Search

5,10-Methylenetetrahydrofolate reductase (MTHFR, MIM #607093) is a key enzyme in the folate cycle that catalyzes the conversion of 5,10-methylenetetrahydrofolate (5,10-MTHF) to 5-methyltetrahydrofolate (5-methylTHF), a critical step for the remethylation of homocysteine to methionine. Methylenetetrahydrofolate reductase deficiency is an autosomal recessive disease and the most common congenital defect in folate metabolism. A deficiency in MTHFR results in elevated serum homocysteine levels. In this study, we evaluated a patient diagnosed with epilepsy and elevated homocysteine levels, who carried compound heterozygous variants c.781-6G>A and c.1316T>C in the MTHFR gene. We primarily focused on the unreported non-canonical splicing variants c.781-6G>A in this patient and identified several complex splicing variant patterns. The c.1316T>C variant results in a substitution of leucine at position 439 with proline and this variant has been previously reported and is considered pathogenic. Our study mainly utilized RNA-seq and TA cloning to reveal the complex splicing patterns exhibited by this non-canonical splicing variant. Additionally, this finding was confirmed through in vitro experiments. This provided deeper insights into the underlying reasons for the patient's disease manifestation. Furthermore, despite apparently normal circulating folate and vitamin B12, we found two family members to exhibit mildly elevated homocysteine levels. While these individuals did not present overt clinical symptoms, the potential harm associated with high homocysteine levels should not be overlooked. This study not only provides additional genetic evidence for the clinical diagnosis of the patient but also broadens our understanding of the clinical manifestations of MTHFR deficiency., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)

Bisphenol compounds (BPs) have various industrial uses and can enter the environment through various sources. To evaluate the ecotoxicity of BPs and identify potential gene candidates involved in the plant toxicity, Arabidopsis thaliana was exposed to bisphenol A (BPA), BPB, BPE, BPF, and BPS at 1, 3, 10 mg/L for a duration of 14 days, and their growth status were monitored. At day 14, roots and leaves were collected for internal BPs exposure concentration detection, RNA-seq (only roots), and morphological observations. As shown in the results, exposure to BPs significantly disturbed root elongation, exhibiting a trend of stimulation at low concentration and inhibition at high concentration. Additionally, BPs exhibited pronounced generation of reactive oxygen species, while none of the pollutants caused significant changes in root morphology. Internal exposure concentration analysis indicated that BPs tended to accumulate in the roots, with BPS exhibiting the highest level of accumulation. The results of RNA-seq indicated that the shared 211 differently expressed genes (DEGs) of these 5 exposure groups were enriched in defense response, generation of precursor metabolites, response to organic substance, response to oxygen-containing, response to hormone, oxidation-reduction process and so on. Regarding unique DEGs in each group, BPS was mainly associated with the redox pathway, BPB primarily influenced seed germination, and BPA, BPE and BPF were primarily involved in metabolic signaling pathways. Our results provide new insights for BPs induced adverse effects on Arabidopsis thaliana and suggest that the ecological risks associated with BPA alternatives cannot be ignored., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this article., (Copyright © 2024. Published by Elsevier B.V.)

Purpose: Radiation-induced gliomas (RIGs) are fatal late complications of radiation therapy, with a median survival time of 6 to 11 months. RIGs demonstrate a unique molecular landscape and may originate from a glial lineage distinct from that of primary malignancies or diffuse midline gliomas (DMGs). This study aimed to explore the intratumoral diversity within RIGs to uncover their cellular origin and characteristics and enhance our understanding of this uncommon tumor type., Methods and Materials: Formalin-fixed, paraffin-embedded samples were collected from 2 RIGs and 2 DMGs for single-nucleus RNA sequencing. A detailed analysis was conducted to assess intratumoral heterogeneity and cellular interactions, including gene set enrichment, pseudotime trajectory, and cell communication analyses. Immunofluorescence staining, proliferation assay, and RNA-seq analysis were also applied to validate our findings., Results: Our analysis revealed distinct heterogeneity in oligodendrocytes (ODs) between the DMG and RIG samples. A unique subpopulation of ODs in RIGs, which was characterized by gene encoding mesenchymal-epithelial transition factor (MET), and therefore termed MET+ ODs, exhibited characteristics typical of cancer cells, such as increased mitotic activity, cancer-related gene expression, and extensive copy number variations. Cell communication studies indicated that MET+ ODs interact vigorously with G1/S and G2/M cycling cells via the neural cell adhesion molecule signaling pathway, potentially enhancing the proliferation of cycling malignant cells. Integrating our results with existing RNA-seq data further supported our hypothesis. The presence of MET+ ODs in RIGs was confirmed by immunostaining, and activation of the neural cell adhesion molecule signaling pathway in vitro significantly promoted the proliferation of RIG tumor cells. Moreover, in vitro radiation induced the transformation of ODs to be more similar to MET+ ODs., Conclusions: RIGs are characterized by an OD composition distinct from that of DMGs. A specific subpopulation of MET+ ODs in RIGs may be crucial in tumorigenesis and promote the growth of malignant cells. Identifying MET+ ODs offers a valuable target for future clinical surveillance and therapeutic strategies., (Copyright © 2024 The Authors. Published by Elsevier Inc. All rights reserved.)

Abstract: Background : Extracorporeal membrane oxygenation (ECMO) is an effective technique for providing short-term mechanical support to the heart, lungs, or both. During ECMO treatment, the inflammatory response, particularly involving cytokines, plays a crucial role in pathophysiology. However, the potential effects of cytokines on patients receiving ECMO are not comprehensively understood. Methods : We acquired three ECMO support datasets, namely two bulk and one single-cell RNA sequencing (RNA-seq), from the Gene Expression Omnibus (GEO) combined with hospital cohorts to investigate the expression pattern and potential biological processes of cytokine-related genes (CRGs) in patients under ECMO. Subsequently, machine learning approaches, including support vector machine (SVM), random forest (RF), modified Lasso penalized regression, extreme gradient boosting (XGBoost), and artificial neural network (ANN), were applied to identify hub CRGs, thus developing a prediction model called CRG classifier. The predictive and prognostic performance of the model was comprehensively evaluated in GEO and hospital cohorts. Finally, we mechanistically analyzed the relationship between hub cytokines, immune cells, and pivotal molecular pathways. Results : Analyzing bulk and single-cell RNA-seq data revealed that most CRGs were significantly differentially expressed; the enrichment scores of cytokine and cytokine-cytokine receptor (CCR) interaction were significantly higher during ECMO. Based on multiple machine learning algorithms, nine key CRGs (CCL2, CCL4, IFNG, IL1R2, IL20RB, IL31RA, IL4, IL7, and IL7R) were used to develop the CRG classifier. The CRG classifier exhibited excellent prognostic values (AUC > 0.85), serving as an independent risk factor. It performed better in predicting mortality and yielded a larger net benefit than other clinical features in GEO and hospital cohorts. Additionally, IL1R2, CCL4, and IL7R were predominantly expressed in monocytes, NK cells, and T cells, respectively. Their expression was significantly positively correlated with the relative abundance of corresponding immune cells. Gene set variation analysis (GSVA) revealed that para-inflammation, complement and coagulation cascades, and IL6/JAK/STAT3 signaling were significantly enriched in the subgroup that died after receiving ECMO. Spearman correlation analyses and Mantel tests revealed that the expression of hub cytokines (IL1R2, CCL4, and IL7R) and pivotal molecular pathways scores (complement and coagulation cascades, IL6/JAK/STAT3 signaling, and para-inflammation) were closely related. Conclusion : A predictive model (CRG classifier) comprising nine CRGs based on multiple machine learning algorithms was constructed, potentially assisting clinicians in guiding individualized ECMO treatment. Additionally, elucidating the underlying mechanistic pathways of cytokines during ECMO will provide new insights into its treatment., Competing Interests: The authors report no conflicts of interest., (Copyright © 2024 The Author(s). Published by Wolters Kluwer Health, Inc. on behalf of the Shock Society.)

