1
|
Chen Z, Ba Y, Zhao N, Dang Q, Xu H, Weng S, Zhang Y, Liu S, Zuo A, Han X, Liu Z. MPDZ is associated with immune infiltration and regulates migration and invasion by switching YAP1 phosphorylation in colorectal cancer. Cell Signal 2024; 114:110967. [PMID: 37949382 DOI: 10.1016/j.cellsig.2023.110967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 11/04/2023] [Accepted: 11/06/2023] [Indexed: 11/12/2023]
Abstract
BACKGROUND Multiple PDZ Domain Crumbs Cell Polarity Complex Component (MPDZ) is involved in a few human cancers. However, the features and potential mechanisms of MPDZ in progression of colorectal cancer (CRC) remains unknown. METHODS The prognostic role of MPDZ in CRC was determined by Kaplan-Meier and univariate regression analysis. Enrichment analysis was performed to characterize crucial pathways of MPDZ. Immune infiltration and immunotherapeutic outcome were further evaluated. CCK8, EDU, transwell, and wound healing assay were used to assess the influence of MPDZ on pernicious performance of CRC cells. CD8+ T cells and CRC cells were co-cultured to explore the effect of MPDZ on the tumor microenvironment. qRT-PCR, western blot, immunoprecipitation (IP), and methylated RNA immunoprecipitation (me-RIP) were implemented in seeking for the potential mechanisms of MPDZ in CRC. RESULTS CRC patients with elevated MPDZ expression suffered from significantly worse prognosis. Enrichment analysis revealed that MPDZ involved in pathways related to metastasis and cell cycle in CRC. In addition, MPDZ expression were related to several immunoinhibitors and had the ability to predict immunotherapy response. Finally, in vitro assays demonstrated that MPDZ knockdown inhibited migration, invasion and immune evasion of CRC cells. Mechanistically, MPDZ knockdown enhanced YAP1 phosphorylation by increased LATS1 expression. Moreover, m6A-MPDZ mRNA may be recognized and degraded by m6A recognition protein YTHDF2. CONCLUSIONS MPDZ was critical for CRC development and could be a promising candidate for the treatment of CRC patients.
Collapse
Affiliation(s)
- Zhuang Chen
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China; Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Yuhao Ba
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Nannan Zhao
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Qin Dang
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Hui Xu
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Siyuan Weng
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Yuyuan Zhang
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Shutong Liu
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Anning Zuo
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Xinwei Han
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China.
| | - Zaoqu Liu
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China; State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China; Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China.
| |
Collapse
|
2
|
Tang L, Wang T, Li W, Yu S, Yao S, Cheng H. Construction of cuproptosis-related lncRNAs/mRNAs model and prognostic prediction of hepatocellular carcinoma. Am J Cancer Res 2022; 12:4693-4707. [PMID: 36381337 PMCID: PMC9641397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 09/15/2022] [Indexed: 06/16/2023] Open
Abstract
Cuproptosis is a recently reported novel form of cell death, which is involved in the regulation of tumor progression. However, the specific role of cuproprosis in hepatocellular carcinoma (HCC) development remains unclear. In this study, we comprehensively analyzed the effect of cuproprosis-related lncRNAs/mRNAs on the prognosis of HCC patients based on the RNA-Seq transcriptome data and clinical data. We identified 6 cuproprosis-related signatures by Cox and Lasso regression analysis, including 3 mRNAs (FBXO30, RNF2, MPDZ) and 3 lncRNAs (PICSAR, LINC00426, AL590705.3). In addition, we constructed a prognostic prediction model for HCC. Risk analysis, RT-qPCR, and Kaplan-Meier analysis showed that the expression of FBXO30, RNF2, AL590705.3 and PICSAR was elevated in HCC, while the expression of MPDZ and LINC00426 was suppressed which was associated with better overall survival. Furthermore, immune response analysis suggested that HCC with high-risk score might respond favorably to immunotherapy. Moreover, the potential drugs that HCC might be sensitive to were screened by drug sensitivity profiling analysis. Taken together, our findings provided important information for the prediction of the prognosis of HCC patients and the development of personalized targeted therapy.
