Radiomic and deep learning characterization of breast parenchyma on full field digital mammograms and specimen radiographs: A pilot study of a potential cancer field effect

Purpose: In women with biopsy-proven breast cancer, histologically normal areas of the parenchyma have shown molecular similarity to the tumor, supporting a potential cancer field effect. The purpose of this work was to investigate relationships of human-engineered radiomic and deep learning features between regions across the breast in mammographic parenchymal patterns and specimen radiographs. Approach: This study included mammograms from 74 patients with at least 1 identified malignant tumor, of whom 32 also possessed intraoperative radiographs of mastectomy specimens. Mammograms were acquired with a Hologic system and specimen radiographs were acquired with a Fujifilm imaging system. All images were retrospectively collected under an Institutional Review Board-approved protocol. Regions of interest (ROI) of 128 × 128 pixels were selected from three regions: within the identified tumor, near to the tumor, and far from the tumor. Radiographic texture analysis was used to extract 45 radiomic features and transfer learning was used to extract 20 deep learning features in each region. Kendall’s Tau-b and Pearson correlation tests were performed to assess relationships between features in each region. Results: Statistically significant correlations in select subgroups of features with tumor, near to the tumor, and far from the tumor ROI regions were identified in both mammograms and specimen radiographs. Intensity-based features were found to show significant correlations with ROI regions across both modalities. Conclusions: Results support our hypothesis of a potential cancer field effect, accessible radiographically, across tumor and non-tumor regions, thus indicating the potential for computerized analysis of mammographic parenchymal patterns to predict breast cancer risk.</p

Inflammatory breast cancer appearance at presentation is associated with overall survival

Background: Inflammatory breast cancer (IBC) is a clinical diagnosis. Here, we examined the association of a "classic" triad of clinical signs, swollen involved breast, nipple change, and diffuse skin change, with overall survival (OS). Method: Breast medical photographs from patients enrolled on a prospective IBC registry were scored by two independent reviewers as classic (triad above), not classic, and difficult to assign. Chi-squared test, Fisher's exact test, and Wilcoxon rank-sum test were used to assess differences between patient groups. Kaplan-Meier estimates and the log-rank test and Cox proportional hazard regression were used to assess the OS. Results: We analyzed 245 IBC patients with median age 54 (range 26-81), M0 versus M1 status (157 and 88 patients, respectively). The classic triad was significantly associated with smoking, post-menopausal status, and metastatic disease at presentation (p = 0.002, 0.013, and 0.035, respectively). Ten-year actuarial OS for not classic and difficult to assign were not significantly different and were grouped for further analyses. Ten-year OS was 29.7% among patients with the classic sign triad versus 57.2% for non-classic (p < 0.0001). The multivariate Cox regression model adjusting for clinical staging (p < 0.0001) and TNBC status (<0.0001) demonstrated classic presentation score significantly associated with poorer OS time (HR 2.6, 95% CI 1.7-3.9, p < 0.0001). Conclusions: A triad of classic IBC signs independently predicted OS in patients diagnosed with IBC. Further work is warranted to understand the biology related to clinical signs and further extend the understanding of physical examination findings in IBC

Chimeric RNAs reveal putative neoantigen peptides for developing tumor vaccines for breast cancer

IntroductionWe present here a strategy to identify immunogenic neoantigen candidates from unique amino acid sequences at the junctions of fusion proteins which can serve as targets in the development of tumor vaccines for the treatment of breastcancer.MethodWe mined the sequence reads of breast tumor tissue that are usually discarded as discordant paired-end reads and discovered cancer specific fusion transcripts using tissue from cancer free controls as reference. Binding affinity predictions of novel peptide sequences crossing the fusion junction were analyzed by the MHC Class I binding predictor, MHCnuggets. CD8+ T cell responses against the 15 peptides were assessed through in vitro Enzyme Linked Immunospot (ELISpot).ResultsWe uncovered 20 novel fusion transcripts from 75 breast tumors of 3 subtypes: TNBC, HER2+, and HR+. Of these, the NSFP1-LRRC37A2 fusion transcript was selected for further study. The 3833 bp chimeric RNA predicted by the consensus fusion junction sequence is consistent with a read-through transcription of the 5’-gene NSFP1-Pseudo gene NSFP1 (NSFtruncation at exon 12/13) followed by trans-splicing to connect withLRRC37A2 located immediately 3’ through exon 1/2. A total of 15 different 8-mer neoantigen peptides discovered from the NSFP1 and LRRC37A2 truncations were predicted to bind to a total of 35 unique MHC class I alleles with a binding affinity of IC50&lt;500nM.); 1 of which elicited a robust immune response.ConclusionOur data provides a framework to identify immunogenic neoantigen candidates from fusion transcripts and suggests a potential vaccine strategy to target the immunogenic neopeptides in patients with tumors carrying the NSFP1-LRRC37A2 fusion

Rapid method for determination of DNA repair capacity in human peripheral blood lymphocytes amongst smokers

