Ductal carcinoma in situ of the breast: finding the balance between overtreatment and undertreatment.

Ductal carcinoma in situ (DCIS) accounts for 15-25% of all breast cancer diagnoses. Its prognosis is excellent overall, the main risk being the occurrence of local breast events, as most cases of DCIS do not progress to invasive cancer. Systematic screening has greatly increased the incidence of this non-obligate precursor of invasion, lending urgency to the need to identify DCIS that is prone to invasive progression and distinguish it from non-invasion-prone DCIS, as the latter can be overdiagnosed and therefore overtreated. Treatment strategies, including surgery, radiotherapy, and optional endocrine therapy, decrease the risk of local events, but have no effect on survival outcomes. Active surveillance is being evaluated as a possible new option for low-risk DCIS. Considerable efforts to decipher the biology of DCIS have led to a better understanding of the factors that determine its variable natural history. Given this variability, shared decision making regarding optimal, personalised treatment strategies is the most appropriate course of action. Well designed, risk-based de-escalation studies remain a major need in this field.

The impact of histologic subtype on primary site surgery in the management of metastatic lobular versus ductal breast cancer: a population based study from the National Cancer Database (NCDB).

PURPOSE: Primary site surgery for metastatic breast cancer improves local control but does not impact overall survival. Whether histologic subtype influences patient selection for surgery is unknown. Given differences in surgical management between early-stage lobular versus ductal disease, we evaluated the impact of histology on primary site surgery in patients with metastatic breast cancer. METHODS: The National Cancer Database (NCDB, 2010-2016) was queried for patients with stage IV HR-positive, HER2-negative invasive lobular carcinoma (ILC) and invasive ductal carcinoma (IDC). We compared clinicopathologic features, primary site surgery rates, and outcomes by histologic subtype. Multivariable Cox proportional hazard models with and without propensity score matching were used for overall survival (OS) analyses. RESULTS: In 25,294 patients, primary site surgery was slightly but significantly less common in the 6,123 patients with ILC compared to the 19,171 patients with IDC (26.9% versus 28.8%, p = 0.004). Those with ILC were less likely to receive chemotherapy (41.3% versus 47.4%, p < 0.0001) or radiotherapy (29.1% versus 37.9%, p < 0.0001), and had shorter OS. While mastectomy rates were similar, those with ILC who underwent lumpectomy had significantly higher positive margin rates (ILC 15.7% versus IDC 11.2%, p = 0.025). In both groups, the odds of undergoing surgery decreased over time, and were higher in younger patients with T2/T3 tumors and higher nodal burden. CONCLUSION: Lobular histology is associated with less primary site surgery, higher positive margin rates, less radiotherapy and chemotherapy, and shorter OS compared to those with HR-positive HER2-negative IDC. These findings support the need for ILC-specific data and treatment approaches in the setting of metastatic disease.

Menstrual Phase and Menopausal Status Classification of Benign Breast Tissue Using Hormone-Regulated Gene Expression and Histomorphology: A Validation Study.

