunofluorescence of choroidal flat mounts, respectively, were observed in a mouse model intravitreally injected with anti-collagen X monoclonal antibody (mAb) compared to the controls. In conclusion, COL10A1 promotes CNV formation and may represent a new candidate target for the treatment and diagnosis of nAMD and other neovascular diseases.
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Affiliation(s)
- Da Lv
- Aier School of Ophthalmology, Central South University, Changsha, China; Aier Eye Institute, Changsha, China
| | | | - Zhijie Wang
- Aier School of Ophthalmology, Central South University, Changsha, China; Aier Eye Institute, Changsha, China
| | | | - Jacey Hongjie Ma
- Aier School of Ophthalmology, Central South University, Changsha, China; Aier Eye Institute, Changsha, China
| | | | - Jiansu Chen
- Aier School of Ophthalmology, Central South University, Changsha, China; Aier Eye Institute, Changsha, China; Key Laboratory for Regenerative Medicine, Ministry of Education, Jinan University, Guangzhou, China; Institute of Ophthalmology, Medical College, Jinan University, Guangzhou, China.
| | - Shibo Tang
- Aier School of Ophthalmology, Central South University, Changsha, China; Aier Eye Institute, Changsha, China; CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China.
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14
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Tissue, age, sex, and disease patterns of matrisome expression in GTEx transcriptome data. Sci Rep 2021; 11:21549. [PMID: 34732773 PMCID: PMC8566510 DOI: 10.1038/s41598-021-00943-x] [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: 08/26/2021] [Accepted: 10/20/2021] [Indexed: 11/08/2022] Open
Abstract
The extracellular matrix (ECM) has historically been explored through proteomic methods. Whether or not global transcriptomics can yield meaningful information on the human matrisome is unknown. Gene expression data from 17,382 samples across 52 tissues, were obtained from the Genotype-Tissue Expression (GTEx) project. Additional datasets were obtained from The Cancer Genome Atlas (TCGA) program and the Gene Expression Omnibus for comparisons. Gene expression levels generally matched proteome-derived matrisome expression patterns. Further, matrisome gene expression properly clustered tissue types, with some matrisome genes including SERPIN family members having tissue-restricted expression patterns. Deeper analyses revealed 382 gene transcripts varied by age and 315 varied by sex in at least one tissue, with expression correlating with digitally imaged histologic tissue features. A comparison of TCGA tumor, TCGA adjacent normal and GTEx normal tissues demonstrated robustness of the GTEx samples as a generalized matrix control, while also determining a common primary tumor matrisome. Additionally, GTEx tissues served as a useful non-diseased control in a separate study of idiopathic pulmonary fibrosis (IPF) matrix changes, while identifying 22 matrix genes upregulated in IPF. Altogether, these findings indicate that the transcriptome, in general, and GTEx in particular, has value in understanding the state of organ ECM.
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Hammerl D, Martens JWM, Timmermans M, Smid M, Trapman-Jansen AM, Foekens R, Isaeva OI, Voorwerk L, Balcioglu HE, Wijers R, Nederlof I, Salgado R, Horlings H, Kok M, Debets R. Spatial immunophenotypes predict response to anti-PD1 treatment and capture distinct paths of T cell evasion in triple negative breast cancer. Nat Commun 2021; 12:5668. [PMID: 34580291 PMCID: PMC8476574 DOI: 10.1038/s41467-021-25962-0] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 09/07/2021] [Indexed: 02/08/2023] Open
Abstract
Only a subgroup of triple-negative breast cancer (TNBC) responds to immune checkpoint inhibitors (ICI). To better understand lack of response to ICI, we analyze 681 TNBCs for spatial immune cell contextures in relation to clinical outcomes and pathways of T cell evasion. Excluded, ignored and inflamed phenotypes can be captured by a gene classifier that predicts prognosis of various cancers as well as anti-PD1 response of metastatic TNBC patients in a phase II trial. The excluded phenotype, which is associated with resistance to anti-PD1, demonstrates deposits of collagen-10, enhanced glycolysis, and activation of TGFβ/VEGF pathways; the ignored phenotype, also associated with resistance to anti-PD1, shows either high density of CD163+ myeloid cells or activation of WNT/PPARγ pathways; whereas the inflamed phenotype, which is associated with response to anti-PD1, revealed necrosis, high density of CLEC9A+ dendritic cells, high TCR clonality independent of neo-antigens, and enhanced expression of T cell co-inhibitory receptors.
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Affiliation(s)
- Dora Hammerl
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - John W M Martens
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Mieke Timmermans
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Marcel Smid
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | | | - Renée Foekens
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Olga I Isaeva
- Division of Tumor Biology & Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Department of Molecular Oncology & Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Leonie Voorwerk
- Division of Tumor Biology & Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Hayri E Balcioglu
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Rebecca Wijers
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Iris Nederlof
- Division of Tumor Biology & Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Roberto Salgado
- Department of Pathology, GZA-ZNA Ziekenhuizen, Antwerp, Belgium
- Division of Research, Peter Mac Callum Cancer Center, Melbourne, Australia
| | - Hugo Horlings
- Division of Tumor Biology & Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Department of Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Marleen Kok
- Division of Tumor Biology & Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands.
- Department of Medical Oncology, The Netherlands Cancer Institute, Amsterdam, The Netherlands.
| | - Reno Debets
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands.
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16
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Bioinformatics analysis of prognostic significance of COL10A1 in breast cancer. Biosci Rep 2021; 40:222087. [PMID: 32043519 PMCID: PMC7029149 DOI: 10.1042/bsr20193286] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Revised: 01/29/2020] [Accepted: 02/10/2020] [Indexed: 01/10/2023] Open
Abstract
Background: Collagen type X alpha 1 (COL10A1) is overexpressed in diverse tumors and displays vital roles in tumorigenesis. However, the prognostic value of COL10A1 in breast cancer remains unclear. Methods: The expression of COL10A1 was analyzed by the Oncomine database and UALCAN cancer database. The relationship between COL10A1 expression level and clinical indicators including prognostic data in breast cancer were analyzed by the Kaplan–Meier Plotter, PrognoScan, and Breast Cancer Gene-Expression Miner (bc-GenExMiner) databases. Results: COL10A1 was up-regulated in different subtypes of breast cancer. Estrogen receptor (ER), progesterone receptor (PR), human epidermal growth factor receptor-2 (HER-2) status and nodal status were positively correlated with COL10A1 expression. Conversely, age, the Scarff–Bloom–Richardson (SBR) grade, basal-like status, and triple-negative status were negatively related to COL10A1 level in breast cancer samples compared with normal tissues. Patients with increased COL10A1 expression level showed worse overall survival (OS), relapse-free survival (RFS), distant metastasis-free survival (DMFS) and disease-free survival (DFS). COL10A1 was positively correlated with metastatic relapse-free survival. GSEA analysis revealed that enrichment of TGF-β signaling pathway. 15-leucine-rich repeat containing membrane protein (LRRC15) is a correlated gene of COL10A1. Conclusion: Bioinformatics analysis revealed that COL10A1 might be considered as a predictive biomarker for prognosis of breast cancer. Further experiments and clinical trials are essential to elucidate the value of COL10A1 in breast cancer treatment.
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17
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Yang W, Wu X, Zhou F. Collagen Type X Alpha 1 (COL10A1) Contributes to Cell Proliferation, Migration, and Invasion by Targeting Prolyl 4-Hydroxylase Beta Polypeptide (P4HB) in Breast Cancer. Med Sci Monit 2021; 27:e928919. [PMID: 33637669 PMCID: PMC7927362 DOI: 10.12659/msm.928919] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Background Breast cancer, a common malignant tumor, has been considered as the leading cause of cancer-related death in women. Collagen type X alpha 1 (COL10A1) is overexpressed in breast cancer. The current study was designed to determine the functional involvement and regulatory mechanism of COL10A1 on the growth and metastasis of breast cancer. Material/Methods COL10A1 and Prolyl 4-hydroxylase beta polypeptide (P4HB) expressions in normal tissues and tumor tissues of breast cancer patients were obtained from the GEPIA dataset. COL10A1 and P4HB levels in breast cancer cell lines were detected by real-time quantitative polymerase chain reaction (RT-qPCR) and western blot analysis. Furthermore, the interaction between COL10A1 and P4HB was confirmed by co-immunoprecipitation (Co-IP) assay. Cell Counting Kit-8 (CCK-8) and colony formation assay were applied to evaluate cell proliferation and clone-forming abilities of breast cancer cells. In addition, wound healing assay and transwell assay were performed to measure cell migration and invasion capabilities, respectively, in breast cancer. Results The GEPIA dataset presented overexpressed COL10A1 and P4HB in tumor tissues of breast cancer patients. COL10A1 and P4HB expression levels were greatly upregulated in breast cancer cell lines. In addition, COL10A1 could directly interact with P4HB. Functionally, overexpressed COL10A1 boosted the proliferation and metastasis of breast cancer cells and silenced COL10A1 impeded the progression of breast cancer. More importantly, knockdown of P4HB weakened the promoting effects of overexpressed COL10A1 on cell proliferation, migration, and invasion in breast cancer. Conclusions COL10A1 promotes the malignant progression of breast cancer by upregulating P4HB expression, indicating that COL10A1 functions as an oncogene in breast cancer.
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Affiliation(s)
- Weibin Yang
- Department of Laboratory Medicine, WuHan PuRen Hospital, Wuhan, Hubei, China (mainland)
| | - Xuan Wu
- Department of Laboratory Medicine, WuHan PuRen Hospital, Wuhan, Hubei, China (mainland)
| | - Fan Zhou
- Department of Laboratory Medicine, WuHan PuRen Hospital, Wuhan, Hubei, China (mainland)
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18
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Karamanos NK, Theocharis AD, Piperigkou Z, Manou D, Passi A, Skandalis SS, Vynios DH, Orian-Rousseau V, Ricard-Blum S, Schmelzer CEH, Duca L, Durbeej M, Afratis NA, Troeberg L, Franchi M, Masola V, Onisto M. A guide to the composition and functions of the extracellular matrix. FEBS J 2021; 288:6850-6912. [PMID: 33605520 DOI: 10.1111/febs.15776] [Citation(s) in RCA: 304] [Impact Index Per Article: 101.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 02/13/2021] [Accepted: 02/18/2021] [Indexed: 12/13/2022]
Abstract
Extracellular matrix (ECM) is a dynamic 3-dimensional network of macromolecules that provides structural support for the cells and tissues. Accumulated knowledge clearly demonstrated over the last decade that ECM plays key regulatory roles since it orchestrates cell signaling, functions, properties and morphology. Extracellularly secreted as well as cell-bound factors are among the major members of the ECM family. Proteins/glycoproteins, such as collagens, elastin, laminins and tenascins, proteoglycans and glycosaminoglycans, hyaluronan, and their cell receptors such as CD44 and integrins, responsible for cell adhesion, comprise a well-organized functional network with significant roles in health and disease. On the other hand, enzymes such as matrix metalloproteinases and specific glycosidases including heparanase and hyaluronidases contribute to matrix remodeling and affect human health. Several cell processes and functions, among them cell proliferation and survival, migration, differentiation, autophagy, angiogenesis, and immunity regulation are affected by certain matrix components. Structural alterations have been also well associated with disease progression. This guide on the composition and functions of the ECM gives a broad overview of the matrisome, the major ECM macromolecules, and their interaction networks within the ECM and with the cell surface, summarizes their main structural features and their roles in tissue organization and cell functions, and emphasizes the importance of specific ECM constituents in disease development and progression as well as the advances in molecular targeting of ECM to design new therapeutic strategies.
