Chromosomal breakpoints in a cohort of head and neck squamous cell carcinoma patients

I P Ribeiro; I M Carreira; L Esteves; F Caramelo; T Liehr; J B Melo

doi:10.1016/j.ygeno.2019.02.009

Chromosomal breakpoints in a cohort of head and neck squamous cell carcinoma patients

Genomics. 2020 Jan;112(1):297-303. doi: 10.1016/j.ygeno.2019.02.009. Epub 2019 Feb 23.

Authors

I P Ribeiro¹, I M Carreira¹, L Esteves², F Caramelo³, T Liehr⁴, J B Melo⁵

Affiliations

¹ Cytogenetics and Genomics Laboratory, Faculty of Medicine, University of Coimbra, Coimbra, Portugal; iCBR-CIMAGO - Center of Investigation on Environment, Genetics and Oncobiology, Faculty of Medicine, University of Coimbra, Coimbra, Portugal.
² Cytogenetics and Genomics Laboratory, Faculty of Medicine, University of Coimbra, Coimbra, Portugal.
³ Laboratory of Biostatistics and Medical Informatics, IBILI - Faculty of Medicine, University of Coimbra, Coimbra, Portugal.
⁴ Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Jena, Germany.
⁵ Cytogenetics and Genomics Laboratory, Faculty of Medicine, University of Coimbra, Coimbra, Portugal; iCBR-CIMAGO - Center of Investigation on Environment, Genetics and Oncobiology, Faculty of Medicine, University of Coimbra, Coimbra, Portugal. Electronic address: citogenetica@fmed.uc.pt.

PMID: 30802597
DOI: 10.1016/j.ygeno.2019.02.009

Abstract

Head and neck squamous cell carcinoma (HNSCC) presents complex chromosomal rearrangements, however, the molecular mechanisms behind HNSCC development remain elusive. The identification of the recurrent chromosomal breakpoints could help to understand these mechanisms. Array-CGH was performed in HNSCC patients and the chromosomal breakpoints involved in gene amplification/loss were analyzed. Frequent breakpoints were clustered in chromosomes 12p, 8p, 3q, 14q, 6p, 4q, Xq and 8q. Chromosomes 6, 14, 3, 8 and X exhibited higher susceptibility to have breaks than other chromosomes. We observed that low copy repeat DNA sequences are localized at or flanking breakpoint sites, ranging from 0 to 200 bp. LINES, SINES and Simple Repeats were the most frequent repeat elements identified in these regions. We conclude that in our cohort specific peri-centromeric and telomeric regions were frequently involved in breakpoints, being the presence of low copy repeats elements one of the explanations for the common rearrangement events observed.

Keywords: Chromosomal breakpoints; DNA repeat elements; Head and neck cancer.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Alu Elements
Centromere
Chromosome Breakpoints*
Cohort Studies
Female
Humans
Long Interspersed Nucleotide Elements
Male
Microsatellite Repeats
Middle Aged
Squamous Cell Carcinoma of Head and Neck / genetics*
Telomere / chemistry