Plasma Autoantibodies Associated with Basal-like Breast Cancers
CANCER EPIDEMIOLOGY BIOMARKERS & PREVENTION
Authors: Wang, Jie; Figueroa, Jonine D.; Wallstrom, Garrick; Barker, Kristi; Park, Jin G.; Demirkan, Gokhan; Lissowska, Jolanta; Anderson, Karen S.; Qiu, Ji; LaBaer, Joshua
Abstract
Background: Basal-like breast cancer (BLBC) is a rare aggressive subtype that is less likely to be detected through mammographic screening. Identification of circulating markers associated with BLBC could have promise in detecting and managing this deadly disease. Methods: Using samples from the Polish Breast Cancer study, a high-quality population-based case-control study of breast cancer, we screened 10,000 antigens on protein arrays using 45 BLBC patients and 45 controls, and identified 748 promising plasma autoantibodies (AAbs) associated with BLBC. ELISA assays of promising markers were performed on a total of 145 BLBC cases and 145 age-matched controls. Sensitivities at 98% specificity were calculated and a BLBC classifier was constructed. Results: We identified 13 AAbs (CTAG1B, CTAG2, TP53, RNF216, PPHLN1, PIP4K2C, ZBTB16, TAS2R8, WBP2NL, DOK2, PSRC1, MN1, TRIM21) that distinguished BLBC from controls with 33% sensitivity and 98% specificity. We also discovered a strong association of TP53 AAb with its protein expression (P = 0.009) in BLBC patients. In addition, MN1 and TP53 AAbs were associated with worse survival [MN1 AAb marker HR = 2.25, 95% confidence interval (CI), 1.03-4.91; P = 0.04; TP53, HR = 2.02, 95% CI, 1.06-3.85; P = 0.03]. We found limited evidence that AAb levels differed by demographic characteristics. Conclusions: These AAbs warrant further investigation in clinical studies to determine their value for further understanding the biology of BLBC and possible detection. Impact: Our study identifies 13 AAb markers associated specifically with BLBC and may improve detection or management of this deadly disease. (C) 2015 AACR.
Induced Pluripotent Stem Cell Differentiation Enables Functional Validation of GWAS Variants in Metabolic Disease
CELL STEM CELL
Authors: Warren, Curtis R.; O'Sullivan, John F.; Friesen, Max; Becker, Caroline E.; Zhang, Xiaoling; Liu, Poching; Wakabayashi, Yoshiyuki; Morningstar, Jordan E.; Shi, Xu; Choi, Jihoon; Xia, Fang; Peters, Derek T.; Florido, Mary H. C.; Tsankov, Alexander M.; Duberow, Eilene; Comisar, Lauren; Shay, Jennifer; Jiang, Xin; Meissner, Alexander; Musunuru, Kiran; Kathiresan, Sekar; Daheron, Laurence; Zhu, Jun; Gerszten, Robert E.; Deo, Rahul C.; Vasan, Ramachandran S.; O'Donnell, Christopher J.; Cowan, Chad A.
Abstract
Genome-wide association studies (GWAS) have highlighted a large number of genetic variants with potential disease association, but functional analysis remains a challenge. Here we describe an approach to functionally validate identified variants through differentiation of induced pluripotent stem cells (iPSCs) to study cellular pathophysiology. We collected peripheral blood cells from Framingham Heart Study participants and reprogrammed them to iPSCs. We then differentiated 68 iPSC lines into hepatocytes and adipocytes to investigate the effect of the 1p13 rs12740374 variant on cardiometabolic disease phenotypes via transcriptomics and metabolomic signatures. We observed a clear association between rs12740374 and lipid accumulation and gene expression in differentiated hepatocytes, in particular, expression of SORT1, CELSR2, and PSRC1, consistent with previous analyses of this variant using other approaches. Initial investigation of additional SNPs also highlighted correlations with gene expression. These findings suggest that iPSC-based population studies hold promise as tools for the functional validation of GWAS variants.