Cancer Systems Biology and Tumour Evolution
Group Leader:
Prof Ramanuj DasGupta
Cancer remains one of the most complex, and devastating diseases of our time, characterized by its ability to evade treatment and adapt to an ever-changing biological landscape with diverse selective pressures. At the forefront of this challenge, our laboratory is pioneering the use of next-generation single-cell and spatial biology tools, paired with functional genomic technologies and relevant murine models, to unravel the developmental origins of cancer.
Specifically, we investigate how damage-associated regenerative programs, activated in the context of chronic inflammatory diseases (fatty liver/MASLD, viral hepatis, colitis, IBD) contribute to cancer initiation and progression.
Lab Reports
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Recent Publications
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Lab Members
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Recent Publications
2026
Owino CO, Narmada BC, Yi Lin G, Aw PPK, Ganesh N, Siying JT, Plissonnier ML, Matan TT, Shirgaonkar N, Bifani P, Levrero M, Periyasamy G, Gee Lim S, DasGupta R. Identification of Cyclin L1 as a Host Factor Regulating Hepatitis B Virus Replication. Viruses. 2026;18(5).
Patten DA, Lumley A, Wilkinson AL, O’Keeffe A, Yin K, Shirgaonkar N, Gao R, DasGupta R, Hoare M, Shetty S. Senescent Human Liver Endothelial Cells Mediate CD4(+) T Cell Recruitment via ICOSL. Immunology. 2026.
2025
Chen Y, Davidson NM, Wan YK, Yao F, Su Y, Gamaarachchi H, Sim A, Patel H, Low HM, Hendra C, Wratten L, Hakkaart C, Sawyer C, Iakovleva V, Lee PL, Xin L, Ng HEV, Loo JM, Ong X, Ng HQA, Wang J, Koh WQC, Poon SYP, Stanojevic D, Tran HD, Lim KHE, Toh SY, Ewels PA, Ng HH, Iyer NG, Thiery A, Chng WJ, Chen L, DasGupta R, Sikic M, Chan YS, Tan BOP, Wan Y, Tam WL, Yu Q, Khor CC, Wüstefeld T, Lezhava A, Pratanwanich PN, Love MI, Goh WSS, Ng SB, Oshlack A, Göke J. A systematic benchmark of Nanopore long-read RNA sequencing for transcript-level analysis in human cell lines. Nat Methods. 2025;22(4):801-812.
Chia S, Wen Seow JJ, Peres da Silva R, Suphavilai C, Shirgaonkar N, Murata-Hori M, Zhang X, Yong EY, Pan J, Thangavelu MT, Periyasamy G, Yap A, Anand P, Muliaditan D, Chan YS, Siyu W, Yong CW, Hong N, Ran G, Sim NL, Guo YA, Yi Teh AX, Wei Ling CC, Wei Tan EK, Pei Cherylin FW, Chang M, Han S, Seow-En I, Chen Hui LR, Hsia Gan AH, Yap CK, Ng HH, Skanderup AJ, Chinswangwatanakul V, Riansuwan W, Trakarnsanga A, Pithukpakorn M, Tanjak P, Chaiboonchoe A, Park D, Kim DK, Iyer NG, Tsantoulis P, Tejpar S, Kim JE, Kim TI, Sampattavanich S, Tan IB, Nagarajan N, DasGupta R. CAN-Scan: A multi-omic phenotype-driven precision oncology platform identifies prognostic biomarkers of therapy response for colorectal cancer. Cell Rep Med. 2025:102053.
Chong WQ, Low JL, Tay JK, Le TBU, Goh GS, Sooi K, Teo HL, Cheo SW, Wong RT, Samol J, Lim MY, Li H, Shirgaonkar N, Chia S, Wang L, Gopinathan A, Eu DK, Tsang RK, Loh KS, Toh HC, Syn N, Kong LR, Dasgupta R, Tai BC, Lim YC, Goh BC. Pembrolizumab with or without bevacizumab in platinum-resistant recurrent or metastatic nasopharyngeal carcinoma: a randomised, open-label, phase 2 trial. Lancet Oncol. 2025;26(2):175-186.
