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Articles by Caner Ercan
Effective tumor kinetics inferred from single routine H&E biopsies enable counterfactual virtual radiotherapy trials
PS and HE declare that a patent application has been filed covering aspects of the method described in this publication. No other competing interests are declared. I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained.
AI-derived tumor-infiltrating lymphocytes enhance the prediction of pathologic complete response in early-stage triple-negative breast cancer
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Abstract Stromal tumor-infiltrating lymphocytes (sTILs) may hold clinical value for triple-negative breast cancer (TNBC) for outcome prediction. Manual scoring of sTILs suffers from inter-observer variability, limiting its clinical adoption.
By Xiaoxi Pan, Caner Ercan, Zhongya Wang, Roland Bassett, Karina Gonzales, Gaiane M. Rauch, Beatriz E. Adrada, Rosalind Candelaria, Debu Tripathy, Jennifer K. Litton, Sharon H. Giordano, Vicente Valero, Banu Arun, Alyson R. Clayborn, Jason WHite, Jason White, Qingqing Ding, Aysegul Sahin, William Fraser Symmans, Clinton Yam, Lei Huo, Yinyin Yuan, Kiran Virani
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Nature
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Gompertz growth with a shared carrying capacity optimally simulates primary and metastatic tumor growth dynamics - British Journal of Cancer
Abstract Cancer is a systemic disease with most deaths attributed to metastatic burden. Primary and metastatic tumors, albeit at different anatomic locations, are interconnected through multiple biological processes. Pre-clinical and clinical observations of growth acceleration of metastases after surgery, or abscopal effects outside the radiation field are widely reported, yet reliably triggering favorable and avoiding unfavorable systemic responses remains an unmet clinical need.
A morphometric signature to identify ductal carcinoma in situ with a low risk of progression - npj Precision Oncology
Abstract Ductal carcinoma in situ (DCIS) may progress to ipsilateral invasive breast cancer (iIBC), but often never will. Because DCIS is treated as early breast cancer, many women with harmless DCIS face overtreatment. To identify features associated with progression, we developed an artificial intelligence-based DCIS morphometric analysis pipeline (AIDmap) on hematoxylin-eosin-stained (H&E) tissue sections.
Targeting the expansion of myeloid-derived suppressor cells in liver cirrhosis
Abstract Background and aims: Previously, we identified immune-suppressive circulating monocytic myeloid-derived suppressor cells (M-MDSC) in patients with cirrhosis and liver failure, which increased with disease severity and were associated with infections and mortality. Impaired immune responses and M-MDSC expansion were reversed by ex vivo polyinosinic:polycytidylic acid (poly(I:C)) treatment.
Author Correction: Bipotent transitional liver progenitor cells contribute to liver regeneration - Nature Genetics
Correction to: Nature Genetics https://doi.org/10.1038/s41588-023-01335-9. Published online 13 March 2023. In the version of this article originally published, reference errors that arose during revisions have now been corrected as follows. In the first sentence of the Results subsection “Bipotent TLPCs differentiate into hepatocytes or BECs,” Thakur, 2019 (Hepatology 70, 1360–1376 (2019)) was cited in error and has now been removed.
Bipotent transitional liver progenitor cells contribute to liver regeneration - Nature Genetics
Abstract Following severe liver injury, when hepatocyte-mediated regeneration is impaired, biliary epithelial cells (BECs) can transdifferentiate into functional hepatocytes. However, the subset of BECs with such facultative tissue stem cell potential, as well as the mechanisms enabling transdifferentiation, remains elusive. Here we identify a transitional liver progenitor cell (TLPC), which originates from BECs and differentiates into hepatocytes during regeneration from severe liver injury.
Transposon-activated POU5F1B promotes colorectal cancer growth and metastasis - Nature Communications
Abstract The treatment of colorectal cancer (CRC) is an unmet medical need in absence of early diagnosis. Here, upon characterizing cancer-specific transposable element-driven transpochimeric gene transcripts (TcGTs) produced by this tumor in the SYSCOL cohort, we find that expression of the hominid-restricted retrogene POU5F1B through aberrant activation of a primate-specific endogenous retroviral promoter is a strong negative prognostic biomarker.
Integrative proteogenomic characterization of hepatocellular carcinoma across etiologies and stages - Nature Communications
Abstract Proteogenomic analyses of hepatocellular carcinomas (HCC) have focused on early-stage, HBV-associated HCCs. Here we present an integrated proteogenomic analysis of HCCs across clinical stages and etiologies. Pathways related to cell cycle, transcriptional and translational control, signaling transduction, and metabolism are dysregulated and differentially regulated on the genomic, transcriptomic, proteomic and phosphoproteomic levels.
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