Background: The occurrence of thoracic aortic dissection (TAD) is closely related to the transformation of vascular smooth muscle cells (VSMCs) from a contractile to a synthetic phenotype. The role of SGK1 (serum- and glucocorticoid-regulated kinase 1) in VSMC phenotypic transformation and TAD occurrence is unclear., Methods: Four-week-old male Sgk1 F/F ( Sgk1 floxed) and Sgk1 F/F ;Tagln Cre (smooth muscle cell-specific Sgk1 knockout) mice were administered β-aminopropionitrile monofumarate for 4 weeks to model TAD. The SGK1 inhibitor GSK650394 was administered daily via intraperitoneal injection to treat the mouse model of TAD. Immunopurification and mass spectrometry were used to identify proteins that interact with SGK1. Immunoprecipitation, immunofluorescence colocalization, and GST (glutathione S-transferase) pull-down were used to detect molecular interactions between SGK1 and SIRT6 (sirtuin 6). RNA-sequencing analysis was performed to evaluate changes in the SIRT6 transcriptome. Quantitative chromatin immunoprecipitation was used to determine the target genes regulated by SIRT6. Functional experiments were also conducted to investigate the role of SGK1-SIRT6-MMP9 (matrix metalloproteinase 9) in VSMC phenotypic transformation. The effect of SGK1 regulation on target genes was evaluated in human and mouse TAD samples., Results: Sgk1 F/F ;Tagln Cre or pharmacological blockade of Sgk1 inhibited the formation and rupture of β-aminopropionitrile monofumarate-induced TADs in mice and reduced the degradation of the ECM (extracellular matrix) in vessels. Mechanistically, SGK1 promoted the ubiquitination and degradation of SIRT6 by phosphorylating SIRT6 at Ser338, thereby reducing the expression of the SIRT6 protein. Furthermore, SIRT6 transcriptionally inhibits the expression of MMP9 through epigenetic modification, forming the SGK1-SIRT6-MMP9 regulatory axis, which participates in the ECM signaling pathway. Additionally, our data showed that the lack of SGK1-mediated inhibition of ECM degradation and VSMC phenotypic transformation is partially dependent on the regulatory effect of SIRT6-MMP9., Conclusions: These findings highlight the key role of SGK1 in the pathogenesis of TAD. A lack of SGK1 inhibits VSMC phenotypic transformation by regulating the SIRT6-MMP9 axis, providing insights into potential epigenetic strategies for TAD treatment., Competing Interests: None.

Aims: This narrative review aims to synthesize current knowledge on integrating single-cell genomics technologies with animal models of periodontitis and peri-implantitis., Review: Single-cell RNA sequencing (scRNAseq) reveals cellular heterogeneity and specific cell roles in periodontitis and peri-implantitis, overcoming the limitations of bulk RNA sequencing. Under controlled conditions and genetic manipulation, animal models facilitate studying disease progression, gene functions and systemic disease links, aiding targeted therapy development. Knockout models have started to elucidate the impact of genetic mutations on periodontal disease and host responses. scRNAseq in animal models has been used to examine connections between periodontitis and systemic diseases, revealing altered immune environments and cellular interactions. Emerging studies are now applying these methods to animal models of peri-implantitis. Integrating these datasets into single-cell and spatially resolved atlases will enable future meta-analyses, providing deeper insights into disease mechanisms considering factors such as sex, strain, and age., Conclusions: Integrating scRNAseq with animal models advances the understanding of periodontitis and peri-implantitis pathogenesis and precision therapies. The combined use of single-cell and spatial genomics and scRNAseq will further enhance data insights significantly for drug discovery and preclinical testing, making these technologies pivotal in validating animal models and translating findings into clinical practice., (© 2024 The Author(s). Journal of Clinical Periodontology published by John Wiley & Sons Ltd.)

Sidedness and staging are major sources of tumor microenvironment (TME) differences in colorectal cancer (CRC). Subpopulation compositions of stromal cells and immune cells, and interactions between cells collectively constitute the immunosuppressive microenvironment of CRC. In this study, we comprehensively collected single-cell RNA sequencing data from public databases. We filtered out 126,279 cells from 55 CRC samples to characterize the differences in cellular composition, and to elucidate the transcriptional features and potential functions of cell types, temporally and positionally. We observed an increased degree of hypoxia in right side-specific cancer cells compared to left-sided cancer. Cancer-associated fibroblasts (CAFs) illustrated molecular signatures tremendously tended to be associated with functions that orchestrate extracellular matrix remodeling and angiogenesis, and right-sided CAFs characterized the stronger cancer invasion signals. Crosstalk between side-specific cancer cells and stromal together with immune cells characterized CRC via different sample groups, and was pertinent to worse prognosis. Our study captured immunosuppressive pattern exhibiting more intricate intercellular interactions in right-sided CRC. Additionally, during malignant progression of CRC, the transformation of CD8+ T cell cytotoxic and exhausted properties and macrophage pro-inflammatory and anti-inflammatory properties epitomized the cellular reprogramming phenomenon that the function of TME shifted from promoting immunity to suppressive immunity. Our study shed lights on refining personalized therapeutic regimens during malignant progression in left- and right-sided CRCs., Competing Interests: Declaration of competing interest The authors declare that they have no competing interests., (Copyright © 2024 The Author(s). Published by Elsevier Inc. All rights reserved.)

Background & Aims: Despite the success of biological therapies in treating inflammatory bowel disease, managing patients remains challenging due to the absence of reliable predictors of therapy response., Methods: In this study, we prospectively sampled 2 cohorts of patients with inflammatory bowel disease receiving the anti-integrin α4β7 antibody vedolizumab. Samples were subjected to mass cytometry; single-cell RNA sequencing; single-cell B and T cell receptor sequencing (BCR/TCR-seq); serum proteomics; and multiparametric flow cytometry to comprehensively assess vedolizumab-induced immunologic changes in the peripheral blood and their potential associations with treatment response., Results: Vedolizumab treatment led to substantial alterations in the abundance of circulating immune cell lineages and modified the T-cell receptor diversity of gut-homing CD4 + memory T cells. Through integration of multimodal parameters and machine learning, we identified a significant increase in proliferating CD4 + memory T cells among nonresponders before treatment compared with responders. This predictive T-cell signature demonstrated an activated T-helper 1/T-helper 17 cell phenotype and exhibited elevated levels of integrin α4β1, potentially making these cells less susceptible to direct targeting by vedolizumab., Conclusions: These findings provide a reliable predictive classifier with significant implications for personalized inflammatory bowel disease management., (Copyright © 2025 The Authors. Published by Elsevier Inc. All rights reserved.)

Ethnopharmacological Relevance: Xiaoyaosan, a classic Chinese herbal formula, exhibits promising antidepressant effects. However, its specific antidepressant mechanisms remain incompletely understood. Previous studies have highlighted the significant role of DNA methylation in the pathogenesis of major depressive disorder (MDD). Yet, whether the effects of Xiaoyaosan are linked to DNA methylation and its regulation remains unclear., Aim of the Study: This study aims to explore and verify the molecular mechanism of Xiaoyaosan in treating MDD via integrated analysis of DNA methylation and RNA sequencing., Materials and Methods: In this study, a chronic unpredictable mild stress (CUMS) model was established to induce MDD in rats, which were subsequently orally treated with Xiaoyaosan, with fluoxetine as a positive control. Antidepressant effects were assessed by the open field test, sucrose preference test, and forced swimming test. Whole-genome bisulfite sequencing (WGBS) and bulk RNA sequencing were performed in the arcuate nucleus of hypothalamus to assess methylation changes and identify differentially expressed genes. Bioinformatics analyses were conducted to explore methylation alterations, RNA sequencing profiles, and their shared epigenetic as well as gene expression changes, to identify candidate genes. Finally, RT-PCR was used to validate the key differential genes., Results: Xiaoyaosan effectively reversed depressive-like behaviors. Further, Xiaoyaosan treatment involved multiple epigenetic modifications. The results of differentially methylated genes showed that there were 1353 overlapped genes between M-vs-C-hypo gene and X-vs-M-hyper gene, 5326 overlapped genes between M-vs-C-hyper gene and X-vs-M-hypo gene. GO and KEGG enrichment analyses indicated these intersecting genes were involved in biological regulation, transcription factors, appetite and endocrine control systems, etc. The analysis of differentially expressed genes from RNA sequencing revealed that there were 25 overlapping genes between the M vs C hypomethylated group and the X vs M hypermethylated group, while 81 overlapping genes were identified between the M vs C hypermethylated group and the X vs M hypomethylated group. Those differential genes regulated by methylation enriched in processes related to brain and neuronal growth, neuropeptide and hormone activation, as well as biological processes and molecular functions associated with protein translation, synthesis, transport, and localization. The integrated analysis of DNA methylation and RNA sequencing screened 14 potentially differential genes, which were associated with appetite regulation, energy metabolism, and neuroreceptor ligands. PCR verification found that Lmx1b, Abcc5, Gpc3 and Cfb showed statistical differences., Conclusions: The antidepressant mechanism of Xiaoyaosan involves the biological regulation in the arcuate nucleus of hypothalamus, including transcription factors, neurotransmitter regulation, neural development, appetite regulation peptides, and endocrine control systems. The methylation level and regulation at the gene locus of Lmx1b, Abcc5, Gpc3, and Cfb may play a key role in the treatment of Xiaoyaosan. These findings provide new insights into the therapeutic mechanisms of Xiaoyaosan., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024. Published by Elsevier B.V.)

