Explanipedia

Mechanisms of tumor persistence in metastatic melanoma following successful immunotherapy Open

Yingxiao Shi, Zoltan Maliga, Tuulia Vallius, Shishir M. Pant, Roxanne J. Pelletier , et al. · 2025

Persistent stable lesions represent a common but ambiguous outcome in melanoma patients receiving immune checkpoint inhibitors (ICIs). However, these lesions are infrequently removed and poorly characterized. Here, we perform in-depth mult…

Integrative single-cell and spatial mapping of oxidative stress response uncovers GCLC+ mesenchymal tumor cell state linked with favorable outcomes in triple negative breast cancer Open

Nomeda Girnius, Tuulia Vallius, Wenqing Chen, Inga-Maria Launonen, Sara Palomino‐Echeverría , et al. · 2025

Inhibiting oxidative stress response (OSR) proteins has been suggested as a therapeutic strategy in triple negative breast cancer (TNBC). However, the cell type specificity and spatial distribution of OSR genes and proteins, such as GCLC a…

Vitessce Link: A Mixed Reality and 2D Display Hybrid Approach for Visual Analysis of 3D Tissue Maps Open

Eric Mörth, Morgan L. Turner, Cydney Nielsen, Xianhao Carton Liu, Mark S. Keller , et al. · 2025

Advances in spatial omics and high-resolution imaging enable the creation of three-dimensional (3D) tissue maps that capture cellular organization and interactions in situ. While these data provide critical insights into tissue function an…

Melanoma to rhabdomyosarcoma plasticity in the setting of immunotherapy Open

Andrew Knight, Emily Robitschek, Jia‐Ren Lin, Dennie T. Frederick, Alvin Shi , et al. · 2025

Acquired resistance to immune checkpoint inhibitors (ICIs) remains a significant challenge in the treatment of metastatic melanoma. Phenotypic plasticity, such as dedifferentiation and transdifferentiation, is an increasingly recognized me…

773 Spatial characterization of the immune microenvironment of localized prostate cancer reveals an immunogenic subset of high-risk tumors Open

Aishwarya Atmakuri, Jeremiah A. Wala, Ali Amiryousefi, Jia-Ren Lin, Brian Labadie , et al. · 2025

488 Integrative molecular and spatial analysis to reveal tumor intrinsic and extrinsic drivers of immunotherapy response in mucosal melanoma Open

Yingxiao Shi, Aikaterini Dedeilia, Jia-Ren Lin, Roxanne J. Pelletier, Tuulia Vallius , et al. · 2025

CRATER tumor niches facilitate CD8+ T cell engagement and correspond with immunotherapy success Open

Aya Ludin, Georgia L. Stirtz, Asaf Tal, Ajit J. Nirmal, Kathleen L. Pfaff , et al. · 2025

T cell-mediated tumor killing underlies immunotherapy success. Here, we used long-term in vivo imaging and high-resolution spatial transcriptomics of zebrafish endogenous melanoma, as well as multiplex imaging of human melanoma, to identif…

Dynamic modelling of cell cycle arrest through integrated single-cell and mathematical modelling approaches Open

Javiera Cortés‐Ríos, María Rodriguez-Fernández, Peter K. Sorger, Fabian Fröhlich · 2025

Highly multiplexed imaging assays allow simultaneous quantification of multiple protein and phosphorylation markers, providing a static snapshots of cell types and states. Pseudo-time techniques can transform these static snapshots of unsy…

Multiomic profiling of a unique in-transit melanoma cohort identifies melanoma differentiation as predictor of tumor progression and therapy response Open

Giuseppe Tarantino, Anne Zaremba, Tuulia Vallius, Mark Woodnorth, Yichao Hua , et al. · 2025

Melanoma patients with in-transit metastasis (ITM), a stage of disease where melanoma has metastasized to sites in between the primary lesion and draining lymph node, vary significantly in their clinical outcomes, but the biology driving d…

Highly multiplexed 3D profiling of cell states and immune niches in human tumors Open

Clarence Yapp, Ajit J. Nirmal, Felix Zhou, Alex Y. H. Wong, Juliann B. Tefft , et al. · 2025

