Mapping the cellular landscape of Atlantic salmon head kidney by single cell and single nucleus transcriptomics

Fish & Shellfish Immunology, Год журнала: 2024, Номер 146, С. 109357 - 109357

Опубликована: Янв. 4, 2024

Single-cell transcriptomics is the current gold standard for global gene expression profiling, not only in mammals and model species, but also non-model fish species. This a rapidly expanding field, creating deeper understanding of tissue heterogeneity distinct functions individual cells, making it possible to explore complexities immunology on highly resolved level. In this study, we compared two single cell transcriptomic approaches investigate cellular within head kidney healthy farmed Atlantic salmon (Salmo salar). We 14,149 transcriptomes assayed by RNA-seq (scRNA-seq) with 18,067 nuclei captured nucleus RNA-Seq (snRNA-seq). Both detected eight major populations common: granulocytes, heamatopoietic stem erythrocytes, mononuclear phagocytes, thrombocytes, B NK-like T cells. Four additional types, endothelial, epithelial, interrenal, mesenchymal were snRNA-seq dataset, appeared be lost during preparation suspension submitted scRNA-seq library generation. identified subpopulations endothelial revealed developmental trajectories cells into differentiated granulocyte phagocyte populations. Gene profiles subtypes IgM IgT-skewed resting lineages provided insights regulation lymphopoiesis. The analysis eleven sub-populations, displaying level comparable that observed mammals, including subsets cd4/cd8-negative such as tcrγ positive, progenitor-like, cytotoxic Although both useful resolve type-specific kidney, pipeline was overall more robust identifying several types subpopulations. While displayed higher levels ribosomal mitochondrial genes, transcription factor genes. However, scRNA-seq-generated data trajectory inference myeloid lineage. conclusion, study systematically outlines relative merits salmon, enhances teleost immune lineages, provides comprehensive list markers significant relevance.

Язык: Английский

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Applications and emerging challenges of single-cell RNA sequencing technology in tumor drug discovery

Drug Discovery Today, Год журнала: 2025, Номер unknown, С. 104290 - 104290

Опубликована: Янв. 1, 2025

Язык: Английский

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Impaired cortical neuronal homeostasis and cognition after diffuse traumatic brain injury are dependent on microglia and type I interferon responses

Glia, Год журнала: 2023, Номер 72(2), С. 300 - 321

Опубликована: Ноя. 8, 2023

Abstract Neuropsychiatric complications including depression and cognitive decline develop in the years after traumatic brain injury (TBI), negatively affecting quality of life. Microglial type 1 interferon (IFN‐I) responses are associated with transition from acute to chronic neuroinflammation diffuse TBI mice. Thus, purpose this study was determine if impaired neuronal homeostasis increased IFN‐I intersected cause impairment. Here, RNA profile neurons microglia (single nucleus RNA‐sequencing) or without depletion (CSF1R antagonist) assessed 7 dpi. There a TBI‐dependent suppression cortical reductions CREB signaling, synaptogenesis, synaptic migration increases RhoGDI PTEN signaling (Ingenuity Pathway Analysis). reversed 50% TBI‐induced gene changes depending on subtype. Moreover, microglial signature dpi stimulator genes (STING) activation responses. Therefore, we sought reduce using STING knockout mice antagonist, chloroquine (CQ). TBI‐associated deficits novel object location recognition (NOL/NOR) tasks at 30 were dependent. In addition, expression, morphological restructuring, inflammatory ( Tnf, Cd68, Ccl2 ) IFN‐related Irf3, Irf7, Ifi27 expression cortex attenuated KO CQ also reduced IFN Irf7 , Sting expression. Collectively, reducing STING‐dependent interventions prolonged

Язык: Английский

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Integrative genomics approach identifies glial transcriptomic dysregulation and risk in the cortex of individuals with Alcohol Use Disorder

