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CDKN1B mutation and copy number variation are associated with tumor aggressiveness in luminal breast cancer.

ABSTRACT: The CDKN1B gene, encoding for the CDK inhibitor p27^kip1 , is mutated in defined human cancer subtypes, including breast, prostate carcinomas and small intestine neuroendocrine tumors. Lessons learned from small intestine neuroendocrine tumors suggest that CDKN1B mutations could be subclonal, raising the question of whether a deeper sequencing approach could lead to the identification of higher numbers of patients with mutations. Here, we addressed this question and analyzed human cancer biopsies from breast (n?=?396), ovarian (n?=?110) and head and neck squamous carcinoma (n?=?202) patients, using an ultra-deep sequencing approach. Notwithstanding this effort, the mutation rate of CDKN1B remained substantially aligned with values from the literature, showing that essentially only hormone receptor-positive breast cancer displayed CDKN1B mutations in a relevant number of cases (3%). However, the analysis of copy number variation showed that another fraction of luminal breast cancer displayed loss (8%) or gain (6%) of the CDKN1B gene, further reinforcing the idea that the function of p27^kip1 is important in this type of tumor. Intriguingly, an enrichment for CDKN1B alterations was found in samples from premenopausal luminal breast cancer patients (n?=?227, 4%) and in circulating cell-free DNA from metastatic luminal breast cancer patients (n?=?59, 8.5%), suggesting that CDKN1B alterations could correlate with tumor aggressiveness and/or occur later during disease progression. Notably, many of the identified somatic mutations resulted in p27^kip1 protein truncation, leading to loss of most of the protein or of its C-terminal domain. Using a gene-editing approach in a luminal breast cancer cell line, MCF-7, we observed that the expression of p27^kip1 truncating mutants that lose the C-terminal domains failed to rescue most of the phenotypes induced by CDKN1B gene knockout, indicating that the functions retained by the C-terminal portion are critical for its role as an oncosuppressor, at least in luminal breast cancer. © 2020 The Authors. The Journal of Pathology published by John Wiley & Sons, Ltd. on behalf of The Pathological Society of Great Britain and Ireland.

SUBMITTER: Viotto D

PROVIDER: S-EPMC7839435 | biostudies-literature | 2020 Nov

REPOSITORIES: biostudies-literature

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CDKN1B mutation and copy number variation are associated with tumor aggressiveness in luminal breast cancer.

Viotto Davide D Russo Francesca F Anania Ilaria I Segatto Ilenia I Rampioni Vinciguerra Gian Luca GL Dall'Acqua Alessandra A Bomben Riccardo R Perin Tiziana T Cusan Martina M Schiappacassi Monica M Gerratana Lorenzo L D'Andrea Sara S Citron Francesca F Vit Filippo F Musco Lorena L Mattevi Maria Chiara MC Mungo Giorgia G Nicoloso Milena S MS Sonego Maura M Massarut Samuele S Sorio Roberto R Barzan Luigi L Franchin Giovanni G Giorda Giorgio G Lucia Emilio E Sulfaro Sandro S Giacomarra Vittorio V Polesel Jerry J Toffolutti Federica F Canzonieri Vincenzo V Puglisi Fabio F Gattei Valter V Vecchione Andrea A Belletti Barbara B Baldassarre Gustavo G

The Journal of pathology 20201204 2

The CDKN1B gene, encoding for the CDK inhibitor p27<sup>kip1</sup> , is mutated in defined human cancer subtypes, including breast, prostate carcinomas and small intestine neuroendocrine tumors. Lessons learned from small intestine neuroendocrine tumors suggest that CDKN1B mutations could be subclonal, raising the question of whether a deeper sequencing approach could lead to the identification of higher numbers of patients with mutations. Here, we addressed this question and analyzed human canc ...[more]

PMID: 33140857

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Project description:Addressing drug resistance is a core challenge in cancer research, but the degree of heterogeneity in resistance mechanisms in cancer is unclear. In this study, we conducted next-generation sequencing (NGS) of circulating tumor cells (CTC) from patients with advanced cancer to assess mechanisms of resistance to targeted therapy and reveal opportunities for precision medicine. Comparison of the genomic landscapes of CTCs and tissue metastases is complicated by challenges in comprehensive CTC genomic profiling and paired tissue acquisition, particularly in patients who progress after targeted therapy. Thus, we assessed by NGS somatic mutations and copy number alterations (CNA) in archived CTCs isolated from patients with metastatic breast cancer who were enrolled in concurrent clinical trials that collected and analyzed CTCs and metastatic tissues. In 76 individual and pooled informative CTCs from 12 patients, we observed 85% concordance in at least one or more prioritized somatic mutations and CNA between paired CTCs and tissue metastases. Potentially actionable genomic alterations were identified in tissue but not CTCs, and vice versa. CTC profiling identified diverse intra- and interpatient molecular mechanisms of endocrine therapy resistance, including loss of heterozygosity in individual CTCs. For example, in one patient, we observed CTCs that were either wild type for ESR1 (n = 5/32), harbored the known activating ESR1 p.Y537S mutation (n = 26/32), or harbored a novel ESR1 p.A569S (n = 1/32). ESR1 p.A569S was modestly activating in vitro, consistent with its presence as a minority circulating subclone. Our results demonstrate the feasibility and potential clinical utility of comprehensive profiling of archived fixed CTCs. Tissue and CTC genomic assessment are complementary, and precise combination therapies will likely be required for effective targeting in advanced breast cancer patients.Significance: These findings demonstrate the complementary nature of genomic profiling from paired tissue metastasis and circulating tumor cells from patients with metastatic breast cancer. Cancer Res; 78(4); 1110-22. ©2017 AACR.

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CDKN1B mutation and copy number variation are associated with tumor aggressiveness in luminal breast cancer.

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CDKN1B mutation and copy number variation are associated with tumor aggressiveness in luminal breast cancer.

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