Spatially organized lymphocytic microenvironments in high grade primary prostate tumors Open

Ali Amiryousefi, Jeremiah A. Wala, Jia‐Ren Lin, Brian Labadie, Aishwarya Atmakuri , et al. · 2025

The spatial organization and composition of the tumor-immune microenvironment (TME) play a critical role in shaping the progression of many solid cancers, but the organization of the TME in primary prostate cancer (PCa) remains poorly char…

Immunoprofiling at an Institutional Scale Reveals That High Numbers of Intratumoral CD8 <sup>+</sup> and PD-1 <sup>+</sup> Cells Predict Superior Patient Survival Across Major Cancer Types Independent of Major Risk Factors Open

Joao V. Alessi, James Lindsay, Anita Giobbie‐Hurder, Bijaya Sharma, Kristen D. Felt , et al. · 2025

PURPOSE Retrospective studies have found associations between the number of intratumoral immune cells and patient outcomes for specific cancers treated with targeted therapies. However, the clinical value of routinely quantifying intratumo…

Virtual Multiplex Staining for Histological Images using a Marker-wise Conditioned Diffusion Model Open

Hyun-Jic Oh, Junsik Kim, Zhiyi Shi, Yichen Wu, Yuan Chen , et al. · 2025

Multiplex imaging is revolutionizing pathology by enabling the simultaneous visualization of multiple biomarkers within tissue samples, providing molecular-level insights that traditional hematoxylin and eosin (H&E) staining cannot provide…

Antigen reactivity defines tissue-resident memory and exhausted T cells in tumours Open

Thomas N. Burn, Jan Schröder, Luke C. Gandolfo, Maleika Osman, Elanor N. Wainwright , et al. · 2025

CD8 + T cells are a key weapon in the therapeutic armamentarium against cancer. While CD8 + CD103 + T cells with a tissue-resident memory T (T RM ) cell phenotype have been favourably correlated with patient prognoses 1–6 , the tumour micr…

SEAL: Spatially-resolved Embedding Analysis with Linked Imaging Data Open

Simon Warchol, Grace Guo, Johannes Knittel, Dan Freeman, Usha Bhalla , et al. · 2025

Dimensionality reduction techniques help analysts make sense of complex, high-dimensional spatial datasets, such as multiplexed tissue imaging, satellite imagery, and astronomical observations, by projecting data attributes into a two-dime…

Corrigendum to "Comprehensive Proteomics Metadata and Integrative Web Portals Facilitate Sharing and Integration of LINCS Multiomics Data". Open

D. Vidović, Behrouz Shamsaei, Stephan C. Schürer, Phillip Kogan, Szymon Chojnacki , et al. · 2025

Morphology-Aware Profiling of Highly Multiplexed Tissue Images using Variational Autoencoders Open

Gregory J. Baker, Edward Novikov, Shannon Coy, Yu‐An Chen, Clemens B. Hug , et al. · 2025

Spatial proteomics (highly multiplexed tissue imaging) provides unprecedented insight into the types, states, and spatial organization of cells within preserved tissue environments. To enable single-cell analysis, high-plex images are typi…

Spatial determinants of tumor cell dedifferentiation and plasticity in primary cutaneous melanoma Open

Tuulia Vallius, Yingxiao Shi, Edward Novikov, Shishir M. Pant, Roxanne J. Pelletier , et al. · 2025

Early detection of melanoma through skin surveillance is critical for preventing metastatic progression. Primary cutaneous melanomas at early stage offer a unique opportunity to uncover fundamental mechanisms of tumor initiation, progressi…

Resident memory T cell development is gradual and shows AP-1 gene expression in mature cells Open

Neal P. Smith, Yu Yan, Youdong Pan, Jason B. Williams, Kasidet Manakongtreecheep , et al. · 2025

Tissue-resident memory T (TRM) cells play a central role in immune responses across all barrier tissues after infection. However, the mechanisms that drive TRM differentiation and priming for their recall effector function remains unclear.…

Supplementary Table S7 from Multimodal Spatial Profiling Reveals Immune Suppression and Microenvironment Remodeling in Fallopian Tube Precursors to High-Grade Serous Ovarian Carcinoma Open