Neo SY, Shuen TWH, Khare S, Chong J, Lau M, Shirgaonkar N, Chua L, Zhao J, Lee K, Tan C, Ba R, Lim J, Chua J, Cheong HS, Chai HM, Chan CY, Chung AYF, Cheow PC, Jeyaraj PR, Teo JY, Koh YX, Chok AY, Chow PKH, Goh B, Wan WK, Leow WQ, Loh TJZ, Tang PY, Karunanithi J, Ngo NT, Lim TKH, Xu S, Dasgupta R, Toh HC, Lam K-P. Atypical memory B cells acquire Breg phenotypes in hepatocellular carcinoma. JCI insight. 2025;10(7):e187025.
Prawira A, Xu H, Mei Y, Leow WQ, Nasir NJM, Reolo MJ, Otsuka M, Rahbari M, Chen Z, Weerasooriya M, Abdullah LB, Wu J, Hazirah SN, Wasser M, Chung A, Goh BK, Chow PK, Albani S, Lee J, Lim TKH, Zhai W, Dan YY, Goh GB, Heikenwälder MF, Zhang Y, Dasgupta R, Tai WMD, Liu H, Chen J, Chew V. Targeting Treg-fibroblast interaction to enhance immunotherapy in steatotic liver disease-related hepatocellular carcinoma. Gut. 2025.
Raeisi Dehkordi S, Wong IT, Ni J, Luebeck J, Zhu K, Prasad G, Krockenberger L, Xu G, Chowdhury B, Rajkumar U, Caplin A, Muliaditan D, Gnanasekar A, Coruh C, Jin Q, Turner K, Teo SX, Pang AWC, Alexandrov LB, Chua CEL, Furnari FB, Maciejowski J, Paulson TG, Law JA, Chang HY, Yue F, DasGupta R, Zhao J, Mischel PS, Bafna V. Breakage fusion bridge cycles drive high oncogene number with moderate intratumoural heterogeneity. Nat Commun. 2025;16(1):1497.
Sun Y, Rodgers Furones A, Gultekin O, Khare S, Neo SY, Shi W, Moyano-Galceran L, Lam KP, Dasgupta R, Fuxe J, Salehi S, Lehti K, Sarhan D. Adaptive NK Cells Exhibit Tumor-Specific Immune Memory and Cytotoxicity in Ovarian Cancer. Cancer Immunol Res. 2025.
Womersley HJ, Muliaditan D, DasGupta R, Cheow LF. Single-nucleus CUT&RUN elucidates the function of intrinsic and genomics-driven epigenetic heterogeneity in head and neck cancer progression. Genome Res. 2025;35(1):162-177.
Wong SQR, Das M, Tenzin K, Shirgaonkar N, Chua H, Chee LX, Sae Yeoh A, Murugiah AA, Chua WY, Theardy MS, Subel EJ, Thangavelu MT, Chan JV, Yap CK, Tan IBH, Tsantoulis P, Tejpar S, Loo JM, DasGupta R. Modeling oxaliplatin resistance in colorectal cancer reveals a SERPINE1-based gene signature (RESIST-M) and therapeutic strategies for pro-metastatic CMS4 subtype. Cell Death Dis. 2025;16(1):529.
Law JH, Shao H, DasGupta R, Huang DQ. Developing risk stratification strategies and biomarkers for recurrent hepatocellular carcinoma. Clin Transl Med. 2025(8):e70410.
Taylor SA, Bader GD, MacParland S, Mullen AC, Andrews T, Cuenca AG, DasGupta R, Gehring AJ, Grün D, Guilliams M, Gulamhusein A, Henderson NC, Hirschfield G, Huppert SS, Itzkovitz S, Jiang ZG, Lauer GM, McGilvray I, Mysore KR, Pirola CJ, Quon G, Rahbari M, Regev A, Ricciuto A, Scott CL, Sharma A, Sookoian S, Tana MM, Teichmann SA, Vallier L, Vlachos IS, Wang B, Zhen M. Towards a reference cell atlas of liver diversity over the human lifespan. Nature reviews. 2025.
2024
Gan WL, Ren X, Ng VHE, Ng L, Song Y, Tano V, Han J, An O, Xie J, Ng BYL, Tay DJT, Tang SJ, Shen H, Khare S, Chong KHC, Young DY, Wu B, DasGupta R, Chen L. Hepatocyte-macrophage crosstalk via the PGRN-EGFR axis modulates ADAR1-mediated immunity in the liver. Cell Rep. 2024;43(7):114400.
