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Genomics of Breast Cancer
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Genomics of Breast Cancer

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Human Genomics and Genetic Diseases".

Deadline for manuscript submissions: closed (20 February 2024) | Viewed by 6154

Special Issue Editor

Dr. Ciara O'Flanagan

E-Mail Website
Guest Editor
Department Molecular Oncology, BC Cancer Research Centre, Vancouver, BC V5Z 1L3, Canada
Interests: breast cancer; ovarian cancer; genomics; transcriptomics; single-cell sequencing; in situ transcriptomics; chemoresistance

Special Issue Information

Dear Colleagues,

Breast cancer is a heterogeneous disease with several clinical and genomic subtypes, making it an exemplary candidate for precision medicine. Advances in next-generation sequencing have shed light on the key mutations associated with breast cancer development and can highlight new therapeutic targets, such as ADP-ribose polymerase (PARP) inhibition in patients with mutations in BRCA1/2 DNA repair genes.

This Special Issue ‘Genomics of Breast Cancer’ aims to present genomic and clinical aspects of breast cancers that broaden our understanding of the disease and we welcome contributions that include, but are not limited to, the topics of genomics, transcriptomics, sequencing, molecular biology, tumour heterogeneity, patient samples or animal models and that advance our understanding of breast cancers or could highlight novel diagnostic and treatment strategies for this disease.

Dr. Ciara O'Flanagan
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Genes is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • breast cancer
  • genomics
  • transcriptomics
  • clusters/subtypes
  • precision medicine
  • heterogeneity
  • mutation

Published Papers (4 papers)

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Research

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13 pages, 1946 KiB  
Article
The Mutational Spectrum of Pre- and Post-Neoadjuvant Chemotherapy Triple-Negative Breast Cancers
by Adriana Aguilar-Mahecha, Najmeh Alirezaie, Josiane Lafleur, Eric Bareke, Ewa Przybytkowski, Cathy Lan, Luca Cavallone, Myriam Salem, Manuela Pelmus, Olga Aleynikova, Celia Greenwood, Amanda Lovato, Cristiano Ferrario, Jean-François Boileau, Catalin Mihalcioiu, Josée-Anne Roy, Elizabeth Marcus, Federico Discepola, Jacek Majewski and Mark Basik
Genes 2024, 15(1), 27; https://doi.org/10.3390/genes15010027 - 23 Dec 2023
Viewed by 1001
Abstract
The response of triple-negative breast cancer (TNBC) patients to pre-operative (neoadjuvant chemotherapy) is a critical factor of their outcome. To determine the effects of chemotherapy on the tumor genome and to identify mutations associated with chemoresistance and sensitivity, we performed whole exome sequencing [...] Read more.
The response of triple-negative breast cancer (TNBC) patients to pre-operative (neoadjuvant chemotherapy) is a critical factor of their outcome. To determine the effects of chemotherapy on the tumor genome and to identify mutations associated with chemoresistance and sensitivity, we performed whole exome sequencing on pre/post-chemotherapy tumors and matched lymphocytes from 26 patients. We observed great inter-tumoral heterogeneity with no gene mutated recurrently in more than four tumors besides TP53. Although the degree of response to chemotherapy in residual tumors was associated with more subclonal changes during chemotherapy, there was minimal evolution between pre/post-tumors. Indeed, gene sets enriched for mutations in pre- and post-chemotherapy tumors were very similar and reflected genes involved in the biological process of neurogenesis. Somatically mutated genes present in chemosensitive tumors included COL1A2, PRMD15, APOBEC3B, PALB2 and histone protein encoding genes, while BRCA1, ATR, ARID1A, XRCC3 and genes encoding for tubulin-associated proteins were present in the chemoresistant tumors. We also found that the mutational spectrum of post-chemotherapy tumors was more reflective of matching metastatic tumor biopsies than pre-chemotherapy samples. These findings support a portrait of modest ongoing genomic instability with respect to single-nucleotide variants induced by or selected for by chemotherapy in TNBCs. Full article
(This article belongs to the Special Issue Genomics of Breast Cancer)
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13 pages, 1030 KiB  
Article
Whole-Exome Sequencing Reveals High Mutational Concordance between Primary and Matched Recurrent Triple-Negative Breast Cancers
by Jaspreet Kaur, Darshan S. Chandrashekar, Zsuzsanna Varga, Bettina Sobottka, Emiel Janssen, Khanjan Gandhi, Jeanne Kowalski, Umay Kiraz, Sooryanarayana Varambally and Ritu Aneja
Genes 2023, 14(9), 1690; https://doi.org/10.3390/genes14091690 - 25 Aug 2023
Cited by 1 | Viewed by 1375
Abstract
Purpose: Triple-negative breast cancer (TNBC) is a molecularly complex and heterogeneous breast cancer subtype with distinct biological features and clinical behavior. Although TNBC is associated with an increased risk of metastasis and recurrence, the molecular mechanisms underlying TNBC metastasis remain unclear. We performed [...] Read more.
Purpose: Triple-negative breast cancer (TNBC) is a molecularly complex and heterogeneous breast cancer subtype with distinct biological features and clinical behavior. Although TNBC is associated with an increased risk of metastasis and recurrence, the molecular mechanisms underlying TNBC metastasis remain unclear. We performed whole-exome sequencing (WES) analysis of primary TNBC and paired recurrent tumors to investigate the genetic profile of TNBC. Methods: Genomic DNA extracted from 35 formalin-fixed paraffin-embedded tissue samples from 26 TNBC patients was subjected to WES. Of these, 15 were primary tumors that did not have recurrence, and 11 were primary tumors that had recurrence (nine paired primary and recurrent tumors). Tumors were analyzed for single-nucleotide variants and insertions/deletions. Results: The tumor mutational burden (TMB) was 7.6 variants/megabase in primary tumors that recurred (n = 9); 8.2 variants/megabase in corresponding recurrent tumors (n = 9); and 7.3 variants/megabase in primary tumors that did not recur (n = 15). MUC3A was the most frequently mutated gene in all groups. Mutations in MAP3K1 and MUC16 were more common in our dataset. No alterations in PI3KCA were detected in our dataset. Conclusions: We found similar mutational profiles between primary and paired recurrent tumors, suggesting that genomic features may be retained during local recurrence. Full article
(This article belongs to the Special Issue Genomics of Breast Cancer)
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13 pages, 4892 KiB  
Article
High Atlastin 2-2 (ATL2-2) Expression Associates with Worse Prognosis in Estrogen-Receptor-Positive Breast Cancer
by Inga Reynisdottir, Adalgeir Arason, Edda S. Freysteinsdottir, Sigrun B. Kristjansdottir, Bylgja Hilmarsdottir, Gunnhildur A. Traustadottir, Oskar T. Johannsson, Bjarni A. Agnarsson and Rosa B. Barkardottir
Genes 2023, 14(8), 1559; https://doi.org/10.3390/genes14081559 - 29 Jul 2023
Viewed by 1323
Abstract
The disruption of endoplasmic reticulum (ER) homeostasis occurs in many human diseases. Atlastins (ATLs) maintain the branched network of the ER. The dysregulation of ATL2, located at ER network junctions, has been associated with cancer. ATL2 is necessary for lipid droplet formation in [...] Read more.
The disruption of endoplasmic reticulum (ER) homeostasis occurs in many human diseases. Atlastins (ATLs) maintain the branched network of the ER. The dysregulation of ATL2, located at ER network junctions, has been associated with cancer. ATL2 is necessary for lipid droplet formation in murine breast tissue. Thus, we analyzed whether ATL2 has a role in human breast cancer (BC) pathology. The expression of ATL2 variant ATL2-2 was analyzed in breast tumors from the BC cohorts of the TCGA, METABRIC, and two independent Icelandic cohorts, Cohort 1 and 2; its association with clinical, pathological, survival, and cellular pathways was explored. ATL2-2 mRNA and protein expression were higher in breast tumors than in normal tissue. ATL2-2 mRNA associated with tumor characteristics that indicate a worse prognosis. In METABRIC, high ATL2-2 mRNA levels were associated with shorter BC-specific survival (BCSS) in patients with estrogen-receptor-positive luminal breast tumors, which remained significant after correction for grade and tumor size (HR 1.334, CI 1.063–1.673). Tumors with high ATL2 mRNA showed an upregulation of hallmark pathways MYC targets v1, E2F targets, and G2M checkpoint genes. Taken together, the results suggest that high levels of ATL2-2 may support BC progression through key cancer driver pathways. Full article
(This article belongs to the Special Issue Genomics of Breast Cancer)
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Review

