Management of breast cancer risk in BRCA1/2 mutation carriers who are unaffected with cancer

Opportunities and barriers in omics-based biomarker discovery for steatotic liver diseases

The rising prevalence of liver diseases related to obesity and excessive use of alcohol is fuelling an increasing demand for accurate biomarkers aimed at community screening, diagnosis of steatohepatitis and significant fibrosis, monitoring, prognostication and prediction of treatment efficacy. Breakthroughs in omics methodologies and the power of bioinformatics have created an excellent opportunity to apply technological advances to clinical needs, for instance in the development of precision biomarkers for personalised medicine. Via omics technologies, biological processes from the genes to circulating protein, as well as the microbiome - including bacteria, viruses and fungi, can be investigated on an axis. However, there are important barriers to omics-based biomarker discovery and validation, including the use of semi-quantitative measurements from untargeted platforms, which may exhibit high analytical, inter- and intra-individual variance. Standardising methods and the need to validate them across diverse populations presents a challenge, partly due to disease complexity and the dynamic nature of biomarker expression at different disease stages. Lack of validity causes lost opportunities when studies fail to provide the knowledge needed for regulatory approvals, all of which contributes to a delayed translation of these discoveries into clinical practice. While no omics-based biomarkers have matured to clinical implementation, the extent of data generated has enabled the hypothesis-free discovery of a plethora of candidate biomarkers that warrant further validation. To explore the many opportunities of omics technologies, hepatologists need detailed knowledge of commonalities and differences between the various omics layers, and both the barriers to and advantages of these approaches.

Oncogenic BRCA1,2 Mutations in the Human Lineage-A By-Product of Sexual Selection?

In this review, we discuss the long-known problem of tissue-specific carcinogenesis in BRCA1 and BRCA2 mutation carriers: while the genes are expressed ubiquitously, increased cancer risk is observed mostly in the breast and ovaries, and to a much lesser extent, in some other tissues such as the prostate or pancreas. We reevaluate hypotheses on the evolutionary origin of these mutations in humans. Also, we align together the reports that at least some great apes have much lower risks of epithelial cancers in general and breast cancer in particular with the fact that humans have more voluminous breast tissue as compared to their closest extant relatives, particularly chimpanzees and bonobos. We conjecture that this disparity may be a consequence of sexual selection, augmented via selection for enhanced lactation. Further, we argue that there is an organ-specific enigma similar to the Peto paradox: breast cancer risk in humans is only minimally correlated with breast size. These considerations lead to the hypothesis that, along with the evolutionary development of larger breasts in humans, additional changes have played a balancing role in suppressing breast cancer. These yet-to-be-discovered mechanisms, while purely speculative, may be valuable to understanding human breast cancer, though they may not be exclusive to the mammary gland epithelial cells. Combining these themes, we review some anti-carcinogenesis preventive strategies and prospects of new interventions against breast cancer.

A Multilabel Text Classifier of Cancer Literature at the Publication Level: Methods Study of Medical Text Classification

BACKGROUND

Given the threat posed by cancer to human health, there is a rapid growth in the volume of data in the cancer field and interdisciplinary and collaborative research is becoming increasingly important for fine-grained classification. The low-resolution classifier of reported studies at the journal level fails to satisfy advanced searching demands, and a single label does not adequately characterize the literature originated from interdisciplinary research results. There is thus a need to establish a multilabel classifier with higher resolution to support literature retrieval for cancer research and reduce the burden of screening papers for clinical relevance.

OBJECTIVE

The primary objective of this research was to address the low-resolution issue of cancer literature classification due to the ambiguity of the existing journal-level classifier in order to support gaining high-relevance evidence for clinical consideration and all-sided results for literature retrieval.

METHODS

We trained a multilabel classifier with scalability for classifying the literature on cancer research directly at the publication level to assign proper content-derived labels based on the "Bidirectional Encoder Representation from Transformers (BERT) + X" model and obtain the best option for X. First, a corpus of 70,599 cancer publications retrieved from the Dimensions database was divided into a training and a testing set in a ratio of 7:3. Second, using the classification terminology of International Cancer Research Partnership cancer types, we compared the performance of classifiers developed using BERT and 5 classical deep learning models, such as the text recurrent neural network (TextRNN) and FastText, followed by metrics analysis.

