Search Results (90)

Oligodendrocytes (OLs) are specialized glial cells essential for the formation and maintenance of the myelin sheath within the central nervous system (CNS). Historically, OLs were considered a functionally homogeneous population. However, the advent and widespread application of single-cell and single-nucleus RNA sequencing (scRNA-seq/snRNA-seq) technologies since 2015 have revealed substantial transcriptional heterogeneity, varying according to developmental stage, anatomical region, and disease state. In this review, we synthesized current advances in the understanding of OL heterogeneity. Nine OL cell classes have been identified in the mouse somatosensory cortex and hippocampal CA1 region, later expanding to 13 distinct subpopulations across ten CNS regions. Furthermore, we characterized disease-associated oligodendrocytes (DAOs)/disease-associated oligodendrocyte lineages (DOLs), identified in various neurological diseases, including multiple sclerosis (MS), Alzheimer’s disease (AD), and spinal cord injury, focusing on their molecular markers, spatial distribution, and pathophysiological roles. We summarized key transcriptional regulatory networks underlying DAO induction, including the signal transducer and activator of transcription (STAT)/interferon regulatory factor (IRF) family, the Yin Yang 1 (YY1)/nuclear factor kappa B (NF-κB) axis, and the SOX9/SOX10 regulatory system. The utility of region-specific brain analyses using spatial transcriptomics (ST) in conjunction with these approaches was also discussed. Finally, we compiled the implications of patient stratification according to white matter glial response patterns derived from large-scale snRNA-seq analyses of patients with progressive MS. Our synthesis shows that oligodendrocytes consist of multiple distinct subtypes that vary across development, brain regions, and disease conditions. In pathological states, they adopt specific disease-associated programs that reflect context-dependent responses and may influence disease progression and repair. This work provides a framework for understanding how oligodendrocyte diversity contributes to neurological disease and may support the development of targeted remyelination therapies. Full article

Diabetic kidney disease (DKD) lacks specific biomarkers reflecting the interplay between mitochondrial dysfunction and immune microenvironment remodeling. To address this, we integrated multi-dataset transcriptomics (GEO, MitoCarta 3.0, GeneCards) with Weighted Gene Co-expression Network Analysis, protein–protein interaction networks, and machine learning algorithms to identify key diagnostic genes. Single-nucleus RNA sequencing was utilized to map cell-type distributions. Subsequently, a single-center cohort of 70 biopsy-confirmed DKD patients was enrolled for validation of the key hub gene, HDAC6. We identified four hub genes: EGF (downregulated), HDAC6, TPM1, and VCAM1 (upregulated). All genes exhibited robust diagnostic efficacy, and single-nucleus analysis revealed distinct renal cell-type enrichment patterns. Clinically, high renal HDAC6 expression correlated with severe interstitial inflammation, elevated complement C3 and cystatin C, and reduced urinary ammonium (a clinical proxy for proximal tubular mitochondrial dysfunction). Crucially, high HDAC6 served as an independent risk factor for both renal endpoints and cardiorenal composite events. In conclusion, EGF, HDAC6, TPM1, and VCAM1 are key regulators in DKD. Specifically, intrarenal HDAC6 quantification serves as a precise histological metric for prognostic stratification and underscores its potential as a therapeutic target for DKD intervention. Full article

Temporal lobe epilepsy (TLE) is the most common focal epilepsy in adults, but cell-type-specific molecular alterations in the epileptic cortex remain incompletely characterized. We performed single-nucleus RNA sequencing on temporal cortex from three patients with drug-resistant TLE and two non-epileptic controls, retaining 66,932 nuclei. Seven major cell types were annotated. Neuropeptide Y (NPY) was significantly upregulated in microglia and oligodendrocytes under stringent criteria (|log₂FC| > 1, adjusted p < 0.01), whereas changes in other cell types did not meet this threshold. Microglia showed enrichment of neuropeptide- and inflammatory-related pathways, together with reduced oxidative phosphorylation signatures. Oligodendrocytes showed altered lipid metabolism, together with reduced mitochondrial energy-related signatures. Inferred intercellular communication was globally reduced in the TLE samples. qPCR in an independent small set showed an upward trend of NPY expression, though not statistically significant. Given the limited cohort size, these results should be interpreted as exploratory. They provide a cell-type-resolved candidate framework for future mechanistic studies of glial-associated responses in human epilepsy. Full article