BACKGROUND: The validation of breast cancer risk biomarkers in benign breast samples (BBS) is a long-sought goal, hampered by the fluctuation of gene and protein expression with menstrual phase (MP) and menopausal status (MS). Previously, we identified hormone-related gene expression and histomorphology parameters to classify BBS by MS/MP. We now evaluate both together, to validate our prior results. PATIENTS AND METHODS: BBS were obtained from consenting women (86 premenopausal, 55 postmenopausal) undergoing reduction mammoplasty (RM) or contralateral unaffected breast (CUB) mastectomy. MP/MS was defined using classical criteria for menstrual dates and hormone levels on the day of surgery. BBS gene expression was measured with reverse transcription quantitative polymerase chain reaction (RT-qPCR) for three luteal phase (LP) genes (TNFSF11, DIO2, MYBPC1) and four menopausal genes (PGR, GREB1, TIFF1, CCND1). Premenopausal samples were classified into LP or non-LP, using published histomorphology parameters. Logistic regression and receiver-operator curve analysis was performed to assess area under the curve (AUC) for prediction of MP/MS. RESULTS: In all 131 women, menopausal genes plus age > 50 years predicted true MS [AUC 0.93, 95% confidence interval (CI) 0.89, 0.97]. Among premenopausal women, high TNFSF11 expression distinguished non-LP from LP samples (AUC 0.80, 95% CI 0.70, 0.91); the addition of histomorphology improved the prediction nonsignificantly (AUC 0.87, 95% CI 0.78, 0.96). In premenopausal subsets, addition of histomorphology improved LP prediction in RM (AUC 0.95, 95% CI 0.87, 1.0), but not in CUB (0.84, 95% CI 0.72, 0.96). CONCLUSIONS: Expression of five-gene set accurately predicts menopausal status and menstrual phase in BBS, facilitating the development of breast cancer risk biomarkers using large, archived sample repositories.

NCCN Guidelines® Insights: Genetic/Familial High-Risk Assessment: Breast, Ovarian, and Pancreatic, Version 2.2024.

The NCCN Guidelines for Genetic/Familial High-Risk Assessment: Breast, Ovarian, and Pancreatic focus primarily on assessment of pathogenic/likely pathogenic (P/LP) variants associated with increased risk of breast, ovarian, pancreatic, and prostate cancer, including BRCA1, BRCA2, CDH1, PALB2, PTEN, and TP53, and recommended approaches to genetic counseling/testing and care strategies in individuals with these P/LP variants. These NCCN Guidelines Insights summarize important updates regarding: (1) a new section for transgender, nonbinary and gender diverse people who have a hereditary predisposition to cancer focused on risk reduction strategies for ovarian cancer, uterine cancer, prostate cancer, and breast cancer; and (2) testing criteria and management associated with TP53 P/LP variants and Li-Fraumeni syndrome.

Primary-Site Local Therapy for Patients with De Novo Metastatic Breast Cancer: An Educational Review.

BACKGROUND: Until 2001, the paradigm guiding the management of women with de novo metastatic breast cancer (dnMBC) stipulated that primary-site locoregional therapy (PSLT) did not alter the course of metastatic disease and was necessary only for palliation of symptoms. Since 2002, retrospective data have begun questioning this paradigm. However, selection biases driving an observed survival advantage associated with PSLT in dnMBC were quickly recognized and led to several randomized clinical trials (RCTs) addressing this question. METHODS AND RESULTS: Four published RCTs have since tested the value of PSLT added to systemic therapy (ST) or not, with overall survival (OS) as the primary end point. The results of three published trials show no OS benefit for the addition of PSLT: Indian Tata Memorial, U.S./Canada E2108, and Austrian POSYTIVE (although POSYTIVE did not reach full accrual). The fourth RCT (Turkey, MF07-01) shows an OS benefit for PSLT at 5 years (42 % vs 24 % in the ST arm; hazard ratio [HR], 0.66; 95 % confidence interval [CI], 0.49-0.88). However, the 5-year survival in the PSLT arm of MF07-01 is similar to that in both arms of E2108, suggesting that the worse survival in the ST arm of MF07-01 is a result of biologically worse disease (from imbalanced randomization). Locoregional control was improved by PSLT in all trials, but without improvement in quality of life. CONCLUSIONS: The current evidence fails to refute the 20th century paradigm guiding management of de novo metastatic breast cancer. Discussion continues regarding the survival value of PSLT for patients with bone-only disease or oligometastases, but unbiased evidence is lacking.

Social cognitive variables and physical activity during chemotherapy for breast cancer: An intensive longitudinal examination.

