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Background & Aims Many patients with pancreatic ductal adenocarcinoma (PDAC) develop recurrent or metastatic diseases after surgery, so it is important to identify those most likely to benefit from aggressive therapy. Disruption of tissue microarchitecture is an early step in pancreatic tumorigenesis and a parameter used in pathology grading of glandular tumors. We investigated whether changes in gene expression during pancreatic epithelial morphogenesis were associated with outcomes of patients with PDAC after surgery. Methods We generated architectures of human pancreatic duct epithelial cells in a 3-dimensional basement membrane matrix. We identified gene expression profiles of the cells during different stages of tubular morphogenesis (tubulogenesis) and of PANC-1 cells during spheroid formation. Differential expression of genes was confirmed by immunoblot analysis. We compared the gene expression profile associated with pancreatic epithelial tubulogenesis with that of PDAC samples from 27 patients, as well as with their outcomes after surgery. Results We identified a gene expression profile associated with tubulogenesis that resembled the profile of human pancreatic tissue with differentiated morphology and exocrine function. Patients with PDACs with this profile fared well after surgery. Based on this profile, we established a 6−28 gene tubulogenesis-specific signature that accurately determined the prognosis of independent cohorts of patients with PDAC (total n = 128; accuracy = 81.2%−95.0%). One gene, ASPM , was down-regulated during tubulogenesis but up-regulated in human PDAC cell lines and tumor samples; up-regulation correlated with patient outcomes (Cox regression P = .0028). Bioinformatic, genetic, biochemical, functional, and clinical correlative studies showed that ASPM promotes aggressiveness of PDAC by maintaining Wnt-β-catenin signaling and stem cell features of PDAC cells. Conclusions We identified a gene expression profile associated with pancreatic epithelial tubulogenesis and a tissue architecture−specific signature of PDAC cells that is associated with patient outcomes after surgery.

Histopathological classification of human prostate cancer (PCA) relies on the morphological assessment of tissue specimens but has limited prognostic value. To address this deficiency, we performed comparative transcriptome analysis of human prostatic acini generated in a three-dimensional basement membrane that recapitulates the differentiated morphological characteristics and gene expression profile of a human prostate glandular epithelial tissue. We then applied an acinar morphogenesis–specific gene profile to two independent cohorts of patients with PCA (total n = 79) and found that those with tumors expressing this profile, which we designated acini-like tumors, had a significantly lower risk of postoperative relapse compared with those tumors with a lower correlation (hazard ratio, 0.078; log-rank test P = 0.009). Multivariate analyses showed superior prognostic prediction performance using this classification system compared with clinical criteria and Gleason scores. We prioritized the genes in this profile and identified programmed cell death protein 4 (PDCD4) and Kruppel-like factor 6 (KLF6) as critical regulators and surrogate markers of prostatic tissue architectures, which form a gene signature that robustly predicts clinical prognosis with a remarkable accuracy in several large series of PCA tumors (total n = 161; concordance index, 0.913 to 0.951). Thus, by exploiting the genomic program associated with prostate glandular differentiation, we identified acini-like PCA and related molecular markers that significantly enhance prognostic prediction of human PCA.

Glandular malignancies such as prostate carcinoma display a considerable heterogeneity in the degree of structural organization while the prognostic role of the associated molecular changes awaits further exploration. Using a three-dimensional (3-D) tissue organization culture model that permits the structural differentiation of prostate glandular epithelium we profiled the transcriptomes of multicellular organoids formed by untransformed prostate epithelial cells (PECs) or prostate carcinoma cells as well as those cultured as cell monolayers. Interrogation into the multiple (n = 6) sets of differentially expressed genes (DEGs) identified that those altered significantly during the structural differentiation process of polarized PEC acini strongly associated with the probability of recurrence in a cohort of 50 prostate cancer patients receiving radical prostatectomy (RP). By contract, the DEGs related to prostate tumor spheroids did not correlate significantly with prognosis. To further explore this association, we prioritized the genes and applied supervised classification algorithms whereby identified a 39-gene structure-associated prognosis signature (SAPS) that shows a remarkable predictivity for the likelihood of post-RP recurrence (overall accuracy 100%, P < 0.001). The SAPS outperformed standard clinicopathological variables, including Gleason scores, as well as existing multigene prognostic predictors of prostate cancer. Our results suggest a distinct contribution by the glandular structural differentiation program to prostate cancer pathology and the usefulness of a robust and biologically relevant genomic predictor of the prognosis of prostate cancer (Supported by NHRI CA-099-PP-19 and Department of Health of Taiwan H99-TD-C-111-004 to KKC).

Systemic chemotherapy inflicts cytotoxic injuries on tumor cells and cells in the stromal compartment and their complex interplay may critically affect therapeutic response and outcome. Evidence has shown that gene expression profiles associated with reactive tumor stroma link to prognosis and treatment outcome in breast cancer; however, the specific stromal alterations underlying these associations await further exploration. We here show that breast carcinoma-associated fibroblasts (CAFs) responded to therapeutically relevant magnitudes of cytotoxic stimuli (TRCS) by engaging in a series of cytostatic and pro-death cell programs in a time-dependent manner. By interrogating clinical samples we found a considerable number of CAFs with similar characteristics in the stroma of breast cancer following neoadjuvant chemotherapy (NACT). Profiling the TRCS-induced transcriptomal changes of breast CAFs demonstrated that the genes involved in the protracted (day 3-7) instead of the early (day 1-3) responses were significantly associated with the responsiveness of breast cancer to NACT. To further substantiate this finding we prioritized gene markers and identified a 30-gene chemotherapy-associated stroma signature (CASS) that can predict pathological complete remission (pCR) of breast cancer following NACT with remarkable accuracy (overall accuracy 80%, P < 0.01). The CASS outperformed and complemented standard clinicopathological variables and existing gene expression signatures for the prediction of pCR in several independent data sets. Thus, by exploiting the distinct pathological role of the stromal cytotoxic responses we identified strong and robust predictive markers for the intrinsic chemosensitivity of breast cancer (Supported by NHRI CA-099-PP-19 and Department of Health of Taiwan H99-TD-C-111-004 to KKT).