Single Cell News

Single Cell News pinned «Dear colleagues! ⚡️ We’re taking a short summer breather to recharge. Hope your summer is filled with sunshine, adventure, and plenty of fun. We’ll be back in September - can’t wait to catch up then! 🏖️ All the best, ASCA Team #ASCAinfo»

Dear colleagues! ⚡️ We’re taking a short summer breather to recharge. Hope your summer is filled with sunshine, adventure, and plenty of fun. We’ll be back in September - can’t wait to catch up then! 🏖️ All the best, ASCA Team #ASCAinfo

A comprehensive epidermal map from a poplar single-cell shoot atlas reveals new trichome-specific genes Anita Giabardo ... C. Robin Buell presented a single-cell RNA-seq atlas of the poplar 717 shoot, including apical meristem, primary and secondary stems, and three stages of leaf development. Key points 🔹159,000 cells, 40 transcriptionally distinct clusters, and 7 major cell types 🔹Focus on the epidermis which constitutes >15% of cells in the shoot atlas 🔹Epidermal cell subclusters corresponding to developmental stages, spatial location, and specialized cell types 🔹Novel trichome markers 🔹A tool to support cell type-targeted-metabolic engineering ➡️ Available here #singlecellnews

HLiCA: An integrated cell atlas of the healthy human liver   Rachel Edgar ... Gary Bader presented the Human Liver Cell Atlas (HLiCA), an integrated reference of non-disease liver cells assembled from eight datasets across six research centers, encompassing more than 525,000 cells from 110 donors. Key points 🔸 Expert-curated cell annotations 🔸 Classifying cells into six lineages and 47 distinct types 🔸 Evaluating the range of ancestral backgrounds represented in the atlas 🔸 Identification of previously unrecognized liver cell types, including NRXN1+ stromal cells localized to periportal regions 🔸 Differential expression of drug metabolism genes in hepatocytes between sexes and mucus-production genes in cholangiocytes, varied with age. #singlecellnews

Pubertal maturation and chemotherapy-associated disruption of the pediatric ovary revealed by multimodal single-cell profiling   Loren Méar … Pauliina Damdimopoulou analyzed ovarian tissue from 16 patients undergoing fertility preservation (aged 1-16 years) and 11 adult controls (aged 22-32 years) using scRNA-seq, spatial transcriptomics, and multiplex immunostaining.    Key points ✔️ Extensive stromal remodeling across puberty, accompanied by vascular and neural maturation and a shift in germline transcriptional programs ✔️ Distinct tissue organization and follicular niche composition between children and adults ✔️ Broader transcriptional alterations in chemotherapy than puberty, including ECM disruption and reduced intercellular communication ✔️ Challenging the direct extrapolation of adult ovarian tissue cryopreservation protocols to prepubertal patients #singlecellnews

⚡Dear Colleagues, 📍 Don't miss the registration for the ASCA CONGRESS 2026, which is open until July 24. The program includes 11 sections with talks by key researchers and technology developers in the field of single-cell and spatial analysis. 📍 Online access is also available. ➡️ More details: https://ascanet.org/events/asca-congress-2026/ Sincerely, Organizing Committee

Four-dimensional molecular mapping from a spatial snapshot reveals the dynamics of hair follicle organogenesis Soichiro Asami ... Reza Kalhor developed 3D DNase-Enhanced Expression Profiling (3DEEP), a tissue-clearing approach that removes genomic DNA to extend spatial transcriptomic profiling hundreds of microns into intact tissues. Highlights 🔸 Spatial pseudotiming reconstructs hair follicle organogenesis in space and time 🔸 Stratification of stem cell compartment along the hair axis precedes bulb formation 🔸 Two cavities emerge between three structures and merge to form the hair canal 🔸 Nude follicles show developmental delay and instability before hair shaft defects. #singlecellnews

