Breast Cancer : Basic and Clinical Research最新文献

{"title":"Caveolin-1, a Determinant of the Fate of MCF-7 Breast Cancer Cells.","authors":"Tina Chai, Wei Yue, Peng Xu, John Gildea, Robin Felder","doi":"10.1177/11782234241226802","DOIUrl":"10.1177/11782234241226802","url":null,"abstract":"<p><strong>Background: </strong>The scaffolding protein, caveolin-1 (Cav-1), participates in multiple cellular functions including promotion of sodium excretion from the kidney. Loss of expression of Cav-1 is associated with tumorigenesis of various types of cancer. We have shown the potential link between hypertension and breast cancer via abnormal function of the G protein-coupled receptor kinase type 4 (GRK4).</p><p><strong>Objective: </strong>The current studies tested the hypothesis that Cav-1 acts as a tumor-suppressive factor in breast cancer cells and enhances the sensitivity to the inhibitory effect of the type 1 dopaminergic receptor (D₁R).</p><p><strong>Methods: </strong>Michigan Cancer Foundation (MCF) MCF-7 cells stably expressing a Cav-1/mCherry fusion protein or mCherry alone were used as models to examine the effect of Cav-1 on cell growth, apoptosis, and senescence. Cell proliferation was determined by cell counting, cell cycle analysis (flow cytometry), and BrdU incorporation. Apoptosis was determined using the Cell Death Detection ELISA kit from Roche Diagnosis. Senescence was determined using the senescence associated beta galactosidase (SA-β-gal) assay. Reactive oxygen species (ROS) was measured using 2',7'-dichlorodihydrofluorescein diacetate. Western blot analysis was used to measure activation of signaling pathway molecules. All statistical analyses were conducted with Microsoft Excel.</p><p><strong>Results: </strong>Overexpression of Cav-1 in MCF-7 cells reduced cellular growth rate. Both inhibition of proliferation and induction of cell death are contributing factors. Multiple signaling pathways were activated in Cav-1-expressing MCF-7 cells. Activation of Akt was prominent. In MCF-7-expressing Cav-1 (MCF-7 Cav-1) cells, the levels of phosphorylated Akt at S⁴⁷³ and T³⁰⁸ were increased 28- and 8.7-fold, respectively. Instead of protecting cells from apoptosis, extremely high levels of activated Akt resulted in increased levels of ROS which led to apoptosis and senescence. The tumor-suppressive effect plus downregulation of GRK4 makes Cav-1-expressing MCF-7 cells significantly more sensitive to the inhibitory effect of the D₁R agonist, SKF38393.</p><p><strong>Conclusion: </strong>Caveolin-1 acts as a tumor-suppressing factor via extreme activation of Akt and down regulation of survival factors such as GRK4, survivin, and cyclin D1.</p>","PeriodicalId":9163,"journal":{"name":"Breast Cancer : Basic and Clinical Research","volume":"18 ","pages":"11782234241226802"},"PeriodicalIF":1.8,"publicationDate":"2024-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10829489/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139650214","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Clinical Outcomes of Breast-Conserving Surgery with Synchronous 50-kV X-ray Intraoperative Partial Breast Irradiation in Patients Aged 64 Years or Older with Low-Risk Breast Cancer","authors":"K. Salari, Andrew Glaza, Joseph S Lee, Neha Sarvepalli, N. Dekhne, Sayee H Kiran, Peter Y Chen, J. Dilworth","doi":"10.1177/11782234231224267","DOIUrl":"https://doi.org/10.1177/11782234231224267","url":null,"abstract":"Background: Breast-conserving surgery with synchronous 50-kV X-ray intraoperative radiation therapy (TARGIT-IORT) is a convenient form of partial breast irradiation; however, the existing literature supports a wide range of local control rates. Objectives: We investigated the treatment effectiveness and toxic effects of TARGIT-IORT in a patient cohort aged 64 years or older with low-risk breast cancer. Design: Retrospective analysis. Methods: Patients who received breast-conserving surgery with synchronous TARGIT-IORT at a single institution from 2016 to 2019 were reviewed. Additional whole breast irradiation was recommended at the discretion of the treating radiation oncologist. Baseline patient demographics and treatment details were recorded. Acute and chronic toxicities, measured