Dr Jeongmin Woo 

Dr Neda Hasan

Mr Chaitanya Vuppusetty (Lab manager)

Dr Praveen Weeratunga 

Dr Harry Tian Hu

Dr Vishal Nathwani 

Dr Sabrina Zulfikar 

Dr Leila Baghaarabani

Dr Yaron Ben-Ami

Affiliates

Prof Daisy Yuejuan Zheng

Dr Andrew Achaiah

See our Spotlight video - https://youtu.be/Dj0uNQgA1Fs

My research group studies how immunological responses impact on mechanisms of lung injury, regeneration and repair. Our projects are divided into mechanistic and translational studies. We have two aims – (1) to understand the contribution of immune cells to chronic progressive lung fibrosis and alveolar regneration (2) to use this knowledge to bring new treatment and improved management to patients with fibrotic lung diseases,focusing on idiopathic pulmonary fibrosis (IPF) and fibrotic sarcoidosis. 

We focus on both the lung tissue and blood in human studies, and longitudinal murine studies. In the lungs, we have developed methods (with mathematicians) to map out the spatial organisation of immune cells using mathematical tools, single cell imaging mass cytometry and single cell transcriptomics. 

Idiopathic Pulmonary Fibrosis (IPF) is a devastating and progressive lung disease in which normal alveolar architecture is replaced by scar tissue, leading to respiratory failure and death. While much attention has been paid to the role of fibroblasts and collagen deposition, it is increasingly clear that failed regeneration of the alveolar epithelium plays a key role in disease progression. Our group recently mapped the spatial landscape of regenerating alveolar niche in IPF (Weeratunga et al., Nature Communications, 2025), revealing a population of abnormal alveolar epithelial cells that are spatially associated with a distinct group of macrophages. Single cell transcriptomic evidence suggest that they may shape epithelial response to injury and drive disease perpetuation. This DPhil project will build on these findings and test the hypothesis that immune–epithelial crosstalk between macrophages and aberrant alveolar intermediates disrupts normal repair and promotes fibrotic progression. The project will generate alveolar organoids which recapitulate features of the regenerating niche in IPF patients and use immunological assays to test the function of interacting macrophages and epithelial cells. Other advanced techniques, including CRISPR-Cas9 gene editing to perturb key ligand–receptor pathways and single-cell RNA sequencing to map cellular responses will be used as necessary.

This project is ideal for a motivated, industrious and smart student with a background in medicine, biomedical sciences, immunology or molecular/cell biology. It offers an opportunity to make a meaningful contribution to a globally important area of disease, working in a Unit at the forefront of immune-mediated diseases and lung immune-epithelial biology. Ultimately, the work could help define new therapeutic strategies for IPF—shifting focus to improving regeneration—and provide insight into how the immune system can be harnessed to restore damaged tissues.

Training Opportunities

The student will be based within the MRC Translational Immune Discovery Unit at the Weatherall Institute of Molecular Medicine, a hub for cutting-edge research in immunology and human disease. Our group is interdisciplinary and translational, with strong links to clinical practice, computational biology, and drug discovery. You will gain hands-on experience in state-of-the-art methods including flow cytometry and mass cytometry (CyTOF),  and opportunities to use single-cell RNA sequencing and spatial transcriptomics, alongside molecular biology and bioinformatics tools for high-dimensional analysis. In addition to technical training, there is a strong emphasis on critical thinking, experimental design, data analysis, presentation skills, and scientific writing—ensuring you develop as an independent and well-rounded researcher.

Contact details: Ling-pei.ho@imm.ox.ac.uk

Temporo-spatial cellular atlas of the regenerating alveolar niche in idiopathic pulmonary fibrosis. Weeratunga P, Hunter B, Sergeant M, Bull J, Clelland C, Denney D, Vuppusetty C, Burgoyne R, Woo JM, Hu T, Borthwick L, Shaw J, Antanavicuete A, Filby A, Byrne HM, Fisher A and Ho L.P.  Nature Comm  2025; https://doi.org/10.1101/2024.04.10.24305440

Single cell spatial analysis reveals inflammatory foci of immature neutrophil and CD8 T cells in COVID-19 lungs.   Weeratunga P, Denney L, Bull J, Repapi E,  Sergeant M, Etherington E,  Vuppussetty C, Turner G,  Clelland C, Woo JM, Cross A, Issa F, de Andrea CE,  Bermejo IM, Sims D,  McGowan S,  Zurke YX, Ahern DJ, Gamez EC, Whalley J, Richards D, Klenerman P, Monaco C, Udalova IA, Dong T, Antanaviciute A, Ogg G, Knight JC, Byrne HM,  Taylor S, Ho L.P. Nature Comm 2023; 14, 7216.