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Affiliation(s)
- Nikos K Karamanos
- Biochemistry, Biochemical Analysis & Matrix Pathobiology Research Group, Laboratory of Biochemistry, Department of Chemistry, University of Patras, Greece.,Foundation for Research and Technology-Hellas (FORTH)/Institute of Chemical Engineering Sciences (ICE-HT), Patras, Greece
| | - Achilleas D Theocharis
- Biochemistry, Biochemical Analysis & Matrix Pathobiology Research Group, Laboratory of Biochemistry, Department of Chemistry, University of Patras, Greece
| | - Zoi Piperigkou
- Biochemistry, Biochemical Analysis & Matrix Pathobiology Research Group, Laboratory of Biochemistry, Department of Chemistry, University of Patras, Greece.,Foundation for Research and Technology-Hellas (FORTH)/Institute of Chemical Engineering Sciences (ICE-HT), Patras, Greece
| | - Dimitra Manou
- Biochemistry, Biochemical Analysis & Matrix Pathobiology Research Group, Laboratory of Biochemistry, Department of Chemistry, University of Patras, Greece
| | - Alberto Passi
- Department of Medicine and Surgery, University of Insubria, Varese, Italy
| | - Spyros S Skandalis
- Biochemistry, Biochemical Analysis & Matrix Pathobiology Research Group, Laboratory of Biochemistry, Department of Chemistry, University of Patras, Greece
| | - Demitrios H Vynios
- Biochemistry, Biochemical Analysis & Matrix Pathobiology Research Group, Laboratory of Biochemistry, Department of Chemistry, University of Patras, Greece
| | - Véronique Orian-Rousseau
- Karlsruhe Institute of Technology, Institute of Biological and Chemical Systems- Functional Molecular Systems, Eggenstein-Leopoldshafen, Germany
| | - Sylvie Ricard-Blum
- University of Lyon, UMR 5246, ICBMS, Université Lyon 1, CNRS, Villeurbanne Cedex, France
| | - Christian E H Schmelzer
- Fraunhofer Institute for Microstructure of Materials and Systems IMWS, Halle (Saale), Germany.,Institute of Pharmacy, Faculty of Natural Sciences I, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Laurent Duca
- UMR CNRS 7369 Matrice Extracellulaire et Dynamique Cellulaire (MEDyC), Team 2: Matrix Aging and Vascular Remodelling, Université de Reims Champagne Ardenne (URCA), UFR Sciences Exactes et Naturelles, Reims, France
| | - Madeleine Durbeej
- Department of Experimental Medical Science, Unit of Muscle Biology, Lund University, Sweden
| | - Nikolaos A Afratis
- Department Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Linda Troeberg
- Norwich Medical School, University of East Anglia, Bob Champion Research and Education Building, Norwich, UK
| | - Marco Franchi
- Department for Life Quality Study, University of Bologna, Rimini, Italy
| | | | - Maurizio Onisto
- Department of Biomedical Sciences, University of Padova, Italy
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19
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Zhuang J, Dai S, Zhang L, Gao P, Han Y, Tian G, Yan N, Tang M, Kui L. Identifying Breast Cancer-induced Gene Perturbations and its Application in Guiding Drug Repurposing. Curr Bioinform 2021. [DOI: 10.2174/1574893615666200203104214] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:
Breast cancer is a complex disease with high prevalence in women, the
molecular mechanisms of which are still unclear at present. Most transcriptomic studies on breast
cancer focus on differential expression of each gene between tumor and the adjacent normal tissues,
while the other perturbations induced by breast cancer including the gene regulation variations, the
changes of gene modules and the pathways, which might be critical to the diagnosis, treatment and
prognosis of breast cancer are more or less ignored.
Objective:
We presented a complete process to study breast cancer from multiple perspectives,
including differential expression analysis, constructing gene co-expression networks, modular
differential connectivity analysis, differential gene connectivity analysis, gene function enrichment
analysis key driver analysis. In addition, we prioritized the related anti-cancer drugs based on
enrichment analysis between differential expression genes and drug perturbation signatures.
Methods:
The RNA expression profiles of 1109 breast cancer tissue and 113 non-tumor tissues were
downloaded from The Cancer Genome Atlas (TCGA) database. Differential expression of RNAs
was identified using the “DESeq2” bioconductor package in R, and gene co-expression networks
were constructed using the weighted gene co-expression network analysis (WGCNA). To compare
the module changes and gene co-expression variations between tumor and the adjacent normal
tissues, modular differential connectivity (MDC) analysis and differential gene connectivity analysis
(DGCA) were performed.
Results:
Top differential genes like MMP11 and COL10A1 were known to be associated with breast
cancer. And we found 23 modules in the tumor network had significantly different co-expression
patterns. The top differential modules were enriched in Goterms related to breast cancer like MHC
protein complex, leukocyte activation, regulation of defense response and so on. In addition, key
genes like UBE2T driving the top differential modules were significantly correlated with the
patients’ survival. Finally, we predicted some potential breast cancer drugs, such as Eribulin,
Taxane, Cisplatin and Oxaliplatin.
Conclusion:
As an indication, this framework might be useful in understanding the molecular
pathogenesis of diseases like breast cancer and inferring useful drugs for personalized medication.
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Affiliation(s)
- Jujuan Zhuang
- School of Science, Dalian Maritime University, Dalian, Liaoning, 116026, China
| | - Shuang Dai
- School of Science, Dalian Maritime University, Dalian, Liaoning, 116026, China
| | - Lijun Zhang
- School of Science, Dalian Maritime University, Dalian, Liaoning, 116026, China
| | - Pan Gao
- School of Science, Dalian Maritime University, Dalian, Liaoning, 116026, China
| | - Yingmin Han
- Geneis Beijing Co., Ltd., Beijing, 100102, China
| | - Geng Tian
- Geneis Beijing Co., Ltd., Beijing, 100102, China
| | - Na Yan
- Geneis Beijing Co., Ltd., Beijing, 100102, China
| | - Min Tang
- Institute of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Ling Kui
- Dana- Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, United States
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Martins Cavaco AC, Dâmaso S, Casimiro S, Costa L. Collagen biology making inroads into prognosis and treatment of cancer progression and metastasis. Cancer Metastasis Rev 2021; 39:603-623. [PMID: 32447477 DOI: 10.1007/s10555-020-09888-5] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Progression through dissemination to tumor-surrounding tissues and metastasis development is a hallmark of cancer that requires continuous cell-to-cell interactions and tissue remodeling. In fact, metastization can be regarded as a tissue disease orchestrated by cancer cells, leading to neoplastic colonization of new organs. Collagen is a major component of the extracellular matrix (ECM), and increasing evidence suggests that it has an important role in cancer progression and metastasis. Desmoplasia and collagen biomarkers have been associated with relapse and death in cancer patients. Despite the increasing interest in ECM and in the desmoplastic process in tumor microenvironment as prognostic factors and therapeutic targets in cancer, further research is required for a better understanding of these aspects of cancer biology. In this review, published evidence correlating collagen with cancer prognosis is retrieved and analyzed, and the role of collagen and its fragments in cancer pathophysiology is discussed.
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Affiliation(s)
- Ana C Martins Cavaco
- Luis Costa Lab, Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, 1649-028, Lisboa, Portugal
| | - Sara Dâmaso
- Serviço de Oncologia, Hospital de Santa Maria-CHULN, 1649-028, Lisboa, Portugal
| | - Sandra Casimiro
- Luis Costa Lab, Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, 1649-028, Lisboa, Portugal
| | - Luís Costa
- Luis Costa Lab, Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, 1649-028, Lisboa, Portugal.
- Serviço de Oncologia, Hospital de Santa Maria-CHULN, 1649-028, Lisboa, Portugal.
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21
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Wang X, Guo J, Yu P, Guo L, Mao X, Wang J, Miao S, Sun J. The roles of extracellular vesicles in the development, microenvironment, anticancer drug resistance, and therapy of head and neck squamous cell carcinoma. J Exp Clin Cancer Res 2021; 40:35. [PMID: 33478586 PMCID: PMC7819156 DOI: 10.1186/s13046-021-01840-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 01/11/2021] [Indexed: 02/06/2023] Open
Abstract
Head and neck squamous cell carcinoma (HNSCC) is one of the main malignant tumours affecting human health, mainly due to delayed diagnosis and high invasiveness. Extracellular vehicles (EVs) are membranous vesicles released by cells into the extracellular matrix that carry important signalling molecules and stably and widely exist in various body fluids, such as plasma, saliva, cerebrospinal fluid, breast milk, urine, semen, lymphatic fluid, synovial fluid, amniotic fluid, and sputum. EVs transport almost all types of bioactive molecules (DNA, mRNAs, microRNAs (miRNAs), proteins, metabolites, and even pharmacological compounds). These "cargoes" can act on recipient cells, reshaping the surrounding microenvironment and altering distant targets, ultimately affecting their biological behaviour. The extensive exploration of EVs has deepened our comprehensive understanding of HNSCC biology. In this review, we not only summarized the effect of HNSCC-derived EVs on the tumour microenvironment but also described the role of microenvironment-derived EVs in HNSCC and discussed how the "mutual dialogue" between the tumour and microenvironment mediates the growth, metastasis, angiogenesis, immune escape, and drug resistance of tumours. Finally, the clinical application of EVS in HNSCC was assessed.
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Affiliation(s)
- Xueying Wang
- Department of Head and Neck Tumors, Harbin Medical University Cancer Hospital, No. 150, Haping Road, Nangang District, 150000, Harbin, Heilongjiang, People's Republic of China
| | - Junnan Guo
- The First Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, No. 150, Haping Road, Nangang District, 150000, Harbin, Heilongjiang, People's Republic of China
| | - Pingyang Yu
- Department of Head and Neck Tumors, Harbin Medical University Cancer Hospital, No. 150, Haping Road, Nangang District, 150000, Harbin, Heilongjiang, People's Republic of China
| | - Lunhua Guo
- Department of Head and Neck Tumors, Harbin Medical University Cancer Hospital, No. 150, Haping Road, Nangang District, 150000, Harbin, Heilongjiang, People's Republic of China
| | - Xionghui Mao
- Department of Head and Neck Tumors, Harbin Medical University Cancer Hospital, No. 150, Haping Road, Nangang District, 150000, Harbin, Heilongjiang, People's Republic of China
| | - Junrong Wang
- Department of Head and Neck Tumors, Harbin Medical University Cancer Hospital, No. 150, Haping Road, Nangang District, 150000, Harbin, Heilongjiang, People's Republic of China
| | - Susheng Miao
- Department of Head and Neck Tumors, Harbin Medical University Cancer Hospital, No. 150, Haping Road, Nangang District, 150000, Harbin, Heilongjiang, People's Republic of China.
| | - Ji Sun
- Department of Head and Neck Tumors, Harbin Medical University Cancer Hospital, No. 150, Haping Road, Nangang District, 150000, Harbin, Heilongjiang, People's Republic of China.
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22
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Chen S, Wei Y, Liu H, Gong Y, Zhou Y, Yang H, Tang L. Analysis of Collagen type X alpha 1 (COL10A1) expression and prognostic significance in gastric cancer based on bioinformatics. Bioengineered 2020; 12:127-137. [PMID: 33371777 PMCID: PMC8291830 DOI: 10.1080/21655979.2020.1864912] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Collagen type X alpha 1 (COL10A1) is a member of the collagen family and the main matrix component. However, COL10A1 expression and prognosis relationship remains unclear in gastric cancer (GC). Through the analysis of database of Oncomine, the Cancer Genome Atlas (TCGA) as well as the Gene Expression Omnibus (GEO), in contrast to the tissue of normal gastric, COL10A1 in gastric cancer, had been upregulated. The high expression of COL10A1 was obviously related to T stage (P = 0.025) and lymph node metastasis (P = 0.025). It has been illustrated by the analysis of logistic regression that COL10A1's heightened expression in gastric cancer had been essentially linked with pathological stage, tumor differentiation, and T classification. The Kaplan-Meier curve in the Kaplan-Meier plotter database (P = 0.0371) and GSE84437 (P = 0.002) indicate that patients with high COL10A1 expression possess poor prognosis, specifically GC patients with lymph node metastasis have it. TCGA's Multivariate analysis (P = 0.025) and GSE84437 dataset (P = 0.034) show that high expression COL10A1 is a key independent predictor of poor overall survival. Searching KEGG pathway enrichment by GSEA, the results suggested that 29 pathways were enriched. qRT-PCR technique was used for verification of the COL10A1's high expression in gastric cancer in contrast to the normal gastric tissues. In conclusion, COL10A1 is of great importance in predicting the survival rate of GC patients.