Papaya (Carica papaya L.) is a widely cultivated tropical and subtropical fruit crop valued for its rich nutritional content, diverse food industry applications, and the medicinal use of papain. However, bitterness in papaya fruit, particularly in fibrous strands, negatively affects fruit quality and consumer acceptance; therefore, the development of papaya cultivars with stable and desirable quality is of great importance. To identify the bitter compounds in papaya fruit fibrous strands and elucidate the molecular mechanisms underlying their biosynthesis, we performed transcriptomic and metabolomic analyses of fibrous strands from two papaya cultivars at three developmental stages. We identified carpaine, dehydrocarpaine II, and their derivative alkaloids. Furthermore, we identified two key regulatory genes, CpNAC82 and CpHD-Zip ANT2, associated with alkaloid biosynthesis. Finally, using single-nucleus RNA sequencing technology, we constructed a comprehensive gene expression atlas of papaya fibrous strands and stems, successfully identifying multiple cell types, including epidermal cells, guard cells, parenchyma cells, and phloem cells. Epidermal and phloem cells serve as the primary sites of alkaloid metabolism in papaya. These findings provide new insights into the molecular mechanisms of bitterness in papaya’s fibrous strands and yield genomic resources for improving fruit quality in papaya. Full article

Background: The cochlea is a specialized sensory organ essential for hearing. To elucidate its cellular and molecular architecture and prioritize candidate genes associated with hearing loss (HL), we constructed a cross-species single-cell transcriptomic atlas of human fetal and postnatal mouse cochleae. Methods: We integrated single-cell and single-nucleus RNA sequencing datasets from human fetal cochleae and postnatal mouse cochleae to build a comprehensive cross-species single-cell transcriptomic atlas. Cell-type annotation, transcriptional regulator analysis, intercellular communication, and disease phenotypes were performed to dissect the cochlear cellular landscape, regulatory programs, and potential HL gene candidates. Results: A total of 19 major cochlear cell types were identified in both species, with conserved cellular composition and transcriptional programs. Comparative analysis revealed strong transcriptional conservation between matched human and mouse cell types, particularly in supporting, schwann cells and hair cells. Cell–cell communication analysis revealed conserved signaling pathways, including the BDNF-NTRK2 axis, potentially involved in cochlear development and auditory function. Regulatory network inference uncovered conserved and previously undercharacterized transcription factors, such as SKOR1, RFX2, and PAX2, predicted to be associated with hair cell identity and function. We further defined a conserved gene module of 3138 hair cell-enriched genes, from which 24 candidate HL-associated genes (e.g., ATP8B1, BDNF, and SOD1) were prioritized through integration with human disease databases and mouse auditory phenotype annotations. Conclusions: This study provides a high-resolution cross-species cochlear atlas, revealing conserved molecular programs and candidate HL-associated genes, offering valuable insights into auditory biology and potential avenues for further investigation. Full article

Glioblastoma (GBM) remains one of the most lethal cancers, and despite advancements in understanding its underlying molecular signature, effective therapeutics are still lacking. The multifaceted challenges of designing treatments for GBM are compounded by the inability to identify a definitive cell of origin, the understanding of which is crucial for developing impactful therapies and ultimately improving patient outcomes. High-resolution technologies, including single-cell and single-nucleus RNA sequencing, spatial transcriptomics, multi-omics, next generation glioma models, bioinformatics, and artificial intelligence are creating an important opportunity to comprehensively map the cellular origin of GBM and its evolutionary dynamics. Accumulating evidence support neural stem cells (NSCs) and oligodendrocyte precursor cells (OPCs) as primary candidates, providing critical insights into the ontogeny of GBM. This comprehensive review synthesizes current knowledge on the cellular origins of GBM and evaluates advanced methodologies, deepening our understanding of its development. Full article