Collapse
Affiliation(s)
- Lingxue Tang
- Department of Oncology, The Second Affiliated Hospital of Anhui Medical UniversityHefei 230601, Anhui, China
| | - Tong Wang
- Department of General Medicine, The Second Affiliated Hospital of Anhui Medical UniversityHefei 230601, Anhui, China
| | - Wen Li
- Department of Oncology, The Second Affiliated Hospital of Anhui Medical UniversityHefei 230601, Anhui, China
| | - Sheng Yu
- Department of Oncology, The Second Affiliated Hospital of Anhui Medical UniversityHefei 230601, Anhui, China
| | - Senbang Yao
- Department of Oncology, The Second Affiliated Hospital of Anhui Medical UniversityHefei 230601, Anhui, China
| | - Huaidong Cheng
- Department of Oncology, The Second Affiliated Hospital of Anhui Medical UniversityHefei 230601, Anhui, China
| |
Collapse
|
3
|
Attique H, Shah S, Jabeen S, Khan FG, Khan A, ELAffendi M. Multiclass Cancer Prediction Based on Copy Number Variation Using Deep Learning. Comput Intell Neurosci 2022; 2022:4742986. [PMID: 35720914 DOI: 10.1155/2022/4742986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 05/21/2022] [Indexed: 12/02/2022]
Abstract
DNA copy number variation (CNV) is the type of DNA variation which is associated with various human diseases. CNV ranges in size from 1 kilobase to several megabases on a chromosome. Most of the computational research for cancer classification is traditional machine learning based, which relies on handcrafted extraction and selection of features. To the best of our knowledge, the deep learning-based research also uses the step of feature extraction and selection. To understand the difference between multiple human cancers, we developed three end-to-end deep learning models, i.e., DNN (fully connected), CNN (convolution neural network), and RNN (recurrent neural network), to classify six cancer types using the CNV data of 24,174 genes. The strength of an end-to-end deep learning model lies in representation learning (automatic feature extraction). The purpose of proposing more than one model is to find which architecture among them performs better for CNV data. Our best model achieved 92% accuracy with an ROC of 0.99, and we compared the performances of our proposed models with state-of-the-art techniques. Our models have outperformed the state-of-the-art techniques in terms of accuracy, precision, and ROC. In the future, we aim to work on other types of cancers as well.
Collapse
|
4
|
Chanez B, Appay R, Guille A, Lagarde A, Colin C, Adelaide J, Denicolai E, Jiguet-jiglaire C, Bequet C, Graillon T, Boissonneau S, Nanni-metellus I, Dufour H, Figarella-branger D, Chinot O, Tabouret E. Genomic analysis of paired IDHwt glioblastomas reveals recurrent alterations of MPDZ at relapse after radiotherapy and chemotherapy. J Neurol Sci 2022. [DOI: 10.1016/j.jns.2022.120207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 02/09/2022] [Accepted: 02/21/2022] [Indexed: 11/17/2022]
|
5
|
Fernandes FG, Silveira HCS, Júnior JNA, da Silveira RA, Zucca LE, Cárcano FM, Sanches AON, Neder L, Scapulatempo-Neto C, Serrano SV, Jonasch E, Reis RM, Evangelista AF. Somatic Copy Number Alterations and Associated Genes in Clear-Cell Renal-Cell Carcinoma in Brazilian Patients. Int J Mol Sci 2021; 22:2265. [PMID: 33668731 PMCID: PMC7956176 DOI: 10.3390/ijms22052265] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 01/13/2021] [Accepted: 01/22/2021] [Indexed: 12/24/2022] Open
Abstract
Somatic copy number aberrations (CNAs) have been associated with clear-cell renal carcinoma (ccRCC) pathogenesis and are a potential source of new diagnostic, prognostic and therapeutic biomarkers. Recurrent CNAs include loss of chromosome arms 3p, 14q, 9p, and gains of 5q and 8q. Some of these regional CNAs are suspected of altering gene expression and could influence clinical outcomes. Despite many studies of CNAs in RCC, there are currently no descriptions of genomic copy number alterations in a Brazilian ccRCC cohort. This study was designed to evaluate the chromosomal profile of CNAs in Brazilian ccRCC tumors and explore clinical associations. A total of 92 ccRCC Brazilian patients that underwent nephrectomy at Barretos Cancer Hospital were analyzed for CNAs by array comparative genomic hybridization. Most patients in the cohort had early-stage localized disease. The most significant alterations were loss of 3p (87.3%), 14q (35.8%), 6q (29.3%), 9p (28.6%) and 10q (25.0%), and gains of 5q (59.7%), 7p (29.3%) and 16q (20.6%). Bioinformatics analysis revealed 19 genes mapping to CNA significant regions, including SETD2, BAP1, FLT4, PTEN, FGFR4 and NSD1. Moreover, gain of 5q34-q35.3 (FLT4 and NSD1) and loss of 6q23.2-q23.3 (MYB) and 9p21.3 (MLLT3) had gene expression levels that correlated with TCGA data and was also associated with advanced disease features, such as larger tumors, Fuhrman 3, metastasis at diagnosis and death. The loss of region 14q22.1 which encompasses the NIN gene was associated with poor overall survival. Overall, this study provides the first CNA landscape of Brazilian patients and pinpoints genomic regions and specific genes worthy of more detailed investigations. Our results highlight important genes that are associated with copy number changes involving large chromosomal regions that are potentially related to ccRCC tumorigenesis and disease biology for future clinical investigations.