Narmada BC, Khakpoor A, Shirgaonkar N, Narayanan S, Aw PPK, Singh M, Ong KH, Owino CO, Ng JWT, Yew HC, Binte Mohamed Nasir NS, Au VB, Sng R, Kaliaperumal N, Khine H, di Tocco FC, Masayuki O, Naikar S, Ng HX, Chia SL, Seah CXY, Alnawaz MH, Wai CLY, Tay AYL, Mangat KS, Chew V, Yu W, Connolly JE, Periyasamy G, Plissonnier ML, Levrero M, Lim SG, DasGupta R. Single-cell landscape of functionally cured chronic hepatitis B patients reveals activation of innate and altered CD4-CTL-driven adaptive immunity. J Hepatol. 2024;81(1):42-61.
Scolaro T, Manco M, Pecqueux M, Amorim R, Trotta R, Van Acker HH, Van Haele M, Shirgaonkar N, Naulaerts S, Daniluk J, Prenen F, Varamo C, Ponti D, Doglioni G, Ferreira Campos AM, Fernandez Garcia J, Radenkovic S, Rouhi P, Beatovic A, Wang L, Wang Y, Tzoumpa A, Antoranz A, Sargsian A, Di Matteo M, Berardi E, Goveia J, Ghesquière B, Roskams T, Soenen S, Voets T, Manshian B, Fendt SM, Carmeliet P, Garg AD, DasGupta R, Topal B, Mazzone M. Nucleotide metabolism in cancer cells fuels a UDP-driven macrophage cross-talk, promoting immunosuppression and immunotherapy resistance. Nat Cancer. 2024;5(8):1206-1226.
Shanmugam R, Majee P, Shi W, Ozturk MB, Vaiyapuri TS, Idzham K, Raju A, Shin SH, Fidan K, Low JL, Chua JYH, Kong YC, Qi OY, Tan E, Chok AY, Seow-En I, Wee I, Macalinao DC, Chong DQ, Chang HY, Lee F, Leow WQ, Murata-Hori M, Xiaoqian Z, Shumei C, Tan CSH, Dasgupta R, Tan IB, Tergaonkar V. Iron-(Fe3+)-Dependent Reactivation of Telomerase Drives Colorectal Cancers. Cancer Discov. 2024;14(10):1940-1963.
Singh V, Mondal A, Adhikary S, Mondal P, Shirgaonkar N, DasGupta R, Roy S, Das C. UBR7 E3 Ligase Suppresses Interferon-β Mediated Immune Signaling by Targeting Sp110 in Hepatitis B Virus-Induced Hepatocellular Carcinoma. ACS Infect Dis. 2024;10(11):3775-3796.
Tan DJH, Ng CH, Muthiah M, Yong JN, Chee D, Teng M, Wong ZY, Zeng RW, Chin YH, Wang JW, Danpanichkul P, Rajaram RB, DasGupta R, Suzuki H, Takahashi H, Tamaki N, Dan YY, Lui R, Duseja A, Siddiqui MS, Yeoh KG, Sanyal A, Wijarnpreecha K, Loomba R, Mantzoros CS, Huang DQ. Rising global burden of cancer attributable to high BMI from 2010 to 2019. Metabolism. 2024;152:155744.
Tostado CP, Da Ong LX, Heng JJW, Miccolis C, Chia S, Seow JJW, Toh YC, DasGupta R. An AI-assisted integrated, scalable, single-cell phenomic-transcriptomic platform to elucidate intratumor heterogeneity against immune response. Bioeng Transl Med. 2024;9(2):e10628.
Womersley H, Muliaditan D, DasGupta R, Cheow LF. Single-nucleus CUT&RUN elucidates the function of intrinsic and genomics-driven epigenetic heterogeneity in head and neck cancer progression. Genome Res. 2024.
Research Assistant
Eilidh McCulloch
I am a research assistant/bioinformatician focused on translational pharmacology and identification of response to therapy biomarkers in cancer patients.
My current research integrates single-cell and spatial profiling approaches to characterise the tumour microenvironment and investigate immune responsiveness and resistance to treatment in hepatocellular carcinoma patients, with the long-term aim of improving patient treatment stratification and identifying novel therapeutic targets.
Before joining the group, I developed pharmacodynamic biomarkers for several other cancer clinical trials at the University of Glasgow and managed a university spin out company, developing and commercialising biomarker assays in the veterinary diagnostic field. Outside of research, I love travelling and animals and like to combine these by going to see wildlife in their natural habitats.