Autism spectrum disorder (ASD) is a neurodevelopmental condition characterized by genetic heterogeneity. Post-transcriptional regulation—particularly alternative polyadenylation (APA)—plays a critical role in the pathogenesis of ASD. APA controls mRNA stability, translational efficiency, and subcellular localization through modulating the length of the 3′ untranslated region of mRNA. APA profiling can uncover functionally relevant post-transcriptional alterations often missed by conventional gene expression analyses. However, current ASD analyses still largely rely on differential gene expression or individual APA event detection, which ignores the collective explanatory power of ASD risk genes or co-dysregulated functional gene modules within specific cell types. In this study, we present an integrative computational framework that combines matrix factorization and machine learning to identify ASD-associated gene modules driven by APA and to predict cell-type-specific ASD-related cells. Applied to human brain single-nucleus RNA sequencing (snRNA-seq) data, our approach systematically uncovers APA regulatory patterns that are specific to cell type, brain region, and sex in ASD. The identified APA modules are significantly enriched in pathways related to synaptic function, neurodevelopment, and immune response, with the strongest signals observed in excitatory neurons of the prefrontal cortex. Using APA genes from these modules as features, we built a classification model that effectively distinguishes ASD cells from normal cells. Moreover, we found that integrating APA with gene expression—two complementary modalities—substantially improves prediction accuracy, underscoring APA as an independent and biologically informative regulatory layer. Our work delineates a high-resolution APA regulatory landscape in ASD, offering novel insights and potential therapeutic avenues beyond transcriptional abundance. Full article

Single-cell RNA sequencing (scRNA-seq) provides a comprehensive understanding of cellular complexity; however, its requirement for fresh or frozen samples limits its flexibility. To overcome this limitation to effectively leverage clinical samples, Chromium Fixed RNA Profiling on formalin-fixed paraffin-embedded (FFPE) tissue blocks (scFFPE-seq) was developed to perform single-nucleus RNA sequencing from nuclei isolated from FFPE. In this study, we utilized fresh tissue samples from colon, ileum, and skin to assess the viability of scFFPE-seq compared to these fresh samples. We were able to recover unique cell types from challenging FFPE tissues and validated scFFPE-seq findings through Hematoxylin and Eosin (H&E) images. The results demonstrated that scFFPE-seq effectively captured the single-cell transcriptome in FFPE tissues, obtaining comparable cell abundance, cell type annotation, and pathway characterization to those in fresh tissues. Overall, the study presents strong evidence of the potential of scFFPE-seq to enhance scientific knowledge by enabling the generation of high-quality, sensitive single-nucleus RNA-seq data from preserved tissue samples. This technique unlocks the vast archives of FFPE samples for extensive retrospective genomic studies. Full article