SenCat: Cataloging human cell senescence through multi-omic profiling of multiple senescent primary cell types Carlos Anerillas ... Myriam Gorospe profiled the transcriptomes and proteomes in 14 different primary human cell types undergoing over 30 senescence paradigms to create a senescence catalog “SenCat”. Key points 🔷 Senescent cells lack universal markers but share metabolic and damage-response pathways implicated in tissue repair 🔷 Machine-learning-refined SenCat signatures enable senescence scoring and identification across multiple human and mouse datasets. #singlecellnews

scEPS integrates genetic and single-cell disease atlas data to provide granular mechanistic insights into complex human diseases Luli Zou ... Huwenbo Shi developed scEPS, an integrative approach for identifying disease-associated cell neighborhoods, where the expression of disease GWAS genes explains more variance in the disease phenotype than randomly selected mean expression matched control genes. Key points ⚡️Capture of the genetic covariance between gene expression and diseases, mitigating the effect of reverse causation and prioritizing cell populations mediating the effects of GWAS genes ⚡️Recapitulation of known and uncovered novel disease-associated cell populations, identifying more significant associations than a CNA-based approach and scDRS ⚡️Detection of different cell populations, contrasting clinical diagnoses vs. their polygenic risk scores, revealing distinct biology for the active/symptomatic vs. preclinical/asymptomatic states of the disease. #singlecellnews

Spatially resolved profiling of extracellular vesicles in tissues with Spatial-EV-seq Qianxi Wen ... Chaoyong Yang presented Spatial-EV-seq, a method for in situ spatial profiling of extracellular vesicles (EVs) within their native microenvironmental context. Key points ☑️ An antibody-engineered capture interface to preserve EVs’ spatial distribution ☑️ Rolling circle amplification with EV surface-binding aptamers, enabling fluorescence imaging and molecular profiling ☑️ Resolving location-specific EV–cell communication networks ☑️ Uncovering a spatially orchestrated immunosuppressive axis in an anti-PD1-treated breast cancer mouse model. #singlecellnews

AI-driven discovery of GPNMB CAR T cells as a multi-cancer therapy Daniel Baker ... Carl June developed an artificial intelligence-driven approach for CAR T cell target discovery by integrating single-cell RNA sequencing datasets from human skin cancer and healthy tissue. Highlights 🔸 Large language models used with biological data nominate tractable CAR T cell targets 🔸 GPNMB is expressed on the surface across a broad range of tumor types 🔸 GPNMB CAR T cells eliminate blood and solid tumors in vivo. #singlecellnews

The Human Pancreas Cell Atlas defines a healthy reference framework for disease contextualization and translational benchmarking Shrey Parikh ... Fabian Theis presented the Human Pancreas Cell Atlas, a reference atlas of the healthy human pancreas integrating 815,126 single-cell and single-nucleus transcriptomes from 109 donors. Key points ✔️ 94 cell types and transcriptional states spanning endocrine, exocrine, immune, and stromal compartments ✔️ Rare endocrine populations, including a putative, spatially supported polyhormonal alpha–beta–delta state ✔️ A unified framework for interpreting pancreatic cellular variation across diverse biological and demographic covariates ✔️ Endocrine and epithelial remodeling relative to healthy pancreatic states ✔️ Injury-associated and malignant epithelial ecosystem regions across donors ✔️ Quantitative benchmarking of murine diabetes models and stem-cell-derived islets against human pancreatic reference states. #singlecellnews

OmniCell: unified foundation modelling of single-cell and spatial transcriptomics for cellular and molecular insights   Jiangshuan Pang ... Xun Xu presented OmniCell, a tissue-contextual transcriptomic foundation model pretrained on 67 million dissociated and spatially resolved profiles.   Key points 🔹 Cell-type-specific programmes and tissue-aligned gene modules 🔹 Robust cell-state structure across batches, species and rare populations 🔹 The reconstruction of spatial cell identity, anatomical domains and cell-type composition. #singlecellnews

A multimodal single-cell epigenomic and 3D genome atlas of the human basal ganglia   Wubin Ding ... Joseph Ecker presented a multimodal single-cell atlas profiling DNA methylation and 3D chromatin conformation in 261,331 nuclei across eight subregions, resolving 12 classes, 31 subclasses, and 59 groups. Highlights 🔸 Neuron-specific loops dominate cell-type-specific 3D contact remodeling in the basal ganglia, whereas most non-neuron-specific loops are constitutive 🔸 Spiny Projection Neuron (SPN) subtypes exhibit regionally organized epigenomic and 3D genome signatures that align with dorsal-ventral identities 🔸 Chromatin loops are the primary distinguishing feature among D1, D2, and eccentric SPN subclasses, with eccentric SPNs being the most 3D-reorganized 🔸 Integrated regulatory maps link cell-type-specific enhancers to disease-associated genetic risk 🔸 Non-SPN interneurons differ in distribution and in transcriptional and epigenetic identity across the matrix-striosome boundary #singlecellnews