using the Common Terminology Criteria for Adverse Events version 3.0 or 4.0 and breast cosmetic outcomes, using the Harvard Cosmesis score, were recorded. Locoregional recurrence, distant metastasis, and overall survival were recorded, and 5-year rates were estimated using the Kaplan-Meier method. Results: 61 patients were included with a median follow-up of 3.5 years and median age of 72 years. Eight (13%) patients received additional whole breast irradiation, and fifty-four (89%) received adjuvant hormone therapy. There were no local, regional, or distance recurrences. One patient died of complications from COVID-19 infection. Grade 2 + acute and chronic toxicities were observed in 6 (12%) and 7 (14%) patients, respectively. One patient experienced a grade 3 acute toxicity. Cosmetic outcome was “excellent” or “good” in 45 (92%) patients. Conclusions: Breast TARGIT-IORT was well tolerated and conferred excellent disease control in this cohort of patients with low-risk breast cancer. While continued follow-up is required, TARGIT-IORT may be an appropriate treatment option for this population.","PeriodicalId":9163,"journal":{"name":"Breast Cancer : Basic and Clinical Research","volume":"315 3","pages":""},"PeriodicalIF":2.9,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139395187","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Sixteen-Year Institutional Review of Magnetic Resonance Imaging-Guided Breast Biopsies: Trends in Histologic Diagnoses With Radiologic Correlation.","authors":"Samaneh A Motanagh, Dennis Dwan, Nasim Azizgolshani, Kristen E Muller, Roberta M diFlorio-Alexander, Jonathan D Marotti","doi":"10.1177/11782234231215193","DOIUrl":"10.1177/11782234231215193","url":null,"abstract":"<p><strong>Background: </strong>Breast magnetic resonance imaging (MRI) is an important imaging tool for the management of breast cancer patients and for screening women at high risk for breast cancer.</p><p><strong>Objectives: </strong>To examine long-term trends in the distribution of histologic diagnoses obtained from MRI-guided breast biopsies.</p><p><strong>Design: </strong>Retrospective analysis.</p><p><strong>Methods: </strong>We retrospectively reviewed the distribution of histologic diagnoses of MRI-guided breast biopsies from 2004 to 2019. All cases underwent central pathology review and lesions were classified based on the most prominent histologic finding present. Magnetic resonance imaging features were extracted from radiology reports when available and correlated with pathology diagnoses.</p><p><strong>Results: </strong>Four hundred ninety-four MRI-guided biopsies were performed on 440 patients; overall, 73% of biopsies were benign and 27% were malignant. The annual percentages of benign and malignant diagnoses remained similar throughout the 16-year period. Of the benign entities commonly identified, the percentage of benign papillary and sclerosing lesions detected in the benign biopsies increased significantly (13% in 2004-2011 vs 31% in 2012-2019, <i>P</i> = .03). The mean size of malignant lesions was larger than benign lesions (30.1 mm compared with 14.2 mm, <i>P</i> = .045); otherwise, there were no distinguishing radiologic features between benign and malignant lesions.</p><p><strong>Conclusion: </strong>The specificity of breast MRI remained constant over a 16-year period; however, there was a shift in the distribution of benign diagnoses with increased detection and biopsy of benign papillary and sclerosing lesions. Monitoring the distribution of breast MRI biopsy diagnoses over time with radiology-pathology correlation might improve the suboptimal specificity of breast MRI.