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Molecular Genetics of Breast Cancer—Recent Progress

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A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Oncology".

Deadline for manuscript submissions: closed (20 September 2025) | Viewed by 7369

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Special Issue Editor

Dr. Virginia Valentini

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Guest Editor

Department of Molecular Medicine, Sapienza University of Rome, 00161 Rome, Italy
Interests: breast cancer; hereditary cancers; cancer genetics and genomics; mutational landscape of cancer; molecular epidemiology

Special Issue Information

Dear Colleagues,

Each year, about 30% of all newly diagnosed cancers in women are breast cancers. Breast cancer is likely to be caused by the concurrent effects of different risk factors, including genetic risk factors. On the other hand, this disease could be characterized as an evolutionary process driven by the accumulation of somatic mutations and clonal selection. Therefore, the genetic profiling of breast cancer is essential to improve our understanding of the molecular etiology of this disease. In this field, next-generation sequencing (NGS) technology allowed for not only the identification and validation of novel susceptibility genes, but also the identification of molecular biomarkers and therapeutic targets.

Expanded knowledge on the molecular genetics of breast cancer is the first step leading to the early diagnosis, preventative strategies and treatment personalization. This molecular characterization is also particularly essential in understudied groups of breast cancer patients, such as men affected by the disease.

This Special Issue will focus on the molecular genetics of breast cancer for improved risk assessment and personalized therapy. We invite researchers to submit original research articles describing novel data, methods, collaborative initiatives and reviews related to these topics.

We look forward to receiving your contributions.

Dr. Virginia Valentini
Guest Editor

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Keywords

hereditary cancer
female breast cancer
male breast cancer
molecular oncology
cancer genetics
NGS of gene panels
transcriptomics
genetic predisposition to breast cancer
breast cancer risk
tumor profiling
predictive biomarkers
personalized treatment

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Published Papers (5 papers)

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21 pages, 5069 KB

Open AccessArticle

Integrated miRNA-mRNA Analyses of Triple-Negative Breast Cancer in Black and White Patients with or Without Obesity

by Fokhrul Hossain, Martha I. Gonzalez-Ramirez, Jone Garai, Diana Polania-Villanueva, Li Li, Farzeen Nafees, Md Manirujjaman, Bolin Liu, Samarpan Majumder, Xiao-Cheng Wu, Chindo Hicks, Luis Del Valle, Denise Danos, Augusto Ochoa, Lucio Miele and Jovanny Zabaleta

Int. J. Mol. Sci. 2025, 26(18), 9101; https://doi.org/10.3390/ijms26189101 - 18 Sep 2025

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Abstract

Triple-negative breast cancer (TNBC) is an aggressive, heterogeneous subtype of breast cancer. miRNAs play an essential role in TNBC pathogenesis and prognosis. Obesity is linked with an increased risk for several cancers, including breast cancer. Obesity is also related to the dysregulation of miRNA expression in adipose tissues. However, there is limited knowledge about race- and obesity-specific differential miRNA expression in TNBC. We performed miRNA sequencing of 48 samples (24 tumor and 24 adjacent non-tumor tissues) and RNA sequencing of 24 tumors samples from Black (AA) and White (EA) TNBC patients with or without obesity. We identified 55 miRNAs exclusively associated with tumors in obese EA patients and 33 miRNAs in obese AA patients, each capable of distinguishing tumor tissues from obese from lean individuals within their respective racial groups. In EA, we detected 41 significant miRNA–mRNA correlations. Notably, miR-181b-5p and miR-877-5p acted as negative regulators of tumor-suppressor genes (e.g., HEY2, MCL2, HAND2), while miR-204-5p and miR-143-3p appeared to indirectly target oncogenes (e.g., RAB10, DR1, PTBP3, NCBP1). Among AA patients, we found 28 significant miRNA–mRNA interactions. miR-195-5p, miR-130a-3p, miR-130a-5p, miR-424-5p, miR-148a-3p, miR-374-5p, and miR-30a-5p each potentially downregulated two or more genes (e.g., CLCN4, PLCB1, CDC25B, AEBP2, ERBB4). Pathway enrichment analysis highlighted KRAS, ESR1, ESR2, RAB10, TNRC6C, and NCAN as the most commonly differentially expressed in EA, whereas ERBB4, PLCB1, and SERPINE1 were most frequently in AA. These findings highlight the importance of considering race-specific miRNA–mRNA signatures in understanding TNBC in the context of obesity, offering insights into biomarker-driven patient stratification for targeted therapeutic strategies. Full article