Background: This study aimed to investigate the key molecular mechanisms underlying keloid pathogenesis by integrating oxidative stress, mitochondria, and immune cells., Methods: Transcriptome sequencing (mRNA, lncRNA, and circRNA expression data), proteomic sequencing, and small RNA sequencing analyses of lesional and non-lesional skin of patients with keloids and healthy control (normal) skin were conducted. By integrating mRNA and publicly available gene expression data (GSE158395), differentially expressed genes related to oxidative stress and mitochondrial function in keloids were identified. Hub genes were identified using various bioinformatics analyses such as immune infiltration analysis, weighted gene co-expression network analysis, machine learning, and expression validation using proteomics sequencing data. Moreover, a competing endogenous RNA (ceRNA) network of hub genes was constructed by combining miRNA, lncRNA, and circRNA expression data. Five hub genes were identified: MGST1, DHCR24, ALDH3A2, ADH1B, and FKBP5., Results: These hub genes had a high diagnostic value for keloids, with an AUC value > 0.8 each. In addition, five hub genes were associated with the infiltration of multiple immune cells. The immune cells with the strongest positive and negative correlations with hub genes were M0 and M1 macrophages. A ceRNA network was constructed, and several ceRNAs, such as AC005062.1/miR-134-5p/FKBP5 and BASP1-AS1/miR-503-5p/ADH1B, were identified. These five hub genes may contribute to keloid pathogenesis., Conclusion: These genes and their related ceRNAs may serve as diagnostic biomarkers and therapeutic targets for keloids., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024. Published by Elsevier B.V.)

Remote research studies are an invaluable tool for reaching populations with limited access to large medical centers or universities. To expand the remote study toolkit, we previously developed homeRNA, which allows for at-home self-collection and stabilization of blood and demonstrated the feasibility of using homeRNA in high temperature climates. Here, we expand upon this work through a systematic study exploring the effects of high temperature on RNA integrity (represented as RNA Integrity Number, RIN) through in-lab and field experiments. Compared to the frozen controls (overall mean RIN of 8.2, n = 8), samples kept at 37 °C for 2, 4, and 8 days had mean RINs of 7.6, 5.9, and 5.2 ( n = 3), respectively, indicating that typical shipping conditions (∼2 days) yield samples suitable for downstream RNA sequencing. Shorter time intervals (6 h) resulted in minimal RNA degradation (median RIN of 6.4, n = 3) even at higher temperatures (50 °C) compared to the frozen control (mean RIN of 7.8, n = 3). Additionally, we shipped homeRNA-stabilized blood from a single donor to 14 states and back during the summer with continuous temperature probes (7.1 median RIN, n = 42). Samples from all locations were analyzed with 3' mRNA-seq to assess differences in gene counts, with the data suggesting that there was no preferential degradation of transcripts as a result of different shipping times, temperatures, and regions. Overall, our data support that homeRNA can be used in elevated temperature conditions, enabling decentralized sample collection for telemedicine, global health, and clinical research.

Objective: This study aims to elucidate the primary signaling communication among papillary craniopharyngioma (PCP) tumor cells., Methods: Five samples of PCP were utilized for single-cell RNA sequencing. The most relevant ligand and receptor interactions among different cells were calculated using the CellChat package in R software. Bulk RNA sequencing of 11 tumor samples and five normal controls was used to investigate the pair interactions detected by single-cell RNA sequencing., Results: Fibroblasts were not found in ACP, whereas they were detected in PCP. InferCNV revealed high CNV scores for the clusters of epithelial cells and fibroblasts using immune cells as a reference. Epithelial Mesenchymal Transition, Interferon Gamma Response, p53 Pathway, and Estrogen Response Early are pathways commonly shared by fibroblasts and epithelial cells, ranking high in priority. The Wnt signaling pathway and PI3K-Akt signaling pathway play a crucial role in facilitating communication between epithelial cells and fibroblasts. Neutrophils were recognized as the main receivers of incoming signals, with ANXA1-FPR1 and MIF-(CD74 + CXCR2) being identified as the primary signals transmitted from fibroblasts to neutrophils., Conclusion: Through analyzing the communication of essential signaling pathways, ligands, and receptors among epithelial cells, fibroblasts, and neutrophils in PCP tumor tissues, we have identified certain molecules with promising prognostic and therapeutic potential., Competing Interests: Declarations. Competing interests: The authors declare that they have no competing interests., (© 2025. The Author(s).)

Background: Pathogenic variants in the DMD gene are associated with dystrophinopathy including Duchenne and Becker muscular dystrophy (DMD/BMD). Targeted DMD gene, gene panels, exomes and genome sequencing have advanced genetic diagnostics, yet some cases remain elusive., Methods: We performed total RNA sequencing (RNAseq) on muscle biopsy from 13 male patients with a clinical diagnosis of DMD/BMD. Splice aberration events are evaluated using the Integrative Genomics Viewers. Targeted DNA sequencing result was used/re-analysed to confirm complex rearrangement events identified., Results: RNAseq identified aberration splicing or expression events in the DMD gene of 12 cases. Splice-altering intronic single nucleotide variant events including c.7309+5G>T, c.7309+5G>A, c.3276+1G>A and c.3603+820G>T were identified in four cases. Splice-altering events were also detected in one case with small indel c.94-38_94del and two cases with intragenic deletions (exons 51-52 and 45-47 deletions). Furthermore, complex DNA rearrangements inducing aberration splicing/expression events were identified in five cases involving exons 44-45, 55-56, 2-79, 45-79 or 68-79, which were concordant with their DNA sequencing reanalysis results. Some cases with exon deletions have presented non-canonical transcripts expression. The RNAseq result showing aberrant splicing/expression in different exon regions in most of these cases corresponded with their immunohistochemical dystrophin staining results and/or clinical symptoms., Conclusion: Our data demonstrated RNAseq is a powerful tool to provide functional data for DMD splice aberration events, especially when integrating with immunohistochemical testing and DNA sequencing, for elucidating the pathogenicity of DMD variants and achieving a precise genetic diagnosis in patients with DMD/BMD clinical presentation but without definitive diagnoses after routine genetic testing., Competing Interests: Competing interests: YP, BRRN, RL, NG, DL, ZM, AM, FG, MH are employees of Revvity Omics and may hold stock or stock options in Revvity. KB and ASM are staff members of Parent Project Muscular Dystrophy., (© Author(s) (or their employer(s)) 2025. No commercial re-use. See rights and permissions. Published by BMJ Group.)

Atopic dermatitis (AD) is characterized by dysregulated T cell immunity and skin microbiome dysbiosis with predominance of Staphylococcus aureus, which is associated with exacerbating AD skin inflammation. Specific glycosylation patterns of S. aureus cell wall structures amplify skin inflammation through interaction with Langerhans cells (LCs). Nevertheless, the role of LCs in AD remains poorly characterized. Here, we performed single cell RNA sequencing of primary epidermal LCs and dermal T cells, isolated from skin biopsies of AD patients and healthy control subjects, alongside specific glycoanalysis of S. aureus strains isolated from the AD lesions. Our findings revealed 4 LC subpopulations ie, 2 steady-state clusters [LC1 and LC1H] and 2 proinflammatory/matured subsets [LC2 and migratory LCs]. The latter 2 subsets were enriched in AD skin. AD LCs showed enhanced expression of C-type lectin receptors, the high-affinity IgE receptor, and activation of prostaglandin and leukotriene biosynthesis pathways, upregulated transcriptional signatures related to T cell activation pathways, and increased expression of CCL17 compared with healthy LCs. Correspondingly, T helper 2 and T regulatory cell populations were increased in AD lesions. Complementary, we performed bulk RNA sequencing of primary LCs stimulated with the S. aureus strains isolated from the AD lesions, which showed upregulation of T helper 2-related pathways. Our study provides proof-of-concept for a role of LCs in connecting the S. aureus-T cell axis in the AD inflammatory cycle., (© The Author(s) 2025. Published by Oxford University Press on behalf of The American Association of Immunologists.)

Background: Malignant clones of primary cutaneous T-cell lymphomas (CTCL) can show a CD4+, CD8+ or T-cell receptor (TCR)-γδ+ phenotype, but their individual impact on tumour biology and skin lesion formation remains ill defined., Objectives: To perform a comprehensive molecular characterization of CD4+ vs. CD8+ and TCR-γδ+ CTCL lesions., Methods: We performed single-cell RNA sequencing (scRNAseq) of 18 CTCL skin biopsies to compare classic CD4+ advanced-stage mycosis fungoides (MF) with TCR-γ/δ+ MF and primary cutaneous CD8+ aggressive epidermotropic cytotoxic T-cell lymphoma (Berti lymphoma)., Results: Malignant clones of TCR-γ/δ+ MF and Bertilymphoma showed similar clustering patterns distinct from CD4+ MF, along with increased expression of cytotoxic markers such as NKG7, CTSW, GZMA and GZMM. Only advanced-stage CD4+ MF clones expressed central memory T-cell markers (SELL, CCR7, LEF1), alongside B1/B2 blood involvement, whereas TCR-γδ+ MF and Berti lymphoma harboured a more tissue-resident phenotype (CD69, CXCR4, NR4A1) without detectable cells in the blood. CD4+ MF and TCR-γδ+ MF skin lesions harboured strong type 2 immune activation across myeloid cells, while Berti lymphoma was more skewed toward type 1 immune responses. Both CD4+ MF and TCR-γδ+ MF lesions showed upregulation of keratinocyte hyperactivation markers such as S100A genes and KRT16. This increase was entirely absent in Berti lymphoma, possibly reflecting an aberrant keratinocyte response to invading tumour cells, which could contribute to the formation of the typical ulceronecrotic lesions within this entity., Conclusions: Our scRNAseq profiling study reveals specific molecular patterns associated with distinct CTCL subtypes., Competing Interests: Conflicts of interest: W.W. has received personal fees from LEO Pharma, Pfizer, Sanofi Genzyme, Eli Lilly, Novartis, Boehringer Ingelheim, AbbVie and Janssen. J.G. has received personal fees from AbbVie, Eli Lilly, Pfizer, Boehringer Ingelheim and Novartis. C.J. has received personal fees from LEO Pharma, UCB Pharma, Pfizer, Recordati Rare Diseases, Eli Lilly, Novartis, Takeda, Kyowa Kirin, Boehringer Ingelheim, Bristol Myers Squibb, AbbVie, Janssen and Almirall. C.J. is an investigator for Eli Lilly, Novartis, Innate Pharma, AbbVie, Incyte, Boehringer Ingelheim and Almirall. P.M.B. has received personal fees from Almirall, Sanofi, Janssen, LEO Pharma, AbbVie, Pfizer, Boehringer Ingelheim, GSK, Regeneron, Eli Lilly, Celgene, Novartis, UCB, Merck, Galderma and BMS. P.M.B. is an investigator for Pfizer and Abbvie. P.M.B has also received research support from Pfizer (grant paid to his institution). The other authors declare no conflicts of interest., (© The Author(s) 2024. Published by Oxford University Press on behalf of British Association of Dermatologists.)