Collapse
Affiliation(s)
- Flávia Gonçalves Fernandes
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos 14784-400, Brazil; (F.G.F.); (H.C.S.S.); (R.A.d.S.)
| | | | - João Neif Antonio Júnior
- Department of Medical Oncology, Barretos Cancer Hospital, Barretos 14784-400, Brazil; (J.N.A.J.); (L.E.Z.); (F.M.C.); (A.O.N.S.); (S.V.S.)
| | - Rosana Antunes da Silveira
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos 14784-400, Brazil; (F.G.F.); (H.C.S.S.); (R.A.d.S.)
| | - Luis Eduardo Zucca
- Department of Medical Oncology, Barretos Cancer Hospital, Barretos 14784-400, Brazil; (J.N.A.J.); (L.E.Z.); (F.M.C.); (A.O.N.S.); (S.V.S.)
| | - Flavio Mavignier Cárcano
- Department of Medical Oncology, Barretos Cancer Hospital, Barretos 14784-400, Brazil; (J.N.A.J.); (L.E.Z.); (F.M.C.); (A.O.N.S.); (S.V.S.)
- Barretos School of Health Sciences Dr Paulo Prata-FACISB, Barretos 14785-002, Brazil
| | - André Octavio Nicolau Sanches
- Department of Medical Oncology, Barretos Cancer Hospital, Barretos 14784-400, Brazil; (J.N.A.J.); (L.E.Z.); (F.M.C.); (A.O.N.S.); (S.V.S.)
| | - Luciano Neder
- Department of Pathology, Barretos Cancer Hospital, Barretos 14784-400, Brazil; (L.N.); (C.S.-N.)
| | | | - Sergio Vicente Serrano
- Department of Medical Oncology, Barretos Cancer Hospital, Barretos 14784-400, Brazil; (J.N.A.J.); (L.E.Z.); (F.M.C.); (A.O.N.S.); (S.V.S.)
- Barretos School of Health Sciences Dr Paulo Prata-FACISB, Barretos 14785-002, Brazil
| | - Eric Jonasch
- Department of Genitourinary Medical Oncology, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA;
| | - Rui Manuel Reis
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos 14784-400, Brazil; (F.G.F.); (H.C.S.S.); (R.A.d.S.)
- Life and Health Sci Research Institute (ICVS), Medical School, University of Minho, 4710-057 Braga, Portugal
- ICVS/3B’s-PT Government Associate Laboratory, 4710-057 Braga/Guimarães, Portugal
| | - Adriane Feijó Evangelista
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos 14784-400, Brazil; (F.G.F.); (H.C.S.S.); (R.A.d.S.)
