Evidence map›Paper›PMID 33371886›Full record

ArticleBMC medical genomics2020

A pan-kidney cancer study identifies subtype specific perturbations on pathways with potential drivers in renal cell carcinoma.

Xiaohui Zhan, Yusong Liu, Christina Y Yu, Tian-Fu Wang, Jie Zhang, Dong Ni, Kun Huang

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In one paragraph

Article in BMC medical genomics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

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2 · The registry

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3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

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4 · The record

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5 · Who and what money

Authors and funding

7 authors.

Xiaohui ZhanNational-Regional Key Technology Engineering Laboratory for Medical Ultrasound, Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, School of Biomedical Engineering, Health Science Center, Shenzhen University, Shenzhen, 518037, China. xhzhan@cqmu.edu.cn.ORCID 0000-0003-1326-6601
Yusong LiuDepartment of Medicine, Indiana University School of Medicine, Indianapolis, IN, 46202, USA.
Christina Y YuDepartment of Medicine, Indiana University School of Medicine, Indianapolis, IN, 46202, USA.
Tian-Fu WangNational-Regional Key Technology Engineering Laboratory for Medical Ultrasound, Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, School of Biomedical Engineering, Health Science Center, Shenzhen University, Shenzhen, 518037, China.
Jie ZhangDepartment of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA.
Dong NiNational-Regional Key Technology Engineering Laboratory for Medical Ultrasound, Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, School of Biomedical Engineering, Health Science Center, Shenzhen University, Shenzhen, 518037, China. nidong@szu.edu.cn.
Kun HuangDepartment of Medicine, Indiana University School of Medicine, Indianapolis, IN, 46202, USA. kunhuang@iu.edu.

Funding

National Key Clinical Specialty Discipline Construction Program of China No. 2019YFC0118300Shenzhen Peacock Plan No. KQTD2016053112051497, KQJSCX20180328095606003
6 · The paper itself

Abstract

backgroundRenal cell carcinoma (RCC) is a complex disease and is comprised of several histological subtypes, the most frequent of which are clear cell renal cell carcinoma (ccRCC), papillary renal cell carcinoma (PRCC) and chromophobe renal cell carcinoma (ChRCC). While lots of studies have been performed to investigate the molecular characterizations of different subtypes of RCC, our knowledge regarding the underlying mechanisms are still incomplete. As molecular alterations are eventually reflected on the pathway level to execute certain biological functions, characterizing the pathway perturbations is crucial for understanding tumorigenesis and development of RCC.

methodsIn this study, we investigated the pathway perturbations of various RCC subtype against normal tissue based on differential expressed genes within a certain pathway. We explored the potential upstream regulators of subtype-specific pathways with Ingenuity Pathway Analysis (IPA). We also evaluated the relationships between subtype-specific pathways and clinical outcome with survival analysis.

resultsIn this study, we carried out a pathway-based analysis to explore the mechanisms of various RCC subtypes with TCGA RNA-seq data. Both commonly altered pathways and subtype-specific pathways were detected. To identify the distinctive characteristics of each subtype, we focused on subtype-specific perturbed pathways. Specifically, we observed that some of the altered pathways were regulated by several recurrent upstream regulators which presenting different expression patterns among distinct RCC subtypes. We also noticed that a large number of perturbed pathways were controlled by the subtype-specific upstream regulators. Moreover, we also evaluated the relationships between perturbed pathways and clinical outcome. Prognostic pathways were identified and their roles in tumor development and progression were inferred.

conclusionsIn summary, we evaluated the relationships among pathway perturbations, upstream regulators and clinical outcome for differential subtypes in RCC. We hypothesized that the alterations of common upstream regulators as well as subtype-specific upstream regulators work together to affect the downstream pathway perturbations and drive cancer initialization and prognosis. Our findings not only increase our understanding of the mechanisms of various RCC subtypes, but also provide targets for personalized therapeutic intervention.

Indexed as

Gene Expression Regulation, NeoplasticGene Regulatory NetworksAdolescentAdultAgedAged, 80 and overBiomarkers, TumorCarcinoma, Renal CellComputational BiologyFemaleGene Expression ProfilingHumansKidney NeoplasmsMaleMiddle AgedPrognosisBiomarkers, TumorccRCCChRCCPathway perturbationPRCCPrognostic pathwayRCCUpstream regulator

Identifiers

PMID33371886
PMCPMC7771093

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.