| Title: |
The effect of germline variants on the genesis of early somatic events in cancer explored via Cas9 genome editing |
| Authors: |
Stringa, Blerta |
| Contributors: |
Stringa, Blerta; Demichelis, Francesca; Gasperini, Paola |
| Publisher Information: |
Trento; Università degli studi di Trento |
| Publication Year: |
2019 |
| Collection: |
Università degli Studi di Trento: CINECA IRIS |
| Subject Terms: |
Germline variants; Genome editing; CRISPR/Cas9; Prostate cancer; Settore BIO/11 - Biologia Molecolare |
| Description: |
Although the understanding of genetic predisposition to prostate cancer (PCa) has been improved through genome-wide association studies (GWAS), little is known about the biological implication of germline variants residing in coding or non-coding regions in cancer development and progression. Our hypothesis is that inherited variants may predispose to specific early recurrent genomic events observed in PCa adenocarcinomas, possibly in the context of variable androgen receptor (AR) signaling that changes during a man’s lifetime. Recent in silico analysis by our group on potential association between germline variants and PCa specific somatic lesions identified a non-coding polymorphic regulatory element at the 7p14.3 locus associated with DNA repair and hormone regulated transcript levels and with an early recurrent prostate cancer specific somatic mutation in the Speckle-Type POZ protein (SPOP) gene (OR=5.54, P=1.22e-08) in human prostate tissue data. In order to functionally characterize the polymorphic 7p14.3 locus (rs1376350, single nucleotide polymorphism, G>A), we set up to establish isogenic cell lines harboring the minor allele by using the CRISPR/Cas9 system. In parallel, CRISPR/Cas9 system was used to knock out different portion of the region encompassing the 7p14.3 variant and to eliminate transcription factors (TFs) binding sites that were identified from previous in silico analysis (i.e. AR and CCAAT/Enhancer Binding Protein (C/EBP) beta (CEBPβ)). The transcriptomes of edited pools and edited single clones from macrodeletion (731 bp), microdeletion (50 bp) and alterations of TFs binding sites were analyzed and compared to the transcriptomes of isogenic cells heterozygous (A/G) and homozygous (A/A) for the minor allele A of the risk variant rs1376350 (with or without AR overexpression). These data identified a set of genes scattered throughout the genome with the same pattern of deregulation suggesting the implication of the variant on the regulation of genes residing in different chromosomes. ... |
| Document Type: |
doctoral or postdoctoral thesis |
| Language: |
English |
| Relation: |
firstpage:1; lastpage:78; numberofpages:78; https://hdl.handle.net/11572/242372 |
| DOI: |
10.15168/11572_242372 |
| Availability: |
https://hdl.handle.net/11572/242372; https://doi.org/10.15168/11572_242372 |
| Rights: |
info:eu-repo/semantics/openAccess ; license:Tutti i diritti riservati (All rights reserved) |
| Accession Number: |
edsbas.A067B2ED |
| Database: |
BASE |