</p>","PeriodicalId":9163,"journal":{"name":"Breast Cancer : Basic and Clinical Research","volume":"17 ","pages":"11782234231215193"},"PeriodicalIF":2.9,"publicationDate":"2023-11-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10685755/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138457911","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Are We Prepared for the CDK4/6 Revolution With HR+/HER2- Breast Cancers?: The Importance of Patient Adherence to Adjuvant Therapies.","authors":"Seyla Azoz, Martin Peters, Graham Jones","doi":"10.1177/11782234231215192","DOIUrl":"10.1177/11782234231215192","url":null,"abstract":"","PeriodicalId":9163,"journal":{"name":"Breast Cancer : Basic and Clinical Research","volume":"17 ","pages":"11782234231215192"},"PeriodicalIF":1.8,"publicationDate":"2023-11-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10685741/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138457908","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Metaplastic Carcinoma of the Axillary Breast With Heterologous Mesenchymal (Chondroid) Differentiation: A Difficult Case and Literature Review.","authors":"Chun-Ming Chang, Ho Yin Pekkle Lam","doi":"10.1177/11782234231215183","DOIUrl":"https://doi.org/10.1177/11782234231215183","url":null,"abstract":"<p><p>Metaplastic breast carcinoma is an invasive carcinoma with a high differentiation rate of the neoplastic epithelium toward mesenchymal-like epithelium. It comprises of only less than 1% of all breast cancers. Although 80% to 90% of metaplastic breast carcinomas are triple-negative cancers, they usually have worse outcomes than other triple-negative breast cancers (TNBCs). Metaplastic carcinoma is also often refractory to cytotoxic chemotherapy. Here, we reported a case of a 61-year-old female patient, presenting with a solitary and pedunculated mass in the right axillary tail breast tissue, whose biopsy revealed metaplastic breast carcinoma with chondroid differentiation. She had failed neoadjuvant chemotherapy and immunotherapy. Although she received debulking surgery, the tumor regrew even faster before surgery. Despite receiving palliative chemotherapy, the patient died 11 weeks after surgery. This case draws attention to physicians that early recognition and surgery may be more beneficial than chemotherapy in combating metaplastic breast carcinoma.</p>","PeriodicalId":9163,"journal":{"name":"Breast Cancer : Basic and Clinical Research","volume":"17 ","pages":"11782234231215183"},"PeriodicalIF":2.9,"publicationDate":"2023-11-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10676630/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138457910","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Assessment of Pathological Complete Response Using Vacuum-Assisted Biopsy in Breast Cancer Patients Who Have Clinical and Radiological Complete Response After Neo-Adjuvant Chemotherapy.","authors":"Siddhant Khare, Irrinki Santosh, Ishita Laroiya, Tulika Singh, Amanjit Bal, Gurpreet Singh","doi":"10.1177/11782234231205698","DOIUrl":"https://doi.org/10.1177/11782234231205698","url":null,"abstract":"<p><strong>Background: </strong>Any treatment protocol that leads to complete elimination of surgery may lead to a better patient acceptance of breast cancer treatments.</p><p><strong>Objectives: </strong>We conducted this study to assess the feasibility of preoperative vacuum-assisted biopsies in identifying pathological complete response (pCR) and its accuracy in correlation to final histopathology report (HPR), in an Indian setting.</p><p><strong>Methods: </strong>This was a prospective study conducted between October 1, 2019, and March 31, 2021. Patients with early breast cancer, estrogen and progesterone receptors negative and either Her2 positive or negative, and who were fit to undergo marker placement at the centre of the tumour and to receive third-generation chemotherapy (4 cycles of 3 weekly doxorubicin and cyclophosphamide followed by 4 cycles of 3 weekly docetaxel) were included in the study. Following the enrolment, a tissue marker was placed at the centre of the tumour and appropriate chemotherapy was started. Patients who achieved clinical complete response were subjected to ultrasound-guided vacuum-assisted biopsy (VAB) from the tumour bed before surgery. Pathology results of the VAB and resected specimen were then compared. Descriptive statistics were used in the study.</p><p><strong>Results: </strong>Eighteen patients were enrolled in the study, with a mean age of 43.6 ± 9.8 years. However, only 10 were eligible for VAB procedure, and sensitivity and specificity were calculated based on the results of these 10 patients only. Vacuum-assisted biopsy showed sensitivity of 50% and specificity of 100% in identifying pCR. Combination of mammography, ultrasonography, and VAB showed sensitivity of 77.8% and specificity of 66.7% in identifying pCR.