Immune checkpoint blockade (ICB) therapies have emerged as a promising avenue for the treatment of various cancers. Despite their success, the efficacy of these treatments is variable across patients and cancer types. Numerous single-cell RNA-sequencing (scRNA-seq) studies have been conducted to unravel cell-specific responses to ICB treatment. However, these studies are limited in their sample sizes and require advanced coding skills for exploration. Here, we have compiled eight scRNA-seq datasets from nine cancer types, encompassing 223 patients, 90,270 cancer cells, and 265,671 other cell types. This compilation forms a unique resource tailored to investigate how cancer cells respond to ICB treatment across cancer types. We meticulously curated, quality-checked, pre-processed, and analyzed the data, ensuring easy access for researchers. Moreover, we designed a user-friendly interface for seamless exploration. By sharing the code and data for creating these interfaces, we aim to assist fellow researchers. These resources offer valuable support to those interested in leveraging and exploring single-cell datasets across diverse cancer types, facilitating a comprehensive understanding of ICB responses., Competing Interests: Competing interests: A.M.C. is a co-founder of and serves as a Scientific Advisory Board member for LynxDx, Esanik Therapeutics, Medsyn, and Flamingo Therapeutics. A.M.C. is a scientific advisor or consultant for EdenRoc, Aurigene Oncology, Ascentage Pharma, Proteovant, Belharra, Rappta Therapeutics, and Tempus., (© 2025. The Author(s).)

Objectives: We investigated the recently generated RNA-sequencing dataset of pulpitis to identify the potential pain-related lncRNAs for pulpitis prediction., Materials and Methods: Differential analysis was performed on the gene expression profile between normal and pulpitis samples to obtain pulpitis-related genes. The co-expressed gene modules were identified by weighted gene coexpression network analysis (WGCNA). Then the hypergeometric test was utilized to screen pain-related core modules. The functional enrichment analysis was performed on the up- and down-regulated genes in the core module of pulpitis pain to explore the underlying mechanisms. A pain-related lncRNA-based classification model was constructed using LASSO. Consensus clustering and gene set variation analysis (GSVA) on the infiltrating immunocytes was used for pulpitis subtyping. miRanda predicts miRNA-target relationship, which was filtered by expression correlation. Hallmark pathway and enrichment analysis was performed to investigate the candidate target pathways of the lncRNAs., Results: A total of 1830 differential RNAs were identified in pulpitis. WGCNA explored seven co-expressed modules, among which the turquoise module is pain-related with hypergeometric test. The up-regulated genes were significantly enriched in immune response related pathways. Down-regulated genes were significantly enriched in differentiation pathways. Eight lncRNAs in the pain-related module were related to inflammation. Among them, MIR181A2HG was downregulated while other seven lncRNAs were upregulated in pulpitis. The LASSO classification model revealed that MIR181A2HG and LINC00426 achieved outstanding predictive performances with perfect ROC-AUC score (AUC = 1). We differentiated the pulpitis samples into two progression subtypes and MIR181A2HG is a progressive marker for pulpitis. The miRNA-mRNA-lncRNA regulatory network of pulpitis pain was constructed, with GATA3 as a key transcription factor. NF-kappa B signaling pathway is a candidate pathway impacted by these lncRNAs., Conclusions: PCED1B-AS1, MIAT, MIR181A2HG, LINC00926, LINC00861, LINC00528, LINC00426 and ITGB2-AS1 may be potential markers of pulpitis pain. A two-lncRNA signature of LINC00426 and MIR181A2HG can accurately predict pulpitis, which could facilitate the molecular diagnosis of pulpitis. GATA3 might regulate these lncRNAs and downstream NF-kappa B signaling pathway., Clinical Relevance: This study identified potential pain-related lncRNAs with underlying molecular mechanism analysis for the prediction of pulpitis. The classification model based on lncRNAs will facilitate the early diagnosis of pulpitis., Competing Interests: Declarations. Ethical approval: Not applicable. Competing interests: The authors declare no competing interests., (© 2025. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

Background: Prolonged spaceflight is known to cause vascular deconditioning and remodeling. Tail suspension, a widely used spaceflight analog, is reported to result in vascular remodeling of rats. However, little is known about the cellular atlas of the heterogeneous cells of CA and FA from hindlimb-unloaded rats., Methods: Firstly, we leveraged scRNA-seq to perform clustering analysis to identify diverse cell populations and sub-clusters within CA and FA from rats subjected to 3 months of hindlimb unloading. The dysregulated genes specific for artery types and cell types in HU group compared to Con were unraveled. Then R package "Cellchat" was used to reveal ligand-receptor cellular communication. At last, the TF network analysis was performed using the SCENIC R package to predict the pivotal TFs in rat artery remodeling induced by hindlimb unloading., Results: Clustering analysis identified ECs, SMCs, fibroblasts, and a spectrum of immune cells, as well as neuronal and stem cells. Notably, an increased percentage of ECs in the CA and a diminished proportion of SMCs in both CA and FA were observed following tail suspension. Intersection of dysregulated genes specific for artery type and cell type after tail suspension revealed several gene sets involved in ECM remodeling, inflammation, vasoconstriction, etc. Fibroblasts, in particular, exhibited the most significant gene expression variability, highlighting their plasticity. Subclustering within ECs, SMCs and fibroblasts revealed specialized subsets engaged in processes such as EndoMT and cell cycle checkpoint regulation. Additionally, enhanced intercellular interactions among major cell types, especially between SMC and fibroblast, underscored the importance of cell communication in vascular remodeling. Several TFs were identified as potentially influential in the vascular remodeling process under simulated microgravity conditions., Conclusions: This study presents the first cellular atlas of the conductive arteries in hindlimb-unloaded rats, revealing a spectrum of dysregulated gene profiles. The identification of the subclusters of ECs, SMCs and fibroblasts, cellular communication analysis and transcription factors prediction are also included in this work. The findings provide a reference for future research on vascular deconditioning following long-duration spaceflight., Competing Interests: Declarations. Ethics approval and consent to participate: All animal procedures conducted in this study were in strict accordance with the “Guidelines for the Care and Use of Laboratory Animals” as stipulated by China, and were duly approved by the Institutional Animal Care and Use Committee at the Fourth Military Medical University, China. Consent for publication: Not applicable. Competing interests: The authors declare no conflict of interest., (© 2025. The Author(s).)

Pigeons and certain other avian species produce a milk-like secretion in their crop sacs to nourish offspring, yet the detailed processes involved are not fully elucidated. This study investigated the crop sacs of 225-day-old unpaired non-lactating male pigeons (MN) and males initiating lactation on the first day after incubation (ML). Using RNA sequencing, ribosome profiling, and single-cell transcriptome sequencing (scRNA-seq), we identified a significant up-regulation of genes associated with ribosome assembly and protein synthesis in ML compared to MN. Results from scRNA-seq analysis identified 12 distinct cell types and 22 clusters, with secretory epithelial cells (SECs) exhibiting marked expression of plasma cell markers, including IGLL1 and MZB1 . RNA fluorescence in situ hybridization (RNA FISH) and IgY quantification confirmed the critical role of SECs in producing endogenous IgY during lactation. We propose that fibroblast-derived BAFF signals activate SECs, mimicking B cell transformation and enhancing protein production through the unfolded protein response (UPR). These findings shed light on the cellular dynamics of pigeon milk production and contribute to a broader understanding of avian biology.