(This article belongs to the Special Issue Molecular Genetics of Breast Cancer—Recent Progress)

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23 pages, 1250 KB

Open AccessArticle

Mitogenomic Alterations in Breast Cancer: Identification of Potential Biomarkers of Risk and Prognosis

by Carlos Jhovani Pérez-Amado, Amellalli Bazan-Cordoba, Laura Gómez-Romero, Julian Ramírez-Bello, Verónica Bautista-Piña, Alberto Tenorio-Torres, Eva Ruvalcaba-Limón, Felipe Villegas-Carlos, Diana Karen Mendiola-Soto, Alfredo Hidalgo-Miranda and Silvia Jiménez-Morales

Int. J. Mol. Sci. 2025, 26(17), 8456; https://doi.org/10.3390/ijms26178456 - 30 Aug 2025

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Abstract

Alterations in the mitochondrial genome (mtDNA) have been shown to be key in cancer development and could be useful as biomarkers for diagnosis, prognosis, and treatment. To identify mtDNA variants associated with breast cancer, we analyzed the whole mtDNA sequence from paired tissues (tumor–peripheral blood) of women with this malignancy and from peripheral blood samples of healthy women. The mtDNA mutational landscape, heteroplasmy levels of the variants, and mitochondrial ancestry were established. Comparative analysis between cases and controls revealed significant differences in the number and location of variants, as well as in the heteroplasmy levels. Cases showed higher mutation number in MT-ND5, tRNAs, and rRNAs genes; increased proportion of missense variants; and elevated mtDNA content, than controls. Notably, a high blood mtDNA mutational burden (OR = 3.83, CI: 1.89–7.95, p = 5.3 × 10⁻⁵) and five mtDNA variants showed association with the risk of breast cancer. Furthermore, a low tumor mutational burden (HR = 7.82, CI: 1.0–63.6, p = 0.05) and the haplogroup L (HR = 12.16, CI: 2.0–72.8, p = 0.0062) were associated with decreased overall and disease-free survival, respectively. Our study adds evidence of the potential usefulness of mtDNA variants as risk and prognosis biomarkers for breast cancer. Full article

(This article belongs to the Special Issue Molecular Genetics of Breast Cancer—Recent Progress)

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22 pages, 6854 KB

Open AccessArticle

Profiling the Expression Level of a Gene from the Caspase Family in Triple-Negative Breast Cancer

by Anna Makuch-Kocka, Janusz Kocki, Jacek Bogucki, Przemysław Kołodziej, Monika Lejman, Karolina Szalast and Anna Bogucka-Kocka

Int. J. Mol. Sci. 2025, 26(15), 7463; https://doi.org/10.3390/ijms26157463 - 1 Aug 2025

Viewed by 447

Abstract

It is believed that caspases may play a significant role in the development of cancer, and the expression levels of genes encoding these proteins may influence the prognosis and clinical course of cancer. Taking into account the information presented, we examined the expression profiles of 11 genes from the caspase family in patients diagnosed with triple-negative breast cancer (TNBC). We qualified 29 patients with TNBC. A fragment of the tumor and a fragment of normal tissue surrounding the tumor were collected from each patient. Then, RNA was isolated, and the reverse transcription process was performed. The expression levels of caspase family genes were determined using the real-time PCR method. The obtained data were correlated with clinical data and compared with data from the Cancer Genome Atlas database using the Breast Cancer Gene Expression Miner v4.8 and Ualcan. Based on the results of the conducted research, it can be assumed that the levels of expression of caspase family genes may be correlated with the clinical course of cancer in patients with TNBC, and further research may indicate that profiling the expression levels of these genes may be used in selecting personalized treatment methods. Full article