Atrial fibrillation (AF) is closely linked to atrial remodeling, while its underlying immune mechanisms remain elusive. This study sought to investigate the role of SPP1⁺ macrophages in the development and progression of AF and further elucidate the underlying mechanisms. Single-nucleus RNA sequencing was performed on right atrial tissues from 3 patients with persistent AF and 3 with sinus rhythm (all with rheumatic valvular heart disease). The results revealed significant immune cell infiltration in AF atrial tissues, with a marked increase in the proportion of SPP1⁺ macrophages, which exhibited the strongest intercellular communication with cardiomyocytes. Phenotypic scoring indicated that apoptosis was the dominant mode of cardiomyocyte death in AF. Immunohistochemical and Western blot analyses confirmed elevated levels of pro-apoptotic proteins (Bax, Cleaved-Caspase3) and reduced levels of the anti-apoptotic protein Bcl2 in AF tissues. In a mouse model with macrophage-specific SPP1 overexpression, increased AF inducibility and duration were observed, accompanied by enhanced cardiomyocyte apoptosis. In vitro co-culture experiments using SPP1-overexpressing RAW264.7 macrophages and HL-1 cardiomyocytes confirmed that SPP1⁺ macrophages could induce cardiomyocyte apoptosis. Mechanistically, KEGG and GSEA analyses identified downregulation of the PI3K/AKT pathway in AF. Treatment with the PI3K/AKT activator Recilisib reversed apoptosis and restored p-PI3K/p-AKT levels in HL-1 cells co-cultured with SPP1-overexpressing RAW264.7 macrophages. These findings demonstrate that SPP1⁺ macrophages accumulate in atrial tissues of AF patients and induce cardiomyocyte apoptosis by downregulating the PI3K/AKT pathway, thereby increasing AF susceptibility. Full article

Hypertrophic cardiomyopathy (HCM) is an inherited cardiac disorder most commonly caused by pathogenic variants in sarcomeric genes, yet many patients remain genotype-negative and the mechanisms linking genetic alterations to disease pathology are not fully understood. Traditional bulk analyses have provided limited insight into the cellular and molecular changes that drive disease progression. Recent advances in single-cell and spatial multi-omics technologies now allow detailed characterization of cell type-specific transcriptional programs, signaling pathways, and tissue remodeling within the human myocardium. These approaches have begun to redefine HCM as a complex, multicellular disease rather than a purely sarcomeric disorder. This review summarizes current single-cell and spatial transcriptomic studies of human septal myectomy tissue, outlines their major findings and limitations, and discusses how these data may inform the development of precision medicine strategies in obstructive HCM. Full article

Body color is the most prominent phenotypic trait in animals. To investigate the molecular regulatory mechanisms underlying skin pigmentation and body color in Channa argus, single-nucleus RNA sequencing technology was employed to analyze cell diversity and functional changes in the skin of normal and albino C. argus. Three pigment-related cell types, seven immune-related cell types, and nine other skin-related structural and functional cell types were identified. The skin of albino C. argus, which appears white to the naked eye, contains numerous melanocytes and iridophores with reflective silver properties. Compared to normal C. argus, melanocytes in albino individuals contained fewer melanin granules, while iridophores exhibited increased chromogenic substances. Melanocyte-specific genes—kitlg, myo5a, and scarb1—were significantly downregulated in albino melanocytes (p < 0.05). Conversely, iridophore-specific genes alk, pnp, and gpnmb were significantly upregulated in albino skin, whereas mlph was significantly downregulated (p < 0.05). Weighted gene co-expression network analysis revealed that scarb1 was associated with the melanocyte module, alk was identified as a core gene, and pnp was linked to the iridophore module. Functionally, scarb1 is involved in pigment transport, pnp in purine synthesis, and alk is essential for iridophore development. Therefore, scarb1, pnp, and alk may be correlated to albinism in C. argus. Overall, this study constructed a single-cell transcriptional atlas of C. argus skin, providing valuable reference data for further research into the regulatory mechanisms governing body color formation and maintenance in this species. Full article

Background: Honeybees sustain vital ecological roles through foraging behavior, which provides pollination services and is likely regulated by dopamine signaling coupled to brain energy metabolism. However, the genetic and metabolic mechanisms underlying this regulation remain unclear. Methods: We treated honeybee workers with the dopamine receptor agonist bromocriptine and employed an integrative approach, combining liquid chromatography–mass spectrometry (LC–MS) metabolomics with single-nucleus RNA sequencing (snRNA-seq). Results: Metabolomics revealed increased levels of N6-carboxymethyllysine (CML) and a coordinated shift in central carbon metabolites, including higher glucose, pyruvate, and lactate within glycolysis, and ribose-5-phosphate in the pentose phosphate pathway (PPP). Integration with transcriptomics showed heterogeneous responses: glial cells exhibited higher glycolysis pathway scores and upregulated hexokinase expression compared to neurons, whereas major PPP enzymes were upregulated in both glial and neuronal subsets. Conclusions: These findings suggest that dopamine receptor activation is associated with altered whole-brain metabolic profiles and concurrent, cell-type-specific upregulation of glycolytic and PPP enzyme genes, particularly in glia. This study characterizes these neuro-metabolic associations, offering insights into the cellular and metabolic basis of foraging behavior in worker bees. Full article