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Affiliation(s)
- Shuai Chen
- Center of Gastrointestinal Disease, The Affiliated Changzhou NO.2 People's Hospital of Nanjing Medical University , Changzhou, China
| | - Yi Wei
- Center of Gastrointestinal Disease, The Affiliated Changzhou NO.2 People's Hospital of Nanjing Medical University , Changzhou, China
| | - Hanyang Liu
- Center of Gastrointestinal Disease, The Affiliated Changzhou NO.2 People's Hospital of Nanjing Medical University , Changzhou, China
| | - Yu Gong
- Center of Gastrointestinal Disease, The Affiliated Changzhou NO.2 People's Hospital of Nanjing Medical University , Changzhou, China
| | - Yan Zhou
- Center of Gastrointestinal Disease, The Affiliated Changzhou NO.2 People's Hospital of Nanjing Medical University , Changzhou, China
| | - Haojun Yang
- Center of Gastrointestinal Disease, The Affiliated Changzhou NO.2 People's Hospital of Nanjing Medical University , Changzhou, China
| | - Liming Tang
- Center of Gastrointestinal Disease, The Affiliated Changzhou NO.2 People's Hospital of Nanjing Medical University , Changzhou, China
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23
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Liang Y, Xia W, Zhang T, Chen B, Wang H, Song X, Zhang Z, Xu L, Dong G, Jiang F. Upregulated Collagen COL10A1 Remodels the Extracellular Matrix and Promotes Malignant Progression in Lung Adenocarcinoma. Front Oncol 2020; 10:573534. [PMID: 33324550 PMCID: PMC7726267 DOI: 10.3389/fonc.2020.573534] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 10/26/2020] [Indexed: 01/27/2023] Open
Abstract
Collagens are major components of the ECM in various organs, including the lungs. Ectopic expression of collagens can regulate the tumor progression and disease outcome through remodeling of the extracellular matrix (ECM). However, it remains largely unexplored whether collagens are involved in the tumor progression of lung adenocarcinoma (LUAD). Analysis of three LUAD transcriptional expression profiles showed that COL10A1 mRNA expression was up-regulated and associated with poor prognosis. Gain- and loss-of-function studies were performed to observe that up-regulated COL10A1 promotes LUAD cell proliferation and invasion in vitro and in vivo. In molecular mechanism study, we found that COL10A1 interacts with DDR2 and affects the downstream FAK signaling pathway to regulate LUAD cell progression. The expression of COL10A1 on tissue microarray (TMA) was also measured to explore the association between COL10A1 expression and patient outcome. The results addressed that COL10A1 is up-regulated and positively correlated with lymph node metastasis in lung adenocarcinoma, and the COL10A1 expression is also an independent prognostic factor. In summary, the up-regulated COL10A1 remodels the ECM and the COL10A1/DDR2/FAK axis regulates the proliferation and metastasis of LUAD cells, implying that COL10A1 is a promising therapeutic target and prognostic marker for LUAD patients.
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Affiliation(s)
- Yingkuan Liang
- The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China.,Department of Thoracic Surgery, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing, China.,Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Nanjing, China.,Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Wenjie Xia
- The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China.,Department of Thoracic Surgery, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing, China
| | - Te Zhang
- The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China.,Department of Thoracic Surgery, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing, China.,Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Nanjing, China
| | - Bing Chen
- The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China.,Department of Thoracic Surgery, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing, China.,Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Nanjing, China
| | - Hui Wang
- The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China.,Department of Thoracic Surgery, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing, China.,Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Nanjing, China
| | - Xuming Song
- The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China.,Department of Thoracic Surgery, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing, China.,Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Nanjing, China
| | - Zeyu Zhang
- The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China.,Department of Thoracic Surgery, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing, China.,Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Nanjing, China
| | - Lin Xu
- The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China.,Department of Thoracic Surgery, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing, China.,Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Nanjing, China
| | - Gaochao Dong
- The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China.,Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Nanjing, China
| | - Feng Jiang
- The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China.,Department of Thoracic Surgery, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing, China.,Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Nanjing, China
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24
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Necula L, Matei L, Dragu D, Pitica I, Neagu AI, Bleotu C, Dima S, Popescu I, Diaconu CC, Chivu-Economescu M. High plasma levels of COL10A1 are associated with advanced tumor stage in gastric cancer patients. World J Gastroenterol 2020; 26:3024-3033. [PMID: 32587446 PMCID: PMC7304107 DOI: 10.3748/wjg.v26.i22.3024] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Revised: 05/14/2020] [Accepted: 05/28/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Gastric cancer (GC) remains an aggressive malignancy with a high rate of mortality, being the third leading cause of cancer-related death. More than one million newly diagnosed cases and 782685 deaths due to GC were reported in 2018. GC is characterized by limited effective treatment options and the lack of consistent biomarkers for the diagnosis and prognosis of these patients. The discovery of new biomarkers useful in the early diagnosis of GC is mandatory.
AIM To evaluate the potential of COL10A1 as a circulating biomarker for the diagnosis and prognosis of gastric adenocarcinoma patients.
METHODS Plasma and tissue obtained from 49 patients with gastric adenocarcinoma have been used in exploring the expression of COL10A1. Real-time PCR and western blot techniques were used to evaluate COL10A1 level in gastric tumor tissue compared to normal adjacent tissue. The circulating level of COL10A1 was also evaluated by ELISA in plasma of gastric adenocarcinoma patients. Survival analysis was made in order to evaluate the potential of COL10A1 as a biomarker for the diagnosis and prognosis of gastric adenocarcinoma patients.
RESULTS Our results showed a significant increase in COL10A1 gene expression and protein levels in gastric tumor tissue compared to adjacent normal tissue (P < 0.05). COL10A1 seems to show an elevated expression from the beginning of carcinogenesis, in the early stages, and its increased level remains elevated during cancer progression. A significant increase of COL10A1 plasma level in gastric adenocarcinoma patients was also identified. Moreover, increased COL10A1 plasma level was associated with poor survival of the patients. Plasma COL10A1 performed a diagnostic value in GC with area under the receiver operating characteristic curve (AUC) of 0.9171 (P = 0.0002), sensitivity of 87.76%, and specificity of 100.0%. Furthermore, this study demonstrated the potential role of plasma COL10A1 in the early detection of GC, as in the early stage, we obtained an AUC of 0.8789 (P = 0.0030), sensitivity of 81.25%, and specificity of 100.0%.
CONCLUSION Circulating expression level of COL10A1 is significantly increased in gastric adenocarcinoma patients being associated with poor survival and is a potential biomarker for early detection of GC.
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Affiliation(s)
- Laura Necula
- Department of Cellular and Molecular Pathology, Stefan S. Nicolau Institute of Virology, Bucharest 030304, Romania
- Titu Maiorescu University, Faculty of Medicine, Bucharest 040441, Romania
| | - Lilia Matei
- Department of Cellular and Molecular Pathology, Stefan S. Nicolau Institute of Virology, Bucharest 030304, Romania
| | - Denisa Dragu
- Department of Cellular and Molecular Pathology, Stefan S. Nicolau Institute of Virology, Bucharest 030304, Romania
| | - Ioana Pitica
- Department of Cellular and Molecular Pathology, Stefan S. Nicolau Institute of Virology, Bucharest 030304, Romania
| | - Ana Iulia Neagu
- Department of Cellular and Molecular Pathology, Stefan S. Nicolau Institute of Virology, Bucharest 030304, Romania
| | - Coralia Bleotu
- Department of Cellular and Molecular Pathology, Stefan S. Nicolau Institute of Virology, Bucharest 030304, Romania
| | - Simona Dima
- Fundeni Clinical Institute, Bucharest 022328, Romania
| | | | - Carmen C Diaconu
- Department of Cellular and Molecular Pathology, Stefan S. Nicolau Institute of Virology, Bucharest 030304, Romania
| | - Mihaela Chivu-Economescu
- Department of Cellular and Molecular Pathology, Stefan S. Nicolau Institute of Virology, Bucharest 030304, Romania
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25
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Yap T, Pruthi N, Seers C, Belobrov S, McCullough M, Celentano A. Extracellular Vesicles in Oral Squamous Cell Carcinoma and Oral Potentially Malignant Disorders: A Systematic Review. Int J Mol Sci 2020; 21:E1197. [PMID: 32054041 PMCID: PMC7072764 DOI: 10.3390/ijms21041197] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 02/08/2020] [Accepted: 02/10/2020] [Indexed: 12/12/2022] Open
Abstract
Extracellular vesicles (EVs) are secreted from most cell types and utilized in a complex network of near and distant cell-to-cell communication. Insight into this complex nanoscopic interaction in the development, progression and treatment of oral squamous cell carcinoma (OSCC) and precancerous oral mucosal disorders, termed oral potentially malignant disorders (OPMDs), remains of interest. In this review, we comprehensively present the current state of knowledge of EVs in OSCC and OPMDs. A systematic literature search strategy was developed and updated to December 17, 2019. Fifty-five articles were identified addressing EVs in OSCC and OPMDs with all but two articles published from 2015, highlighting the novelty of this research area. Themes included the impact of OSCC-derived EVs on phenotypic changes, lymph-angiogenesis, stromal immune response, mechanisms of therapeutic resistance as well as utility of EVs for drug delivery in OSCC and OPMD. Interest and progress of knowledge of EVs in OSCC and OPMD has been expanding on several fronts. The oral cavity presents a unique and accessible microenvironment for nanoparticle study that could present important models for other solid tumours.
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Affiliation(s)
- Tami Yap
- Melbourne Dental School, The University of Melbourne, 720 Swanston Street, Carlton, VIC 3053, Australia; (N.P.); (C.S.); (S.B.); (M.M.); (A.C.)
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26
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Li Y, Wang X, Shi L, Xu J, Sun B. Predictions for high COL1A1 and COL10A1 expression resulting in a poor prognosis in esophageal squamous cell carcinoma by bioinformatics analyses. Transl Cancer Res 2020; 9:85-94. [PMID: 35117161 PMCID: PMC8798449 DOI: 10.21037/tcr.2019.11.11] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 10/18/2019] [Indexed: 12/12/2022]
Abstract
Background Esophageal squamous cell carcinoma (ESCC) is one of the most common malignant neoplasms of the digestive tract worldwide. The lack of key molecular biomarkers is associated with the poor prognosis in ESCC patients. The present study was aimed to identify candidate genes for diagnostic, prognostic, and therapeutic applications in ESCC by bioinformatics. Methods Two datasets of ESCC (GSE20347 and GSE70409) from gene expression omnibus (GEO) were analyzed using GEO2R online tool to identify the differentially expressed genes (DEGs). Subsequently, functions and pathways enrichment analyses of DEGs and their protein-protein interaction (PPI) network analyses were performed. When key DEGs were identified, their relationship with ESCC prognosis was further validated. Results There were 134 commonly changed DEGs (33 up-regulated and 101 down-regulated) from GSE20347 and GSE70409 datasets were identified using integrated bioinformatical analysis. Gene ontology (GO) and pathway enrichment analysis was performed to annotate genes and gene products, highlight biological processes (BPs) and systemic functional information. Through the PPI network and cluster analysis, two clusters containing 21 key DEGs were detected and 14 of them were validated based on TCGA and GTEx data. Among these key DEGs, COL1A1 and COL10A1 were significantly associated with the prognosis in ESCC cases. Conclusions In conclusion, a total of 14 key DEGs and outcome in ESCC were identified by integrated bioinformatics analyses. COL1A1 and COL10A1 might be novel potential diagnostic and prognostic biomarkers in ESCC.