RESULTS

After comparing various combined deep learning models, we obtained a classifier based on the optimal combination "BERT + TextRNN," with a precision of 93.09%, a recall of 87.75%, and an F1-score of 90.34%. Moreover, we quantified the distinctive characteristics in the text structure and multilabel distribution in order to generalize the model to other fields with similar characteristics.

CONCLUSIONS

The "BERT + TextRNN" model was trained for high-resolution classification of cancer literature at the publication level to support accurate retrieval and academic statistics. The model automatically assigns 1 or more labels to each cancer paper, as required. Quantitative comparison verified that the "BERT + TextRNN" model is the best fit for multilabel classification of cancer literature compared to other models. More data from diverse fields will be collected to testify the scalability and extensibility of the proposed model in the future.

Evaluation of disparities in perceived healthcare discrimination among BRCA1/2-positive women from medically underserved populations

The current study evaluated associations between disparities relating to race/ethnicity, poverty status, educational status, and odds of experiencing healthcare discrimination among women with BRCA1/2 mutations. We conducted a cross-sectional study of United States (US)-based women (18+ years) who have tested positive for BRCA1/2 mutations within the past 5 years and who identify with one or more medically underserved populations. 211 women were recruited from BRCA1/2-oriented support groups and completed an online survey. Adjusted odds ratios (aORs) and 95 percent confidence intervals (CIs) were estimated using multivariable logistic regression models for associations between race/ethnicity, poverty status, education, and perceived healthcare discrimination adjusting for covariates. 182 women were included (31.3 percent were cancer survivors). Most were NHW (67.2 percent) and younger than 50 years (83.2 percent). Racial/ethnic minorities were 2.6 times more likely to report receiving poorer service than NHW women (95 percent CI, 1.26-5.33, p = .01). Associations with poverty status, education, and healthcare discrimination outcomes were not statistically significant. Improving patient-provider interactions that can contribute to medical mistrust should become a priority for the care of high-risk US minority women with BRCA1/2 mutations.

In vivo assignment of methylmalonic acid in breast tissue using 2D MRS and relationship with breast density, menopausal status and cancer risk

BACKGROUND

Methylmalonic acid (MMA) is linked to progression and aggressiveness of tumours. A recent study showed that high levels of circulatory MMA directed genetic programs promoting cancer progression.

PURPOSE

To evaluate in vivo two-dimensional correlated spectroscopy (2D COSY) data from women at elevated risk of breast cancer to determine if resonances consistent with MMA are present, and if so to correlate levels with breast density, menopausal status and risk categories.

MATERIALS AND METHODS

With institutional review board approval, 106 women at elevated risk (mean age 47), including 46 participants at medium risk, 43 at high risk with no known mutation and 17 BRCA-mutation carriers, were recruited. Breast density was assessed using a T₂ sequence. A T₁ sequence was used to place the voxel for the 2D COSY data. Peak volumes were normalized to the methylene peak at (1.30, 1.30) ppm. Chi-squared and Mann-Whitney tests were used.

RESULTS

Two resonances are assigned on the diagonal at 3.15 ppm and 3.19 ppm consistent with and denoted MMA1 and MMA2 respectively. MMA1 and MMA2 increased in parallel with increased risk. BRCA-mutation carriers recorded an increase in mean MMA1 of 120% (p = 0.033) and MMA2 of 127% (p = 0.020) in comparison with participants with no known mutation. BRCA-mutation carriers with dense breasts recorded a significant increase in mean MMA1 of 137% (p = 0.002) and in mean MMA2 of 143% (p = 0.004) compared with BRCA-mutation participants with low-density breast tissue. MMA1 and MMA2 were higher in premenopausal women with dense breasts compared with those with low-density tissue. The highest values of MMA were recorded in BRCA-mutation carriers.

CONCLUSION

Two tentative assignments are made for MMA in breast tissue of women at elevated risk for cancer. BRCA-mutation carriers exhibited higher values of MMA than those with no known mutation. Premenopausal women with BRCA mutation and dense breasts recorded the highest levels of MMA compared with other categories.

