Breast cancer genomic analyses reveal genes, mutations, and signaling networks

IF 3.9 4区生物学 Q1 GENETICS & HEREDITY Functional & Integrative Genomics Pub Date : 2024-11-04 DOI:10.1007/s10142-024-01484-y

Gowrang Kasaba Manjunath, Srihari Sharma, Disha Nashier, Shruthi Vasanthaiah, Spriha Jha, Saloni Bage, Tamoghna Mitra, Pankaj Goyal, Muniasamy Neerathilingam, Abhishek Kumar

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Abstract

Breast cancer (BC) is the most commonly diagnosed cancer and the predominant cause of death in women. BC is a complex disorder, and the exploration of several types of BC omic data, highlighting genes, perturbations, signaling and cellular mechanisms, is needed. We collected mutational data from 9,555 BC samples using cBioPortal. We classified 1174 BC genes (mutated ≥ 40 samples) into five tiers (BCtier_I-V) and subjected them to pathway and protein‒protein network analyses using EnrichR and STRING 11, respectively. BCtier_I possesses 12 BC genes with mutational frequencies > 5%, with only 5 genes possessing > 10% frequencies, namely, PIK3CA (35.7%), TP53 (34.3%), GATA3 (11.5%), CDH1 (11.4%) and MUC16 (11%), and the next seven BC genes are KMT2C (8.8%), TTN (8%), MAP3K1 (8%), SYNE1 (7.2%), AHNAK2 (7%), USH2A (5.5%), and RYR2 (5.4%). Our pathway analyses revealed that the five top BC pathways were the PI3K-AKT, TP53, NOTCH, HIPPO, and RAS pathways. We found that BC panels share only seven genes. These findings show that BC arises from genetic disruptions evident in BC signaling and protein networks.

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乳腺癌基因组分析揭示了基因、突变和信号网络。

乳腺癌（BC）是最常见的癌症，也是导致女性死亡的主要原因。乳腺癌是一种复杂的疾病，需要探索多种类型的乳腺癌 omic 数据，突出基因、扰动、信号传导和细胞机制。我们利用 cBioPortal 收集了 9555 个 BC 样本的突变数据。我们将 1174 个 BC 基因（突变≥ 40 个样本）分为五层（BCtier_I-V），并分别使用 EnrichR 和 STRING 11 对它们进行了通路和蛋白质-蛋白质网络分析。BCtier_I 有 12 个 BC 基因的突变频率大于 5%，只有 5 个基因的突变频率大于 10%，分别是 PIK3CA（35.7%）、TP53（34.3%）、GATA3（11.5%）、CDH1（11.4%）和MUC16（11%），接下来的7个BC基因分别是KMT2C（8.8%）、TTN（8%）、MAP3K1（8%）、SYNE1（7.2%）、AHNAK2（7%）、USH2A（5.5%）和RYR2（5.4%）。我们的通路分析表明，五大 BC 通路分别是 PI3K-AKT、TP53、NOTCH、HIPPO 和 RAS 通路。我们发现，BC 小组只共享 7 个基因。这些研究结果表明，BC源于BC信号转导和蛋白质网络中明显的基因紊乱。

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来源期刊

Functional & Integrative Genomics 生物-遗传学

CiteScore

3.50

自引率

3.40%

发文量

审稿时长

2 months

期刊介绍： Functional & Integrative Genomics is devoted to large-scale studies of genomes and their functions, including systems analyses of biological processes. The journal will provide the research community an integrated platform where researchers can share, review and discuss their findings on important biological questions that will ultimately enable us to answer the fundamental question: How do genomes work?