| |
Collapse
|
6
|
Nguyen QH, Nguyen H, Nguyen T, Le DH. Multi-Omics Analysis Detects Novel Prognostic Subgroups of Breast Cancer. Front Genet 2020; 11:574661. [PMID: 33193681 PMCID: PMC7594512 DOI: 10.3389/fgene.2020.574661] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 09/23/2020] [Indexed: 12/02/2022] Open
Abstract
The unprecedented proliferation of recent large-scale and multi-omics databases of cancers has given us many new insights into genomic and epigenomic deregulation in cancer discovery in general. However, we wonder whether or not there exists a systematic connection between copy number aberrations (CNA) and methylation (MET)? If so, what is the role of this connection in breast cancer (BRCA) tumorigenesis and progression? At the same time, the PAM50 intrinsic subtypes of BRCA have gained the most attention from BRCA experts. However, this classification system manifests its weaknesses including low accuracy as well as a possible lack of association with biological phenotypes, and even further investigations on their clinical utility were still needed. In this study, we performed an integrative analysis of three-omics profiles, CNA, MET, and mRNA expression, in two BRCA patient cohorts (one for discovery and another for validation) – to elucidate those complicated relationships. To this purpose, we first established a set of CNAcor and METcor genes, which had CNA and MET levels significantly correlated (and anti-correlated) with their corresponding expression levels, respectively. Next, to revisit the current classification of BRCA, we performed single and integrated clustering analyses using our clustering method PINSPlus. We then discovered two biologically distinct subgroups that could be an improved and refined classification system for breast cancer patients, which can be validated by a third-party data. Further studies were then performed and realized each-subgroup-specific genes and different interactions between each of the two identified subgroups with the age factor. These findings can show promise as diagnostic and prognostic values in BRCA, and a potential alternative to the PAM50 intrinsic subtypes in the future.
Collapse
Affiliation(s)
- Quang-Huy Nguyen
- Department of Computational Biomedicine, Vingroup Big Data Institute, Hanoi, Vietnam.,Faculty of Pharmacy, Dainam University, Hanoi, Vietnam
| | - Hung Nguyen
- Department of Computer Science and Engineering, University of Nevada, Reno, Reno, NV, United States
| | - Tin Nguyen
- Department of Computer Science and Engineering, University of Nevada, Reno, Reno, NV, United States
| | - Duc-Hau Le
- Department of Computational Biomedicine, Vingroup Big Data Institute, Hanoi, Vietnam.,School of Computer Science and Engineering, Thuyloi University, Hanoi, Vietnam
| |
Collapse
|
7
|
Sayeeram D, Katte TV, Bhatia S, Jai Kumar A, Kumar A, Jayashree G, Rachana D, Nalla Reddy HV, Arvind Rasalkar A, Malempati RL, Reddy S DN. Identification of potential biomarkers for lung adenocarcinoma. Heliyon 2020; 6:e05452. [PMID: 33251353 PMCID: PMC7677689 DOI: 10.1016/j.heliyon.2020.e05452] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 04/21/2020] [Accepted: 09/21/2020] [Indexed: 12/14/2022] Open
Abstract
Lung adenocarcinoma (LUAD) is the most predominant subtype of lung cancers and is one of the leading causes of cancer related mortality worldwide. Despite the advancements in the field of cancer diagnostics and therapeutics, detection at an early stage using reliable biomarkers is an unmet clinical need for a plethora of cancers, including LUAD, thus attributing to poor prognosis. In view of this, to identify potential biomarkers and therapeutic candidate genes, the expression of all known human genes was screened in the publicly available 'The Cancer Genome Atlas' (TCGA) samples of LUAD patients which resulted in the identification of overexpressed genes. Further analysis of these genes across various patient sample datasets revealed that ZNF687, ODR4, PBXIP1, PYGO2, METTL3, PIGM and RAD1 are consistently more highly expressed in LUAD. Higher expression of these genes either alone or in combination is correlated with poor survival of LUAD patients. Hence, in this study we propose that these identified genes could serve as potential candidates as gene signatures or biomarkers for LUAD that require further investigation in large cohorts of LUAD samples.