<p>Abstract</p> <p>Background</p> <p>DNA repair capacity is an important determinant of susceptibility to cancer. The hOGG1 enzyme is crucial for repairing the 8-oxoguanine lesion that occurs either as a byproduct of oxidative metabolism or as a result of exogenous sources such as exposure to cigarette smoke. It has been previously reported that smokers with low hOGG1 activity had significantly higher risk of developing lung cancer as compared to smokers with high hOGG1 activity.</p> <p>Methods</p> <p>In the current study we elucidate the association between plasma levels of 8-OHdG and the OGG1 repair capacity. We used the commercially available 8-OHdG ELISA (enzyme-linked immunosorbent assay), the Comet assay/FLARE hOGG1 (Fragment Length Analysis by Repair Enzymes) assay for quantification of the levels of 8-OHdG and measured the constitutive, induced and unrepaired residual damage, respectively. We compared the DNA repair capacity in peripheral blood lymphocytes following H₂O₂exposure in 30 lung cancer patients, 30 non-, 30 former and 30 current smoker controls matched by age and gender.</p> <p>Results</p> <p>Our results show that lung cancer cases and current smoker controls have similar levels of 8-OHdG lesions that are significantly higher compared to the non-smokers controls. However, lung cancer cases showed significantly poorer repair capacity compared to all controls tested, including the current smokers controls. After adjustment for age, gender and family history of smoking-related cancer using linear regression, we observed a 5-fold increase in risk of lung cancer associated with high levels of residual damage/reduced repair capacity. Reduced OGG1 activity could be expected to be a risk factor in other smoking-related cancers.</p> <p>Conclusion</p> <p>Our study shows that the Comet/FLARE assay is a relatively rapid and useful method for determination of DNA repair capacity. Using this assay we could identify individuals with high levels of residual damage and hence poor repair capacity who would be good candidates for intensive follow-up and screening.</p

Cytokinesis-blocked micronucleus assay and cancer risk assessment

Cancer risk assessment is a multidisciplinary process that goes beyond the scope of classical epidemiology to include the biological evaluation of individual differences to carcinogenic exposures. The inclusion of genetic biomarkers such as mutagen sensitivity or cytokinesis-blocked micronucleus (CBMN) assay end points into risk assessment models allows for a more comprehensive determination of cancer risk that includes known demographic (age and gender), lifestyle exposures (smoking and alcohol) and occupational or environmental exposures. The CBMN assay generates multiple correlated end points that, after applying data reduction methods, could be combined into a summary measure that incorporates information from each individual variable into a single (or possible multiple, uncorrelated) measure of risk. In this article, we highlight the use of the CBMN assay in radiosensitivity assessment. In addition, we demonstrate the potential use of the combined summary measures in cancer risk assessment as a result of chronic exposure to tobacco carcinogens. The simplicity, rapidity and sensitivity of the CBMN assay not only make it a valuable tool for screening but also the multiple end points simultaneously generated lead to a better understanding of the underlying mechanisms involved in the carcinogenic process that could in turn substantially improve risk predictions

Genetic polymorphism and their contribution to cancer susceptibility

Since the majority of chemical carcinogens are not capable of causing hazardous effects per se, the metabolism of these compounds is a crucial part of the initial host response to the environmental exposure. Disturbances in the balance between activation and detoxification may thus explain the individual variations in responses to exposures to carcinogens. The amount of the ultimate carcinogen produced depends on the action of competing activation and detoxification pathways involving cytochrome P450 and glutathione-S-transferases enzymes

Genetic polymorphism and their contribution to cancer susceptibility

Since the majority of chemical carcinogens are not capable of causing hazardous effects per se, the metabolism of these compounds is a crucial part of the initial host response to the environmental exposure. Disturbances in the balance between activation and detoxification may thus explain the individual variations in responses to exposures to carcinogens. The amount of the ultimate carcinogen produced depends on the action of competing activation and detoxification pathways involving cytochrome P450 and glutathione-S-transferases enzymes

Polimorfismo genético e sua contribuição na susceptibilidade ao câncer

Uma vez que a maioria dos carcinogênicos químicos não é capaz de causar efeitos danosos per se, o metabolismo desses compostos é a parte crucial da resposta inicial à exposição ambiental. Os distúrbios causados no balanço entre os processos de ativação e destoxificação podem, assim, explicar as variações individuais em resposta à exposição aos carcinogênicos. A quantidade de compostos carcinogênicos finais produzida depende da ação competitiva entre os passos de ativação e destoxificação, envolvendo as enzimas do citocromo P450 e das S-glutatião transferases.Since the majority of chemical carcinogens are not capable of causing hazardous effects per se, the metabolism of these compounds is a crucial part of the initial host response to the environmental exposure. Disturbances in the balance between activation and detoxification may thus explain the individual variations in responses to exposures to carcinogens. The amount of the ultimate carcinogen produced depends on the action of competing activation and detoxification pathways involving cytochrome P450 and glutathione-S-transferases enzymes