OBJECTIVE: Although physical activity is associated with better health outcomes in breast cancer survivors (BCS), activity often declines during cancer treatment. Social cognitive theory (SCT) constructs have been associated with physical activity in post-treatment BCS, but little is known about the relation between these constructs and physical activity during chemotherapy. METHODS: BCS (n = 67; Mage  = 48.6 [SD = 10.3]) undergoing chemotherapy wore accelerometers and completed prompts in the morning and at night assessing same-day and next-day exercise self-efficacy, physical and psychological outcome expectations, and goal-setting for 10 consecutive days (3 days pre-, day of, and 6 days post-chemotherapy dose) at three time points (beginning, middle, and end of chemotherapy). Separate mixed models assessed between- and within-person associations of each of the SCT constructs associations with same- and next-day moderate to vigorous physical activity (MVPA) and light physical activity (LPA), independently. RESULTS: Within-person differences in all SCT variables were statistically significantly related to same-day MVPA (p's < 0.001) and LPA (p's < 0.001). Every one-point increase in SCT construct related to an increase in MVPA ranging from (a) 3.70 (self-efficacy) to 8.02 (physical outcome expectations) minute increase in MVPA and (b) 12.72 (self-efficacy) to 20.38 (physical outcome expectations) increase in LPA that day. No same-day between-person effects nor any next-day effects were significant. CONCLUSION: MVPA and LPA were related to same-day within-person differences in SCT variables. Interventions targeted at increasing or mitigating chemotherapy-related declines in daily within-person changes in SCT constructs could help to increase physical activity among BCS during chemotherapy.

Using ecological momentary assessment to understand associations between daily physical activity and symptoms in breast cancer patients undergoing chemotherapy.

PURPOSE: Understanding real-time relationships between physical activity (PA) and symptoms during chemotherapy (CT) could have important implications for intervention. This study used ecological momentary assessment to examine the relationship between objective PA and symptoms during CT. METHODS: Breast cancers patients (n = 67; Mage = 48.6 (SD = 10.3)) participated in data collection at three time points during CT: beginning, middle, and end. At each time point, participants answered four prompts assessing symptoms and wore an accelerometer for 10 days (3 days pre-CT, day of CT, and 6 days post-CT). Multilevel linear regression models examined the between- and within-person associations between moderate to vigorous (MVPA) and light-intensity physical activity (LPA) and same and next-day symptom ratings controlling for covariates. RESULTS: On days when individuals engaged in more LPA or MVPA, separately, they reported improved affect, anxiety, fatigue, physical functioning (walking and activities of daily living), pain, and cognition that day (p < 0.001 for all). Findings were consistent for next-day symptom ratings with the exception that only previous day LPA was related to next-day fatigue and neither LPA nor MVPA were related to next-day cognition (p < 0.001 for all). No between-person effects were found. CONCLUSIONS: Within person higher than usual PA on a given day, regardless of intensity, is associated with improved symptoms ratings on the current and next day. IMPLICATIONS FOR CANCER SURVIVORS: Encouraging breast cancer patients undergoing CT to engage in daily PA could help manage CT-associated symptoms.

Deep learning for cancer type classification and driver gene identification.

BACKGROUND: Genetic information is becoming more readily available and is increasingly being used to predict patient cancer types as well as their subtypes. Most classification methods thus far utilize somatic mutations as independent features for classification and are limited by study power. We aim to develop a novel method to effectively explore the landscape of genetic variants, including germline variants, and small insertions and deletions for cancer type prediction. RESULTS: We proposed DeepCues, a deep learning model that utilizes convolutional neural networks to unbiasedly derive features from raw cancer DNA sequencing data for disease classification and relevant gene discovery. Using raw whole-exome sequencing as features, germline variants and somatic mutations, including insertions and deletions, were interactively amalgamated for feature generation and cancer prediction. We applied DeepCues to a dataset from TCGA to classify seven different types of major cancers and obtained an overall accuracy of 77.6%. We compared DeepCues to conventional methods and demonstrated a significant overall improvement (p < 0.001). Strikingly, using DeepCues, the top 20 breast cancer relevant genes we have identified, had a 40% overlap with the top 20 known breast cancer driver genes. CONCLUSION: Our results support DeepCues as a novel method to improve the representational resolution of DNA sequencings and its power in deriving features from raw sequences for cancer type prediction, as well as discovering new cancer relevant genes.