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Affiliation(s)
- Yang Li
- Department of Gastroenterology, the First Affiliated Hospital of Anhui Medical University, Hefei 230001, China
| | - Xu Wang
- Department of Gastroenterology, the First Affiliated Hospital of Anhui Medical University, Hefei 230001, China
| | - Liangliang Shi
- Department of Gastroenterology, Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing University, Nanjing 210008, China
| | - Jianming Xu
- Department of Gastroenterology, the First Affiliated Hospital of Anhui Medical University, Hefei 230001, China
| | - Bin Sun
- Department of Gastroenterology, the First Affiliated Hospital of Anhui Medical University, Hefei 230001, China
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27
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Zhao CL, Singh K, Brodsky AS, Lu S, Graves TA, Fenton MA, Yang D, Sturtevant A, Resnick MB, Wang Y. Stromal ColXα1 expression correlates with tumor-infiltrating lymphocytes and predicts adjuvant therapy outcome in ER-positive/HER2-positive breast cancer. BMC Cancer 2019; 19:1036. [PMID: 31675929 PMCID: PMC6825361 DOI: 10.1186/s12885-019-6134-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 09/04/2019] [Indexed: 12/21/2022] Open
Abstract
Background The breast cancer microenvironment contributes to tumor progression and response to chemotherapy. Previously, we reported that increased stromal Type X collagen α1 (ColXα1) and low TILs correlated with poor pathologic response to neoadjuvant therapy in estrogen receptor and HER2-positive (ER+/HER2+) breast cancer. Here, we investigate the relationship of ColXα1 and long-term outcome of ER+/HER2+ breast cancer patients in an adjuvant setting. Methods A total of 164 cases with at least 5-year follow-up were included. Immunohistochemistry for ColXα1 was performed on whole tumor sections. Associations between ColXα1expression, clinical pathological features, and outcomes were analyzed. Results ColXα1 expression was directly proportional to the amount of tumor associated stroma (p = 0.024) and inversely proportional to TILs. Increased ColXα1 was significantly associated with shorter disease free survival and overall survival by univariate analysis. In multivariate analysis, OS was lower in ColXα1 expressing (HR = 2.1; 95% CI = 1.2–3.9) tumors of older patients (> = 58 years) (HR = 5.3; 95% CI = 1.7–17) with higher stage (HR = 2.6; 95% CI = 1.3–5.2). Similarly, DFS was lower in ColXα1 expressing (HR = 1.8; 95% CI = 1.6–5.7) tumors of older patients (HR = 3.2; 95% CI = 1.3–7.8) with higher stage (HR = 2.7; 95% CI = 1.6–5.7) and low TILs. In low PR+ tumors, higher ColXα1 expression was associated with poorer prognosis. Conclusion ColXα1 expression is associated with poor disease free survival and overall survival in ER+/HER2+ breast cancer. This study provides further support for the prognostic utility of ColXα1 as a breast cancer associated stromal factor that predicts response to chemotherapy. Electronic supplementary material The online version of this article (10.1186/s12885-019-6134-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Chaohui Lisa Zhao
- Department of Pathology and Laboratory Medicine, Rhode Island Hospital and Lifespan Medical Center, Warren Alpert Medical School of Brown University, 593 Eddy St, APC 12, Providence, RI, 02903, USA
| | - Kamaljeet Singh
- Department of Pathology and Laboratory Medicine, Women and Infant Hospital, Warren Alpert Medical School of Brown University, Providence, RI, 02903, USA
| | - Alexander S Brodsky
- Department of Pathology and Laboratory Medicine, Rhode Island Hospital and Lifespan Medical Center, Warren Alpert Medical School of Brown University, 593 Eddy St, APC 12, Providence, RI, 02903, USA
| | - Shaolei Lu
- Department of Pathology and Laboratory Medicine, Rhode Island Hospital and Lifespan Medical Center, Warren Alpert Medical School of Brown University, 593 Eddy St, APC 12, Providence, RI, 02903, USA
| | - Theresa A Graves
- Department of Surgery, Rhode Island Hospital and Lifespan Medical Center, Warren Alpert Medical School of Brown University, Providence, USA
| | - Mary Anne Fenton
- Department of Medicine, Rhode Island Hospital and Lifespan Medical Center, Warren Alpert Medical School of Brown University, Providence, USA
| | - Dongfang Yang
- Department of Pathology and Laboratory Medicine, Rhode Island Hospital and Lifespan Medical Center, Warren Alpert Medical School of Brown University, 593 Eddy St, APC 12, Providence, RI, 02903, USA
| | - Ashlee Sturtevant
- Department of Pathology and Laboratory Medicine, Rhode Island Hospital and Lifespan Medical Center, Warren Alpert Medical School of Brown University, 593 Eddy St, APC 12, Providence, RI, 02903, USA
| | - Murray B Resnick
- Department of Pathology and Laboratory Medicine, Rhode Island Hospital and Lifespan Medical Center, Warren Alpert Medical School of Brown University, 593 Eddy St, APC 12, Providence, RI, 02903, USA
| | - Yihong Wang
- Department of Pathology and Laboratory Medicine, Rhode Island Hospital and Lifespan Medical Center, Warren Alpert Medical School of Brown University, 593 Eddy St, APC 12, Providence, RI, 02903, USA.
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28
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Malvia S, Bagadi SAR, Pradhan D, Chintamani C, Bhatnagar A, Arora D, Sarin R, Saxena S. Study of Gene Expression Profiles of Breast Cancers in Indian Women. Sci Rep 2019; 9:10018. [PMID: 31292488 PMCID: PMC6620270 DOI: 10.1038/s41598-019-46261-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 06/25/2019] [Indexed: 02/06/2023] Open
Abstract
Breast cancer is the most common cancer among women globally. In India, the incidence of breast cancer has increased significantly during the last two decades with a higher proportion of the disease at a young age compared to the west. To understand the molecular processes underlying breast cancer in Indian women, we analysed gene expression profiles of 29 tumours and 9 controls using microarray. In the present study, we obtained 2413 differentially expressed genes, consisting of overexpressed genes such as COL10A1, COL11A1, MMP1, MMP13, MMP11, GJB2, and CST1 and underexpressed genes such as PLIN1, FABP4, LIPE, AQP7, LEP, ADH1A, ADH1B, and CIDEC. The deregulated pathways include cell cycle, focal adhesion and metastasis, DNA replication, PPAR signaling, and lipid metabolism. Using PAM50 classifier, we demonstrated the existence of molecular subtypes in Indian women. In addition, qPCR validation of expression of metalloproteinase genes, MMP1, MMP3, MMP11, MMP13, MMP14, ADAMTS1, and ADAMTS5 showed concordance with that of the microarray data; wherein we found a significant association of ADAMTS5 down-regulation with older age (≥55 years) of patients. Together, this study reports gene expression profiles of breast tumours from the Indian subcontinent, throwing light on the pathways and genes associated with the breast tumourigenesis in Indian women.
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Affiliation(s)
- Shreshtha Malvia
- Tumour Biology Division, ICMR-National Institute of Pathology, New Delhi, 110029, India
| | | | - Dibyabhaba Pradhan
- Bioinformatics Cell, ICMR-National Institute of Pathology, New Delhi, 110029, India
| | | | - Amar Bhatnagar
- Department of Cancer Surgery, Safdarjung Hospital, New Delhi, 110029, India
| | - Deepshikha Arora
- Department of Pathology, Indraprastha Apollo Hospital, New Delhi, 110076, India
| | - Ramesh Sarin
- Department of Surgery, Indraprastha Apollo Hospital, New Delhi, 110076, India
| | - Sunita Saxena
- Tumour Biology Division, ICMR-National Institute of Pathology, New Delhi, 110029, India.
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29
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RAD51B (rs8017304 and rs2588809), TRIB1 (rs6987702, rs4351379, and rs4351376), COL8A1 (rs13095226), and COL10A1 (rs1064583) Gene Variants with Predisposition to Age-Related Macular Degeneration. DISEASE MARKERS 2019; 2019:5631083. [PMID: 31191752 PMCID: PMC6525907 DOI: 10.1155/2019/5631083] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 03/27/2019] [Indexed: 12/16/2022]
Abstract
Background Age-related macular degeneration (AMD) is a progressive neurodegenerative disease of a central part of the neural retina (macula) and a leading cause of blindness in elderly people. While it is known that the AMD is a multifactorial disease, genetic factors involved in lipid metabolism, inflammation, and neovascularization are currently being widely studied in genome-wide association studies (GWAS). The aim of our study was to evaluate the impact of new single nucleotide polymorphisms (SNPs) in RAD51B, TRIB1, COL8A1, and COL10A1 genes on AMD development. Methods Case-control study involved 254 patients diagnosed with early AMD, 244 patients with exudative AMD, and 942 control subjects. The genotyping of RAD51B (rs8017304 and rs2588809), TRIB1 (rs6987702, rs4351379, and rs4351376), COL8A1 (rs13095226), and COL10A1 (rs1064583) was carried out using TaqMan assays by a real-time polymerase chain reaction (RT-PCR) method. Results Statistically significant difference was found in genotype (TT, TC, and CC) distribution of COL8A1 rs13095226 between exudative AMD and control groups (60.2%, 33.6%, and 6.1% vs. 64.9%, 32.3%, and 2.9%, respectively, p = 0.036). Also, comparing with TT+TC, rs13095226 CC genotype was associated with 3.5-fold increased odds of exudative AMD development (OR = 3.540; 95% CI: 1.415-8.856; p = 0.007). Conclusion Our study revealed a strong association between a variant in COL8A1 (rs13095226) and exudative AMD development.
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30
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Exosomes derived from microRNA-101-3p-overexpressing human bone marrow mesenchymal stem cells suppress oral cancer cell proliferation, invasion, and migration. Mol Cell Biochem 2019; 458:11-26. [PMID: 31165315 DOI: 10.1007/s11010-019-03526-7] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 03/15/2019] [Indexed: 10/26/2022]
Abstract
Dysregulation of microRNAs (miRNAs) has been found to disrupt the progression of oral cancer. However, which miRNAs are most effective against oral cancer and how these miRNAs should be delivered are major unanswered problems. We aimed at investigating if human bone marrow mesenchymal stem cells (hBMSCs)-derived exosomes affect oral cancer development, and the potential regulatory mechanism associated with COL10A1 and miR-101-3p. COL10A1 was upregulated, while miR-101-3p was downregulated in oral cancer, and miR-101-3p targeted COL10A1 as verified by dual-luciferase reporter gene assay. Meanwhile, exosomes derived from hBMSCs were isolated and then co-cultured with oral cancer cells to identify the role of exosomes, and the results suggested that hBMSCs-derived exosomes overexpressing miR-101-3p inhibited oral cancer progression. Furthermore, tumorigenicity assay in nude mice further confirmed the inhibitory effects of hBMSCs-derived exosomes, loaded with miR-101-3p, on oral cancer, which provides a new theoretical basis in the treatment of oral cancer.
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31
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Zhao X, Xu M, Cai Z, Yuan W, Cui W, Li MD. Identification of LIFR, PIK3R1, and MMP12 as Novel Prognostic Signatures in Gallbladder Cancer Using Network-Based Module Analysis. Front Oncol 2019; 9:325. [PMID: 31119098 PMCID: PMC6504688 DOI: 10.3389/fonc.2019.00325] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 04/10/2019] [Indexed: 01/17/2023] Open
Abstract
Background: Gallbladder cancer (GBC) is a rare and aggressive malignancy of the biliary tract with a dismal survival rate. Effective biomarkers and therapeutic targets are urgently needed. Methods: We analyzed gene expression profiles of GBC to identify differentially expressed genes (DEGs) and then used these DEGs to identify functional module biomarkers based on protein functional interaction (FI) networks. We further evaluated the module-gene protein expression and clinical significance with immunohistochemistry staining (IHC) in a tissue microarray (TMA) from 80 GBC samples. Results: Five functional modules were identified. Module 0 included classical cancer signaling pathways, such as Ras and PI3K-Akt; and modules 1–4 included genes associated with muscle cells, fibrinogen, extracellular matrix, and integrins, respectively. We validated the expression of LIFR, PIK3R1, and MMP12, which were hubs or functional nodes in modules. Compared with paired peritumoural tissues, we found that the expression of LIFR (P = 0.002) and PIK3R1 (P = 0.046) proteins were significantly downregulated, and MMP12 (P = 0.006) was significantly upregulated. Further prognostic analysis showed that patients with low expression of LIFR had shorter overall survival than those with high expression (log-rank test P = 0.028), the same trend as for PIK3R1 (P = 0.053) and MMP12 (P = 0.006). Multivariate analysis indicated that expression of MMP12 protein (hazard ratio [HR] = 0.429; 95% confidence interval [CI] 0.198, 0.930; P = 0.032) was one of the significant independent prognostic factors for overall survival. Conclusions: We found a highly reliable FI network, which revealed LIFR, PIK3R1, and MMP12 as novel prognostic biomarker candidates for GBC. These findings could accelerate biomarker discovery and therapeutic development in this cancer.
