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Single-cell or single-nucleus transcriptomics is a powerful tool for identifying cell types and cell states. However, hypotheses derived from these assays, including gene expression information, require validation, and their functional relevance needs to be established. The choice of validation depends on numerous factors. Here, we present types of orthogonal and functional validation experiment to strengthen preliminary findings obtained using single-cell and single-nucleus transcriptomics as well as the challenges and limitations of these approaches.
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http://dx.doi.org/10.1038/s41593-024-01814-0 | DOI Listing |
Cancer Cell
July 2025
Department of Lymphoma and Myeloma, University of Texas (UT) MD Anderson Cancer Center, Houston, TX, USA; Lymphoid Malignancies Program, UT MD Anderson Cancer Center, Houston, TX, USA; Department of Genomic Medicine, UT MD Anderson Cancer Center, Houston, TX, USA. Electronic address: mgreen5@mdander
Large B cell lymphomas (LBCL) are clinically and biologically heterogeneous lymphoid malignancies with complex microenvironments that are central to disease etiology. Here, we have employed single-nucleus multiome profiling of 232 tumor and control biopsies to characterize diverse cell types and subsets that are present in LBCL tumors, effectively capturing the lymphoid, myeloid, and non-hematopoietic cell compartments. Cell subsets co-occurred in stereotypical lymphoma microenvironment archetype profiles (LymphoMAPs) defined by; (1) a sparsity of T cells and high frequencies of cancer-associated fibroblasts and tumor-associated macrophages (FMAC); (2) lymph node architectural cell types with naive and memory T cells (LN); or (3) activated macrophages and exhausted CD8 T cells (TEX).
View Article and Find Full Text PDFCell Rep
September 2025
Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA; Center for Neurogenetics, Weill Cornell Medicine, New York, NY, USA. Electronic address:
Progranulin-deficient frontotemporal dementia (GRN-FTD) is a major cause of familial FTD with TAR DNA-binding protein 43 (TDP-43) pathology, which is linked to exon dysregulation. However, little is known about this dysregulation in glial and neuronal cells. Here, using splice-junction-covering enrichment probes, we introduce single-nuclei long-read RNA sequencing 2 (SnISOr-Seq2), targeting 3,630 high-interest genes without loss of precision, and complete the first single-cell, long-read-resolved case-control study for neurodegeneration.
View Article and Find Full Text PDFCell type markers have been instrumental to physiological and molecular investigation of the human brain and remain essential for annotating cell type clusters in single-cell expression data and for targeted validation studies. However, expression of canonical markers in the target cell type (which we termed as the expression 'fidelity') as well as expression in unrelated cell types (which we termed as the 'background expression') across cortical regions remains poorly characterized. Using nearly 500,000 high-quality single-nucleus profiles from 19 studies, we quantified marker fidelity, revealing substantial regional variability.
View Article and Find Full Text PDFCell Mol Gastroenterol Hepatol
September 2025
Ajmera Transplant Centre, University Health Network, Toronto, ON; Department of Immunology, University of Toronto, Toronto, ON; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON. Electronic address:
Background & Aims: Interleukin-4 (IL-4) is a key contributor to liver regeneration but its effects remain poorly understood due to a lack of models that preserve the complex cellular interactions of the liver. Here, we use murine precision-cut liver slices (PCLS), a 3D tissue culture system that maintains both parenchymal and non-parenchymal cells, to investigate the role of IL-4 in hepatic cell reprogramming. Through longitudinal single-cell transcriptomics and protein-level validation, we demonstrate the pro-regenerative potential of IL-4.
View Article and Find Full Text PDFNeural Regen Res
September 2025
Shenzhen Key Laboratory of Systems Medicine in Inflammatory Diseases, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong Province, China.
Mitochondrial DNA variants have been linked to cognitive progression in Parkinson's disease; however, the mechanisms by which mitochondrial DNA variants or haplogroups contribute to this process remain unclear. In the present study, we analyzed single-nucleus RNA sequencing data from 241 post-mortem brain samples across five regions to investigate the dysregulatory mechanisms associated with mitochondrial DNA haplogroup H and haplogroups J, T, and U#. Our findings revealed significant alterations in the proportions of astrocyte subtypes CHI3L1 and GRM3 in the neocortical regions of haplogroup H.
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