Progesterone receptor antagonists reverse stem cell expansion and the paracrine effectors of progesterone action in the mouse mammary gland.

BACKGROUND: The ovarian hormones estrogen and progesterone (EP) are implicated in breast cancer causation. A specific consequence of progesterone exposure is the expansion of the mammary stem cell (MSC) and luminal progenitor (LP) compartments. We hypothesized that this effect, and its molecular facilitators, could be abrogated by progesterone receptor (PR) antagonists administered in a mouse model. METHODS: Ovariectomized FVB mice were randomized to 14 days of treatment: sham, EP, EP + telapristone (EP + TPA), EP + mifepristone (EP + MFP). Mice were then sacrificed, mammary glands harvested, and mammary epithelial cell lineages separated by flow cytometry using cell surface markers. RNA from each lineage was sequenced and differential gene expression was analyzed using DESeq. Quantitative PCR was performed to confirm the candidate genes discovered in RNA seq. ANOVA with Tukey post hoc analysis was performed to compare relative expression. Alternative splicing events were examined using the rMATs multivariate analysis tool. RESULTS: Significant increases in the MSC and luminal mature (LM) cell fractions were observed following EP treatment compared to control (p < 0.01 and p < 0.05, respectively), whereas the LP fraction was significantly reduced (p < 0.05). These hormone-induced effects were reversed upon exposure to TPA and MFP (p < 0.01 for both). Gene Ontology analysis of RNA-sequencing data showed EP-induced enrichment of several pathways, with the largest effect on Wnt signaling in MSC, significantly repressed by PR inhibitors. In LP cells, significant induction of Wnt4 and Rankl, and Wnt pathway intermediates Lrp2 and Axin2 (confirmed by qRTPCR) were reversed by TPA and MFP (p < 0.0001). Downstream signaling intermediates of these pathways (Lrp5, Mmp7) showed similar effects. Expression of markers of epithelial-mesenchymal transition (Cdh1, Cdh3) and the induction of EMT regulators (Zeb1, Zeb2, Gli3, Snai1, and Ptch2) were significantly responsive to progesterone. EP treatment was associated with large-scale alternative splicing events, with an enrichment of motifs associated with Srsf, Esrp, and Rbfox families. Exon skipping was observed in Cdh1, Enah, and Brd4. CONCLUSIONS: PR inhibition reverses known tumorigenic pathways in the mammary gland and suppresses a previously unknown effect of progesterone on RNA splicing events. In total, our results strengthen the case for reconsideration of PR inhibitors for breast cancer prevention.

Preoperative Breast MRI for Newly Diagnosed Ductal Carcinoma in Situ: Imaging Features and Performance in a Multicenter Setting (ECOG-ACRIN E4112 Trial).