Pseudomonas aeruginosa is a Gram-negative bacterium that is notorious for airway infections in cystic fibrosis (CF) subjects. Bacterial quorum sensing (QS) coordinates virulence factor expression and biofilm formation at population level. Better understanding of QS in the bacterium-host interaction is required. Here, we set up a new P. aeruginosa infection model, using 2D upper airway nasal organoids that were derived from 3D organoids. Using dual RNA-sequencing, we dissected the interaction between organoid epithelial cells and WT or QS-mutant P. aeruginosa strains. Since only a single healthy individual and a single CF subject were used as donors for the organoids, conclusions about CF-specific effects could not be deduced. However, P. aeruginosa induced epithelial inflammation, whereas QS signaling did not affect the epithelial airway cells. Conversely, the epithelium influenced infection-related processes of P. aeruginosa, including QS-mediated regulation. Comparison of our model with samples from the airways of CF subjects indicated that our model recapitulates important aspects of infection in vivo. Hence, the 2D airway organoid infection model is relevant and may help to reduce the future burden of P. aeruginosa infections in CF., Competing Interests: Declarations. Competing interests: HC is the head of Pharma Research and Early Development at Roche, Basel and holds several patents related to organoids technology. HC’s full disclosure is given at https://www.uu.nl/staff/JCClevers/. The other authors declare no conflict of interest., (© 2025. The Author(s).)

Barley leaf stripe, a disease mainly caused by Pyrenophora graminea (P. graminea) infection, severely affects barley yield and quality and is one of the most widespread diseases in barley production. However, little is known about the underlying molecular mechanisms of leaf stripe resistance. In this study, the transcript expression profiles of normal and infected leaves of resistant Tibetan hulless barley (Hordeum vulgare L. var. nudum Hook. f.) variety Kunlun 14 and susceptible variety Z1141 were analyzed by RNA sequencing (RNA-seq). The results showed a total of 7,669 and 5,943 differentially expressed genes (DEGs) were found in resistant and susceptible Kunlun 14 and Z1141, respectively, with 8,916 DEGs found between Kunlun 14 and Z1141. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of the 8,916 DEGs identified many significantly enriched categories and pathways, of which a plant-pathogen interaction pathway, containing a total of 102 genes (100 known genes and two novel genes), was found, that was very important for the study of the leaf stripe resistance mechanism. Using RNA-seq, small RNA sequencing (miRNA-seq) combined with degradome sequencing (degradome-seq), four pairs associated with leaf-stripe miRNAs and target genes were obtained, namely Hvu-miR168-5p and Argonaute1 (HvAGO1), Hvu-novel-52 and growth-regulating factor 6 (HvGRF6), Hvu-miR6195 and chemocyanin-like protein (CLP), and Hvu-miR159b and gibberellin-dependent MYB (GAMYB). Transformation of the important target gene HvAGO1 into Arabidopsis verified that HvAGO1 could against Botrytis cinerea. Then RNA-seq and miRNA-seq of Arabidopsis transformed with overexpressed of HvAGO1 were performed. Based on the above research results, we constructed a Protein-Protein Interaction (PPI) network of barley leaf stripe resistance. This study lays the foundation for the study of the barley leaf stripe resistance mechanism and provides new targets for the genetic improvement of disease-resistant barley varieties., Competing Interests: Declarations. Institutional review board statement: Not applicable. Informed consent: Not applicable. Competing interests: The authors declare no competing interests., (© 2025. The Author(s).)

Background: Cancer remains one of the most significant public health challenges worldwide. A widely recognized hallmark of cancer is the ability to sustain proliferative signaling, which is closely tied to various cell cycle processes. Centromere Protein A (CENPA), a variant of the standard histone H3, is crucial for selective chromosome segregation during the cell cycle. Despite its importance, a comprehensive pan-cancer bioinformatic analysis of CENPA has not yet been conducted., Methods: Data on genomes, transcriptomes, and clinical information were retrieved from publicly accessible databases. We analyzed CENPA's genetic alterations, mRNA expression, functional enrichment, association with stemness, mutations, expression across cell populations and cellular locations, link to the cell cycle, impact on survival, and its relationship with the immune microenvironment. Additionally, a prognostic model for glioma patients was developed to demonstrate CENPA's potential as a biomarker. Furthermore, drugs targeting CENPA in cancer cells were identified and predicted using drug sensitivity correlations and protein-ligand docking., Results: CENPA exhibited low levels of gene mutation across various cancers. It was found to be overexpressed in nearly all cancer types analyzed in TCGA, relative to normal controls, and was predominantly located in the nucleus of malignant cells. CENPA showed a strong association with the cancer cell cycle, particularly as a biomarker for the G2 phase. It also emerged as a valuable diagnostic and prognostic biomarker across multiple cancer types. In glioma, CENPA demonstrated reliable prognostic potential when used alongside other prognostic factors. Additionally, CENPA was linked to the immune microenvironment. Drugs such as CD-437, 3-Cl-AHPC, Trametinib, BI-2536, and GSK461364 were predicted to target CENPA in cancer cells., Conclusion: CENPA serves as a crucial biomarker for the cell cycle in cancers, offering both diagnostic and prognostic value., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2025 Liu et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Background: There was evidence that ERP44 played vital roles in a variety of cancers. However, currently, ERP44 was rarely mentioned in gliomas. Therefore, we firstly integrated proteomics, bulk, as well as single-cell RNA-sequencing (scRNA-seq) to study the possible functions of ERP44 in glioma patients., Methods: From online databases, we obtained bulk RNA-seq, scRNA-seq, and proteomic data of ERP44 in gliomas and verified the expression of ERP44 by qRT-PCR. Then, the Noman diagram, gene set enrichment analysis (GSEA), and univariate/multivariate Cox regression analysis were all carried out in turn. Further discussions were also conducted regarding tumor immunity and ERP44 expression., Results: ERP44 in glioma tissues was found to be considerably higher than that in normal tissues (P<0.05) in the TCGA dataset, as well as the verification of GSE50161, GSE4290, and qRT-PCR results. High ERP44 expression indicated poorer overall survival (OS) for glioma (P<0.05), and it might also be used to predict gliomas' OS independently (P<0.05). In order to estimate these patients' survival prognosis, a Noman chart was created with effectiveness. According to GSEA analysis, ERP44 might be implicated in five significant pathways in gliomas. The levels of immune cell infiltration of LGG, the tumor immune microenvironments, the immunological checkpoints of LGG, and GBM were all strongly linked with ERP44 in terms of tumor immunity (P<0.05). Further scRNA-seq analysis revealed that ERP44 could be expressed in various cell types, including T cells, Mono/Macrophages, and malignant cells., Conclusions: ERP44 was an oncogenic gene in gliomas, serving as a bridge mediating prognosis and immunity., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)

Background: Type 2 Diabetes Mellitus (T2DM) represents a major global health challenge, marked by chronic hyperglycemia, insulin resistance, and immune system dysfunction. Immune cells, including T cells and monocytes, play a pivotal role in driving systemic inflammation in T2DM; however, the underlying single-cell mechanisms remain inadequately defined., Methods: Single-cell RNA sequencing of peripheral blood mononuclear cells (PBMCs) from 37 patients with T2DM and 11 healthy controls (HC) was conducted. Immune cell types were identified through clustering analysis, followed by differential expression and pathway analysis. Metabolic heterogeneity within T cell subpopulations was evaluated using Gene Set Variation Analysis (GSVA). Machine learning models were constructed to classify T2DM subtypes based on metabolic signatures, and T-cell-monocyte interactions were explored to assess immune crosstalk. Transcription factor (TF) activity was analyzed, and drug enrichment analysis was performed to identify potential therapeutic targets., Results: In patients with T2DM, a marked increase in monocytes and a decrease in CD4+ T cells were observed, indicating immune dysregulation. Significant metabolic diversity within T cell subpopulations led to the classification of patients with T2DM into three distinct subtypes (A-C), with HC grouped as D. Enhanced intercellular communication, particularly through the MHC-I pathway, was evident in T2DM subtypes. Machine learning models effectively classified T2DM subtypes based on metabolic signatures, achieving an AUC > 0.84. Analysis of TF activity identified pivotal regulators, including NF-kB, STAT3, and FOXO1, associated with immune and metabolic disturbances in T2DM. Drug enrichment analysis highlighted potential therapeutic agents targeting these TFs and related pathways, including Suloctidil, Chlorpropamide, and other compounds modulating inflammatory and metabolic pathways., Conclusion: This study underscores significant immunometabolic dysfunction in T2DM, characterized by alterations in immune cell composition, metabolic pathways, and intercellular communication. The identification of critical TFs and the development of drug enrichment profiles highlight the potential for personalized therapeutic strategies, emphasizing the need for integrated immunological and metabolic approaches in T2DM management., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2025 Li, Zou, Long and Zhan.)