scParadise: tunable, highly accurate multi-level cell type annotation, unknown cell type identification, and modality imputation Elizaveta Chechekhina ... Vadim Chechekhin proposed scParadise, a Python framework comprising three integrated tools (scAdam, scEve, and scNoah) designed to transform single-cell RNA sequencing datasets into accurate cell types and interpretable multi-omic states. Key points 🔹scAdam enables tunable multi-level cell annotation and unknown cell identification, outperforming existing methods. 🔹scEve provides accurate cross-tissue protein imputation, significantly improving cell clustering. 🔹scParadise corrected major annotation errors in the Tabula Muris Senis atlas, accurately redefining granulocyte and macrophage clusters. 🔹scParadise identified three novel NKT cell subsets in visceral adipose tissue linked to obesity-related immune crosstalk. #singlecellnews

Lamprey 3D single-cell transcriptomics reveals ancestral and specialized features of the vertebrate brain Haixu Wu ... Bing Su sing generated a three-dimensional molecular atlas of the lamprey brain, identifying 209 distinct cell clusters across 14 regions using spatial transcriptomics and single-nucleus RNA sequencing.   Key points 📍 Cross-species conservation of regional spatial architecture, defining an ancestral organizational blueprint 📍 Emerging marked lineage-specific divergence 📍 Extensive neuronal specialization across vertebrate lineages 📍 A cerebellum-like architecture predates the jawed vertebrate cerebellum. #singlecellnews

⚡Dear colleagues! We are glad to announce the 2026 ASCA-MGI-Helicon Spatial Omics Atlas Research (SOAR) Grant Results! 📍Winner📍 ✨Ekaterina Gorshkova, "The Role of Gut-Associated Lymphoid Tissue in Cancer Resistance of Naked Mole-Rats". 📍Top 10% Applicants📍 ✨Tatiana Shnaider, "Defining the Cellular and Spatial Contexts in Which Human Accelerated Regions within the CNTN6 Locus Regulate Human Cortical Development" ✨Nadezhda Tverdova, "Characterization of Spatial Organization and Clonal Architecture of T Cell Immunity in Human Atherosclerotic Plaques" ✨Nikolay Shakhpazyan, "Spatial Transcriptomics of SARIFA in Colorectal Cancer". Congratulations! 🎉 📍The Top 10% Applicants and other eligible participants will receive exclusive discounts on Stereo-seq and single-cell library preparation services and the corresponding sequencing reagents. Eligible applicants will be contacted separately with further details. #ASCAinfo

Multimodal Hypersampling of the adult human heart resolves tissue-specific cell states and disease-associated variants James Cranley ... Sarah Teichmann profiled 28 regions of the adult human heart from 36 donors, combining paired single-nucleus RNA and chromatin accessibility assays with spatial transcriptomics. Key points 📌1,059,175 expression profiles, 452,614 chromatin accessibility profiles, and spatial niches across the heart 📌A valve fibroblast-macrophage niche linked to aortic stenosis susceptibility 📌Pulmonary vein myocardial sleeve cardiomyocytes connected to the PITX2/4q25 atrial fibrillation locus 📌A synthetic smooth muscle cell state defining the coronary subintima, a potential substrate for atherosclerosis 📌Integration of cell state-resolved chromatin accessibility with allele-specific accessibility and fine-tuned sequence-to-function models to prioritise cell type-specific genetic mechanisms. #singlecellnews

A generalizable Hi-C foundation model for chromatin architecture, single-cell and multiomics analysis across species Xiao Wang ... Sheng Wang proposed HiCFoundation, a foundation model trained on massive Hi-C data for integrative analysis linking chromatin structure to downstream regulatory function. Key points ✔️State-of-the-art performance and generalizability across species on various 3D genome analysis ✔️Reproducibility analysis, resolution enhancement and loop detection ✔️Predicting various epigenomic activities from Hi-C ✔️Easy adaptation to single-cell Hi-C data. #singlecellnews

Dear colleagues! ⚡ ➡️️ The program of the ASCA CONGRESS 2026 is already available here 📍Registration is open until July 24, 2026 The program includes 11 sections with talks by key researchers and technology developers in the field of single-cell and spatial analysis. See you soon in Moscow! Sincerely, Organizing Committee #ASCAinfo