Background There are limited data from clinical trials describing preoperative MRI features and performance in the evaluation of mammographically detected ductal carcinoma in situ (DCIS). Purpose To report qualitative MRI features of DCIS, MRI performance in the identification of additional disease, and associations of imaging features with pathologic, genomic, and surgical outcomes from the Eastern Cooperative Oncology Group-American College of Radiology Imaging Network (ECOG-ACRIN) E4112 trial. Materials and Methods Secondary analyses of a multicenter prospective clinical trial from the ECOG-ACRIN Cancer Research Group included women with DCIS diagnosed with conventional imaging techniques (mammography and US), confirmed via core-needle biopsy (CNB), and enrolled between March 2015 and April 2016 who were candidates for wide local excision (WLE) based on conventional imaging and clinical examination results. DCIS MRI features and pathologic features from CNB and excision were recorded. Each woman without invasive upgrade of the index DCIS at WLE received a 12-gene DCIS score. MRI performance metrics were calculated. Associations of imaging features with invasive upgrade, dichotomized DCIS score (<39 vs ≥39), and single WLE success were estimated in uni- and multivariable analyses. Results Among 339 women (median age, 60 years; interquartile range, 51-66 years), most DCIS cases showed nonmass enhancement (NME) (195 of 339 [58%]) on MRI scans with larger median size than on mammograms (19 mm vs 12 mm; P < .001). Positive predictive value of MRI-prompted CNBs was 32% (21 of 66) (95% CI: 22, 44), yielding an additional cancer detection rate of 6.2% (21 of 339) (95% CI: 4.1, 9.3). MRI false-positive rate was 14.2% (45 of 318) (95% CI: 10.7, 18.4). No imaging features were associated with invasive upgrade or DCIS score (P = .05 to P = .95). Smaller size and focal NME distribution at MRI were linked to single WLE success (P < .001). Conclusion Preoperative MRI depicted ductal carcinoma in situ (DCIS) diagnosed with conventional imaging most commonly as nonmass enhancement, with larger median span than mammography, and additional cancer detection rate of 6.2%. MRI features of this subset of DCIS did not enable prediction of pathologic or genomic outcomes. Clinical trial registration no. NCT02352883 © RSNA, 2021 Online supplemental material is available for this article. See also the editorial by Kuhl in this issue. An earlier incorrect version of this article appeared online. This article was corrected on August 4, 2021.

High-Resolution Full-3D Specimen Imaging for Lumpectomy Margin Assessment in Breast Cancer.

BACKGROUND: Two-dimensional (2D) specimen radiography (SR) and tomosynthesis (DBT) for breast cancer yield data that lack high-depth resolution. A volumetric specimen imager (VSI) was developed to provide full-3D and thin-slice cross-sectional visualization at a 360° view angle. The purpose of this prospective trial was to compare VSI, 2D SR, and DBT interpretation of lumpectomy margin status with the final pathologic margin status of breast lumpectomy specimens. METHODS: The study enrolled 200 cases from two institutions. After standard imaging and interpretation was performed, the main lumpectomy specimen was imaged with the VSI device. Image interpretation was performed by three radiologists after surgery based on VSI, 2D SR, and DBT. A receiver operating characteristic (ROC) curve was created for each method. The area under the curve (AUC) was computed to characterize the performance of the imaging method interpreted by each user. RESULTS: From 200 lesions, 1200 margins were interpreted. The AUC values of VSI for the three radiologists were respectively 0.91, 0.90, and 0.94, showing relative improvement over the AUCs of 2D SR by 54%, 13%, and 40% and DBT by 32% and 11%, respectively. The VSI has sensitivity ranging from 91 to 94%, specificity ranging from 81 to 85%, a positive predictive value ranging from 25 to 30%, and a negative predicative value of 99%. CONCLUSIONS: The ROC curves of the VSI were higher than those of the other specimen imaging methods. Full-3D specimen imaging can improve the correlation between the main lumpectomy specimen margin status and surgical pathology. The findings from this study suggest that using the VSI device for intraoperative margin assessment could further reduce the re-excision rates for women with malignant disease.

Genetic/Familial High-Risk Assessment: Breast, Ovarian, and Pancreatic, Version 2.2021, NCCN Clinical Practice Guidelines in Oncology.

The NCCN Guidelines for Genetic/Familial High-Risk Assessment: Breast, Ovarian, and Pancreatic focus primarily on assessment of pathogenic or likely pathogenic variants associated with increased risk of breast, ovarian, and pancreatic cancer and recommended approaches to genetic testing/counseling and management strategies in individuals with these pathogenic or likely pathogenic variants. This manuscript focuses on cancer risk and risk management for BRCA-related breast/ovarian cancer syndrome and Li-Fraumeni syndrome. Carriers of a BRCA1/2 pathogenic or likely pathogenic variant have an excessive risk for both breast and ovarian cancer that warrants consideration of more intensive screening and preventive strategies. There is also evidence that risks of prostate cancer and pancreatic cancer are elevated in these carriers. Li-Fraumeni syndrome is a highly penetrant cancer syndrome associated with a high lifetime risk for cancer, including soft tissue sarcomas, osteosarcomas, premenopausal breast cancer, colon cancer, gastric cancer, adrenocortical carcinoma, and brain tumors.