Background: Psoriasis is a chronic inflammatory skin disease affecting 2-3% of the global population, characterised by red scaly patches that significantly affect patients' quality of life. Recent studies have suggested that cell senescence, a state in which cells cease to divide and secrete inflammatory mediators, plays a critical role in various chronic diseases, including psoriasis. However, the involvement and mechanisms of action of senescence-related genes in psoriasis remain unclear., Methods: This study aimed to identify senescence-related genes associated with psoriasis and explore their molecular mechanisms. RNA sequencing data from psoriasis and control samples were obtained from the GEO database. Differential expression analysis was performed using DESeq2 to identify differentially expressed genes (DEGs). The intersection of DEGs with cell senescence-related genes from the CellAge database was used to identify the candidate genes. Protein-protein interaction networks, Gene Ontology, and Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway enrichment analyses were conducted to explore the functions and pathways of these genes. Machine learning algorithms, including Least Absolute Shrinkage and Selection Operator (LASSO) regression and Support vector machine-recursive feature elimination (SVE-RFE), were used to select feature genes that were validated by qRT-PCR. Additionally, an immune cell infiltration analysis was performed to understand the roles of these genes in the immune response to psoriasis., Results: This study identified 4,913 DEGs in psoriasis, of which 46 were related to cell senescence. Machine learning highlighted four key genes, CXCL1, ID4, CCND1, and IRF7, as significant. These genes were associated with immune cell infiltration and validated by qRT-PCR, suggesting their potential as therapeutic targets for psoriasis., Conclusions: This study identified and validated key senescence-related genes involved in psoriasis, providing insights into their molecular mechanisms and potential therapeutic targets and offering a foundation for developing targeted therapies for psoriasis., Competing Interests: The authors declare that they have no competing interests., (© 2025 Deng et al.)

Background: Chronic obstructive pulmonary disease (COPD) is a leading cause of morbidity and mortality worldwide. Single-cell RNA sequencing (scRNA-seq) provides gene expression profiles at the single-cell level. Hence, we evaluated gene expression in the peripheral blood of patients with COPD., Methods: Peripheral blood samples from seven healthy controls and eight patients with COPD were obtained in this study. The 10X Genomics Chromium Instrument and cDNA synthesis kit were utilized to generate a barcoded cDNA library for single cell RNA-sequencing. We compared the scRNA-seq data between the COPD and control groups using computational analysis. Functional analyses were performed using Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses., Results: scRNA-seq was used to analyze the transcriptome of peripheral blood mononuclear cells from seven normal controls and eight patients with COPD. We found an increased number of monocyte/macrophages in the COPD group compared to the normal control group. Among the differentially expressed genes (DEGs) in monocyte/macrophages, we identified 15 upregulated genes (EGR1, NR4A1, CCL3, CXCL8, PTGS2, CD83, BCL2A1, SGK1, IL1B, BTG2, NFKBIZ, DUSP2, MAFB, PLAUR and CCL3L1) and 7 downregulated genes (FOLR3, RPS4Y1, HLA-DRB5, NAMPT, CD52, TMEM176A and TMEM176B) in the COPD group compared to the normal control group., Conclusions: Using scRNA-seq, we found differences in cell type distribution, especially in monocyte/ macrophages. Several upregulated and downregulated genes were found in the monocyte/macrophages of the COPD group., Competing Interests: Declarations. Ethics approval and consent to participate: The authors are responsible for all aspects of the work, ensuring that any questions related to the accuracy or integrity of any part of the study are appropriately investigated and resolved. The study was conducted in accordance with the Declaration of Helsinki (2013 revision). Study approval was obtained from the Institutional Review Board of Kangwon National University Hospital (IRB No. 2012-06-007-061), and written informed consent was acquired from each participant before enrollment. Consent for publication: Written informed consent was obtained from all the participants. Competing interests: The authors declare no competing interests., (© 2025. The Author(s).)

This study aims to investigate the follicle microenvironment of individuals with premature ovarian insufficiency (POI), normal ovarian reserve (normal), and advanced maternal age (AMA), and identify potential therapeutic targets. A total of nine women, including three POI, three normal, and three AMA women, who underwent in vitro fertilization or intracytoplasmic sperm injection were included in this study. For each participant, the first punctured follicle not containing cumulus cells were submitted to single-cell RNA sequencing to explore the characteristics of the follicle microenvironment of POI, normal, and AMA individuals. A total of 87,323 cells were isolated and grouped into six clusters: T cells, B cells, neutrophils, basophils, mononuclear phagocytes, and granulosa cells. Further analysis demonstrated that the population of granulosa cells in cluster 6 was increased in AMA and POI patients, whereas the population of gamma delta T (GDT) cells was decreased. We also found that the genes that were differentially expressed between GDT cells and monocytes were enriched in ribosome- and endoplasmic reticulum (ER)-related pathways. In addition, it showed that VEGFA-FLT1 interaction between the monocytes and granulosa cells may be lost in the AMA and POI patients as compared with the normal group. Loss of the VEGFA-FLT1 interaction in monocytes and granulosa cells, along with enriched ER- and ribosome-related pathways, may drive excess inflammation, accelerating granulosa cell senility and contributing to infertility. This study provides new insights into the pathogenesis of POI and aging and highlights the VEGFA-FLT1 interaction may be a potential therapeutic target for reducing inflammation and treating POI., (© The Author(s) 2024. Published by Oxford University Press on behalf of Society for the Study of Reproduction.)

Age-related muscle wasting, sarcopenia is an extensive loss of muscle mass and strength with age and a major cause of disability and accidents in the elderly. Mechanisms purported to be involved in muscle ageing and sarcopenia are numerous but poorly understood, necessitating deeper study. Hence, we employed high-throughput RNA sequencing to survey the global changes in protein-coding gene expression occurring in skeletal muscle with age. Caloric restriction (CR) is a known prophylactic intervention against sarcopenia. Therefore, total RNA was isolated from the muscle tissue of both rats fed ad libitum and CR rats. RNA-seq data were subjected to Gene Ontology, pathway, co-expression, and interaction network analyses. This revealed the functional pathways most activated by both ageing and CR, as well as the key "hub" proteins involved in their activation.RNA-seq revealed 442 protein-coding genes to be upregulated and 377 to be downregulated in aged muscle, compared to young muscle. Upregulated genes were commonly involved in protein folding and immune responses; meanwhile, downregulated genes were often related to developmental biology. CR was found to suppress 69.7% and rescue 57.8% of the genes found to be upregulated and downregulated in aged muscle, respectively. In addition, CR uniquely upregulated 291 and downregulated 304 protein-coding genes. Hub genes implicated in both ageing and CR included Gc, Plg, Irf7, Ifit3, Usp18, Rsad2, Blm and RT1-A2, whilst those exclusively implicated in CR responses included Alb, Apoa1, Ambp, F2, Apoh, Orm1, Mx1, Oasl2 and Rtp4. Hub genes involved in ageing but unaffected by CR included Fgg, Fga, Fgb and Serpinc1. In conclusion, this comprehensive RNA sequencing study highlights gene expression patterns, hub genes and signalling pathways most affected by ageing in skeletal muscle. This data may provide the initial evidence for several targets for potential future therapeutic interventions against sarcopenia., Competing Interests: Declarations. Ethics approval and consent to participate: The animal study from which samples were collected [25] received ethical approval from the University of Liverpool’s Animal Welfare Committee and adhered to the Animal (Scientific Procedures) Act 1986 and its amendments. The research proposal underwent an ethical review and scoring process before grant submission, followed by additional review from the funding body. After funding approval, a Project Licence (PPL 40/2533), classified as "Mild," was obtained from the Home Office Animal Inspectorate, which involved detailed scrutiny and compliance with the principles of Replace, Reduce, and Refine. The Home Office conducted unannounced visits to ensure adherence to protocols, and animals were humanely euthanised by cervical dislocation after stunning, as required by law. The process was overseen by licensed officials to maintain high standards of animal welfare and ethical compliance. Consent for publication: Not applicable. Competing interests: JPM is CSO of YouthBio Therapeutics, an advisor/consultant for the BOLD Longevity Growth Fund, 199 Biotechnologies, and NOVOS, and the founder of Magellan Science Ltd, a company providing consulting services in longevity science. There are no competing interests declared by any other authors. There are no competing interests declared by any other authors., (© 2025. The Author(s).)

Mitophagy, the selective degradation of mitochondria by autophagy, plays a crucial role in cancer progression and therapy response. This study aims to elucidate the role of mitophagy-related genes (MRGs) in cutaneous melanoma (CM) through single-cell RNA sequencing (scRNA-seq) and machine learning approaches, ultimately developing a predictive model for patient prognosis. The scRNA-seq data, bulk transcriptomic data, and clinical data of CM were obtained from publicly available databases. The single-sample gene set enrichment analysis (ssGSEA) and weighted gene co-expression network analysis (WGCNA) were used to identify gene modules associated with mitophagy phenotypes. A machine learning framework employing ten different algorithms was used to develop the prognostic model. Based on scRNA-seq data, we identified 16 distinct cell subpopulations in melanoma, and melanoma cells exhibited significantly higher mitophagy scores. The turquoise module identified via WGCNA showed the strongest correlation with mitophagy scores. A prognostic model incorporating seven genes was developed through machine learning algorithms, achieving an average C-index of 0.754 across training and validation cohorts. Functionally, low-risk patients were enriched in interferon-gamma response and inflammatory processes, whereas high-risk patients showed enrichment in glycolysis regulation and signaling pathways such as KRAS and Wnt/β-catenin. Notably, low-risk patients demonstrated enhanced immune infiltration and greater sensitivity to immunotherapy. RT-qPCR validated the expression level of 7 model genes in human melanoma cell lines and normal melanocyte cell lines. Our study provides a comprehensive understanding of MRGs in melanoma and presents a novel prognostic model. These findings enhance our understanding of the tumor microenvironment and may guide personalized treatment strategies for CM patients., Competing Interests: Declarations. Conflict of interest: The authors declare that they have no conflict of interest., (© 2025. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.)