Collapse
Affiliation(s)
- Deepak Sayeeram
- Department of Biotechnology, BMS College of Engineering, Bengaluru, India
| | - Teesta V. Katte
- Department of Biotechnology, BMS College of Engineering, Bengaluru, India
| | - Saloni Bhatia
- Department of Biotechnology, BMS College of Engineering, Bengaluru, India
| | - Anushree Jai Kumar
- Department of Biotechnology, BMS College of Engineering, Bengaluru, India
| | - Avinesh Kumar
- Department of Biotechnology, BMS College of Engineering, Bengaluru, India
| | - G. Jayashree
- Department of Biotechnology, BMS College of Engineering, Bengaluru, India
| | - D.S. Rachana
- Department of Biotechnology, BMS College of Engineering, Bengaluru, India
| | | | - Avinash Arvind Rasalkar
- inDNA Life Sciences Private Limited, Plot 368, 3 Floor, North View, Infocity Avenue, Patia, Bhubaneswar, Odisha 751024, India
| | | | | |
Collapse
|
8
|
Li Y, Shen Y, Zhu Z, Wen H, Feng C. Comprehensive analysis of copy number variance and sensitivity to common targeted therapy in clear cell renal cell carcinoma: In silico analysis with in vitro validation. Cancer Med 2020; 9:6020-6029. [PMID: 32628820 PMCID: PMC7433817 DOI: 10.1002/cam4.3281] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 05/15/2020] [Accepted: 06/17/2020] [Indexed: 12/20/2022] Open
Abstract
Background Chromosomal rearrangements are common in clear cell renal cell carcinoma (ccRCC) and their roles in mediating sensitivity to tyrosine kinase inhibitors (TKIs) and mTOR inhibitors (mTORi) remain elusive. Methods We developed an in silico strategy by screening copy number variance (CNV) that was potentially related to TKI or mTORi sensitivity in ccRCC by reproducing the TCGA and GDSC datasets. Candidate genes should be both significantly prognostic and related to drug sensitivity or resistance, and were then validated in vitro. Results ADCYAP1 loss and GNAS gain were associated with sensitivity and resistance and to Cabozantinib, respectively. ACRBP gain and CTBP1 loss were associated with sensitivity and resistance and to Pazopanib, respectively. CDKN2A loss and SULT1A3 gain were associated with sensitivity and resistance and to Temsirolimus, respectively. CCNE1 gain was associated with resistance to Axitinib and LRP10 loss was associated with resistance to Sunitinib. Mutivariate analysis showed ADCYAP1, GNAS, and CCNE1 remained independently prognostic when adjusted for the rest. Conclusion Here we show CNVs of several genes that are associated with sensitivity and resistance to commonly used TKIs and mTORi in ccRCC. Further validation and functional analyses are therefore needed.
Collapse
Affiliation(s)
- Yuqing Li
- Department of Urology, Huashan Hospital, Fudan University, Shanghai, PR China
| | - Yanyun Shen
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai, PR China
| | - Zhidong Zhu
- Department of Cardiology, Huashan Hospital, Fudan University, Shanghai, PR China
| | - Hui Wen
- Department of Urology, Huashan Hospital, Fudan University, Shanghai, PR China
| | - Chenchen Feng
- Department of Urology, Huashan Hospital, Fudan University, Shanghai, PR China
| |
Collapse
|
9
|
Shao X, Lv N, Liao J, Long J, Xue R, Ai N, Xu D, Fan X. Copy number variation is highly correlated with differential gene expression: a pan-cancer study. BMC Med Genet 2019; 20:175. [PMID: 31706287 PMCID: PMC6842483 DOI: 10.1186/s12881-019-0909-5] [Citation(s) in RCA: 135] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 10/15/2019] [Indexed: 12/13/2022]
Abstract
BACKGROUND Cancer is a heterogeneous disease with many genetic variations. Lines of evidence have shown copy number variations (CNVs) of certain genes are involved in development and progression of many cancers through the alterations of their gene expression levels on individual or several cancer types. However, it is not quite clear whether the correlation will be a general phenomenon across multiple cancer types. METHODS In this study we applied a bioinformatics approach integrating CNV and differential gene expression mathematically across 1025 cell lines and 9159 patient samples to detect their potential relationship. RESULTS Our results showed there is a close correlation between CNV and differential gene expression and the copy number displayed a positive linear influence on gene expression for the majority of genes, indicating that genetic variation generated a direct effect on gene transcriptional level. Another independent dataset is utilized to revalidate the relationship between copy number and expression level. Further analysis show genes with general positive linear influence on gene expression are clustered in certain disease-related pathways, which suggests the involvement of CNV in pathophysiology of diseases. CONCLUSIONS This study shows the close correlation between CNV and differential gene expression revealing the qualitative relationship between genetic variation and its downstream effect, especially for oncogenes and tumor suppressor genes. It is of a critical importance to elucidate the relationship between copy number variation and gene expression for prevention, diagnosis and treatment of cancer.
Collapse
Affiliation(s)
- Xin Shao
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Ning Lv
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Jie Liao
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Jinbo Long
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Rui Xue
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Ni Ai
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Donghang Xu
- Department of Pharmacy, The 2nd Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310009, China.
| | - Xiaohui Fan
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China.
| |
Collapse
|