(This article belongs to the Special Issue Molecular Genetics of Breast Cancer—Recent Progress)

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25 pages, 3194 KB

Open AccessArticle

High- and Moderate-Risk Variants Among Breast Cancer Patients and Healthy Donors Enrolled in Multigene Panel Testing in a Population of Central Russia

by Syuykum Shumilova, Anastasia Danishevich, Sergey Nikolaev, George Krasnov, Anna Ikonnikova, Darya Isaeva, Sergei Surzhikov, Alexander Zasedatelev, Natalia Bodunova and Tatiana Nasedkina

Int. J. Mol. Sci. 2024, 25(23), 12640; https://doi.org/10.3390/ijms252312640 - 25 Nov 2024

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Abstract

Assessments of breast cancer (BC) risk in carriers of pathogenic variants identified by gene panel testing in different populations are highly in demand worldwide. We performed target sequencing of 78 genes involved in DNA repair in 860 females with BC and 520 age- and family history-matched controls from Central Russia. Among BC patients, 562/860 (65.3%) were aged 50 years or less at the time of diagnosis. In total, 190/860 (22%) BC patients were carriers of 198 pathogenic/likely pathogenic (P/LP) variants in 30 genes, while among controls, 32/520 (6.2%) carriers of P/LP variants in 17 genes were identified. The odds ratio [95% confidence interval] was 16.3 [4.0–66.7] for BRCA1; 12.0 [2.9–45.9] for BRCA2; and 7.3 [0.9–56.7] for ATM (p < 0.05). Previously undescribed BRCA1/2, ATM, and PALB2 variants, as well as novel recurrent mutations, were identified. The contribution to BC susceptibility of truncating variants in the genes BARD1, RAD50, RAD51C, NBEAL1 (p. E1155*), and XRCC2 (p. P32fs) was evaluated. The BLM, NBN, and MUTYH genes did not demonstrate associations with BC risk. Finding deleterious mutations in BC patients is important for diagnosis and management; in controls, it opens up the possibility of prevention and early diagnostics. Full article

(This article belongs to the Special Issue Molecular Genetics of Breast Cancer—Recent Progress)

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9 pages, 1201 KB

Open AccessCase Report

BRCA1 Intragenic Duplication Combined with a Likely Pathogenic TP53 Variant in a Patient with Triple-Negative Breast Cancer: Clinical Risk and Management

by Vuthy Ea, Claudine Berthozat, Hélène Dreyfus, Clémentine Legrand, Estelle Rousselet, Magalie Peysselon, Laura Baudet, Guillaume Martinez, Charles Coutton and Marie Bidart

Int. J. Mol. Sci. 2024, 25(11), 6274; https://doi.org/10.3390/ijms25116274 - 6 Jun 2024

Cited by 1 | Viewed by 2351

Abstract

For patients with hereditary breast and ovarian cancer, the probability of carrying two pathogenic variants (PVs) in dominant cancer-predisposing genes is rare. Using targeted next-generation sequencing (NGS), we investigated a 49-year-old Caucasian woman who developed a highly aggressive breast tumor. Our analyses identified an intragenic germline heterozygous duplication in BRCA1 with an additional likely PV in the TP53 gene. The BRCA1 variant was confirmed by multiplex ligation probe amplification (MLPA), and genomic breakpoints were characterized at the nucleotide level (c.135-2578_442-1104dup). mRNA extracted from lymphocytes was amplified by RT-PCR and then Sanger sequenced, revealing a tandem duplication r.135_441dup; p.(Gln148Ilefs*20). This duplication results in the synthesis of a truncated and, most likely, nonfunctional protein. Following functional studies, the TP53 exon 5 c.472C > T; p.(Arg158Cys) missense variant was classified as likely pathogenic by the Li-Fraumeni Syndrome (LFS) working group. This type of unexpected association will be increasingly identified in the future, with the switch from targeted BRCA sequencing to hereditary breast and ovarian cancer (HBOC) panel sequencing, raising the question of how these patients should be managed. It is therefore important to record and investigate these rare double-heterozygous genotypes. Full article

(This article belongs to the Special Issue Molecular Genetics of Breast Cancer—Recent Progress)

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