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Affiliation(s)
- Xinyi Zhao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Mengxiang Xu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Zhen Cai
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Wenji Yuan
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Wenyan Cui
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Ming D Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Research Center for Air Pollution and Health, Zhejiang University, Hangzhou, China.,Institute of Neuroimmune Pharmacology, Seton Hall University, South Orange, NJ, United States
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32
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Frezzetti D, De Luca A, Normanno N. Extracellular matrix proteins as circulating biomarkers for the diagnosis of non-small cell lung cancer patients. J Thorac Dis 2019; 11:S1252-S1256. [PMID: 31245101 DOI: 10.21037/jtd.2019.02.46] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Daniela Frezzetti
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G.Pascale, Naples, Italy
| | - Antonella De Luca
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G.Pascale, Naples, Italy
| | - Nicola Normanno
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G.Pascale, Naples, Italy
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MiR-384 induces apoptosis and autophagy of non-small cell lung cancer cells through the negative regulation of Collagen α-1(X) chain gene. Biosci Rep 2019; 39:BSR20181523. [PMID: 30442874 PMCID: PMC6356039 DOI: 10.1042/bsr20181523] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 11/05/2018] [Accepted: 11/12/2018] [Indexed: 12/14/2022] Open
Abstract
The present study aims to investigate the mechanism of miR-384 in non-small cell lung cancer (NSCLC) cell apoptosis and autophagy by regulating Collagen α-1(X) chain (COL10A1). Bioinformatics methods were applied to evaluate potential miRNAs and genes that might correlate with NSCLC. Tumor tissues and adjacent tissues from 104 NSCLC patients were collected and human NSCLC A549 cell line was selected for subsequent experiments. A549 cells were treated with miR-384 mimic, miR-384 inhibitor, or knockdown of COL10A1. Quantitative real-time PCR (qRT-PCR) and Western blotting were utilized to detect the levels of miR-384, COL10A, Survivin, Bcl-2, Bax, Bcl-xl, Beclin 1, and LC3 in tissues and cells. A series of biological assays including MTT assay, Annexin V-FITC/PI (propidium iodide) staining, immunofluorescence, monodansylcadaverine (MDC) staining were conducted to investigate the effects of miR-384 and COL10A1 on NSCLC cells. Tumorigenicity assay for nude rats was applied. Results obtained from the present study indicated that miR-384 down-regulated COL10A1 by targetting it. Compared with adjacent tissues, miR-384 expression was obviously reduced while COL10A1 expression was significantly enhanced in NSCLC tissues (all P<0.05). Outcomes in vivo and in vitro suggested that cell proliferation and tumorigenicity were inhibited while cell apoptosis and autophagy were induced in NSCLC cells treated with up-regulation of miR-384 or silence of COL10A1. In miR-384 inhibitor group, cell proliferation was improved, while cell apoptosis was reduced and cell autophagy was decreased whereas tumorigenicity of cells was strengthened. Based on the findings of our study, it was established that miR-384 could down-regulate COL10A1 levels, subsequently inhibiting cell proliferation and promoting cell apoptosis and autophagy in NSCLC cells.
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Comprehensive and in-depth analysis of microRNA and mRNA expression profile in salivary adenoid cystic carcinoma. Gene 2018; 678:349-360. [PMID: 30098429 DOI: 10.1016/j.gene.2018.08.023] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 07/19/2018] [Accepted: 08/06/2018] [Indexed: 12/24/2022]
Abstract
OBJECTIVES To conduct an integrated analysis of microRNA and mRNA expression profile and further discover vital molecules to uncover novel pathogenic mechanisms in salivary adenoid cystic carcinoma (SACC). MATERIALS AND METHODS MicroRNA and mRNA expression profiles were obtained from six paired primary SACC tumors and corresponding adjacent normal glands using high-throughput next-generation sequencing technology followed by an overall integrated bioinformatics analysis and subsequently molecular biology techniques validation. RESULTS Compared with adjacent noncancerous normal gland, 2107 significant differentially expressed mRNA were determined in SACC. Gene ontology and KEGG pathway analysis suggested that the differentially expressed genes were relevant to many significant biological implications. Venn diagram analysis of differentially expressed genes in different group identified 29 differentially expressed overlapping mRNA. 40 differentially expressed microRNAs were also identified in SACC. Furthermore, integrated analysis of microRNA and mRNA expression profiles recognized a core microRNA-mRNA regulatory network and unmasked many novel genes including SCUBE3, CA6, hsa-miR-885-5p and other molecules which may play an essential role in the carcinogenesis of SACC. Also, Q-PCR and immunohistochemistry results reveal the high expression and distribution of SCUBE3 in SACC and dual luciferase reporter assay also preliminarily validated that SCUBE3 was a target of hsa-miR-885-5p. CONCLUSION Contemporary microRNA/mRNA analysis have uncovered many mRNAs and microRNAs worthy further exploration in SACC. These are bound to help us shed light on the overall genetic background of SACC and further elucidate the potential molecular mechanism of SACC.
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35
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Li T, Huang H, Shi G, Zhao L, Li T, Zhang Z, Liu R, Hu Y, Liu H, Yu J, Li G. TGF-β1-SOX9 axis-inducible COL10A1 promotes invasion and metastasis in gastric cancer via epithelial-to-mesenchymal transition. Cell Death Dis 2018; 9:849. [PMID: 30154451 PMCID: PMC6113209 DOI: 10.1038/s41419-018-0877-2] [Citation(s) in RCA: 124] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 05/22/2018] [Accepted: 06/13/2018] [Indexed: 12/14/2022]
Abstract
Molecular biomarkers that predict disease progression might promote drug development and therapeutic strategies in aggressive cancers, such as gastric cancer (GC). High-throughput mRNA sequencing (RNA-seq) revealed that collagen type X alpha 1 (COL10A1) is a disease progression-associated gene. Analysis of 103 GC patients showed that high COL10A1 mRNA expression was associated with GC metastasis and reduced survival. We analyzed the COL10A1 promoter using the UCSC genome website and JASPAR database, and we found potential SOX9 binding site. Here, we demonstrated that SOX9 and COL10A1 were both up-regulated in GC. We observed a positive correlation between the expression patterns of SOX9 and COL10A1 in GC cells and tissues. The results of electrophoretic mobility shift assay (EMSA), chromatin immunoprecipitation (ChIP) assay and promoter reporter indicated that SOX9 could directly bind to the COL10A1 gene promoter and activate its transcription. Biological function experiments showed that COL10A1 regulated the migration and invasion of GC cells. Knockdown COL10A1 inhibited lung and abdominal cavity metastasis in a nude mouse model. Moreover, transforming growth factor-β1 (TGF-β1) treatment up-regulated the phosphorylation of Smad2 and increased SOX9 and COL10A1 expression. COL10A1 was confirmed to be a potential inducer of epithelial-to-mesenchymal transition (EMT). SOX9 was essential for COL10A1-mediated EMT, and cell migration, invasion and metastasis. Co-expression of SOX9 and COL10A1 was associated with tumor progression and was strongly predictive of overall survival in GC patients. In summary, this study elucidated the mechanistic link between COL10A1 and the TGF-β1-SOX9 axis. These findings indicated that COL10A1 might play a crucial role in GC progression and serve as a potential biomarker and therapeutic target in GC patients.
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Affiliation(s)
- Tingting Li
- Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Haipeng Huang
- Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, China.,Department of Gastrointestinal Surgery, Guangdong Provincial Hospital of Traditional Chinese Medicine, Guangzhou, China
| | - Guangyao Shi
- Division of Cardiology, Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Liying Zhao
- Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Tuanjie Li
- Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Ze Zhang
- Departments of Maxillofacial and Otorhinolaryngology Oncology; Department of Head and Neck Surgery, Tianjin Medical University Cancer Institute and Hospital; National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin; Tianjin's Clinical Research Center for Cancer, Tianjin, China
| | - Ruoyan Liu
- Department of Gynecologic Oncology, Tianjin Medical University Cancer Institute and Hospital; National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, Tianjin's Clinical Research Center for Cancer, Tianjin, China
| | - Yanfeng Hu
- Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Hao Liu
- Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, China.
| | - Jiang Yu
- Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, China.
| | - Guoxin Li
- Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, China.
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36
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Coghlan RF, Oberdorf JA, Sienko S, Aiona MD, Boston BA, Connelly KJ, Bahney C, LaRouche J, Almubarak SM, Coleman DT, Girkontaite I, von der Mark K, Lunstrum GP, Horton WA. A degradation fragment of type X collagen is a real-time marker for bone growth velocity. Sci Transl Med 2018; 9:9/419/eaan4669. [PMID: 29212713 PMCID: PMC6516194 DOI: 10.1126/scitranslmed.aan4669] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Revised: 08/11/2017] [Accepted: 10/12/2017] [Indexed: 12/20/2022]
Abstract
Despite its importance as a key parameter of child health and development, growth velocity is difficult to determine in real timebecause skeletal growth is slowand clinical tools to accurately detect very small increments of growth do not exist. We report discovery of a marker for skeletal growth in infants and children. The intact trimeric noncollagenous 1 (NC1) domain of type X collagen, the markerwe designated as CXMfor Collagen X Marker, is a degradation by-product of endochondral ossification that is released into the circulation in proportion to overall growth plate activity. Thismarker corresponds to the rate of linear bone growth at timeofmeasurement. Serumconcentrations of CXMplotted against age showa pattern similar to well-established height growth velocity curves and correlate with height growth velocity calculated from incremental height measurements in this study. The CXM marker is stable once collected and can be accurately assayed in serum, plasma, and dried blood spots. CXMtestingmay be useful for monitoring growth in the pediatric population, especially responses of infants and children with genetic and acquired growth disorders to interventions that target the underlying growth disturbances. The utility of CXM may potentially extend to managing other conditions such as fracture healing, scoliosis, arthritis, or cancer.
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Affiliation(s)
- Ryan F Coghlan
- Research Center, Shriners Hospitals for Children, Portland, OR 97239, USA
| | - Jon A Oberdorf
- Research Center, Shriners Hospitals for Children, Portland, OR 97239, USA.,Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, OR 97239, USA
| | - Susan Sienko
- Research Center, Shriners Hospitals for Children, Portland, OR 97239, USA
| | - Michael D Aiona
- Research Center, Shriners Hospitals for Children, Portland, OR 97239, USA
| | - Bruce A Boston
- Department of Pediatrics, Oregon Health and Science University, Portland, OR 97239, USA
| | - Kara J Connelly
- Department of Pediatrics, Oregon Health and Science University, Portland, OR 97239, USA
| | - Chelsea Bahney
- Department of Orthopedic Surgery, University of California Medical School, San Francisco, CA 94111, USA
| | - Jeremie LaRouche
- Department of Orthopedic Surgery, University of California Medical School, San Francisco, CA 94111, USA
| | - Sarah M Almubarak
- Department of Orthopedic Surgery, University of California Medical School, San Francisco, CA 94111, USA
| | - Daniel T Coleman
- Graduate School of Social Service, Fordham University, Lincoln Center, New York, NY 10023, USA
| | - Irute Girkontaite
- Department of Immunology, State Research Institute, Vilnius University, Vilnius, Lithuania
| | | | - Gregory P Lunstrum
- Research Center, Shriners Hospitals for Children, Portland, OR 97239, USA
| | - William A Horton
- Research Center, Shriners Hospitals for Children, Portland, OR 97239, USA. .,Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, OR 97239, USA
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Wu SX, Huang J, Liu ZW, Chen HG, Guo P, Cai QQ, Zheng JJ, Qin HD, Zheng ZS, Chen X, Zhang RY, Chen SL, Lin TX. A Genomic-clinicopathologic Nomogram for the Preoperative Prediction of Lymph Node Metastasis in Bladder Cancer. EBioMedicine 2018; 31:54-65. [PMID: 29655996 PMCID: PMC6014062 DOI: 10.1016/j.ebiom.2018.03.034] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 03/29/2018] [Accepted: 03/29/2018] [Indexed: 02/05/2023] Open
Abstract
Preoperative lymph node (LN) status is important for the treatment of bladder cancer (BCa). Here, we report a genomic-clinicopathologic nomogram for preoperatively predicting LN metastasis in BCa. In the discovery stage, 325 BCa patients from TCGA were involved and LN-status-related mRNAs were selected. In the training stage, multivariate logistic regression analysis was used to developed a genomic-clinicopathologic nomogram for preoperative LN metastasis prediction in the training set (SYSMH set, n=178). In the validation stage, we validated the nomogram using two independent sample sets (SYSUCC set, n=142; RJH set, n=104) with respect to its discrimination, calibration and clinical usefulness. As results, we identified five LN-status-related mRNAs, including ADRA1D, COL10A1, DKK2, HIST2H3D and MMP11. Then, a genomic classifier was developed to classify patients into high- and low-risk groups in the training set. Furthermore, a nomogram incorporating the five-mRNA-based classifier, image-based LN status, transurethral resection (TUR) T stage, and TUR lymphovascular invasion (LVI) was constructed in the training set, which performed well in the training and validation sets. Decision curve analysis demonstrated the clinical value of our nomogram. Thus, our genomic-clinicopathologic nomogram shows favorable discriminatory ability and may aid in clinical decision-making, especially for cN-patients.
