Exploratory analysis using machine learning to predict for chest wall pain in patients with stage I non-small-cell lung cancer treated with stereotactic body radiation therapy.

Background and purposeChest wall toxicity is observed after stereotactic body radiation therapy (SBRT) for peripherally located lung tumors. We utilize machine learning algorithms to identify toxicity predictors to develop dose-volume constraints.Materials and methodsTwenty-five patient, tumor, and dosimetric features were recorded for 197 consecutive patients with Stage I NSCLC treated with SBRT, 11 of whom (5.6%) developed CTCAEv4 grade ≥2 chest wall pain. Decision tree modeling was used to determine chest wall syndrome (CWS) thresholds for individual features. Significant features were determined using independent multivariate methods. These methods incorporate out-of-bag estimation using Random forests (RF) and bootstrapping (100 iterations) using decision trees.ResultsUnivariate analysis identified rib dose to 1 cc < 4000 cGy (P = 0.01), chest wall dose to 30 cc < 1900 cGy (P = 0.035), rib Dmax < 5100 cGy (P = 0.05) and lung dose to 1000 cc < 70 cGy (P = 0.039) to be statistically significant thresholds for avoiding CWS. Subsequent multivariate analysis confirmed the importance of rib dose to 1 cc, chest wall dose to 30 cc, and rib Dmax. Using learning-curve experiments, the dataset proved to be self-consistent and provides a realistic model for CWS analysis.ConclusionsUsing machine learning algorithms in this first of its kind study, we identify robust features and cutoffs predictive for the rare clinical event of CWS. Additional data in planned subsequent multicenter studies will help increase the accuracy of multivariate analysis

Chronic pharmacologic inhibition of EGFR leads to cardiac dysfunction in C57BL/6J mice

Molecule-targeted therapies like those against the epidermal growth factor receptor (EGFR) are becoming widely used in the oncology clinic. With improvements in treatment efficacy, many cancers are being treated as chronic diseases, with patients having prolonged exposure to several therapies that were previously only given acutely. The consequence of chronic suppression of EGFR activity may lead to unexpected toxicities like altered cardiac physiology, a common organ site for adverse drug effects. To explore this possibility, we treated C57BL/6J (B6) mice with two EGFR small molecule tyrosine kinase inhibitors (TKIs), irreversible EKB-569 and reversible AG-1478, orally for three months. In B6 female mice, chronic exposure to both TKIs depressed body weight gain and caused significant changes in left ventricular (LV) wall thickness and cardiac function. No significant differences were observed in heart weight or cardiomyocyte size but histological analysis revealed an increase in fibrosis and in the numbers of TUNEL-positive cells in the hearts from treated female mice. Consistent with histological results, LV apoptotic gene expression was altered, with significant downregulation of the anti-apoptotic gene Bcl2l1. Although there were no significant differences in any of these endpoints in treated male mice, suggesting sex may influence susceptibility to TKI mediated toxicity, the LVs of treated male mice had significant upregulation of Egf, Erbb2 and Nppb over controls. Taken together, these data suggest that chronic dietary exposure to TKIs may result in pathological and physiological changes in the heart

Basal-like Breast cancer DNA copy number losses identify genes involved in genomic instability, response to therapy, and patient survival

Breast cancer is a heterogeneous disease with known expression-defined tumor subtypes. DNA copy number studies have suggested that tumors within gene expression subtypes share similar DNA Copy number aberrations (CNA) and that CNA can be used to further sub-divide expression classes. To gain further insights into the etiologies of the intrinsic subtypes, we classified tumors according to gene expression subtype and next identified subtype-associated CNA using a novel method called SWITCHdna, using a training set of 180 tumors and a validation set of 359 tumors. Fisher’s exact tests, Chi-square approximations, and Wilcoxon rank-sum tests were performed to evaluate differences in CNA by subtype. To assess the functional significance of loss of a specific chromosomal region, individual genes were knocked down by shRNA and drug sensitivity, and DNA repair foci assays performed. Most tumor subtypes exhibited specific CNA. The Basal-like subtype was the most distinct with common losses of the regions containing RB1, BRCA1, INPP4B, and the greatest overall genomic instability. One Basal-like subtype-associated CNA was loss of 5q11–35, which contains at least three genes important for BRCA1-dependent DNA repair (RAD17, RAD50, and RAP80); these genes were predominantly lost as a pair, or all three simultaneously. Loss of two or three of these genes was associated with significantly increased genomic instability and poor patient survival. RNAi knockdown of RAD17, or RAD17/RAD50, in immortalized human mammary epithelial cell lines caused increased sensitivity to a PARP inhibitor and carboplatin, and inhibited BRCA1 foci formation in response to DNA damage. These data suggest a possible genetic cause for genomic instability in Basal-like breast cancers and a biological rationale for the use of DNA repair inhibitor related therapeutics in this breast cancer subtype.Electronic supplementary materialThe online version of this article (doi:10.1007/s10549-011-1846-y) contains supplementary material, which is available to authorized users

Women with endometriosis have higher comorbidities: Analysis of domestic data in Taiwan