NCCN Guidelines Insights: Genetic/Familial High-Risk Assessment: Breast, Ovarian, and Pancreatic, Version 1.2020.

The NCCN Guidelines for Genetic/Familial High-Risk Assessment: Breast, Ovarian, and Pancreatic provide recommendations for genetic testing and counseling for hereditary cancer syndromes, and risk management recommendations for patients who are diagnosed with syndromes associated with an increased risk of these cancers. The NCCN panel meets at least annually to review comments, examine relevant new data, and reevaluate and update recommendations. These NCCN Guidelines Insights summarize the panel's discussion and most recent recommendations regarding criteria for high-penetrance genes associated with breast and ovarian cancer beyond BRCA1/2, pancreas screening and genes associated with pancreatic cancer, genetic testing for the purpose of systemic therapy decision-making, and testing for people with Ashkenazi Jewish ancestry.

Breast cancer risk assessment and management programs: A practical guide.

Breast cancer risk assessment continues to evolve as emerging knowledge of breast cancer risk drivers and modifiers enables better identification of high-risk women who may benefit from increased screening or targeted risk-reduction protocols. The ongoing development of breast cancer Risk Assessment and Management Programs (RAMPs) presents an opportunity to decrease breast cancer disease incidence with evidence-based interventions. The goal of this review was to provide a practical guide for providers seeking to establish or update a breast cancer risk assessment and management program. We outline genetic/familial, personal, reproductive, and lifestyle-related factors while discussing the incorporation of risk modeling for precise risk estimate personalization. We further describe the process for determining a risk management plan: information gathering, generation of a risk profile, and articulation and implementation of risk reduction. We also include an overview of clinical workflows in breast cancer management programs and underlines the logistics of establishing a program as well as general principles for guiding the formulation of an individualized risk management plan. We discuss practical considerations, such as clinic structure and operation, allocation of resources, and patient education. Other critical aspects of program design, including identification of the target population, delineation of the core components of the clinical experience, definition of provider roles, description of referral mechanisms, and the launching of a marketing plan are also addressed. The process of risk assessment is both anxiety-provoking and empowering for women at increased risk. New knowledge has enabled strategies to both understand the risk and control it through evidence-based risk management. These benefits can now be realized by an increasing number of unaffected, high-risk patients collaborating with risk management practitioners. Continuation of these efforts will lead to further progress in both risk stratification and risk management of women at elevated breast cancer risk in the near future.

BRCA1 mutation influences progesterone response in human benign mammary organoids.

BACKGROUND: Women, who carry a germline BRCA1 gene mutation, have a markedly increased risk of developing breast cancer during their lifetime. While BRCA1 carriers frequently develop triple-negative, basal-like, aggressive breast tumors, hormone signaling is important in the genesis of BRCA1 mutant breast cancers. We investigated the hormone response in BRCA1-mutated benign breast tissue using an in vitro organoid system. METHODS: Scaffold-free, multicellular human breast organoids generated from benign breast tissues from non-carrier or BRCA1 mutation carriers were treated in vitro with a stepwise menstrual cycle hormone regimen of estradiol (E2) and progesterone (P4) over the course of 28 days. RESULTS: Breast organoids exhibited characteristics of the native breast tissue, including expression of hormone receptors, collagen production, and markers of luminal and basal epithelium, and stromal fibroblasts. RNA sequencing analysis revealed distinct gene expression in response to hormone treatment in the non-carrier and BRCA1-mutated organoids. The selective progesterone receptor modulator, telapristone acetate (TPA), was used to identify specifically PR regulated genes. Specifically, extracellular matrix organization genes were regulated by E2+P4+TPA in the BRCA1-mutated organoids but not in the non-carrier organoids. In contrast, in the non-carrier organoids, known PR target genes such as the cell cycle genes were inhibited by TPA. CONCLUSIONS: These data show that BRCA1 mutation influences hormone response and in particular PR activity which differs from that of non-carrier organoids. Our organoid model system revealed important insights into the role of PR in BRCA1-mutated benign breast cells and the critical paracrine actions that modify hormone receptor (HR)-negative cells. Further analysis of the molecular mechanism of BRCA1 and PR crosstalk is warranted using this model system.

