The paper expands the concept of MHC Class I peptide binding promiscuity to support vaccine discovery across cancers by analyzing data from 2,323 samples.

bioRxiv · May 8, 2025 · PreprintBioinformatics

Angiogenic and Immune Predictors of Neoadjuvant Axitinib Response in Renal Cell Carcinoma with Venous Tumour Thrombus

Rebecca Wray, Hania Paverd, Ines Prata Machado, Johanna Barbieri, Farhana Easita, Abigail R. Edwards, Ferdia Aidan Gallagher, Iosif Alexandru Mendichovszky, Thomas J. Mitchell, Maike de la Roche, Jacqueline D. Shields, Stephan Ursprung, Lauren Wallis, Anne Yvonne Warren, Sarah Joanne Welsh, , Robert J. Jones

The paper assesses neoadjuvant axitinib response in RCC with VTT using multiparametric analysis and identifies angiogenic and immune predictors of treatment response.

Nature Communications · Apr 28, 2025Peer-reviewedCancer Biology

Plasma Cell-Free DNA in Acute and Chronic Aortic Syndromes.

Ruwan Alwis Weerakkody, Martyna Joanna Adamowicz, Christelle Robert, John D. Pound, Maaz B. J. Syed, Caroline Pumpe, Anwar Muhammad Bilal, Alexander Laird, Duncan B. McLaren, Orwa Falah, Andrew L. Tambyraja, Matthew James Reed, David Ernest Newby, Timothy J. Aitman

The paper shows plasma short-fragment cfDNA concentration is higher in acute and chronic aortic disease compared to controls and is higher in acute cases, suggesting it could be a diagnostic biomarker.

bioRxiv · Jan 6, 2025 · PreprintGenomics

DNA methylation subtypes inferred from transcriptomes guide sunitinib and immunotherapy selection in renal cancer

Florian Jeanneret, Sarah Schoch, Pedro J. Ballester, Stefan Nicholas Symeonides, Alexander Laird, Håkan Axelson, Delphine Pflieger, Christophe Battail

The paper identifies DNA methylation subtypes from transcriptomes to guide sunitinib and immunotherapy selection in renal cancer, finding hyper-methylated tumors respond better to atezolizumab plus bevacizumab.

bioRxiv · Nov 5, 2024 · PreprintBioinformatics

Long-read Spatial Transcriptomic Profiling of Patient-derived ccRCC Tumoroids Reveals Heterogeneity in Isoform and Gene Expression

Mustafa Elshani, Hazem Abdullah, Ying Zhang, Alexander Laird, Peter Mullen, David James Harrison

The paper uses long-read spatial transcriptomics on ccRCC tumoroids to reveal gene and isoform expression heterogeneity, identifying distinct functional tumor clusters and isoform-specific patterns.

bioRxiv · Oct 16, 2024 · PreprintCancer Biology

Spatial Metabolomics co-registered with Multiplex Phenotyping for the Evaluation of Human Kidney Tissue

Greice Michele Zickuhr, In Hwa Um, Alexander Laird, David James Harrison, Alison L. Dickson

The paper evaluates a workflow for spatially co-registering molecular and phenotypical data from human kidney tissue using DESI-MSI under varying conditions.

bioRxiv · Nov 10, 2023 · PreprintSystems Biology

Microenvironment of metastasis reveals key predictors of PD-1 blockade response in renal cell carcinoma

Florian Jeanneret, Pauline Bazelle, Sarah Schoch, Catherine Pillet, In Hwa Um, Assilah Bouzit, Bertrand Evrard, Evan Seffar, Frédéric Chalmel, Javier A. Alfaro, Cátia Pesquita, Fabio Massimo Zanzotto, Mark D. Stares, Stefan Nicholas Symeonides, Alexander Laird, , Christophe Battail

The paper identifies key predictors of PD-1 blockade response in renal cell carcinoma by analyzing the tumor microenvironment of metastatic sites and developing a predictive TID score.

bioRxiv · Jul 17, 2023 · PreprintBioinformatics

The immunopeptidome from a genomic perspective: Establishing immune-relevant regions for cancer vaccine design

Georges Bedran, Tongjie Wang, Dominika Pankanin, Kenneth Weke, Alexander Laird, Christophe Battail, Fabio Massimo Zanzotto, Cátia Pesquita, Håkan Axelson, Ajitha Rajan, David James Harrison, Aleksander Pałkowski, Maciej Pawlik, Maciej Parys, J. Robert O’Neill, , Javier A. Alfaro

The paper develops COD-dipp to map MHC Class I antigens from cancer studies and identifies immune-relevant genomic regions for vaccine design.

bioRxiv · Jan 13, 2022 · PreprintBioinformatics