AbstractEndometriosis, defined by the presence of viable extrauterine endometrial glands and stroma, can grow or bleed cyclically, and possesses characteristics including a destructive, invasive, and metastatic nature. Since endometriosis may result in pelvic inflammation, adhesion, chronic pain, and infertility, and can progress to biologically malignant tumors, it is a long-term major health issue in women of reproductive age. In this review, we analyze the Taiwan domestic research addressing associations between endometriosis and other diseases. Concerning malignant tumors, we identified four studies on the links between endometriosis and ovarian cancer, one on breast cancer, two on endometrial cancer, one on colorectal cancer, and one on other malignancies, as well as one on associations between endometriosis and irritable bowel syndrome, one on links with migraine headache, three on links with pelvic inflammatory diseases, four on links with infertility, four on links with obesity, four on links with chronic liver disease, four on links with rheumatoid arthritis, four on links with chronic renal disease, five on links with diabetes mellitus, and five on links with cardiovascular diseases (hypertension, hyperlipidemia, etc.). The data available to date support that women with endometriosis might be at risk of some chronic illnesses and certain malignancies, although we consider the evidence for some comorbidities to be of low quality, for example, the association between colon cancer and adenomyosis/endometriosis. We still believe that the risk of comorbidity might be higher in women with endometriosis than that we supposed before. More research is needed to determine whether women with endometriosis are really at risk of these comorbidities

Examination of the BRCA1-dependent DNA repair pathway in basal-like breast cancers

Human breast cancer is a diverse disease, exhibiting variety in morphology, natural history, and therapeutic response. Multiple studies have shown that breast tumors can be segregated into distinct subtypes, characterized by similarities in the genes they express. One subtype, called basal-like breast tumors (BBT), represents 10-20% of breast cancer diagnoses and is typically associated with poor outcomes. Our work has shown that BBT occurs with significantly higher frequency in women with germline mutations in breast cancer 1 (BRCA1). Given the link between BRCA1-germline mutations and BBT, we proposed to determine whether the BRCA1-dependent DNA repair pathway is deficient during sporadic BBT formation. Our initial step was to identify BBT specific regions of aberration and determine if they affected important genetic pathways. One region located on chromosome 5q contained multiple BRCA1-dependent repair pathway genes. These genes exhibited frequent co-associated loss with each other and with other cancer relevant genes. Exogenous disruption of these genes in normal breast epithelial cell lines increased sensitivity to DNA damage and impaired BRCA1 localization and function. We further characterized the genomic instability aspect of BBT by examining a previously undetectable form of genomic aberration we termed micro-aberrations. These small-scale genomic changes (<5kb in some cases) are detectable using a high-resolution tiling array. We found these events were functional, relevant for survival, preferentially located in the promoter regions of cell cycle genes, and appear most frequently in BBT. Lastly, we examined BBT-specific loss of the tumor suppressor INPP4B. We found that DNA, RNA, and protein expression of INPP4B are highly correlated with BBT and that it functions as an excellent marker of this subtype as well as predicting survival and response to therapy. It is critical to gain a greater understanding of BBT function as BBT poses a significant challenge to the US health care system; if BBT were to be treated as a unique disease separate from other breast cancers, it would represent the fourth leading cause of cancer deaths among women. My work here describes newly discovered functional basal-specific aberrations that explain much of the biology of BBT

Micro-Scale Genomic DNA Copy Number Aberrations as Another Means of Mutagenesis in Breast Cancer

<div><h3>Introduction</h3><p>In breast cancer, the basal-like subtype has high levels of genomic instability relative to other breast cancer subtypes with many basal-like-specific regions of aberration. There is evidence that this genomic instability extends to smaller scale genomic aberrations, as shown by a previously described micro-deletion event in the <em>PTEN</em> gene in the Basal-like SUM149 breast cancer cell line.</p> <h3>Methods</h3><p>We sought to identify if small regions of genomic DNA copy number changes exist by using a high density, gene-centric Comparative Genomic Hybridizations (CGH) array on cell lines and primary tumors. A custom tiling array for CGH (244,000 probes, 200 bp tiling resolution) was created to identify small regions of genomic change, which was focused on previously identified basal-like-specific, and general cancer genes. Tumor genomic DNA from 94 patients and 2 breast cancer cell lines was labeled and hybridized to these arrays. Aberrations were called using SWITCHdna and the smallest 25% of SWITCHdna-defined genomic segments were called micro-aberrations (<64 contiguous probes, ∼ 15 kb).</p> <h3>Results</h3><p>Our data showed that primary tumor breast cancer genomes frequently contained many small-scale copy number gains and losses, termed micro-aberrations, most of which are undetectable using typical-density genome-wide aCGH arrays. The basal-like subtype exhibited the highest incidence of these events. These micro-aberrations sometimes altered expression of the involved gene. We confirmed the presence of the <em>PTEN</em> micro-amplification in SUM149 and by mRNA-seq showed that this resulted in loss of expression of all exons downstream of this event. Micro-aberrations disproportionately affected the 5′ regions of the affected genes, including the promoter region, and high frequency of micro-aberrations was associated with poor survival.</p> <h3>Conclusion</h3><p>Using a high-probe-density, gene-centric aCGH microarray, we present evidence of small-scale genomic aberrations that can contribute to gene inactivation. These events may contribute to tumor formation through mechanisms not detected using conventional DNA copy number analyses.</p> </div