Coping Self-Efficacy and Its Relationship with Psychological Morbidity after Genetic Test Result Disclosure: Results from Cancer-Unaffected BRCA1/2 Mutation Carriers

Women who are found to carry a BRCA1/2 pathogenic variant experience psychological distress due to an increased risk of breast and ovarian cancer. They may decide between different preventive options. In this secondary analysis of data collected alongside a larger randomized controlled trial, we are looking at 130 newly found BRCA1/2 pathogenic variant carriers and how their coping self-efficacy immediately after genetic test result disclosure is related to their psychological burden and status of preventive decision making. Participants received the Coping Self-Efficacy Scale, the Hospital Anxiety and Depression Scale, the Impact of Event Scale, the Decisional Conflict Scale, and the Stage of Decision-Making Scale after positive genetic test result disclosure. We found that women with higher coping self-efficacy showed fewer symptoms of anxiety or depression and were less affected by receiving the genetic test result in terms of post-traumatic stress. However, coping self-efficacy had no relationship with any decision-related criteria, such as decisional conflict or stage of decision making. This shows that despite its buffering capacity on psychological burden, possessing coping self-efficacy does not lead to more decisiveness in preference-sensitive decisions.

Prevalence and clinical implications of germline mutations among Jordanian patients with ovarian cancer. The Jordanian exploratory cancer genetics ( Jo‐ECAG ) ovarian study

BACKGROUND

Ovarian cancer is one of the most common gynecological malignancies. Due to the absence of effective screening methods, ovarian cancer is usually diagnosed at late stages. Patients with pathogenic and likely-pathogenic germline variants (PGVs) in BRCA1 or BRCA2 harbor elevated risk of developing both ovarian and breast cancers. Identifying PGVs may help in both cancer prevention and active disease treatment. Worldwide prevalence of PGVs varies and the matter is poorly addressed among Arab patients.

METHODS

Patients with epithelial ovarian, fallopian tube or primary peritoneal cancers were offered the universal 20 or 84-multi-gene panel testing as per standard guidelines. Cascade family screening was also offered to all first and second-degree relatives of PGV positive patients. Genetic testing was done at a referral lab using a next generation sequencing (NGS)-based platform.

RESULTS

During the study period, 152 patients, median age (range): 50 (18-79) years old, were tested. The majority (n = 100, 65.8%) had high-grade serous carcinoma, and 106 patients (69.7%) had metastatic disease at presentation. In total, 38 (25.0%) had PGVs, while 47 (30.9%) others had variants of uncertain significance (VUS). PGVs were mostly in BRCA1 (n = 21, 13.8%) and in BRCA2 (n = 12, 7.9%), while 6 (3.9%) others had PGVs in non-BRCA1/2 genes. PGV rates were significantly higher among 15 patients with a positive family history of ovarian cancer (60.0%, p = .022) and among 52 patients with a positive family history of breast cancer (40.4%, p = .017).

CONCLUSIONS

PGVs are common among Jordanian women with ovarian cancer, and mostly occur in BRCA1/2. Given its clinical impact on disease prevention and precision therapy, universal testing should be routinely offered.

Overview on population screening for carriers with germline BRCA mutation in China

Carriers with BRCA1/2 germline pathogenic variants are associated with a high risk of breast and ovarian cancers (also pancreatic and prostate cancers). While the spectrum on germline BRCA mutations among the Chinese population shows ethnic specificity, the identification of carriers with germline BRCA mutation before cancer onset is the most effective approach to protect them. This review focused on the current status of BRCA1/2 screening, the surveillance and prevention measures, and discussed the issues and potential impact of BRCA1/2 population screening in China. We conducted literature research on databases PubMed and Google Scholar, as well as Chinese databases CNKI and Wangfang Med Online database (up to 31 March 2022). Latest publications on germline BRCA1/2 prevalence, spectrum, genetic screening as well as carrier counseling, surveillance and prevention were captured where available. While overall 15,256 records were retrieved, 72 publications using germline BRCA1/2 testing were finally retained for further analyses. Germline BRCA1/2 mutations are common in Chinese patients with hereditary breast, ovarian, prostate and pancreatic cancers. Within previous studies, a unique BRCA mutation spectrum in China was revealed. Next-generation sequencing panel was considered as the most common method for BRCA1/2 screening. Regular surveillance and preventive surgeries were tailored to carriers with mutated-BRCA1/2. We recommend that all Chinese diagnosed with breast, ovarian, pancreatic or prostate cancers and also healthy family members, shall undergo BRCA1/2 gene test to provide risk assessment. Subsequently, timely preventive measures for mutation carriers are recommended after authentic genetic counseling.

