The paper identifies increased MCT4-associated lactate export in myeloid cells during HNSCC progression using single-cell RNA-sequencing and metabolic flux analysis.

bioRxiv · Oct 16, 2026 · PreprintCancer Biology

ETS1 Orchestrates a Hybrid EMT Program Driving in vivo Metastasis and Immune Evasion

Benjamin Ziman, Talia A. Wenger, Chehyun Nam, Qian Yang, Daniel Arnaudov, Thomas Tilton, Megha Sheth, Zhixuan Jing, Yuhao Pan, Joseph A. Vargas, Yong Teng, Uttam K. Sinha, Young Min Park, De‐Chen Lin

This study identifies ETS1 as a master regulator of a hybrid EMT program in UASCC that drives metastasis and immune evasion, and shows HSP90 inhibitors can target ETS1-driven tumors.

Cancer Research · May 19, 2026Peer-reviewedCancer Biology

Genomic and single-cell characterization of patient-derived tumor organoid models of head and neck squamous cell carcinoma

Jung Hyun Um, Yueyuan Zheng, Qiong Mao, Chehyun Nam, Hua Zhao, Yoon Woo Koh, Su‐Jin Shin, Young Min Park, De‐Chen Lin

This study establishes patient-derived tumor organoids (PDOs) from 31 HNSCC patients, faithfully recapitulating tumor characteristics and predicting cisplatin responses, revealing hEMT-driven resistance and AREG as a therapeutic target.

Cancer Research · Apr 22, 2025Peer-reviewedCancer Biology

Genetically Defined Organoid Models Reveal Mechanisms Driving Squamous Cell Neoplastic Evolution and Identify Potential Therapeutic Vulnerabilities

Hua Zhao, Young Min Park, Yueyuan Zheng, Qiong Mao, Casey Collet, Boyan Hu, Tianming Zhou, Luda Lin, Stephanie K. Wong, Yuhao Pan, Anette Vistoro Monreal, Uttam K. Sinha, Parish Paymon Sedghizadeh, Alice Soragni, De‐Chen Lin

bioRxiv · Jan 18, 2025 · PreprintCancer Biology

A local sequence signature defines a subset of heterochromatin-associated CpGs with minimal loss of methylation in healthy tissues but extensive loss in cancer

Dror Bar, Lior Fishman, Yueyuan Zheng, Irene Unterman, Devorah Schlesinger, Amir Eden, De‐Chen Lin, Benjamin P. Berman

The paper identifies a sequence signature that predicts CpG methylation loss in healthy tissues and cancer, revealing slow-loss CpGs with minimal methylation loss in health but significant loss in cancer.

bioRxiv · Aug 16, 2022 · PreprintGenomics

EuRBPDB: a comprehensive resource for annotation, functional and oncological investigation of eukaryotic RNA binding proteins (RBPs)

Jian‐You Liao, Bing Yang, Yu‐Chan Zhang, Xiaojuan Wang, Yushan Ye, Jing-Wen Peng, Zhi-Zhi Yang, Jiehua He, Yin Zhang, Kaishun Hu, De‐Chen Lin, Dong Yin

EuRBPDB is a database that compiles eukaryotic RNA binding proteins (RBPs) using computational and proteomic methods, and provides cancer-related annotations and a web interface for exploration.

Nucleic Acids Research · Oct 8, 2019Peer-reviewedBioinformatics

ELMER v.2: An R/Bioconductor package to reconstruct gene regulatory networks from DNA methylation and transcriptome profiles

Tiago C. Silva, Simon G. Coetzee, Nicole Gull, Lijing Yao, Dennis J. Hazelett, Houtan Noushmehr, De‐Chen Lin, Benjamin P. Berman

ELMER v.2 reconstructs gene regulatory networks from DNA methylation and transcriptome data to identify Master Regulators in diseases like breast cancer.

Bioinformatics · Oct 25, 2018Peer-reviewedBioinformatics