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Affiliation(s)
- Shao-Xu Wu
- Department of Urology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China; Guangdong Province Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Research Center of Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Jian Huang
- Department of Urology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Zhuo-Wei Liu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Department of Urology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Hai-Ge Chen
- Department of Urology, Renji Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Pi Guo
- Department of Preventive Medicine, Shantou University Medical College, Shantou, China
| | - Qing-Qing Cai
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Department of Medical Oncology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Jun-Jiong Zheng
- Department of Urology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Hai-De Qin
- Guangdong Province Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Research Center of Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Zao-Song Zheng
- Department of Urology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Xin Chen
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Department of Urology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Rui-Yun Zhang
- Department of Urology, Renji Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Si-Liang Chen
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Department of Urology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Tian-Xin Lin
- Department of Urology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China.
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38
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Huang H, Li T, Ye G, Zhao L, Zhang Z, Mo D, Wang Y, Zhang C, Deng H, Li G, Liu H. High expression of COL10A1 is associated with poor prognosis in colorectal cancer. Onco Targets Ther 2018; 11:1571-1581. [PMID: 29593423 PMCID: PMC5865565 DOI: 10.2147/ott.s160196] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Background High expression of collagen type X alpha 1 chain (COL10A1), a member of the collagen family, had been observed in various human cancers, but the detailed function and molecular mechanism of COL10A1 were largely unclear. Aim The aim of this study was to investigate the expression of COL10A1 in colorectal cancer (CRC) tissues and cells and to reveal its biological function and mechanism in CRC. Materials and methods Immunohistochemistry (IHC), real-time quantitative polymerase chain reaction (QPCR) and Western blot experiments were used to determine the clinical relevance between expression levels of COL10A1 and CRC. Results Compared with normal tissues, COL10A1 expression was significantly higher in CRC tissues. Biological functional experiments showed that overexpression of COL10A1 enhanced proliferation, migration, and invasion of CRC cells, and knockdown of COL10A1 inhibited tumorigenesis in vivo. Western blot assays showed that COL10A1 promoted the process of epithelial–mesenchymal transition (EMT). The overexpression of COL10A1 was associated with adverse prognosis in CRC by tissue microarray (TMA) analysis. Conclusion Our findings had provided evidences to support the fact that COL10A1 was abnormally up-expressed in CRC and involved in the progression of CRC and the process of EMT. Furthermore, we demonstrated that the high-level expression of COL10A1 was an independent risk factor of prognosis and overall survival in CRC patients. These suggested that COL10A1 might be a new potential target for cancer therapy in the future.
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Affiliation(s)
- Haipeng Huang
- Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangdong Provincial Engineering Technology Research Center of Minimally Invasive Surgery, Guangzhou, China
| | - Tingting Li
- Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangdong Provincial Engineering Technology Research Center of Minimally Invasive Surgery, Guangzhou, China
| | - Gengtai Ye
- Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangdong Provincial Engineering Technology Research Center of Minimally Invasive Surgery, Guangzhou, China
| | - Liying Zhao
- Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangdong Provincial Engineering Technology Research Center of Minimally Invasive Surgery, Guangzhou, China
| | - Zhenzhan Zhang
- Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangdong Provincial Engineering Technology Research Center of Minimally Invasive Surgery, Guangzhou, China
| | - Debin Mo
- Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangdong Provincial Engineering Technology Research Center of Minimally Invasive Surgery, Guangzhou, China
| | - Yiming Wang
- Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangdong Provincial Engineering Technology Research Center of Minimally Invasive Surgery, Guangzhou, China
| | - Ce Zhang
- Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangdong Provincial Engineering Technology Research Center of Minimally Invasive Surgery, Guangzhou, China
| | - Haijun Deng
- Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangdong Provincial Engineering Technology Research Center of Minimally Invasive Surgery, Guangzhou, China
| | - Guoxin Li
- Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangdong Provincial Engineering Technology Research Center of Minimally Invasive Surgery, Guangzhou, China
| | - Hao Liu
- Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangdong Provincial Engineering Technology Research Center of Minimally Invasive Surgery, Guangzhou, China
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Barrett AS, Maller O, Pickup MW, Weaver VM, Hansen KC. Compartment resolved proteomics reveals a dynamic matrisome in a biomechanically driven model of pancreatic ductal adenocarcinoma. JOURNAL OF IMMUNOLOGY AND REGENERATIVE MEDICINE 2018; 1:67-75. [PMID: 36908331 PMCID: PMC10003644 DOI: 10.1016/j.regen.2018.03.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is characterized by a severe fibrotic component that compromises treatment, alters the immune cell profile and contributes to patient mortality. It has been shown that early on in this process, dynamic changes in tissue biomechanics play an integral role in supporting pancreatic cancer development and progression. Despite the acknowledgement of its importance, a granular view of how stromal composition changes during the course of PDAC progression remains largely unknown. To mimic the quasi-mesenchymal phenotype and pronounced desmoplastic response observed clinically, we utilized a genetically engineered mouse model of PDAC that is driven by a KrasG12D mutation and loss of Tgfbr2 expression. Application of compartment resolved proteomics revealed that PDAC progression in this KTC model is associated with dynamic stromal alterations that are indicative of a wound healing program. We identified an early provisional matricellular fibrosis that was accompanied by markers of macrophage activation and infiltration, consistent with the inflammatory phase of wound healing. At 20 weeks a proliferative phenotype was observed with increased fibroblast markers, further collagen deposition and loss of basement membrane and native cell markers.
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Affiliation(s)
- Alexander S Barrett
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, Colorado, USA
| | - Ori Maller
- Department of Surgery, University of California San Francisco, San Francisco, California, USA
| | - Michael W Pickup
- Department of Surgery, University of California San Francisco, San Francisco, California, USA
| | - Valerie M Weaver
- Department of Surgery, University of California San Francisco, San Francisco, California, USA
| | - Kirk C Hansen
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, Colorado, USA
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40
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Zhao Q, Eichten A, Parveen A, Adler C, Huang Y, Wang W, Ding Y, Adler A, Nevins T, Ni M, Wei Y, Thurston G. Single-Cell Transcriptome Analyses Reveal Endothelial Cell Heterogeneity in Tumors and Changes following Antiangiogenic Treatment. Cancer Res 2018; 78:2370-2382. [PMID: 29449267 DOI: 10.1158/0008-5472.can-17-2728] [Citation(s) in RCA: 126] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Revised: 11/27/2017] [Accepted: 02/12/2018] [Indexed: 11/16/2022]
Abstract
Angiogenesis involves dynamic interactions between specialized endothelial tip and stalk cells that are believed to be regulated in part by VEGF and Dll4-Notch signaling. However, our understanding of this process is hampered by limited knowledge of the heterogeneity of endothelial cells and the role of different signaling pathways in specifying endothelial phenotypes. Here, we characterized by single-cell transcriptomics the heterogeneity of mouse endothelial cells and other stromal cells during active angiogenesis in xenograft tumors as well as from adult normal heart, following pharmacologic inhibition of VEGF and Dll4-Notch signaling. We classified tumor endothelial cells into three subpopulations that appeared to correspond with tip-like, transition, and stalk-like cells. Previously identified markers for tip and stalk cells were confirmed and several novel ones discovered. Blockade of VEGF rapidly inhibited cell-cycle genes and strongly reduced the proportion of endothelial tip cells in tumors. In contrast, blockade of Dll4 promoted endothelial proliferation as well as tip cell markers; blockade of both pathways inhibited endothelial proliferation but preserved some tip cells. We also phenotypically classified other tumor stromal cells and found that tumor-associated fibroblasts responded to antiangiogenic drug treatments by upregulating hypoxia-associated genes and producing secreted factors involved in angiogenesis. Overall, our findings better define the heterogeneity of tumor endothelial and other stromal cells and reveal the roles of VEGF and Dll4-Notch in specifying tumor endothelial phenotype, highlighting the response of stromal cells to antiangiogenic therapies.Significance: These findings provide a framework for defining subpopulations of endothelial cells and tumor-associated fibroblasts and their rapid changes in gene expression following antiangiogenic treatment. Cancer Res; 78(9); 2370-82. ©2018 AACR.
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Affiliation(s)
- Qi Zhao
- Regeneron Pharmaceuticals Inc., Tarrytown, New York
| | | | - Asma Parveen
- Regeneron Pharmaceuticals Inc., Tarrytown, New York
| | | | - Ying Huang
- Regeneron Pharmaceuticals Inc., Tarrytown, New York
| | - Wei Wang
- Regeneron Pharmaceuticals Inc., Tarrytown, New York
| | - Yueming Ding
- Regeneron Pharmaceuticals Inc., Tarrytown, New York
| | | | | | - Min Ni
- Regeneron Pharmaceuticals Inc., Tarrytown, New York
| | - Yi Wei
- Regeneron Pharmaceuticals Inc., Tarrytown, New York
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Identification of differentially expressed genes regulated by molecular signature in breast cancer-associated fibroblasts by bioinformatics analysis. Arch Gynecol Obstet 2017; 297:161-183. [PMID: 29063236 DOI: 10.1007/s00404-017-4562-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 09/21/2017] [Indexed: 12/18/2022]
Abstract
OBJECTIVE Breast cancer is a severe risk to public health and has adequately convoluted pathogenesis. Therefore, the description of key molecular markers and pathways is of much importance for clarifying the molecular mechanism of breast cancer-associated fibroblasts initiation and progression. Breast cancer-associated fibroblasts gene expression dataset was downloaded from Gene Expression Omnibus database. METHODS A total of nine samples, including three normal fibroblasts, three granulin-stimulated fibroblasts and three cancer-associated fibroblasts samples, were used to identify differentially expressed genes (DEGs) between normal fibroblasts, granulin-stimulated fibroblasts and cancer-associated fibroblasts samples. The gene ontology (GO) and pathway enrichment analysis was performed, and protein-protein interaction (PPI) network of the DEGs was constructed by NetworkAnalyst software. RESULTS Totally, 190 DEGs were identified, including 66 up-regulated and 124 down-regulated genes. GO analysis results showed that up-regulated DEGs were significantly enriched in biological processes (BP), including cell-cell signalling and negative regulation of cell proliferation; molecular function (MF), including insulin-like growth factor II binding and insulin-like growth factor I binding; cellular component (CC), including insulin-like growth factor binding protein complex and integral component of plasma membrane; the down-regulated DEGs were significantly enriched in BP, including cell adhesion and extracellular matrix organization; MF, including N-acetylgalactosamine 4-sulfate 6-O-sulfotransferase activity and calcium ion binding; CC, including extracellular space and extracellular matrix. WIKIPATHWAYS analysis showed the up-regulated DEGs were enriched in myometrial relaxation and contraction pathways. WIKIPATHWAYS, REACTOME, PID_NCI and KEGG pathway analysis showed the down-regulated DEGs were enriched endochondral ossification, TGF beta signalling pathway, integrin cell surface interactions, beta1 integrin cell surface interactions, malaria and glycosaminoglycan biosynthesis-chondroitin sulfate/dermatan sulphate. The top 5 up-regulated hub genes, CDKN2A, MME, PBX1, IGFBP3, and TFAP2C and top 5 down-regulated hub genes VCAM1, KRT18, TGM2, ACTA2, and STAMBP were identified from the PPI network, and subnetworks revealed these genes were involved in significant pathways, including myometrial relaxation and contraction pathways, integrin cell surface interactions, beta1 integrin cell surface interaction. Besides, the target hsa-mirs for DEGs were identified. hsa-mir-759, hsa-mir-4446-5p, hsa-mir-219a-1-3p and hsa-mir-26a-5p were important miRNAs in this study. CONCLUSIONS We pinpoint important key genes and pathways closely related with breast cancer-associated fibroblasts initiation and progression by a series of bioinformatics analysis on DEGs. These screened genes and pathways provided for a more detailed molecular mechanism underlying breast cancer-associated fibroblasts occurrence and progression, holding promise for acting as molecular markers and probable therapeutic targets.
