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Abstract
BackgroundComplex genomic changes that arise in tumors are a consequence of chromosomal instability. In tumor cells genomic aberrations disrupt core signaling pathways involving various genes, thus delineating of signaling pathways can help understand the pathogenesis of cancer. The bioinformatics tools can further help in identifying networks of interactions between the genes to get a greater biological context of all genes affected by chromosomal instability.MethodsKaryotypic analyses was done in 150 clinically confirmed breast cancer patients and 150 age and gender matched healthy controls after 72 h Peripheral lymphocyte culturing and GTG-banding. Reactome database from Cytoscape software version 3.7.1 was used to perform in-silico analysis (functional interaction and gene enrichment).ResultsFrequency of chromosomal aberrations (structural and numerical) was found to be significantly higher in patients as compared to controls. The genes harbored by chromosomal regions showing increased aberration frequency in patients were further analyzed in-silico. Pathway analysis on a set of genes that were not linked together revealed that genes HDAC3, NCOA1, NLRC4, COL1A1, RARA, WWTR1, and BRCA1 were enriched in the RNA Polymerase II Transcription pathway which is involved in recruitment, initiation, elongation and dissociation during transcription.ConclusionThe current study employs the information inferred from chromosomal instability analysis in a non-target tissue for determining the genes and the pathways associated with breast cancer. These results can be further extrapolated by performing either mutation analysis in the genes/pathways deduced or expression analysis which can pinpoint the relevant functional impact of chromosomal instability.
Highlights
IntroductionComplex genomic changes that arise in tumors are a consequence of chromosomal instability
Complex genomic changes that arise in tumors are a consequence of Chromosomal Instability (CIN), which leads to numerical [(N)-CIN] as well as structural chromosomal instability [(S)-CIN] [1]
The current study employs the information inferred from chromosomal instability for determining the genes and the pathways associated with breast cancer
Summary
Complex genomic changes that arise in tumors are a consequence of chromosomal instability. Complex genomic changes that arise in tumors are a consequence of Chromosomal Instability (CIN), which leads to numerical [(N)-CIN] as well as structural chromosomal instability [(S)-CIN] [1]. Kour et al BMC Med Genomics (2020) 13:168 is distinct from structural changes and aneuploidy arises by disruptions in cell cycle checkpoints and errors in mitotic segregation [2, 7]. A link between aneuploidy and/or CIN and poor clinical outcome has been identified by several studies [16]. An association between aneuploidy and chromosomal instability with distinctive clinical and histopathological features and poor prognosis has been reported in various cancers [20,21,22]. The need to target CIN with new combinatorial strategies has been suggested [23]
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