</p><p><strong>Conclusion: </strong>Vacuum-assisted biopsy of tumour bed may not be sensitive enough to eliminate surgery even in patients who have had exceptional response to neo-adjuvant chemotherapy.</p>","PeriodicalId":9163,"journal":{"name":"Breast Cancer : Basic and Clinical Research","volume":"17 ","pages":"11782234231205698"},"PeriodicalIF":2.9,"publicationDate":"2023-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10655653/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138457909","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Coping in Post-Mastectomy Breast Cancer Survivors and Need for Intervention: Systematic Review.","authors":"Anju Mishra, Jayajith Nair, Anjali Midha Sharan","doi":"10.1177/11782234231209126","DOIUrl":"10.1177/11782234231209126","url":null,"abstract":"<p><strong>Background: </strong>Breast cancer is the most prominent cancer type to affect women. Surgical treatment of invasive breast cancers involves mastectomy. Due to mastectomy, women are subjected to social, emotional, and cultural problems which need to be addressed.</p><p><strong>Objective: </strong>The objective of the study is to understand how women cope with body image-related issues, trauma, anxiety, and depression post-mastectomy.</p><p><strong>Design: </strong>A systematic literature review was conducted for understanding the coping in post-mastectomy patients. The methods for identifying the studies were based on Preferred Reporting Items for Systematic reviews and Meta-analysis (PRISMA) guidelines.</p><p><strong>Databases: </strong>Medline/PubMed, PsycInfo, and Cochrane databases were used for searching relevant articles. A final of 19 studies were analyzed for the work.</p><p><strong>Methods: </strong>Search strings such as \"coping strategies and post mastectomy,\" \"body image coping and post mastectomy\" and \"anxiety coping and post mastectomy\" were used for identification of references from databases. Eligibility criteria were used for finalizing the references.</p><p><strong>Results: </strong>Analysis of the 19 studies has clearly shown that women who undergo mastectomy suffer from anxiety, stress, and trauma. This study has observed that women have problems with their body image post-mastectomy along with bouts of depression. Self-coping has been observed in relatively few studies. Psychological interventions before surgery have been observed to be a better coping strategy. In most of the studies, women opted for breast reconstruction to overcome the trauma associated with mastectomy.</p><p><strong>Conclusion: </strong>Mastectomy has a severe impact on women's appearance and psychology. Breast reconstruction and acceptance have played an important role in coping among these women. However, breast reconstruction is not accepted by many women due to a multitude of factors. Thus, it is essential to have proper intervention programs in place to ensure women can cope with this situation and can lead healthy lives.</p><p><strong>Registration: </strong>Systematic literature review (SLR) is submitted to PROSPERO. The application confirmation number is 449135.Registration awaited from the database.</p>","PeriodicalId":9163,"journal":{"name":"Breast Cancer : Basic and Clinical Research","volume":"17 ","pages":"11782234231209126"},"PeriodicalIF":2.9,"publicationDate":"2023-11-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10638885/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"89716912","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Implementation of Risk-Stratified Breast Cancer Prevention With a Polygenic Risk Score Test in Clinical Practice.","authors":"Peeter Padrik,&nbsp;Mikk Puustusmaa,&nbsp;Neeme Tõnisson,&nbsp;Berit Kolk,&nbsp;Regina Saar,&nbsp;Anna Padrik,&nbsp;Tõnis Tasa","doi":"10.1177/11782234231205700","DOIUrl":"10.1177/11782234231205700","url":null,"abstract":"<p><strong>Background: </strong>Breast cancer (BC) screening with mammography reduces mortality but considers currently only age as a risk factor. Personalized risk-based screening has been proposed as a more efficient alternative. For that, risk prediction tools are necessary. Genome-wide association studies have identified numerous genetic variants (single-nucleotide polymorphisms [SNPs]) associated with BC. The effects of SNPs are combined into a polygenic risk score (PRS) as a risk prediction tool.