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22 pages, 1728 KiB  
Review
Genomic Features of Homologous Recombination Deficiency in Breast Cancer: Impact on Testing and Immunotherapy
by Umer Ali, Sunitha Vungarala and Venkataswarup Tiriveedhi
Genes 2024, 15(2), 162; https://doi.org/10.3390/genes15020162 - 26 Jan 2024
Viewed by 1883
Abstract
Genomic instability is one of the well-established hallmarks of cancer. The homologous recombination repair (HRR) pathway plays a critical role in correcting the double-stranded breaks (DSB) due to DNA damage in human cells. Traditionally, the BRCA1/2 genes in the HRR pathway have been [...] Read more.
Genomic instability is one of the well-established hallmarks of cancer. The homologous recombination repair (HRR) pathway plays a critical role in correcting the double-stranded breaks (DSB) due to DNA damage in human cells. Traditionally, the BRCA1/2 genes in the HRR pathway have been tested for their association with breast cancer. However, defects in the HRR pathway (HRD, also termed ‘BRCAness’), which has up to 50 genes, have been shown to be involved in tumorigenesis and treatment susceptibility to poly-ADP ribose polymerase inhibitors (PARPis), platinum-based chemotherapy, and immune checkpoint inhibitors (ICIs). A reliable consensus on HRD scores is yet to be established. Emerging evidence suggests that only a subset of breast cancer patients benefit from ICI-based immunotherapy. Currently, albeit with limitations, the expression of programmed death-ligand 1 (PDL1) and tumor mutational burden (TMB) are utilized as biomarkers to predict the favorable outcomes of ICI therapy in breast cancer patients. Preclinical studies demonstrate an interplay between the HRR pathway and PDL1 expression. In this review, we outline the current understanding of the role of HRD in genomic instability leading to breast tumorigenesis and delineate outcomes from various clinical trials. Furthermore, we discuss potential strategies for combining HRD-targeted therapy with immunotherapy to achieve the best healthcare outcomes in breast cancer patients. Full article
(This article belongs to the Special Issue Genomics of Breast Cancer)
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