Gametogenesis is a process in which dysfunctions lead to infertility, a growing health and social problem worldwide. In both spermatogenesis and oogenesis, post-transcriptional gene expression regulation is crucial. Essentially, all mRNAs possess non-templated poly(A) tails, whose composition and dynamics (elongation, shortening, and modifications) determine the fate of mRNA. Moreover, gametogenesis, especially oogenesis, represents a unique instance of the complexity of poly(A) tails metabolism, with oocyte-specific waves of cytoplasmic polyadenylation. In this context, we provide a comprehensive transcriptomic dataset focusing on mRNA poly(A) tail composition and dynamics in murine testes and ovaries. It consists of RNA samples isolated from wild-type and transgenic mice lacking TENT5 polymerases, which can extend poly(A) tails in the cytoplasm. TENT5 deficiencies have serious consequences. For instance, the defect of TENT5D causes infertility in humans. The data described here are generated mainly using the Oxford Nanopore Direct RNA Sequencing (DRS) method, which provides ground-truth information about mRNA molecules, including poly(A) tail length and nucleotide content. For instance, we show the prevalence of uridilated tails in testicular mRNAs., Competing Interests: Competing interests: The authors declare no competing interests., (© 2025. The Author(s).)

Turner syndrome (TS) can be determined by karyotype analysis, marked by the loss of one X chromosome in females. However, the genes involved in autoimmunity in TS patients remain unclear. In this study, we aimed to analyze differences in immune gene expression between a patient with TS, a healthy female, and a female patient with Graves' disease using single-cell RNA sequencing (scRNA-seq) analysis of antigen-specific CD4(+) T cells. We identified 43 differentially expressed genes in the TS patient compared with the healthy female and the female patient with Graves' disease. Many of these genes have previously been suggested to play a role in immune system regulation. This study provides valuable insights into the differences in immune-related gene expression between TS patients, healthy individuals, and those with autoimmune diseases.

Macrophages play important roles in metabolic dysfunction-associated steatohepatitis (MASH), an advanced and inflammatory stage of metabolic dysfunction-associated steatotic liver disease (MASLD). In humans and mice, the cellular heterogeneity and diverse function of hepatic macrophages in MASH have been investigated by single cell RNA sequencing (scRNA-seq). However, little is known about their roles in rats. Here, we collected liver tissues at the postnatal week 16, when our previously characterized Lep ∆I14/∆I14 rats developed MASH phenotypes. By scRNA-seq, we found an increase in the number of macrophages and endothelial cells and a decrease in that of NK and B cells. Hepatic macrophages in rats underwent a unique M1 to M2 transition without expression of the classical markers such as Arg1 and Nos2, except for Cd163. Lipid-associated macrophages (LAMs) were increased, which could be detected by the antibody against Cd63. In the microenvironment, macrophages had an increased number of interactions with hepatocytes, myofibroblasts, T cells, neutrophils, and dendritic cells, while their interaction strengths remained unchanged. Finally, the macrophage migration inhibitory factor (MIF) pathway was identified as the top upregulated cell-communication pathway in MASH. In conclusion, we dissected hepatic macrophage dynamics during MASH at single cell resolution and provided fundamental tools for the investigation of MASH in rat models.

The utility of environmental RNA (eRNA) in capturing biological responses to stresses has been discussed previously; however, the limited number of genes detected remains a significant hindrance to its widespread implementation. Here, we investigated the potential of eRNA to assess the health status of Japanese medaka fish exposed to linear alkylbenzene sulfonate. Analyzing eRNA and organismal RNA (oRNA) in aquarium water within 12 h, we achieved high mapping rates and 10 times more differentially expressed genes than previously reported. This advancement has facilitated the previously unattainable capability of gene ontology (GO) analysis. The GO analysis revealed that eRNA can detect nuclear genes associated with cellular components and reflect cumulative gene expression signatures over time, while oRNA provided short-term gene expression signatures in biological process. Moreover, eRNA exhibited high sensitivity in responding to genes associated with sphingolipid and ceramide biosynthesis, which are involved in inflammatory responses possibly originating from impaired cells. This finding aligns with the observations made in oRNA. In conclusion, eRNA-sequencing (eRNA-seq) using aquarium water emerges as a valuable high sensitivity tool for analyzing physiological stress. The findings of this study lay the foundation for further development of eRNA-seq technologies., Competing Interests: Declaration of competing interest Authors declare that they have no competing interests., (Copyright © 2024 The Authors. Published by Elsevier B.V. All rights reserved.)

Background: Adenocarcinoma of the esophagogastric junction (AEGJ) is a highly aggressive tumor that frequently metastasizes to the liver. Understanding the cellular and molecular mechanisms that drive this process is essential for developing effective therapies., Methods: We employed single-cell RNA sequencing to analyze the tumor heterogeneity and microenvironmental landscape in patients with AEGJ liver metastases. This approach enabled us to characterize the diverse cell populations involved in the liver metastatic process., Results: Our analysis revealed a significant involvement of fibroblasts and mural cells in AEGJ liver metastasis. We identified a specific fibroblast type in AEGJ liver metastasis and observed distinct gene expression patterns between adenocarcinoma of the esophagogastric junction and other stomach adenocarcinomas. Our study demonstrated high expression of the SFRP2 gene in pericyte cells during the liver metastasis of AEGJ. The incorporation of GEO, TCGA, and immunofluorescence staining of SFRP2 expression enhanced our study. High expression of SFRP2 in pericytes may influence vascular stability and angiogenesis through the Wnt pathway., Conclusion: Our study provides novel insights into the cellular interactions and molecular mechanisms that underlie AEGJ liver metastasis. Targeting the identified subtype of fibroblasts or influencing SFRP2 gene expression in pericytes may offer new therapeutic strategies for combating this aggressive tumor., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2025 Xu, Sadiq, Zhao, Xia, Liu, Zhang and Xu.)

Tooth development is a complex process of the orderly interaction between epithelium originating from the ectoderm and mesenchyme derived from cranial neural crest cells, which not only depends on cell genes regulatory network but also involves crosstalk between cells and their surrounding environment. Even within the same type of cellular populations, obvious heterogeneity may be observed. Single-cell RNA sequencing is a novel technology aimed at sequencing the transcriptome of individual cell. As a critical bridge linking genetic information from the genome to the functional proteome, transcriptome analysis at the single-cell level enables a deeper understanding of cellular heterogeneity and organ developmental trajectories. This approach provides a powerful tool for elucidating complex biological processes and identifying potential therapeutic targets. Here, we summarize the latest advances in employing single-cell RNA sequencing analysis to the process of tooth development, which will help provide insights into a better understanding of prosthodontics and regeneration.

Background: Cervical cancer is the fourth most common cancer in women globally, and the main cause of the disease has been found to be ongoing HPV infection. Cervical cancer remains the primary cause of cancer-related death despite major improvements in screening and treatment approaches, especially in low- and middle-income nations. Therefore, it is crucial to investigate the tumor microenvironment in advanced cervical cancer in order to identify possible treatment targets., Materials and Methods: In order to better understand malignant cervical cancer epithelial cells (EPCs), this study used bulk RNA-seq data from UCSC in conjunction with single-cell RNA sequencing data from the ArrayExpress database. After putting quality control procedures into place, cell type identification and clustering analysis using the Seurat software were carried out. To clarify functional pathways, enrichment analysis and differential gene expression were carried out. The CIBERSORT and ESTIMATE R packages were used to evaluate the immune microenvironment characteristics, and univariate and multivariate Cox regression analyses were used to extract prognostic features. Furthermore, assessments of drug sensitivity and functional enrichment were carried out., Results: Eight cell types were identified, with EPCs showing high proliferative and stemness features. Five EPC subpopulations were defined, with C1 NNMT+ CAEPCs driving tumor differentiation. A NNMT CAEPCs Risk Score (NCRS) model was developed, revealing a correlation between elevated NCRS scores and adverse patient outcomes characterized by immune evasion. In vitro experiments validated that the prognostic gene PLOD2 significantly enhances proliferation, migration, and invasion of cervical cancer cells., Conclusion: This investigation delineated eight cell types and five subpopulations of malignant EPCs in cervical cancer, establishing the C1 NNMT+ CAEPCs as a crucial therapeutic target. The NCRS model demonstrated its prognostic capability, indicating that higher scores are associated with poorer clinical outcomes. The validation of PLOD2 as a prognostic gene highlights its therapeutic potential, underscoring the critical need for integrating immunotherapy and targeted treatment strategies to enhance diagnostic and therapeutic approaches in cervical cancer., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2025 Lin, Wang, Yin, Li, Bai, Zhang, Sui, Cao, Su, Xu and Wang.)