What does risk of future cancer mean to breast cancer patients?

PURPOSE: Newly diagnosed breast cancer patients greatly overestimate their risk of developing contralateral breast cancer (CBC). Better understanding of patient conceptions of risk would facilitate doctor-patient communication and surgical decision making. In this mixed methods study, we prospectively examined breast cancer patients' perceived risk of future cancer and the reported factors that drove their risk perceptions. METHODS: Women age 21-60 diagnosed with breast cancer without a BRCA mutation or known distant metastases completed a study interview between surgical consult and surgical treatment. Participants completed a 12-item Perceived Risk Questionnaire, which assessed 10-year and lifetime risks of ipsilateral local recurrence, CBC, and distant recurrence. Patients provided qualitative explanations for their answers. RESULTS: Sixty-three patients completed study interviews (mean age 50.3). Participants were primarily White (85.7%) and 90.5% had attended college. Patients estimated their 10-year risk of CBC as 22.0%, nearly 4 times the established 10-year risk. Women attributed their risk perceptions to "gut feelings" about future cancer, even when women knew those feelings contradicted medically established risk. Perceptions of risk also reflected beliefs that cancer is random and that risk for local recurrence, CBC, and distant recurrence are the same. CONCLUSIONS: Our findings point to the need for novel ways of presenting factual information regarding both risk of recurrence and of new primary cancers, as well as the necessity of acknowledging cognitive and affective processes many patients use when conceptualizing risk. By differentiating women's intuitive feelings about risk from their knowledge of medically estimated risk, doctors can enhance informed decision making.

Cancer classification and pathway discovery using non-negative matrix factorization.

OBJECTIVES: Extracting genetic information from a full range of sequencing data is important for understanding disease. We propose a novel method to effectively explore the landscape of genetic mutations and aggregate them to predict cancer type. DESIGN: We applied non-smooth non-negative matrix factorization (nsNMF) and support vector machine (SVM) to utilize the full range of sequencing data, aiming to better aggregate genetic mutations and improve their power to predict disease type. More specifically, we introduce a novel classifier to distinguish cancer types using somatic mutations obtained from whole-exome sequencing data. Mutations were identified from multiple cancers and scored using SIFT, PP2, and CADD, and collapsed at the individual gene level. nsNMF was then applied to reduce dimensionality and obtain coefficient and basis matrices. A feature matrix was derived from the obtained matrices to train a classifier for cancer type classification with the SVM model. RESULTS: We have demonstrated that the classifier was able to distinguish four cancer types with reasonable accuracy. In five-fold cross-validations using mutation counts as features, the average prediction accuracy was 80% (SEM = 0.1%), significantly outperforming baselines and outperforming models using mutation scores as features. CONCLUSION: Using the factor matrices derived from the nsNMF, we identified multiple genes and pathways that are significantly associated with each cancer type. This study presents a generic and complete pipeline to study the associations between somatic mutations and cancers. The proposed method can be adapted to other studies for disease status classification and pathway discovery.

Feasibility and acceptability of intensive longitudinal data collection of activity and patient-reported outcomes during chemotherapy for breast cancer.