</p><p><strong>Objectives: </strong>We aimed to develop a clinical-grade PRS test suitable for BC risk-stratified screening with clinical recommendations and implementation in clinical practice.</p><p><strong>Design and methods: </strong>In the first phase of our study, we gathered previously published PRS models for predicting BC risk from the literature and validated them using the Estonian Biobank and UK Biobank data sets. We selected the best performing model based on prevalent data and independently validated it in both incident data sets. We then conducted absolute risk simulations, developed risk-based recommendations, and implemented the PRS test in clinical practice. In the second phase, we carried out a retrospective analysis of the PRS test's performance results in clinical practice.</p><p><strong>Results: </strong>The best performing PRS included 2803 SNPs. The C-index of the Cox regression model associating BC status with PRS was 0.656 (SE = 0.05) with a hazard ratio of 1.66. The PRS can stratify individuals with more than a 3-fold risk increase. A total of 2637 BC PRS tests have been performed for women between the ages 30 and 83. Results in clinical use overlap well with expected PRS performance with 5.7% of women with more than 2-fold and 1.4% with more than 3-fold higher risk than the population average.</p><p><strong>Conclusion: </strong>The PRS test separates different BC risk levels and is feasible to implement in clinical practice.</p>","PeriodicalId":9163,"journal":{"name":"Breast Cancer : Basic and Clinical Research","volume":"17 ","pages":"11782234231205700"},"PeriodicalIF":2.9,"publicationDate":"2023-10-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/ac/9c/10.1177_11782234231205700.PMC10571698.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41232373","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Real-World Survival and Treatment Regimens Across First- to Third-Line Treatment for Advanced Triple-Negative Breast Cancer.","authors":"Alan Celik,&nbsp;Tobias Berg,&nbsp;Maj-Britt Jensen,&nbsp;Erik Jakobsen,&nbsp;Hanne Melgaard Nielsen,&nbsp;Iben Kümler,&nbsp;Vesna Glavicic,&nbsp;Jeanette Dupont Jensen,&nbsp;Ann Knoop","doi":"10.1177/11782234231203292","DOIUrl":"10.1177/11782234231203292","url":null,"abstract":"<p><strong>Background: </strong>Metastatic triple-negative breast cancer (mTNBC) is an aggressive subtype of breast cancer with poor survival. Currently, the literature lacks comprehensive real-world evidence on locally recurrent and mTNBC patients. To validate the optimal treatment for patients with mTNBC, real-world evidence in combination with data from clinical trials must be evaluated as complementary.</p><p><strong>Objectives: </strong>The objective of the study is to examine outcomes and treatment patterns of patients with advanced triple-negative breast cancer (TNBC) utilizing real-world data of patients from all oncology sites across Denmark.</p><p><strong>Design: </strong>This is a retrospective, non-interventional, multi-site, population-based observational study conducted across all oncology departments in Denmark.</p><p><strong>Methods: </strong>We included all women diagnosed with metastatic or locally recurrent TNBC from January 1, 2017, to December 31, 2019, using the national Danish Breast Cancer Group database. The primary endpoints were overall survival (OS) and progression-free survival (PFS) in the first to third treatment line.</p><p><strong>Results: </strong>The study included 243 women diagnosed with metastatic or recurrent TNBC. The median OS (mOS) was 11.6 months after the first line of treatment, 6.5 months after the second line, and 6.5 months after the third line. De novo mTNBC was associated with shorter OS (mOS: 8.3 vs 14.2 months), and those with a relapse within 18 months of primary diagnosis had shorter OS than those with a relapse after 18 months (mOS: 10.0 vs 18.2). In the first line, taxane was the preferred choice of treatment for patients with de novo mTNBC, whereas capecitabine was preferred for patients with recurrent TNBC.