PhD Student
Gideon Adeniyi
My journey into cancer research started with the death of a friend to the disease in 2013. Since then, my research experience has revolved around chemical carcinogenesis, chemotherapy-induced side effects, and integrative oncology. My PhD research centers on utilizing single-cell and multiomics approaches to understand MASLD progression to HCC in time and space. Outside the lab? I love volunteering, jogging, hiking, and playing tennis.
Research Associate
Kerrie Hargrave
I am a postdoctoral researcher in Ram’s lab with a background in immunology and immunometabolism. My previous research has been varied where I have explored dendritic cell metabolism during parasitic infections, investigated lung APC-T cell interactions during influenza infection and developed nanoparticles that deliver drugs into the brain.
Now transitioning into cancer research, my current project focuses on how high fat diet alters the liver microenvironment including myeloid immunometabolism which consequently effects immune cell activation and contributes to the progression of hepatocellular carcinoma (HCC). Outside the lab, I enjoy travelling to sunny destinations, following the drama of Formula 1 and listening to crime podcasts.
PhD Student
Khushi Tanwar
Hi, I’m Khushi. I am curious to understand how tumours evolve across time and space, with a particular focus on colorectal cancer (CRC) metastasis to the liver. Inspired by Paget’s “seed and soil” hypothesis, I’m interested in understanding why CRC cells (the seed) preferentially colonise the liver, and what makes the hepatic microenvironment (the soil) such a fertile niche for metastatic growth.
When I’m not thinking about metastatic ecosystems, you’ll probably find me at the gym, chasing endorphins, hiking up a mountain, or exploring fashion as another form of creativity, because whether it’s science, style, or life, I’m all about exploring new terrains.
Research Associate
Mengwei Li
I am a postdoctoral researcher in Ram’s lab. My work sits at the interface between bioinformatics and biology. I focus on connecting computational methods with real biological questions, aiming to make data analysis easier for biologists so they can spend more time thinking about the biology itself. For example, I developed DISCO, a large-scale single-cell data platform that supports data integration, annotation, and biological discovery. My broader research interests include single-cell and spatial omics, cancer, liver disease progression, ageing, and computational tool development. Outside the lab, I enjoy climbing, drinking, and playing Dota.
Associate Scientist
Niranjan Shirgaonkar
I’m a computational biologist focused on decoding tumour pathology, using spatial transcriptomics and machine learning to map how cell states shape cellular morphology. I spend my time diving into high dimensional data to uncover how cells organise and interact across various cancer models, with a particular focus on liver and other solid tumours.
Outside the lab, my world revolves around my new role as a father. There's nothing better than taking my baby daughter out for walks in the fresh air. When I do get a bit of downtime, I love winding down with an authentic cup of chai or logging on for some online gaming.
Research Associate
Ran Gao
I am Ran Gao, a postdoctoral researcher in Ram’s lab. I am broadly interested in combining single-cell and spatial technologies to explore the evolution of chronic liver diseases. My current work focus on characterizing cellular ecosystem changes and investigating how the microenvironment establishes pre-tumorigenic niches during the transition from MAFLD to hepatocellular carcinoma (HCC). In my spare time, I enjoy hiking and playing video games.
Research Fellow
Shruti Khare
I am a postdoctoral researcher with a particular interest in how the tissue microenvironment influences disease initiation, progression, and epithelial plasticity. My work spans MASLD-HCC, stomach cancer, and colorectal cancer, combining clinical data analysis with single-cell and spatial transcriptomics approaches, including scRNA-seq, Visium, and CosMx, to better understand tumor heterogeneity and cellular interactions within diseased tissues.
When I’m not wrangling large datasets or troubleshooting analysis pipelines, I enjoy reading and occasionally dancing, thanks to my background in Kathak, which these days, serves to entertain my baby girl.
Clinical Research Fellow
Dan Field
My name is Dan, I am a CRUK TRACC Clinical Research Training Fellow in Histopathology currently embarking on my PhD training. My PhD project aims to harness archival human tissue to explore the key drivers of early carcinogenesis in the liver, in particular, looking at the interactions between the background chronically damaged liver and evolving dysplastic (pre-cancerous) lesions. Most importantly, I am interested in exploring how these early changes can be targeted to prevent cancer development. I am a strong advocate for the inclusion of pathologists in research/clinical trials and I am currently the chair of the Trainees’ Subcommittee of the Pathological Society of GB and Ireland.
Outside of work I can be usually found either on a beach/sea cliff/remote island photographing birds as a published amateur wildlife photographer, running, reading a book, or playing the violin!