Broad Institute of MIT and Harvard’s Post

Morphology and gene functions…

This study represents significant strides in cell classification and morphology for human kidney tissue. The latest research utilizes both targeted and whole-transcriptome spatial platforms to accurately identify individual immune cells in renal mouse tissue. By integrating these findings into a topological pipeline based on multiparameter persistent homology, the scientists uncovered spatial relationships characteristic of lupus nephritis in mice. These discoveries were validated experimentally through immunofluorescence, marking a milestone in the understanding of this condition. What's more, this framework is designed to be adaptable, paving the way for its application across various platforms. This represents a leap forward in connecting the dots from genes to tissues, enhancing one's ability to understand and treat complex diseases p/b University of Oxford, University of Chinese Academy of Sciences, BGI · Research, University of Cambridge, MPI-CBG - Max Planck Institute of Molecular Cell Biology and Genetics, aneesha bhandari, Jessica Kepple, Shane Zhouchun SHANG, PhD, Oliver McCallion, Heather Harrington #BiomedicalResearch #CellBiology #TranslationalMedicine https://lnkd.in/gwkD3aQW

We started a blog! New on Terrain's website, we created a place to share our thinking on the fast-moving proteomics space. Our blog 'Compass' (as a way to talk about the direction of the industry) is going to be jointly written by my co-founders Brian Dranka, Kenneth (Kirby) Bloom, and I. Our goal is to foster meaningful conversations, provide insights into emerging trends, and highlight the potential of spatial proteomics to revolutionize diagnostics and therapeutic strategies. In the coming posts, we’ll explore topics like integrating spatial proteomics into clinical workflows, overcoming challenges in biomarker discovery, relevance of multi-omics, and the role of LLM and AI in tackling the workflow and analytic challenges we have today. To start, I will describe my early motivation that led to the development of FISSEQ and the evolution of my priorities that directed me to spatial proteomics, as well as the huge impact I foresee it having on precision medicine if we do it right. Check it out here --> https://lnkd.in/eSmffYNW

A groundbreaking toolkit lets scientists map RNA activity at the subcellular level with single-molecule precision—like a GPS for cells! This innovation reveals RNA interactions critical to life, opening new frontiers in biology and medicine. https://bit.ly/4fcD2zs #spatialtranscriptomics #biomedicalengineering #georgiatech

🔬 Advancing Cell–Cell Communication (CCC) Inference 🧬 So MANY (Over 100 tools) now enhance single-cell and spatial transcriptomics analysis, focusing mainly on protein-mediated interactions. However, emerging multi-omics promise broader insights into intercellular signaling. 🌐 LIANA+ may be a a game-changer—an all-in-one CCC framework published in nature cell biology. Applied to Parkinson’s and heart disease models, it reveals key intercellular programs and drivers of disease processes. 🚀 https://lnkd.in/duqDGQ4r #Bioinformatics #SingleCell #Spatialomics #CCC #MultiOmics

The formation and maintenance of tissue integrity requires complex, coordinated activities by thousands of genes and their encoded products. Until recently, transcript levels could only be quantified for a few genes in tissues, but advances in DNA sequencing, oligonucleotide synthesis and fluorescence microscopy have enabled the invention of a suite of spatial transcriptomics technologies capable of measuring the expression of many, or all, genes in situ. These technologies have evolved rapidly in sensitivity, multiplexing and throughput. As such, they have enabled the determination of the cell-type architecture of tissues, the querying of cell–cell interactions and the monitoring of molecular interactions between tissue components. The rapidly evolving spatial genomics landscape will enable generalized high-throughput genomic measurements and perturbations to be performed in the context of tissues. These advances will empower hypothesis generation and biological discovery and bridge the worlds of tissue biology and genomics. https://lnkd.in/gfSpbbi9

Scientists uncover how transcription drives motion within the genome by New York University "[...] The Nature Communications study investigated how a motion of a single actively transcribed gene affects the motions of the genome around it in live human cells. To do so, the authors employed CRISPR technology to fluorescently label single genes, two-color high-resolution live cell microscopy to visualize the motion of these labeled genes, and displacement correlation spectroscopy (DCS) to simultaneously map flows of the genome across the nucleus. The high-resolution imaging data were then processed through a physical and mathematical analysis, uncovering a never-before-seen physical picture of how genes move inside the cell. [...]" "More information: Transcription-dependent mobility of single genes and genome-wide motions in live human cells, Nature Communications (2024). DOI: 10.1038/s41467-024-51149-4 Journal information: Nature Communications "

Empowering Single-Cell Genomics with 10X Precision. Let's embark on a journey of discovery, pushing the boundaries of scientific exploration one cell at a time. 10x Genomics has officially launched its latest breakthrough product, #Chromium GEM-X. With Chromium GEM-X, researchers can delve deeper into the complexity of cellular diversity, unraveling the intricacies of gene expression, and uncovering rare cell populations with unprecedented clarity. By capturing vast amounts of single-cell data, GEM-X empowers scientists to explore diverse biological landscapes with enhanced sensitivity and resolution. Featuring advanced microfluidics and chemistry, GEM-X delivers robust performance and streamlined workflows, making single-cell analysis more accessible than ever before. From unraveling the mysteries of disease progression to unlocking the secrets of developmental biology.  This innovative platform revolutionizes single-cell genomics, offering unparalleled precision and scalability. Join us in embracing the future of single-cell genomics with 10X Genomics' Chromium GEM-X. Read more here 👉https://lnkd.in/emgCaAbJ For more information contact GeneTiCA Group! If you want to know more visit the 10xG Experience meeting in Prague on the 14th of May 2024. It is coming up! https://lnkd.in/esBGttpb

ST-GEARS: Advancing 3D downstream research through accurate spatial information recovery Existing 3D Spatial Transcriptomics reconstruction approaches often overlook spatial information or experiment-induced distortions. Here, authors propose ST-GEARS to bridge the gap between in vivo cell locations and in vitro analysis, accurately recovering spatial profiles. https://lnkd.in/ghNZ2wvg

🌟 Method of the year! 🌟 Spatial transcriptomics has been named Method of the Year by Nature Methods. Working in this field, I’ve seen firsthand how this revolutionary technology is transforming how we study tissues. It’s not just about understanding gene expression anymore; it’s about seeing where it happens within the intricate architecture of tissues. On a personal note, being part of this cutting-edge field has been such a rewarding experience. I’ve loved collaborating with researchers to explore these new horizons, troubleshoot challenges, and celebrate discoveries. Each day brings new questions and possibilities, and that's what keeps me motivated! I’m excited to see how this recognition inspires more scientists to dive into spatial biology and push the boundaries of what we can achieve together. #SpatialTranscriptomics #MethodOfTheYear #SpatialBiology #InnovationInScience #ProudScientist