Advancing Spatial Transcriptomics Through International Collaboration
A New York Research Exchange Advancing Hepatobiliary Cancer Research
Luke McNickle is a Clinical Research Fellow and PhD student who is undertaking research into colorectal cancer liver metastasis as part of our CYGNUS project. Leading the Hepatobiliary Cancer exemplar, Luke applies advanced multi-modal spatial technologies to study the molecular characteristics of different tumor growth patterns, aiming to uncover insights that could improve diagnosis, treatment, and patient care.
To further advance spatial transcriptomics capabilities within the exemplar and strengthen the wider spatial biology ecosystem, Luke completed a one‑month placement in August 2025 at Weill Cornell Medicine in New York. Supported by the ROBIN Young Scientist Exchange Programme, he worked within Dr Nir Ben Chetrit’s laboratory, generating meaningful benefits for the exemplar while also enhancing his own professional development and translational research skills.
Key Achievements and Outputs
- Technical Development: Computational pipelines that integrate single-cell RNA sequencing with Visium HD data were developed, with direct applications to other spatial technologies including CosMx. These pipelines are now utilised by colleagues in Glasgow, extending impact beyond the individual researcher.
- Novel Analytical Approaches: Expertise was built in analysing spatial data in ways that go beyond looking at individual genes. Importantly, it helped establish approaches that treat spatial data as a distinct data type, rather than applying methods designed for single-cell pipelines - a key distinction that has reshaped analytical practice.
- Sustained International Collaboration: An ongoing working relationship with Dr. Ben Chetrit was established, involving regular meetings, data sharing, and continued mentorship. This collaboration is expected to extend into post-doctoral work, creating lasting transatlantic research links.
Together, these achievements strengthen CYGNUS’s ability to generate clinically meaningful insights from spatial data, accelerating progress towards more personalised and effective patient care.
Impact on CYGNUS
The skills and methods developed during the New York placement are enabling deeper biological analysis of complex spatial transcriptomics datasets within the CYGNUS hepatobiliary exemplar.
By treating spatial data as a distinct data type, these approaches support a deeper understanding of tumour biology, spatial heterogeneity, and disease-relevant interactions, helping to inform future patient-focused research.
Key applications include:
- Cholangiocarcinoma analysis
- Advanced analysis of colorectal liver metastasis (CRLM) CosMx data, a core component of the CYGNUS exemplar
Impact on Spatial Biology Ecosystem
The placement proved invaluable in developing the technical capabilities and international networks necessary to advance spatial transcriptomics research both within the CYGNUS framework and beyond, leading to:
- Sustained international partnerships that enable knowledge exchange and data sharing.
- Transferable computational pipelines that benefit the wider research group.
- Bridges between breast cancer and hepatobiliary spatial biology communities.
- Demonstrated value of clinical academics engaging in computational biology training.
Professional Development & Research Direction
The experience provided Luke with valuable exposure to research culture and working practices in a leading US medical institution, resulting in:
- Reinforced focus on the spatial dimension of spatial transcriptomics analysis, moving beyond treating spatial data as simply single-cell data with coordinates.
- Continued development of computational tools and analytical pathways.
- Broadened career perspectives for a surgical trainee undertaking PhD research, highlighting opportunities for international research collaboration in surgical academia.