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Common Subcluster Mining in Microarray Data for Molecular Biomarker Discovery. Interdiscip Sci 2017; 11:348-359. [PMID: 29022249 DOI: 10.1007/s12539-017-0262-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Revised: 08/07/2017] [Accepted: 09/12/2017] [Indexed: 12/11/2022]
Abstract
Molecular biomarkers can be potential facilitators for detection of cancer at early stage which is otherwise difficult through conventional biomarkers. Gene expression data from microarray experiments on both normal and diseased cell samples provide enormous scope to explore genetic relations of disease using computational techniques. Varied patterns of expressions of thousands of genes at different cell conditions along with inherent experimental error make the task of isolating disease related genes challenging. In this paper, we present a data mining method, common subcluster mining (CSM), to discover highly perturbed genes under diseased condition from differential expression patterns. The method builds heap through superposing near centroid clusters from gene expression data of normal samples and extracts its core part. It, thus, isolates genes exhibiting the most stable state across normal samples and constitute a reference set for each centroid. It performs the same operation on datasets from corresponding diseased samples and isolates the genes showing drastic changes in their expression patterns. The method thus finds the disease-sensitive genesets when applied to datasets of lung cancer, prostrate cancer, pancreatic cancer, breast cancer, leukemia and pulmonary arterial hypertension. In majority of the cases, few new genes are found over and above some previously reported ones. Genes with distinct deviations in diseased samples are prospective candidates for molecular biomarkers of the respective disease.
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Liu Q, Diao R, Feng G, Mu X, Li A. Risk score based on three mRNA expression predicts the survival of bladder cancer. Oncotarget 2017; 8:61583-61591. [PMID: 28977887 PMCID: PMC5617447 DOI: 10.18632/oncotarget.18642] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 05/23/2017] [Indexed: 01/08/2023] Open
Abstract
Bladder cancer (BLCA) is one of the most malignant cancers worldwide, and its prognosis varies. 1214 BLCA samples in five different datasets and 2 platforms were enrolled in this study. By utilizing the gene expression in The Cancer Genome Atlas (TCGA) dataset, and another two datasets, in GSE13507 and GSE31684, we constructed a risk score staging system with Cox multivariate regression to evaluate predict the outcome of BLCA patients. Three genes consist of RCOR1, ST3GAL5, and COL10A1 were used to predict the survival of BLCA patients. The patients with low risk score have a better survival rate than those with high risk score, significantly. The survival profiles of another two datasets (GSE13507 and GSE31684), which were used for candidate gene selection, were similar as the training dataset (TCGA). Furthermore, survival prediction effect of risk score staging system in another 2 independent datasets, GSE40875 and E-TABM-4321, were also validated. Compared with other clinical observations, and the risk score performs better in evaluating the survival of BLCA patients. Moreover, the correlation between radiation were also evaluated, and we found that patients have a poor survival in high risk group, regardless of radiation. Gene Set Enrichment Analysis was also implemented to find the difference between high-risk and low-risk groups on biological pathways, and focal adhesion and JAK signaling pathway were significantly enriched. In summary, we developed a risk staging model for BLCA patients with three gene expression. The model is independent from and performs better than other clinical information.
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Affiliation(s)
- Qingzuo Liu
- Yantai Yuhuangding Hospital, Zhifu District, Yantai 264000, China
| | - Ruigang Diao
- Yantai Yuhuangding Hospital, Zhifu District, Yantai 264000, China
| | - Guoyan Feng
- Yantai Yuhuangding Hospital, Zhifu District, Yantai 264000, China
| | - Xiaodong Mu
- Yantai Yuhuangding Hospital, Zhifu District, Yantai 264000, China
| | - Aiqun Li
- Yantai Affiliated Hospital of Binzhou Medical University, Muping District, Yantai 264003, China
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Liu Y, Yin X, Zhong J, Guan N, Luo Z, Min L, Yao X, Bo X, Dai L, Bai H. Systematic Identification and Assessment of Therapeutic Targets for Breast Cancer Based on Genome-Wide RNA Interference Transcriptomes. Genes (Basel) 2017; 8:genes8030086. [PMID: 28245581 PMCID: PMC5368690 DOI: 10.3390/genes8030086] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 01/24/2017] [Accepted: 02/13/2017] [Indexed: 12/15/2022] Open
Abstract
With accumulating public omics data, great efforts have been made to characterize the genetic heterogeneity of breast cancer. However, identifying novel targets and selecting the best from the sizeable lists of candidate targets is still a key challenge for targeted therapy, largely owing to the lack of economical, efficient and systematic discovery and assessment to prioritize potential therapeutic targets. Here, we describe an approach that combines the computational evaluation and objective, multifaceted assessment to systematically identify and prioritize targets for biological validation and therapeutic exploration. We first establish the reference gene expression profiles from breast cancer cell line MCF7 upon genome-wide RNA interference (RNAi) of a total of 3689 genes, and the breast cancer query signatures using RNA-seq data generated from tissue samples of clinical breast cancer patients in the Cancer Genome Atlas (TCGA). Based on gene set enrichment analysis, we identified a set of 510 genes that when knocked down could significantly reverse the transcriptome of breast cancer state. We then perform multifaceted assessment to analyze the gene set to prioritize potential targets for gene therapy. We also propose drug repurposing opportunities and identify potentially druggable proteins that have been poorly explored with regard to the discovery of small-molecule modulators. Finally, we obtained a small list of candidate therapeutic targets for four major breast cancer subtypes, i.e., luminal A, luminal B, HER2+ and triple negative breast cancer. This RNAi transcriptome-based approach can be a helpful paradigm for relevant researches to identify and prioritize candidate targets for experimental validation.
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Affiliation(s)
- Yang Liu
- Research Center for Clinical & Translational Medicine, Beijing 302 Hospital, Beijing 100039, China.
| | - Xiaoyao Yin
- Science and technology on Parallel and Distributed Processing Laboratory, National University of Defense Technology, Changsha 410073, China.
| | - Jing Zhong
- Huzhou Key Laboratory of Molecular Medicine, Huzhou Central Hospital, Huzhou 313000, China.
| | - Naiyang Guan
- Science and technology on Parallel and Distributed Processing Laboratory, National University of Defense Technology, Changsha 410073, China.
| | - Zhigang Luo
- Science and technology on Parallel and Distributed Processing Laboratory, National University of Defense Technology, Changsha 410073, China.
| | - Lishan Min
- Huzhou Key Laboratory of Molecular Medicine, Huzhou Central Hospital, Huzhou 313000, China.
| | - Xing Yao
- Huzhou Key Laboratory of Molecular Medicine, Huzhou Central Hospital, Huzhou 313000, China.
| | - Xiaochen Bo
- Beijing Institute of Radiation Medicine, Beijing 100850, China.
| | - Licheng Dai
- Huzhou Key Laboratory of Molecular Medicine, Huzhou Central Hospital, Huzhou 313000, China.
| | - Hui Bai
- Beijing Institute of Radiation Medicine, Beijing 100850, China.
- No. 451 Hospital of PLA, Xi'an 710054, China.
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Gene expression profiling of breast cancer in Lebanese women. Sci Rep 2016; 6:36639. [PMID: 27857161 PMCID: PMC5114572 DOI: 10.1038/srep36639] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 10/13/2016] [Indexed: 12/20/2022] Open
Abstract
Breast cancer is commonest cancer in women worldwide. Elucidation of underlying biology and molecular pathways is necessary for improving therapeutic options and clinical outcomes. Molecular alterations in breast cancer are complex and involve cross-talk between multiple signaling pathways. The aim of this study is to extract a unique mRNA fingerprint of breast cancer in Lebanese women using microarray technologies. Gene-expression profiles of 94 fresh breast tissue samples (84 cancerous/10 non-tumor adjacent samples) were analyzed using GeneChip Human Genome U133 Plus 2.0 arrays. Quantitative real-time PCR was employed to validate candidate genes. Differentially expressed genes between breast cancer and non-tumor tissues were screened. Significant differences in gene expression were established for COL11A1/COL10A1/MMP1/COL6A6/DLK1/S100P/CXCL11/SOX11/LEP/ADIPOQ/OXTR/FOSL1/ACSBG1 and C21orf37. Pathways/diseases representing these genes were retrieved and linked using PANTHER®/Pathway Studio®. Many of the deregulated genes are associated with extracellular matrix, inflammation, angiogenesis, metastasis, differentiation, cell proliferation and tumorigenesis. Characteristics of breast cancers in Lebanese were compared to those of women from Western populations to explain why breast cancer is more aggressive and presents a decade earlier in Lebanese victims. Delineating molecular mechanisms of breast cancer in Lebanese women led to key genes which could serve as potential biomarkers and/or novel drug targets for breast cancer.
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Brodsky AS, Xiong J, Yang D, Schorl C, Fenton MA, Graves TA, Sikov WM, Resnick MB, Wang Y. Identification of stromal ColXα1 and tumor-infiltrating lymphocytes as putative predictive markers of neoadjuvant therapy in estrogen receptor-positive/HER2-positive breast cancer. BMC Cancer 2016; 16:274. [PMID: 27090210 PMCID: PMC4835834 DOI: 10.1186/s12885-016-2302-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 04/07/2016] [Indexed: 12/15/2022] Open
Abstract
Background The influence of the tumor microenvironment and tumor-stromal interactions on the heterogeneity of response within breast cancer subtypes have just begun to be explored. This study focuses on patients with estrogen receptor-positive/human epidermal growth factor receptor 2-positive (ER+/HER2+) breast cancer receiving neoadjuvant chemotherapy and HER2-targeted therapy (NAC+H), and was designed to identify novel predictive biomarkers by combining gene expression analysis and immunohistochemistry with pathologic response. Methods We performed gene expression profiling on pre-NAC+H tumor samples from responding (no or minimal residual disease at surgery) and non-responding patients. Gene set enrichment analysis identified potentially relevant pathways, and immunohistochemical staining of pre-treatment biopsies was used to measure protein levels of those pathways, which were correlated with pathologic response in both univariate and multivariate analysis. Results Increased expression of genes encoding for stromal collagens, including Col10A1, and reduced expression of immune-associated genes, reflecting lower levels of total tumor-infiltrating lymphocytes (TILs), were strongly associated with poor pathologic response. Lower TILs in tumor biopsies correlated with reduced likelihood of achieving an optimal pathologic response, but increased expression of the Col10A1 gene product, colXα1, had greater predictive value than stromal abundance for poor response (OR = 18.9, p = 0.003), and the combination of increased colXα1 expression and low TILs was significantly associated with poor response in multivariate analysis. ROC analysis suggests strong specificity and sensitivity for this combination in predicting treatment response. Conclusions Increased expression of stromal colXα1 and low TILs correlate with poor pathologic response in ER+/HER2+ breast tumors. Further studies are needed to confirm their predictive value and impact on long-term outcomes, and to determine whether this collagen exerts a protective effect on the cancer cells or simply reflects other factors within the tumor microenvironment. Electronic supplementary material The online version of this article (doi:10.1186/s12885-016-2302-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Alexander S Brodsky
- Department of Pathology and Laboratory Medicine, Rhode Island Hospital and Lifespan Medical Center, Warren Alpert Medical School of Brown University, Providence, USA. .,Department of Pathology, Rhode Island Hospital and Lifespan Medical Center, Providence, RI, 02903, USA.
| | - Jinjun Xiong
- Department of Pathology, Women and Infants Hospital, Warren Alpert Medical School of Brown University, Providence, USA
| | - Dongfang Yang
- Department of Pathology and Laboratory Medicine, Rhode Island Hospital and Lifespan Medical Center, Warren Alpert Medical School of Brown University, Providence, USA
| | - Christoph Schorl
- Molecular Biology, Cell Biology, & Biochemistry, Brown University, Providence, USA
| | - Mary Anne Fenton
- Department of Medicine, Rhode Island Hospital and Lifespan Medical Center, Warren Alpert Medical School of Brown University, Providence, USA
| | - Theresa A Graves
- Department of Surgery, Rhode Island Hospital and Lifespan Medical Center, Warren Alpert Medical School of Brown University, Providence, USA
| | - William M Sikov
- Program in Women's Oncology, Women and Infants Hospital, Warren Alpert Medical School of Brown University, Providence, USA
| | - Murray B Resnick
- Department of Pathology and Laboratory Medicine, Rhode Island Hospital and Lifespan Medical Center, Warren Alpert Medical School of Brown University, Providence, USA
| | - Yihong Wang
- Department of Pathology and Laboratory Medicine, Rhode Island Hospital and Lifespan Medical Center, Warren Alpert Medical School of Brown University, Providence, USA. .,Department of Pathology, Rhode Island Hospital and Lifespan Medical Center, Providence, RI, 02903, USA.