Rates of Variants of Uncertain Significance Among Patients With Breast Cancer Undergoing Genetic Testing: Regional Perspectives

Purpose

Contrary to BRCA pathogenic variants, recommendations for management of variants of uncertain significance (VUS) are not clear and focus more on the patient’s family and personal history of cancer. Local and regional data on VUS are scarce. In this paper, we study patterns and frequency of VUS among breast cancer patients undergoing genetic testing.

Patients and Methods

Patients with breast cancer at high risk for pathogenic variants, as per the National Comprehensive Cancer Network (NCCN) guidelines, were tested at reference laboratories. Related surgical interventions were reviewed.

Results

Among a group of 1,197 patients with breast cancer who underwent genetic testing and counseling, 110 (9.2%) had VUS; most (n = 79, 71.8%) were in BRCA2. Median age (range) was 39 (25–66) years with 65 (59.1%) patients who were 40 years or younger at diagnosis. Among 103 patients with non-metastatic disease, 48 (46.6%) had breast-conserving surgery (BCS) while only 5 (4.9%) had bilateral mastectomies; all were due to bilateral disease and not prophylactic. VUS diagnosis was known prior to initial surgery in 34 (33.0%) patients; 11 (32.4%) of them had BCS only. Over the study period, only one VUS variant was upgraded to “likely positive.” The recent introduction of multiple-gene panel testing had resulted in a surge in VUS rate (22.2%) in genes other than BRCA1 or BRCA2, like PALB2, CHEK2, and ATM.

Conclusions

Rates of VUS are relatively high and increasing, mostly in non-BRCA1 or BRCA2, and this had no impact on the therapeutic or prophylactic surgical decisions. Adherence to guidelines is extremely important to avoid unnecessary procedures.

Federated analysis of BRCA1 and BRCA2 variation in a Japanese cohort

More than 40% of the germline variants in ClinVar today are variants of uncertain significance (VUSs). These variants remain unclassified in part because the patient-level data needed for their interpretation is siloed. Federated analysis can overcome this problem by "bringing the code to the data": analyzing the sensitive patient-level data computationally within its secure home institution and providing researchers with valuable insights from data that would not otherwise be accessible. We tested this principle with a federated analysis of breast cancer clinical data at RIKEN, derived from the BioBank Japan repository. We were able to analyze these data within RIKEN's secure computational framework without the need to transfer the data, gathering evidence for the interpretation of several variants. This exercise represents an approach to help realize the core charter of the Global Alliance for Genomics and Health (GA4GH): to responsibly share genomic data for the benefit of human health.

Development of decision aids for female BRCA1 and BRCA2 mutation carriers in Germany to support preference-sensitive decision-making

BACKGROUND

Women with pathogenic BRCA1 and BRCA2 mutations possess a high risk of developing breast and ovarian cancer. They face difficult choices when considering preventive options. This study presents the development process of the first decision aids to support this complex decision-making process in the German healthcare system.

METHODS

A six-step development process based on the International Patient Decision Aid Standards was used, including a systematic literature review of existing decision aids, a topical medical literature review, preparation of the decision aids, focus group discussions with women with BRCA1/2 mutations, internal and external reviews by clinical and self-help experts, and user tests. All reviews were followed by iterative revisions.

RESULTS

No existing decision aids were transferable to the German setting. The medical research revealed a need to develop separate decision aids for women with BRCA1/2 mutations (A) without a history of cancer (previvors) and (B) with a history of unilateral breast cancer (survivors). The focus group discussions confirmed a high level of approval for the decision aids from both target groups. Additionally, previvors requested more information on risk-reducing breast surgery, risk-reducing removal of both ovaries and Fallopian tubes, and psychological aspects; survivors especially wanted more information on breast cancer on the affected side (e.g. biological parameters, treatment, and risk of recurrence).

CONCLUSIONS

In a structured process, two target-group-specific DAs for previvors/survivors with BRCA1/2 mutations were developed to support decision-making on risk-adapted preventive options. These patient-oriented tools offer an important addition to existing specialist medical care in Germany.