Housheng Hansen He

At a Glance

• Cancer Genetics and Epigenetics
• Noncoding RNA, RNA Therapy
• Data Science and Computational Biology

Research Synopsis

Cancer arises from breakdown in the normal cellular regulatory system. This malfunction can be a consequence of genetic mutation as well as epigenetic changes. Key epigenetic alterations, including histone modification and DNA methylation, often result in global as well as localized chromatin packaging that influences the transcription of genes important to cancer. Drugs that modify the epigenetic state promise to be effective new cancer therapies. However, the mechanism(s) underlying the epigenetic regulation of cancer cells, as well as the way in which drugs manipulate the epigenetic state and transcription, remain largely unknown. Moreover, as epigenetic regulation is critical for maintaining normal cellular function, the characterization of cancer-specific epigenetic reprogramming is an essential step for increasing specificity of epigenetic therapy. Noncoding RNAs, particularly long non-coding RNA (lncRNA) and circular RNA (circRNA), have recently become a new area of focus in cancer biology, with evidence suggesting that they are essential to epigenetic reprogramming during cancer development and progression.

Our laboratory applies a variety of genomic, epigenomic experimental and computational approaches to elucidate the functional role of epigenetic regulation in cancer development, progression, drug response and resistance, with a special focus on the interplay between epigenetic regulator and noncoding RNA under stress conditions such as hypoxia. Our research focuses on three major directions. 

1. Understand epigenetic regulation in cancer development, progression, drug response and resistance
2. Identify epigenetic biomarkers in tumor and liquid biopsies.
3. Target cancer specific epigenetic regulation for cancer therapy, in particular RNA therapy.

Recent Publications

1. Teng M*, Guo J*, Xin X*, Ci X, Mo Y, Chen S, Guo W, Bakht M, Ku S, Sigouros M, Xia Z, Chen M, Haq S, Yang W, Berlin A, van der Kwast T, Ellis L, Zoubeidi A, Zheng G, Ming J, Wang YZ, Lok B, Raught B, Beltran H^#, Qin J^#, He H^#. Circular RMST cooperates with lineage-driving transcription factors to govern neuroendocrine transdifferentiation. Cancer Cell. 2025. PMID: 40250444.

2. Xu X*,  Zhu H*, Hugh-White R*, Livingstone J*, Eng S, Chen S, Sheng M, Houlahan K, Guo W, Wang M, Zeng Y, Wang S, Zhu G, Gao T, Chen W, Wang Y, Ci X, Xu K, Orain M, Picard V, Hovington H, Bergeron A, Lacombe L, Têtu B, Fradet Y, Bristow R, Fleshner N, Wu X, Shao Y, Berlin A, Tvan der Kwast T, Leong H, Boutros P^#, He H^#. The Landscape of N6-Methyladenosine in Localized Primary Prostate Cancer. Nature Genetics. 2025. PMID: 40128621.

3. Wang S*, Zeng Y*, Xin X, Zhu H, Chen S, Ahmed M, Soares F, Chen M, Moran M, Tsao M^#, He H^#. The m6A epitranscriptome landscape in lung adenocarcinoma. Cancer Discovery. 2024. IPMID: 38922581.

4. Su P*, Liu Y*, Chen T*, Xue Y, Zeng Y, Ahmed M, Chen S, Harding S, Brooks D, Schramek D, Ming T^#, He H^#. In vivo functional genomics screen identifies dual function of MEN1 in regulating tumor-microenvironment interactions. Nature Genetics. 2024. PMID: 39227744.

5. Wang S*, Gao S*, Zeng Y*, Zhu L, Wong C, Su P, Zhai J, Soares F, Xu X, Yang Z, Cheung H, Chen H, O’Brian C, Rottapel R, Kang W, Cai Z, Wu J, Yu J^#, He H^#. N6-methyladenosine reader YTHDF1 promoted colorectal tumorigenesis and metastasis through ARHGEF2. Gastroenterology. 2022. PMID: 34968454. Patent number: US63/299,054.

6. Chen S*, Zhu G*, Yang Y*, Wang F*, Xiao Y, Zhang N, Bian X, Zhu Y, Yu Y, Liu F, Dong K, Mariscal J, Liu Y, Soares F, Yau H, Zhang B, Chen W, Wang C, Chen D, Guo Q, Yi Z, Liu M, Fraser M, De Carvalho D, Boutros P, Vizio D, Jiang Z, Kwast T, Berlin A, Wu S, Wang J^#, He H^#, Ren S^#. Single-cell analysis reveals transcriptomic remodellings in distinct cell types that contribute to human prostate cancer progression. Nature Cell Biology. 2021. PMID: 33420488.

7. Gao S*, Chen S*, Han D, Zhou F, Barrett D, Luong MP, Han W, Avery AM, Petricca J, Yuan M, Asara JM, Macoska JA, Balk SP^#, He H^#, Cai C^#. Chromatin binding of FOXA1 is promoted by LSD1-mediated demethylation in prostate cancer. Nature Genetics. 2020. PMID: 32868907.

8. Chen S*, Huang V*, Xu Xin*, Julie L*, Soares F*, Jeon J, Zeng Y, Hua J, Petricca J, Guo H, Wang M, Yousif F, Zhang Y, Donmez N, Ahmed M, Volik S, Lapuk A, Chua M, Heisler L, Foucal A, Fox N, Fraser M, Bhandari V, Shiah Y, Guan J, Orian M, Picar V, Hovington H, Bergeron A, Lacombe L, Fradet Y, Tetu B, Liu S, Feng F, Wu X, Y Shao, Komor M, Sahinalp C, Collins C, Hoogstrate Y, Jong M, Fijneman R, Fei T, Jenster G, van der Kwat T, Bristow RG, Boutros P^#, He H^#. Widespread and functional RNA circularization in localized prostate cancer. Cell. 2019. PMID: 30735634.

9. Hua J, Ahmed M, Guo H, Zhang Y, Chen S, Soares F, Lu J, Zhou S, Wang M, Li H, Larson N, McDonnell S, Patel P, Liang Y, Yao CQ, Kwast T, Lupien M, Feng F, Zoubeidi A, Tsao M, Thibodeau SN, Boutros P, He H. Risk SNP-Mediated Promoter-Enhancer Switching Drives Prostate Cancer through lncRNA PCAT19. Cell. 2018. PMID: 30033362.

10. Guo H, A.M., Liang Y, Hua J, Langstein J, Poon C, Bailey S, Desai K, Fei T, Li Q, Prensner JR, Pomerantz M, Feng FY, Freedman M, Lupien M, He H. Modulation of long noncoding RNAs underlying genetic predispositions to prostate cancer. Nature Genetics. 2016. PMID: 27526323.

Graduate Students

Vivian Chu
Peter Her
Peiran Su
Mona Teng
Lin Yang
Helen Zhu