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Uehara Y, Oda K, Ikeda Y, Koso T, Tsuji S, Yamamoto S, Asada K, Sone K, Kurikawa R, Makii C, Hagiwara O, Tanikawa M, Maeda D, Hasegawa K, Nakagawa S, Wada-Hiraike O, Kawana K, Fukayama M, Fujiwara K, Yano T, Osuga Y, Fujii T, Aburatani H. Integrated copy number and expression analysis identifies profiles of whole-arm chromosomal alterations and subgroups with favorable outcome in ovarian clear cell carcinomas. PLoS One 2015; 10:e0128066. [PMID: 26043110 PMCID: PMC4456367 DOI: 10.1371/journal.pone.0128066] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Accepted: 04/23/2015] [Indexed: 12/11/2022] Open
Abstract
Ovarian clear cell carcinoma (CCC) is generally associated with chemoresistance and poor clinical outcome, even with early diagnosis; whereas high-grade serous carcinomas (SCs) and endometrioid carcinomas (ECs) are commonly chemosensitive at advanced stages. Although an integrated genomic analysis of SC has been performed, conclusive views on copy number and expression profiles for CCC are still limited. In this study, we performed single nucleotide polymorphism analysis with 57 epithelial ovarian cancers (31 CCCs, 14 SCs, and 12 ECs) and microarray expression analysis with 55 cancers (25 CCCs, 16 SCs, and 14 ECs). We then evaluated PIK3CA mutations and ARID1A expression in CCCs. SNP array analysis classified 13% of CCCs into a cluster with high frequency and focal range of copy number alterations (CNAs), significantly lower than for SCs (93%, P < 0.01) and ECs (50%, P = 0.017). The ratio of whole-arm to all CNAs was higher in CCCs (46.9%) than SCs (21.7%; P < 0.0001). SCs with loss of heterozygosity (LOH) of BRCA1 (85%) also had LOH of NF1 and TP53, and LOH of BRCA2 (62%) coexisted with LOH of RB1 and TP53. Microarray analysis classified CCCs into three clusters. One cluster (CCC-2, n = 10) showed more favorable prognosis than the CCC-1 and CCC-3 clusters (P = 0.041). Coexistent alterations of PIK3CA and ARID1A were more common in CCC-1 and CCC-3 (7/11, 64%) than in CCC-2 (0/10, 0%; P < 0.01). Being in cluster CCC-2 was an independent favorable prognostic factor in CCC. In conclusion, CCC was characterized by a high ratio of whole-arm CNAs; whereas CNAs in SC were mainly focal, but preferentially caused LOH of well-known tumor suppressor genes. As such, expression profiles might be useful for sub-classification of CCC, and might provide useful information on prognosis.
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Affiliation(s)
- Yuriko Uehara
- Genome Science Division, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
- Department of Obstetrics and Gynecology, The University of Tokyo, Tokyo, Japan
| | - Katsutoshi Oda
- Department of Obstetrics and Gynecology, The University of Tokyo, Tokyo, Japan
- * E-mail:
| | - Yuji Ikeda
- Department of Obstetrics and Gynecology, The University of Tokyo, Tokyo, Japan
| | - Takahiro Koso
- Genome Science Division, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
- Department of Obstetrics and Gynecology, The University of Tokyo, Tokyo, Japan
| | - Shingo Tsuji
- Genome Science Division, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Shogo Yamamoto
- Genome Science Division, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Kayo Asada
- Genome Science Division, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
- Department of Obstetrics and Gynecology, The University of Tokyo, Tokyo, Japan
| | - Kenbun Sone
- Department of Obstetrics and Gynecology, The University of Tokyo, Tokyo, Japan
| | - Reiko Kurikawa
- Department of Obstetrics and Gynecology, The University of Tokyo, Tokyo, Japan
| | - Chinami Makii
- Department of Obstetrics and Gynecology, The University of Tokyo, Tokyo, Japan
| | - Otoe Hagiwara
- Department of Obstetrics and Gynecology, The University of Tokyo, Tokyo, Japan
| | - Michihiro Tanikawa
- Department of Obstetrics and Gynecology, The University of Tokyo, Tokyo, Japan
| | - Daichi Maeda
- Department of Pathology, The University of Tokyo, Tokyo, Japan
| | - Kosei Hasegawa
- Department of Obstetrics and Gynecology, Saitama Medical University International Medical Center, Saitama, Japan
| | - Shunsuke Nakagawa
- Department of Obstetrics and Gynecology, Teikyo University International, Tokyo, Japan
| | - Osamu Wada-Hiraike
- Department of Obstetrics and Gynecology, The University of Tokyo, Tokyo, Japan
| | - Kei Kawana
- Department of Obstetrics and Gynecology, The University of Tokyo, Tokyo, Japan
| | | | - Keiichi Fujiwara
- Department of Obstetrics and Gynecology, Saitama Medical University International Medical Center, Saitama, Japan
| | - Tetsu Yano
- Department of Obstetrics and Gynecology, National Center for Global Health and Medicine, Tokyo, Japan
| | - Yutaka Osuga
- Department of Obstetrics and Gynecology, The University of Tokyo, Tokyo, Japan
| | - Tomoyuki Fujii
- Department of Obstetrics and Gynecology, The University of Tokyo, Tokyo, Japan
| | - Hiroyuki Aburatani
- Genome Science Division, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
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Bioinformatics approach reveals systematic mechanism underlying lung adenocarcinoma. TUMORI JOURNAL 2015; 101:281-6. [PMID: 26045113 DOI: 10.5301/tj.5000278] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/30/2015] [Indexed: 01/22/2023]
Abstract
BACKGROUND The purpose of this work was to explore the systematic molecular mechanism of lung adenocarcinoma and gain a deeper insight into it. METHODS Comprehensive bioinformatics methods were applied. Initially, significant differentially expressed genes (DEGs) were analyzed from the Affymetrix microarray data (GSE27262) deposited in the Gene Expression Omnibus (GEO). Subsequently, gene ontology (GO) analysis was performed using online Database for Annotation, Visualization and Integration Discovery (DAVID) software. Finally, significant pathway crosstalk was investigated based on the information derived from the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. RESULTS According to our results, the N-terminal globular domain of the type X collagen (COL10A1) gene and transmembrane protein 100 (TMEM100) gene were identified to be the most significant DEGs in tumor tissue compared with the adjacent normal tissues. The main GO categories were biological process, cellular component and molecular function. In addition, the crosstalk was significantly different between non-small cell lung cancer pathways and inositol phosphate metabolism pathway, focal adhesion signal pathway, vascular smooth muscle contraction signal pathway, peroxisome proliferator-activated receptor (PPAR) signaling pathway and calcium signaling pathway in tumor. CONCLUSIONS Dysfunctional genes and pathways may play key roles in the progression and development of lung adenocarcinoma. Our data provide a systematic perspective for understanding this mechanism and may be helpful in discovering an effective treatment for lung adenocarcinoma.
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Wan Q, Dingerdissen H, Fan Y, Gulzar N, Pan Y, Wu TJ, Yan C, Zhang H, Mazumder R. BioXpress: an integrated RNA-seq-derived gene expression database for pan-cancer analysis. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2015; 2015:bav019. [PMID: 25819073 PMCID: PMC4377087 DOI: 10.1093/database/bav019] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
BioXpress is a gene expression and cancer association database in which the expression levels are mapped to genes using RNA-seq data obtained from The Cancer Genome Atlas, International Cancer Genome Consortium, Expression Atlas and publications. The BioXpress database includes expression data from 64 cancer types, 6361 patients and 17 469 genes with 9513 of the genes displaying differential expression between tumor and normal samples. In addition to data directly retrieved from RNA-seq data repositories, manual biocuration of publications supplements the available cancer association annotations in the database. All cancer types are mapped to Disease Ontology terms to facilitate a uniform pan-cancer analysis. The BioXpress database is easily searched using HUGO Gene Nomenclature Committee gene symbol, UniProtKB/RefSeq accession or, alternatively, can be queried by cancer type with specified significance filters. This interface along with availability of pre-computed downloadable files containing differentially expressed genes in multiple cancers enables straightforward retrieval and display of a broad set of cancer-related genes. Database URL:http://hive.biochemistry.gwu.edu/tools/bioxpress
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Affiliation(s)
- Quan Wan
- Department of Biochemistry and Molecular Medicine and McCormick Genomic and Proteomic Center, The George Washington University, Washington, DC 20037, USA
| | - Hayley Dingerdissen
- Department of Biochemistry and Molecular Medicine and McCormick Genomic and Proteomic Center, The George Washington University, Washington, DC 20037, USA
| | - Yu Fan
- Department of Biochemistry and Molecular Medicine and McCormick Genomic and Proteomic Center, The George Washington University, Washington, DC 20037, USA
| | - Naila Gulzar
- Department of Biochemistry and Molecular Medicine and McCormick Genomic and Proteomic Center, The George Washington University, Washington, DC 20037, USA
| | - Yang Pan
- Department of Biochemistry and Molecular Medicine and McCormick Genomic and Proteomic Center, The George Washington University, Washington, DC 20037, USA
| | - Tsung-Jung Wu
- Department of Biochemistry and Molecular Medicine and McCormick Genomic and Proteomic Center, The George Washington University, Washington, DC 20037, USA
| | - Cheng Yan
- Department of Biochemistry and Molecular Medicine and McCormick Genomic and Proteomic Center, The George Washington University, Washington, DC 20037, USA
| | - Haichen Zhang
- Department of Biochemistry and Molecular Medicine and McCormick Genomic and Proteomic Center, The George Washington University, Washington, DC 20037, USA
| | - Raja Mazumder
- Department of Biochemistry and Molecular Medicine and McCormick Genomic and Proteomic Center, The George Washington University, Washington, DC 20037, USA Department of Biochemistry and Molecular Medicine and McCormick Genomic and Proteomic Center, The George Washington University, Washington, DC 20037, USA
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50
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Discovery and validation of new potential biomarkers for early detection of colon cancer. PLoS One 2014; 9:e106748. [PMID: 25215506 PMCID: PMC4162553 DOI: 10.1371/journal.pone.0106748] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Accepted: 08/01/2014] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Accurate detection of characteristic proteins secreted by colon cancer tumor cells in biological fluids could serve as a biomarker for the disease. The aim of the present study was to identify and validate new serum biomarkers and demonstrate their potential usefulness for early diagnosis of colon cancer. METHODS The study was organized in three sequential phases: 1) biomarker discovery, 2) technical and biological validation, and 3) proof of concept to test the potential clinical use of selected biomarkers. A prioritized subset of the differentially-expressed genes between tissue types (50 colon mucosa from cancer-free individuals and 100 normal-tumor pairs from colon cancer patients) was validated and further tested in a series of serum samples from 80 colon cancer cases, 23 patients with adenoma and 77 cancer-free controls. RESULTS In the discovery phase, 505 unique candidate biomarkers were identified, with highly significant results and high capacity to discriminate between the different tissue types. After a subsequent prioritization, all tested genes (N = 23) were successfully validated in tissue, and one of them, COL10A1, showed relevant differences in serum protein levels between controls, patients with adenoma (p = 0.0083) and colon cancer cases (p = 3.2e-6). CONCLUSION We present a sequential process for the identification and further validation of biomarkers for early detection of colon cancer that identifies COL10A1 protein levels in serum as a potential diagnostic candidate to detect both adenoma lesions and tumor. IMPACT The use of a cheap serum test for colon cancer screening should improve its participation rates and contribute to decrease the burden of this disease.
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