</p><p><strong>Conclusions: </strong>This real-world, nationwide study demonstrated poor OS among patients with metastatic or recurrent TNBC, with a mOS of 11.6 months (95% CI, 9.9-17.3). Patients who presented with de novo mTNBC or who had a relapse of their breast cancer within 18 months of primary diagnosis had shorter OS.</p><p><strong>Registration: </strong>The study was registered and approved by the Danish Capital Regions research overview (P-2021-605).</p>","PeriodicalId":9163,"journal":{"name":"Breast Cancer : Basic and Clinical Research","volume":"17 ","pages":"11782234231203292"},"PeriodicalIF":2.9,"publicationDate":"2023-10-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/4f/08/10.1177_11782234231203292.PMC10552450.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41107546","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Homologous Recombination Abnormalities Associated With <i>BRCA1/2</i> Mutations as Predicted by Machine Learning of Targeted Next-Generation Sequencing Data.","authors":"Maher Albitar,&nbsp;Hong Zhang,&nbsp;Andrew Pecora,&nbsp;Stanley Waintraub,&nbsp;Deena Graham,&nbsp;Mira Hellmann,&nbsp;Donna McNamara,&nbsp;Ahmad Charifa,&nbsp;Ivan De Dios,&nbsp;Wanlong Ma,&nbsp;Andre Goy","doi":"10.1177/11782234231198979","DOIUrl":"https://doi.org/10.1177/11782234231198979","url":null,"abstract":"<p><strong>Background: </strong>Homologous recombination deficiency (HRD) is the hallmark of breast cancer gene 1/2 (<i>BRCA1/2</i>)-mutated tumors and the unique biomarker for predicting response to double-strand break (DSB)-inducing drugs. The demonstration of HRD in tumors with mutations in genes other than <i>BRCA1/2</i> is considered the best biomarker of potential response to these DSB-inducer drugs.</p><p><strong>Objectives: </strong>We explored the potential of developing a practical approach to predict in any tumor the presence of HRD that is similar to that seen in tumors with <i>BRCA1/2</i> mutations using next-generation sequencing (NGS) along with machine learning (ML).</p><p><strong>Design: </strong>We use copy number alteration (CNA) generated from routine-targeted NGS data along with a modified naïve Bayesian model for the prediction of the presence of HRD.</p><p><strong>Methods: </strong>The CNA from NGS of 434 targeted genes was analyzed using CNVkit software to calculate the log2 of CNA changes. The log2 values of various sequencing reads (bins) were used in ML to train the system on predicting tumors with <i>BRCA1/2</i> mutations and tumors with abnormalities similar to those detected in <i>BRCA1/2</i> mutations.</p><p><strong>Results: </strong>Using 31 breast or ovarian cancers with <i>BRCA1/2</i> mutations and 84 tumors without mutations in any of 12 homologous recombination repair (HRR) genes, the ML demonstrated high sensitivity (90%, 95% confidence interval [CI] = 73%-97.5%) and specificity (98%, 95% CI = 90%-100%). Testing of 114 tumors with mutations in HRR genes other than <i>BRCA1/2</i> showed 39% positivity for HRD similar to that seen in <i>BRCA1/2</i>. Testing 213 additional wild-type (WT) cancers showed HRD positivity similar to <i>BRCA1/2</i> in 32% of cases. Correlation with proportional loss of heterozygosity (LOH) as determined using whole exome sequencing of 51 samples showed 90% (95% CI = 72%-97%) concordance. The approach was also validated in an independent set of 1312 consecutive tumor samples.</p><p><strong>Conclusions: </strong>These data demonstrate that CNA when combined with ML can reliably predict the presence of <i>BRCA1/2</i> level HRD with high specificity. Using <i>BRCA1/2</i> mutant cases as gold standard, this ML can be used to predict HRD in cancers with mutations in other HRR genes as well as in WT tumors.</p>","PeriodicalId":9163,"journal":{"name":"Breast Cancer : Basic and Clinical Research","volume":"17 ","pages":"11782234231198979"},"PeriodicalIF":2.9,"publicationDate":"2023-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/bc/c3/10.1177_11782234231198979.PMC10542224.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41103801","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}