Biological Psychiatry, Год журнала: 2025, Номер unknown

Опубликована: Фев. 1, 2025

Язык: Английский

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A Comprehensive Review on Circulating cfRNA in Plasma: Implications for Disease Diagnosis and Beyond

Diagnostics, Год журнала: 2024, Номер 14(10), С. 1045 - 1045

Опубликована: Май 17, 2024

Circulating cfRNA in plasma has emerged as a fascinating area of research with potential applications disease diagnosis, monitoring, and personalized medicine. RNA sequencing technology allows for the non-invasive collection important information about expression target genes, eliminating need biopsies. This comprehensive review aims to provide detailed overview current knowledge advancements study cfRNA, focusing on its diverse landscape biological functions, detection methods, diagnostic prognostic various diseases, challenges, future perspectives.

Язык: Английский

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Single-cell and spatially resolved transcriptomics for liver biology

Hepatology, Год журнала: 2023, Номер 80(3), С. 698 - 720

Опубликована: Апрель 1, 2023

Single-cell transcriptomics enables the identification of rare cell types and inference state transitions, whereas spatially resolved allows quantification cells genes in context tissues. The recent progress these new technologies is improving our understanding landscape its roles diseases. Here, we review key biological insights into liver homeostasis, development, regeneration, chronic disease, cancer obtained from single-cell transcriptomics. We highlight atlas that characterizes comprehensive cellular composition; diversity function; spatial architecture such as zonation, communication, proximity; identity conversion cell-specific alterations are associated with pathology; therapeutic targets. further discuss outstanding challenges, advanced experimental technologies, computational methods help to address challenges.

Язык: Английский

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Adipose tissue macrophage heterogeneity in the single-cell genomics era

Molecules and Cells, Год журнала: 2024, Номер 47(2), С. 100031 - 100031

Опубликована: Фев. 1, 2024

It is now well accepted that obesity-induced inflammation plays an important role in the development of insulin resistance and Type 2 Diabetes (T2D). A key source murine epididymal human visceral adipose tissue. The current paradigm obesity activates multiple pro-inflammatory immune cell types tissue, including adipose-tissue macrophages (ATMs), Th1 T cells, NK while concomitantly suppressing anti-inflammatory cells such as Th2 Tregs. feature induces M2 ATMs lean tissue to polarize into M1 ATMs. However, recent single-cell transcriptomics studies suggest story much more complex. Here we describe genomics technologies have been developed recently, emerging results from using these technologies. While further are needed, it clear highly heterogeneous. Moreover, a variety ATM clusters with quite distinct features found be expanded by obesity, none truly resemble classical likely technology will revolutionize field, thereby promoting our understanding ATMs, inflammation, accelerating therapies for T2D.

Язык: Английский

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Techniques and analytic workflow for spatial transcriptomics and its application to allergy and inflammation

Journal of Allergy and Clinical Immunology, Год журнала: 2025, Номер 155(3), С. 678 - 687

Опубликована: Янв. 19, 2025

Язык: Английский

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Single-cell RNA sequencing in autoimmune diseases: New insights and challenges

Pharmacology & Therapeutics, Год журнала: 2025, Номер unknown, С. 108807 - 108807

Опубликована: Янв. 1, 2025

Язык: Английский

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A versatile and efficient method to isolate nuclei from low-input cryopreserved tissues for single-nuclei transcriptomics

Scientific Reports, Год журнала: 2025, Номер 15(1)

Опубликована: Фев. 15, 2025

Clinical samples are vital for understanding diseases, but their scarcity requires refined research methods. Emerging single-cell technologies offer detailed views of tissue heterogeneity need sufficient fully characterized tissues. We developed an optimized single-nuclei RNA sequencing (snRNA-seq) protocol to extract nuclei from just 15 mg cryopreserved human tissue. Applied four cancer tissues (brain, bladder, lung, prostate), it profiled 1550–7468 per tissue, revealing comparable public atlases. This method enhances the use and sharing rare, biospecimens, supporting where sample quantity is limited full characterization needed.

Язык: Английский

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