Type I IFN-activated lung monocytes and macrophages as initiators and drivers of fibrosis at the alveolar barrier in  IPF. Nathwani V*, Weeratunga P*, Woo JM*, Denney L, Vuppusetty C, Hu T,  Zulfikar S,  Achaiah A, Parker H,  Chuang HW , Mazurczyk M, Fedorov A,  Simmons A, Clelland C, Rehwinkel R,  Antanaviciute A and Ho L.P. MedRxV 2025. doi: https://doi.org/10.1101/2025.05.09.25326523

Immune mechanisms of granuloma formation in sarcoidosis and tuberculosis. Weeratunga P, Moller DR and Ho LP. J Clin Invest 2024 134 (1):e175264

COVID-19 therapeutics: Challenges and directions for the future. Robinson PC, Liew DFL, Tanner HL, Grainger JR, Dwek RA, Reisler RB, Steinman L, Feldmann M, Ho L.P., Hussell T, Moss P, Richards D, Zitzmann N. Proc Natl Acad Sci U S A. 2022;119:e2119893119.

Multi-modal characterization of monocytes in idiopathic pulmonary fibrosis reveals a primed type I interferon immune phenotype. Fraser E, Denney L, Blirando K, Vuppusetty C, Antanviciute A, Zheng Y, Repapi E, Iotchkova V, Ashley N, St Noble V, Benamore R, Hoyles R, Clelland C, Rastick JM, Hardman CS, Alham NK, Rigby RE, Rehwinkel J, Ho L.P. Frontiers Immunology 2021;12:623430.

A blood atlas of COVID-19 defines hallmarks of disease severity and specificity. COvid-19 Multi-omics Blood ATlas (COMBAT) Consortium. Cell 2022;185(5):916-938.e58. 

Safety and efficacy of inhaled nebulised interferon beta-1a (SNG001) for treatment of SARS-CoV-2 infection: a randomised, double-blind, placebo-controlled, phase 2 trial. Monk P, Marsden R, Tear V, Brookes J, Batten TTN, Mankowski M, Gabbay F, Davies D, Holgate S, Ho L.P, Clark T, Djukanovic R, and Wilkinson T. Lancet Respiratory Medicine. 2020, 12;S2213

Longitudinal immune profiling reveals key myeloid signatures associated with COVID-19.  Mann E, Menon M, Knight S, Konkel J, Jagger C, Shaw T, Krishnan S, Rattray M, Ustianowski A, Bakerly ND, Dark P, Lord G, Simpson A, Felton T, Ho L.P, NIHR Respiratory TRC, Feldmann M, CIRCO, Grainger J, Hussell T. Science Immunology. 2020, 5;51

Immune mechanisms in fibrotic pulmonary sarcoidosis. Weeratunga P, Moller DR, Ho L.P. Eur Respir Rev 2023; 31 (166).

Spatial transcriptomic characterization of COVID-19 pneumonitis identifies immune circuits related to tissue injury.Cross, A. R., C. E. de Andrea, M. Villalba-Esparza, M. F. Landecho, L. Cerundolo, P. Weeratunga, R. E. Etherington, L. Denney, G. Ogg, L. P. Ho, I. S. Roberts, J. Hester, P. Klenerman, I. Melero, S. N. Sansom and F. Issa (2023).  J Clin Invest Insight 2023; 8(2):e157837

Increased monocyte level is a risk factor for radiological progression in patients with early fibrotic interstitial lung abnormality. A. Achaiah, P. Lyon, E. Fraser, P. Saunders, R. Hoyles, R. Benamore, Ling-Pei Ho. Eur Resp J Open Res 2022 ;8:3

M1-like monocytes are a major immunological determinant of severity in previously healthy adults with life-threatening influenza. SL Cole, J Dunning, WL Kok, KH Benam, A Benlahrech, E Repapi, F Martinez, L Drumright, TJ Powell, M Bennett, R Elderfield, MOSAIC Investigators, T Dong, J McCauley, EFY Liew, S Taylor, W Barclay, V Cerundolo, PJ Openshaw, AJ McMichael and L.P Ho. J Clin Invest Insight 2017; 6;2:e91868

Namilumab or infliximab compared with standard of care in hospitalised patients with COVID-19 (CATALYST): a randomised, multicentre, multi-arm, multistage, open-label, adaptive, phase 2, proof-of-concept trial. Fisher BA, et al. Lancet Respir Med. 2022;10(3):255-266. 

Clinical characteristics with inflammation profiling of long COVID and association with 1-year recovery following hospitalisation in the UK: a prospective observational study. PHOSP-COVID Collaborative Group. Lancet Respir Med. 2022:S2213-2600(22)00127-8.

Genetic programs expressed in resting and IL-4 alternatively activated mouse and human macrophages: similarities and differences. F Martinez, L Helming, R Mueller, A Varin, B Melgert, C Draijer, B Thomas, M Fabbri, A Crawshaw, L.P Ho, N Ten Hacken, V Jiménez, N Kootstra, J Hamann, D Greaves, M Locati, A Mantovani and S Gordon. Blood 2013; 28;121(9):e57-69.

Gene-set Analysis of Lung Samples Provides Insight into Pathogenesis of Progressive, Fibrotic Pulmonary Sarcoidosis. HE Lockstone, Sanderson S, Kulakova N, Baban D, Leonard A, Kok WL, McGowan S, McMichael AJ, Ho LP. Am J Respir Crit Care Med. 2010;181(12):1367-75.