BioCAsia Seminar Series

BioCAsia Seminar Series

Date: 14th July Tuesday
Time: 4:00 – 5:00pm
Location: QUT Kelvin Grove, Q block, and you can register to join on Zoom
Speaker: Dharmesh Bhuva

Bioconductor Asia’s monthly Seminar Series

Dr Dharmesh Bhuva

A Single-Cell Spatially-Resolved Human Whole Transcriptome Atlas of Non-Small Cell Lung Cancer (NSCLC) Associates Spatial Features with Clinical Response

Spatial transcriptomics enables in situ interrogation of tumour ecosystems but integrating molecular, pathological, and clinical data remains challenging. We generated a single-cell, spatially resolved whole-transcriptome atlas of non-small cell lung cancer (NSCLC), comprising ~750,000 cells from 527 patient biopsies profiled using CosMx Whole Transcriptome imaging. The atlas captures expression of 18,935 genes per cell and integrates five independent clinical cohorts, providing a large-scale resource for characterising the tumour microenvironment (TME).
To analyse these data, we developed a computational framework incorporating existing Bioconductor infrastructure and a novel quality control pipeline, a new normalisation approach (SpaNorm), a background-aware spatially variable gene detection method (SpaNormSVG), and a spatial influence differential expression model (SpiDE). Integration with pathology-guided annotations enabled accurate cell typing and identification of six conserved tissue neighbourhoods, revealing histology-, stage-, and sex-specific changes in cellular composition and transcriptional programs.

Dr Dharmesh D Bhuva

NHMRC Emerging Leadership Fellow

Frazer Institute, University of Queensland

Dr Dharmesh D Bhuva is an NHMRC Emerging Leadership Fellow (EL1) at the Frazer Institute, University of Queensland, who is passionate about understanding how complex systems of gene regulation and signalling lead to organisation of healthy and diseased tissues. He completed his PhD in 2020 at the University of Melbourne and WEHI where he developed new systems biology approaches to study molecular function and gene regulation in cancer. He then undertook his post-doctoral studies at the world-renowned WEHI Bioinformatics division, where he embarked on developing novel approaches to study cancer tissues using spatial molecular data. In 2023, he joined the computational systems oncology division at the South Australian Immunogenomics Cancer Institute (SAiGENCI) to continue his cutting-edge research in developing computational approaches to study tissue architecture. Computational methods developed by Dr. Bhuva have been downloaded >240,000 times globally. Dr. Bhuva has been recently awarded a MRFF grant and a NHMRC investigator grant (EL1) to identify spatial biomarkers in cancer systems, particularly biomarkers of response to immunotherapies in NSCLC.