Single-cell and spatial omics: exploring hypothalamic heterogeneity DOI Creative Commons
Muhammad Junaid, Eun Jeong Lee, Su Bin Lim

et al.

Neural Regeneration Research, Journal Year: 2024, Volume and Issue: 20(6), P. 1525 - 1540

Published: July 10, 2024

Elucidating the complex dynamic cellular organization in hypothalamus is critical for understanding its role coordinating fundamental body functions. Over past decade, single-cell and spatial omics technologies have significantly evolved, overcoming initial technical challenges capturing analyzing individual cells. These high-throughput now offer a remarkable opportunity to comprehend spatiotemporal patterns of transcriptional diversity cell-type characteristics across entire hypothalamus. Current single-nucleus RNA sequencing methods comprehensively quantify gene expression by exploring distinct phenotypes various subregions However, single-cell/single-nucleus requires isolating cell/nuclei from tissue, potentially resulting loss information concerning neuronal networks. Spatial transcriptomics methods, bypassing cell dissociation, can elucidate intricate neural networks through their imaging technologies. In this review, we highlight applicative value molecular-genetic hypothalamic types, driven recent achievements.

Language: Английский

Mapping the cellular landscape of Atlantic salmon head kidney by single cell and single nucleus transcriptomics DOI Creative Commons
Adriana Magalhães Santos Andresen, Richard S. Taylor, Johanna Hol Fosse

et al.

Fish & Shellfish Immunology, Journal Year: 2024, Volume and Issue: 146, P. 109357 - 109357

Published: Jan. 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.

Language: Английский

Citations

10
Applications and emerging challenges of single-cell RNA sequencing technology in tumor drug discovery DOI
Lu Zhang,

Yueying Yang,

Jianjun Tan

et al.

Drug Discovery Today, Journal Year: 2025, Volume and Issue: unknown, P. 104290 - 104290

Published: Jan. 1, 2025

Language: Английский

Citations

1
Integrative genomics approach identifies glial transcriptomic dysregulation and risk in the cortex of individuals with Alcohol Use Disorder DOI
Anna S. Warden, Nihal A. Salem, Eric Brenner

et al.

Biological Psychiatry, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 1, 2025

Language: Английский

Citations

1
Impaired cortical neuronal homeostasis and cognition after diffuse traumatic brain injury are dependent on microglia and type I interferon responses DOI
Jonathan M. Packer, Chelsea E. Bray,

Nicolas B. Beckman

et al.

Glia, Journal Year: 2023, Volume and Issue: 72(2), P. 300 - 321

Published: Nov. 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

Language: Английский

Citations

17
Adipose tissue macrophage heterogeneity in the single-cell genomics era DOI Open Access

Haneul Kang,

Jongsoon Lee

Molecules and Cells, Journal Year: 2024, Volume and Issue: 47(2), P. 100031 - 100031

Published: Feb. 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.

Language: Английский

Citations

5
A Comprehensive Review on Circulating cfRNA in Plasma: Implications for Disease Diagnosis and Beyond DOI Creative Commons

Pengqiang Zhong,

Lu Bai,

Mengzhi Hong

et al.

Diagnostics, Journal Year: 2024, Volume and Issue: 14(10), P. 1045 - 1045

Published: May 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.

Language: Английский

Citations

5
Single-cell and spatially resolved transcriptomics for liver biology DOI
Ping Lin, Xi Yan, Siyu Jing

et al.

Hepatology, Journal Year: 2023, Volume and Issue: 80(3), P. 698 - 720

Published: April 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.

Language: Английский

Citations

12
SGK1 drives hippocampal demyelination and diabetes-associated cognitive dysfunction in mice DOI Creative Commons

Ziying Jiang,

Bin Liu,

Tangsheng Lu

et al.

Nature Communications, Journal Year: 2025, Volume and Issue: 16(1)

Published: Feb. 17, 2025

Diabetes-associated cognitive dysfunction (DACD) is increasingly recognized as a critical complication of diabetes. The complex pathology DACD remains unknown. Here, we performed single-nucleus RNA sequencing (snRNA-seq) to demonstrate unique cellular and molecular patterns the hippocampus from mouse model More in-depth analysis oligodendrocytes (OLs) distinguished five subclusters, indicating different functional states OLs transcriptional changes in each subcluster. Based on results snRNA-seq experiments vivo, observed demyelination disharmony oligodendroglial lineage cell composition male diabetic mice. Serum/glucocorticoid regulated kinase 1 (SGK1) expression was significantly increased mice, SGK1 knockdown reversed via N-myc downstream-regulated gene (NDRG1)-mediated pathway. findings illustrated landscape hippocampal substantiated impaired myelination DACD. Our provided direct evidence that inhibition or promotion might be potential therapeutic strategy for authors show drives regulating NDRG1 phosphorylation.

Language: Английский

Citations

0
Single-cell omics and heterogeneity of neuroglial cells DOI

Sylvie Lahaie,

Naama Brezner,

Keith K. Murai

et al.

Handbook of clinical neurology, Journal Year: 2025, Volume and Issue: unknown, P. 265 - 275

Published: Jan. 1, 2025

Language: Английский

Citations

0
Techniques and analytic workflow for spatial transcriptomics and its application to allergy and inflammation DOI
Haihan Zhang, Matthew T. Patrick, Jingyu Zhao

et al.

Journal of Allergy and Clinical Immunology, Journal Year: 2025, Volume and Issue: 155(3), P. 678 - 687

Published: Jan. 19, 2025

Language: Английский

Citations

0