10x Genomics

We are creating advanced end-to-end pipelines featuring cutting-edge technologies that fill the gaps in current #precisionmedicine workflows, uplifting capacity. These precision medicine pipelines are available to all researchers and clinicians across Australia, who can drop off their samples and tell us about their project, and then be as hands-off or as hands-on as they desire. We take samples and have an integrated collaboration of experienced specialists from histology, biobank, genomics, cytometry, imaging, bioresources and bioinformatics, who complete high-quality analysis to generate useful insights from these samples. Here, you can see our Genomics Specialist Dr David Dawei Zheng using the 10x Genomics Visium Cytassist to spatially map close to 20,000 genes in a transplanted kidney biopsy to identify specific gene signatures and key cell types which serve as biomarkers or predictors of rejection. The Westmead Institute for Medical Research #futureofhealthcare #innovation Maggie Wang Philip O'Connell Prof Denis C. Bauer, GAICD Kirstie Bertram Joanne Reed Emily Blyth Hilda Pickett Simon Ringer

We've just completed our first run on the 10x Genomics Xenium, which maps gene activity at unprecedented resolution within tissue samples while maintaining the spatial arrangement of cells, revealing how genes and cells function and interact in their natural environment. This is crucial for #precisionmedicine, as it helps identify specific cellular behaviours and disease markers, leading to more personalised therapies for conditions such as cancer and neurological disorders. Watch our The Westmead Institute for Medical Research Genomics experts Dr Joey Lai and Dr David Dawei Zheng explain more about this incredible technology! Stay tuned on our socials for future videos showcasing some of the preliminary results, and to hear more about the exciting precision medicine projects that are using our pipelines. University of Sydney Western Sydney Local Health District NSW Health Pathology CSIRO Infrastructure Technologies CMRI Hospital Maggie Wang Philip O'Connell Prof Denis C. Bauer, GAICD Kirstie Bertram Joanne Reed Emily Blyth Hilda Pickett Simon Ringer

Check our last paper in collaboration with Vincenzo Corbo and Peter Bailey. Finally on Nature! Our beloved 10x Genomics Xenium helped to unravel ecDNA-driven heterogeneity in pancreatic cancer. https://lnkd.in/dndKDsUk

Behind the Scenes of Our Recently Published Nature Paper Spatial immune scoring system predicts hepatocellular carcinoma recurrence https://lnkd.in/gAVavF4W Using AI, spatial proteomics (mass spec), and comprehensive immune modeling, our team not only developed an implementable scoring system to identify high-risk patients for treatment escalation but also uncovered a novel NK cell mechanism—paving the way for new NK cell therapy development. How It All Began: In early 2021, amidst the pandemic, I began contemplating how we could leverage the latest breakthroughs in spatial techs from Bruker Spatial Biology and 10x Genomics. Fortunately, our lab had some extra funding from immuno-profiling services we provided during the pandemic, particularly to industry and regional collaborators. Given the state of spatial techs at the time, I decided that the best approach would be to focus on surgical samples (early-stage tumors). These samples offer well-demarcated regions—stroma (normal), invasive front (border), and tumor center—allowing us to study the dynamic spatial distribution of immune cells. One key question emerged: "Is there a subset of immune cells that infiltrates and penetrates the tumor in a linear fashion toward its center, potentially contributing to better clinical outcomes?" Another crucial question was whether we could identify high-risk patients for adjuvant immunotherapy to prevent or delay relapse. The Search for Clinical Samples: During the pandemic, we had ongoing collaborations with Prof. Tian and his team, who generously provided HCC samples and facilitated the legal processes for their shipment. The Long Road to Nature Portfolio: After 2 years of intensive work, we submitted our first manuscript to Nature in 2023. The revision request (thankfully!) came back, but the reviewers demanded extensive additional work—particularly mechanistic validation using NK cell-specific KO models. The challenges felt almost insurmountable, and we nearly gave up. However, our Chinese collaborators stepped forward. We discussed with the editors, explaining that if they were willing to wait another year, we would do our best to address the reviewers' concerns. To our relief, the editors agreed. A year later, we submitted the revised manuscript, which received largely favorable reviews. A Step Toward Spatial Medicine: Eric Topol, MD To the spatial community, e.g. JEDIs—what excites me most about this work is how it: • Starting with spatial discovery • Validating findings with spatial proteomics (mass spec and mIF) • Applying AI (H&E 2.0-like) to develop a clinically implementable scoring system that outperforms existing evaluation tools Treatment escalation could benefit this high-risk patient group, as demonstrated in ex vivo, in vivo, and specific patient cohorts. Could this mark the dawn of spatial medicine? Perhaps it’s just the end of the beginning. Singapore General Hospital Institute of Molecular and Cell Biology (IMCB)

EYE CATCHING and THOUGHT PROVOKING! Sarah Murphy's image, Morphological Masterpiece, of human choroid plexus brain tissue is a small example of the morphological intricacies that the choroid plexus presents. The image displays a stain consisting of 6 different markers and a nuclear stain.  The vessels of the choroid plexus show elongated nuclei, creating an appearance like flowing water. The dendrite branching of the neuronal cells, also seen in this image, show a similar display of flow. Take a moment and consider how information is likely being passed between these cells, following the flow of its morphology. INCREDIBLE. VOTE NOW for #ArtoftheBrain Image #22 Most 🧡💛♥️s wins! View the 2024 Art of the Brain virtual exhibition: https://shorturl.at/fELRX #FriedmanBrainInstitute #NashNeuroscience #BrainAwarenessWeek #BAW2025 Icahn School of Medicine at Mount Sinai The Mount Sinai Hospital Graduate School of Biomedical Sciences at the Icahn School of Medicine Dana Foundation Center for Excellence in Youth Education (CEYE)

🚨 New preprint alert! 🚨 Excited to share our latest work from the DUTRENEO trial, now available on medRxiv! 🧬🔬 In this prospective, biomarker-driven study, we tested whether the 18-gene Tumor Inflammation Signature (TIS)could guide treatment selection for muscle-invasive bladder cancer (MIBC) patients receiving neoadjuvant immune checkpoint inhibitors (ICI) or chemotherapy (NAC). While TIS alone did not significantly enrich for ICI responders, we generated one of the largest spatial transcriptomics datasets in bladder cancer (Visium, Xenium) and integrated multi-omics to reveal key insights into tumor-immune interactions and treatment resistance: 🔹 Spatial immune proximity drives ICI response – Cancer-immune colocalization, not just inflammation, predicts benefit. Where immune cells are matters. 🔹 Phenotypic plasticity fuels NAC resistance – Not genetic diversity, but transcriptional reprogramming allows tumors to evade chemotherapy. 🔹 Bulk RNA "immune" signatures are misleading – Response-associated genes primarily originate from cancer cells, not the microenvironment. 🔹 Checkpoint expression alone is not enough – The spatial context of immune checkpoints and cellular neighborhoods determines therapeutic response. 🔹 Retrospective ≠ prospective biomarkers – TIS was promising in retrospective studies but did not prospectively enrich for responders, underscoring the need for spatial and multi-modal biomarkers in clinical trials. With spatial transcriptomics and AI poised to transform precision oncology, these findings provide a roadmap for integrating spatial biomarkers into future clinical trials. Huge thanks to our amazing collaborators—looking forward to discussions and feedback from the community! 🔗 Read the full preprint: https://lnkd.in/dz2H_kZ7 #BladderCancer #SpatialTranscriptomics #Immunotherapy #PrecisionOncology #DUTRENEO #CancerResearch #Visium #Xenium #AIinOncology