Microarray data for inflammatory breast cancer cases

Inflammatory breast cancer (IBC) is a rare and aggressive type of breast cancer (BC) whose molecular basis is poorly understood. We performed a comprehensive molecular analysis of 24 fresh frozen IBC biopsies naïve of treatment, using a high-resolution microarray platform The most common genes covered by copy number alterations included gains of MYC and MDM4, and losses affecting TP53 and RB1. MYC and MDM4 genes have been related to IBC aggressiveness, and MDM4 might also represent a new therapeutic target in IBC. Thirteen IBC cases presented copy-neutral of heterozygosity (cnLOH) or losses covering CHL1, which gives additional evidence of its role as a tumor suppressor. Functional enrichment analysis with the most common alterations revealed genes associated with inflammatory regulation and immune response. Particularly, IL6R and IL7 could represent therapeutic targets for IBC treatment. Chromothripsis patterns were identified in nine cases and chromosomal instability in 50% of cases. High homologous recombination (HR) deficiency scores were observed in triple-negative IBC and those with metastasis. High telomeric allelic imbalance (TAI) score was detected in patients having worse overall survival (OS). TAI score could also be useful to predict deficiency in homologous recombination (HR) genes and to identify patients for platinum or PARP inhibitor therapy. Our study describes the most common genomic alterations in IBC and their association with clinical findings, providing a framework for improved diagnosis and therapeutic opportunities for this aggressive tumor type. Genomic DNA was isolated from fresh-frozen IBC tissue biopsies. The CytoScan HD Array (Affymetrix, Santa Clara, CA, USA) platform was used to evaluate CNAs and copy-neutral loss of heterozygosity (cnLOH) according to the manufacturer's recommendations. The microarray analyses were performed using ChAS (Chromosome Analysis Suite), CoNVaQ and WebGestalt (WEB-based Gene SeT AnaLysis ToolKit) softwares. Additionally, microarray data was also used to estimate chromothripsis, genomic instability and homologous recombination deficiency scores.