Human adult cardiomyocytes (CMs) have limited regenerative capacity, posing a significant challenge in restoring cardiac function following substantial CM loss due to an acute ischemic event or chronic hemodynamic overload. Nearly half of patients show no improvement in left ventricular ejection fraction during recovery from acute myocardial infarction. At baseline, both humans and mice exhibit low but continuous cell turnover originating from the existing CMs. Moreover, myocardial infarction can induce endogenous CM cell cycling. Consequently, research has focused on identifying drivers of CM rejuvenation and proliferation from pre-existing CMs. High-throughput screening has facilitated the discovery of novel pro-proliferative targets through small molecules, microRNAs, and pathway-specific interventions. More recently, omics-based approaches such as single-nucleus RNA sequencing and spatial transcriptomics have expanded our understanding of cardiac cellular heterogeneity. The big-data strategies provide critical insights into why only a subset of CMs re-enter the cell cycle while most remain quiescent. In this review, we compare several high-throughput screening strategies used to identify novel targets for CM proliferation. We also summarize the benefits and limitations of various screening models—including zebrafish embryos, rodent CMs, human induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs), and cardiac organoids—underscoring the importance of integrating multiple systems to uncover new regenerative mechanisms. Further work is needed to identify translatable and safe targets capable of inducing functional CM expansion in clinical settings. By integrating high-throughput screening findings with insights into CM heterogeneity, this review provides a comprehensive framework for advancing cardiac regeneration research and guiding future therapeutic development. Full article

The fields of medical diagnostics, nephrology, and the sequencing of cellular genetic material are pivotal for precise quantification of kidney diseases. Single-cell sequencing, enhanced by automation and software tools, enables efficient examination of biopsies at the individual cell level. This approach shows the complex cellular mosaic that shapes organ function. By quantifying gene expression following injury, single-cell analysis provides insight into disease progression. In this review, new developments in single-cell analysis methods, spatial integration of single-cell analysis, single-nucleus RNA sequencing, and emerging methods, including expression quantitative trait loci, whole-genome sequencing, and whole-exome sequencing in nephrology, are discussed. These advancements are poised to enhance kidney disease diagnostic processes, therapeutic strategies, and patient prognosis. Full article

The United States is currently facing a drug overdose epidemic. The nucleus accumbens core (NAcore), a brain region critical for reward and aversion behaviors, undergoes structural and functional synaptic adaptations in response to chronic drug exposure. However, the molecular mechanisms underlying these adaptations remain poorly understood. In this study, we investigate the role of dual-specificity phosphatase 5 (DUSP5), a phosphatase known to deactivate extracellular signal-regulated kinase (ERK), in cocaine-induced neuroplasticity. While prior research has linked other DUSP family members to various drugs of abuse, the specific role of DUSP5 in cocaine addiction remains unexplored. We hypothesized that lack of DUSP5 contributes to cocaine-induced maladaptive synaptic plasticity in NAcore. To test this, we employed a rat cocaine self-administration model and molecular analyses and mined publicly available single-cell RNA sequencing data from cocaine-treated NAcore. Our findings reveal a role for DUSP5 in cocaine-related synaptic and behavioral adaptations, highlighting DUSP5 and DUSP5-associated signaling pathways as potential mechanisms underlying substance use disorders and as candidates for therapeutic intervention. Full article