PURPOSE: Ecological momentary assessment (EMA) may help us better understand biopsychosocial determinants and outcomes of physical activity during chemotherapy, but may be burdensome for patients. The purpose of this study was to determine the feasibility and acceptability of using EMA to assess activity, symptoms, and motivation among early-stage breast cancer patients undergoing chemotherapy. METHODS: Women were instructed to wear an accelerometer 24/7 (hip during day and wrist overnight). Text message prompts were sent 4 times/day concerning patient-reported symptoms and motivational factors for 10 consecutive days (3 days pre-, day of, and 6 days post-chemotherapy dose). These measures occurred at the beginning, middle, and end of a full course of chemotherapy. At study conclusion, participants reported on perceived study acceptability, burden, and reactivity. RESULTS: Of the 75 women who consented to participate, 63 (84%) completed all 3 assessment time points. Participants responded to 86% of total text prompts and had valid accelerometer data on 82% of study days. Compliance was similar across all time points. The majority (78%) rated their study experience as positive; 100% were confident in their ability to use study technology. Reactivity varied with 27% indicating answering symptom questions did not affect how they felt and 44% and 68% indicated answering questions and wearing the accelerometer, respectively, made them want to increase activity. CONCLUSIONS: Findings indicate EMA methods are feasible for breast cancer patients undergoing chemotherapy. EMA may help us better understand the biopsychosocial processes underlying breast cancer patients' activity in the context of daily life.

Cyberlindnera fabianii fungaemia outbreak in preterm neonates in Kuwait and literature review.

BACKGROUND: Cyberlindnera fabianii has rarely been reported as a human pathogen. Here, we describe an outbreak of C. fabianii fungaemia involving 10 preterm neonates during a seven-month period in Kuwait and review the published reports. METHODS: Blood cultures were processed, and yeast isolates were initially identified by ID 32 C and/or VITEK 2. Molecular identification was done by PCR sequencing of internally transcribed spacer (ITS) region and D1/D2 domains of rDNA. Fingerprinting was performed with microsatellite-based and minisatellite-based primers to examine genetic relatedness among the isolates. Antifungal susceptibility testing of the isolates was done by Etest. FINDINGS: All infected neonates were preterm, received prior antibiotics and had an intravascular catheter in place. All bloodstream isolates were initially identified as Candida utilis by ID 32 C and/or VITEK 2 and showed reduced susceptibility to triazoles. PCR sequencing of rDNA identified all isolates as Cyberlindnera fabianii. Fingerprinting studies yielded identical patterns indicating clonality. One neonate died before treatment, one died during treatment, and eight neonates survived treatment with amphotericin B with/without fluconazole or caspofungin. Source of infection remained unknown despite surveillance cultures. CONCLUSION: The outbreak highlights emergence of C. fabianii as a neonatal pathogen and reinforces importance of molecular methods in its accurate identification.

Clinical Trials for Ductal Carcinoma In Situ of the Breast.

Ductal carcinoma in situ (DCIS) of the breast is a non-obligatory precursor to invasive breast carcinoma, with a variable natural history and biological potential for progression to invasive disease. Over the past 30 years, clinical trials have applied the therapeutic principles used for invasive carcinoma to treat DCIS (surgery, with or without breast radiotherapy, and post-operative endocrine therapy), with excellent survival outcomes, and in-breast recurrence rates that range from 0.5 to 1% annually. However, half of such recurrences are again in-situ lesions, and intensive therapy is likely not necessary for all patients. Current clinical research is focused on a better characterization of the potential of individual lesions to progress to invasive disease, and to identify women who would do well with lesser treatment. Three ongoing trials in the United States and Europe randomize women to active surveillance (with or without endocrine therapy) versus usual treatment with surgery and radiotherapy. The use of pre-operative endocrine therapy has been evaluated in a recently completed trial of letrozole use in postmenopausal women with DCIS; and in on-going trials of tamoxifen, used either orally, or as a 4-hydroxytamoxifen gel formulation for application to the breast skin. This review summaries the major past and current clinical trials of DCIS, and the likely trajectories of DCIS management in the near future.