Progress in biology has generated numerous lists of genes that share some property. But advancing from these lists of genes to understanding their roles is slow and unsystematic. Here we use RNA silencing in Caenorhabditis elegans to illustrate an approach for prioritizing genes for detailed study given limited resources. The partially subjective relationships between genes forged by both deduced functional relatedness and biased progress in the field were captured as mutual information and used to cluster genes that were frequently identified yet remain understudied. Some proteins encoded by these understudied genes are predicted to physically interact with known regulators of RNA silencing, suggesting feedback regulation. Predicted interactions with proteins that act in other processes and the clustering of studied genes among the most frequently perturbed suggest regulatory links connecting RNA silencing to other processes like the cell cycle and asymmetric cell division. Thus, among the gene products altered when a process is perturbed could be regulators of that process acting to restore homeostasis, which provides a way to use RNA sequencing to identify candidate protein-protein interactions. Together, the analysis of perturbed transcripts and potential interactions of the proteins they encode could help prioritize candidate regulators of any process., (© The Author(s) 2025. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Identifying cell populations associated with risk variants is essential for uncovering cell-specific mechanisms that drive disease development and progression. Integrating genome-wide association studies (GWAS) with single-cell RNA sequencing (scRNA-seq) has become an effective strategy for detecting trait-cell relationships. The accumulation of trait-related single cell data has led to an urgent need for its comprehensively processing. To address this, we developed sc2GWAS (https://bio.liclab.net/sc2GWAS/), which aims to document large-scale GWAS trait-cell regulatory pairs at single-cell resolution and provide comprehensive annotations and enrichment analyses for these related pairs. The current version of sc2GWAS curates a total of 15 078 310 candidate trait-cell pairs from > 6 300 000 individual cells, offering a valuable resource for exploring complex regulatory relationships between traits and cells. We applied strict quality control measures on both scRNA-seq data and GWAS data, ensuring the reliability and accuracy of the datasets for the identification of trait-relevant cells and genes. In addition, sc2GWAS provides ranked lists of trait-relevant genes and extensive (epi) genetic annotations, making it a valuable resource for downstream analyses. We demonstrate the utility of the platform by investigating Alzheimer's disease, where we identified significant associations between the disease and microglial cells, with the APOE gene emerging as particularly significant. This platform facilitates detailed research into complex trait-cell and trait-gene interactions, we anticipate that sc2GWAS will become a comprehensive and valuable platform for exploring GWAS trait-cell regulatory mechanisms., (© The Author(s) 2024. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Background: Dilated cardiomyopathy (DCM) is one of the most common causes of heart failure. Infiltration and alterations in non-cardiomyocytes of the human heart involve crucially in the occurrence of DCM and associated immunotherapeutic approaches., Methods: We constructed a single-cell transcriptional atlas of DCM and normal patients. Then, the xCell algorithm, EPIC algorithm, MCP counter algorithm, and CIBERSORT method were applied to identify DCM-related cell types with a high degree of precision and specificity using RNA-seq datasets. We further analyzed the heterogeneity among cell types, performed trajectory analysis, examined transcription factor regulatory networks, investigated metabolic heterogeneity, and conducted intercellular communication analysis. Finally, we used bulk RNA-seq data to confirm the roles of M2-like2 subpopulations and GAS6 in DCM., Results: We integrated and analyzed Single-cell sequencing (scRNA-seq) data from 7 DCM samples and 3 normal heart tissue samples, totaling 70,958 single-cell data points. Based on gene-specific expression and prior marker genes, we identified 9 distinct subtypes, including fibroblasts, endothelial cells, myeloid cells, pericytes, T/NK cells, smooth muscle cells, neuronal cells, B cells, and cardiomyocytes. Using machine learning methods to quantify bulk RNA-seq data, we found significant differences in fibroblasts, T cells, and macrophages between DCM and normal samples. Further analysis revealed high heterogeneity in tissue preference, gene expression, functional enrichment, immunodynamics, transcriptional regulatory factors, metabolic changes, and communication patterns in fibroblasts and myeloid cells. Among fibroblast subpopulations, proliferative F3 cells were implicated in the fibroblast transition process in DCM, while myofibroblast F6 cells promoted the fibroblast transition to a late cell state in DCM. Additionally, two subpopulations of M2 macrophages, M2-like1 and M2-like2, were identified with distinct features. The M2-like2 cell subpopulation, which was enriched in glycolysis and fatty acid metabolism, involved in inflammation inhibition and fibrosis promotion. Cell‒cell communication analysis indicated the GAS6-MERTK axis might exhibit interaction between M2 macrophage and M2-like1 macrophage. Furthermore, deconvolution analysis for bulk RNA-seq data revealed a significant increase in M2-like2 subpopulations in DCM, suggesting a more important role for this cell population in DCM., Conclusions: We revealed the heterogeneity of non-cardiomyocytes in DCM and identified subpopulations of myofibroblast and macrophages engaged in DCM, which suggested a potential significance of non-cardiomyocytes in treatment of DCM., Competing Interests: Declarations. Ethics approval and consent to participate: Not applicable. Consent for publication: Not applicable. Competing interests: The authors declare that they have no competing interests in this section., (© 2024. The Author(s).)

Single-cell sequencing technology has enabled the discovery and characterization of subpopulations of immune cells with unique functions, which is critical for revealing immune responses under healthy or disease conditions. Efforts have been made to collect and curate single-cell RNA sequencing (scRNA-seq) data, yet an immune-specific single-cell multi-omics atlas with harmonized metadata is still lacking. Here, we present scImmOmics (https://bio.liclab.net/scImmOmics/home), a manually curated single-cell multi-omics immune database constructed based on high-quality immune cells with known immune cell labels. Currently, scImmOmics documents >2.9 million cell-type labeled immune cells derived from seven single-cell sequencing technologies, involving 131 immune cell types, 47 tissues and 4 species. To ensure data consistency, we standardized the nomenclature of immune cell types and presented them in a hierarchical tree structure to clearly describe the lineage relationships within the immune system. scImmOmics also provides comprehensive immune regulatory information, including T-cell/B-cell receptor sequencing clonotype information, cell-specific regulatory information (e.g. gene/chromatin accessibility/protein/transcription factor states within known cell types, cell-to-cell communication and co-expression networks) and immune cell responses to cytokines. Collectively, scImmOmics is a comprehensive and valuable platform for unraveling the heterogeneity and diversity of immune cells and elucidating the specific regulatory mechanisms at the single-cell level., (© The Author(s) 2024. Published by Oxford University Press on behalf of Nucleic Acids Research.)

The Rfam database, a widely used repository of non-coding RNA families, has undergone significant updates in release 15.0. This paper introduces major improvements, including the expansion of Rfamseq to 26 106 genomes, a 76% increase, incorporating the latest UniProt reference proteomes and additional viral genomes. Sixty-five RNA families were enhanced using experimentally determined 3D structures, improving the accuracy of consensus secondary structures and annotations. R-scape covariation analysis was used to refine structural predictions in 26 families. Gene Ontology (GO) and Sequence Ontology annotations were comprehensively updated, increasing GO term coverage to 75% of families. The release adds 14 new Hepatitis C Virus RNA families and completes microRNA family synchronization with miRBase, resulting in 1603 microRNA families. New data types, including FULL alignments, have been implemented. Integration with APICURON for improved curator attribution and multiple website enhancements further improve user experience. These updates significantly expand Rfam's coverage and improve annotation quality, reinforcing its critical role in RNA research, genome annotation and the development of machine learning models. Rfam is freely available at https://rfam.org., (© The Author(s) 2024. Published by Oxford University Press on behalf of Nucleic Acids Research.)

The field of single-cell RNA sequencing (scRNA-seq) has advanced rapidly in the past decade, generating significant amounts of valuable data for researchers to study complex tumor profiles. This data is crucial for gaining innovative insights into cancer biology. CancerSCEM (https://ngdc.cncb.ac.cn/cancerscem) is a public resource that integrates, analyzes and visualizes scRNA-seq data related to cancer, and it provides invaluable support to numerous cancer-related studies. With CancerSCEM 2.0, scRNA-seq data have increased from 208 to 1466 datasets, covering tumor, matching-normal and peripheral blood samples across 127 research projects and 74 cancer types. The new version of this resource enhances transcriptome analysis by adding copy number variation evaluation, transcription factor enrichment, pseudotime trajectory construction, and diverse biological feature scoring. It also introduces a new cancer metabolic map at the single-cell level, providing an intuitive understanding of metabolic regulation across different cancer types. CancerSCEM 2.0 has a more interactive analysis platform, including four modules and 14 analytical functions, allowing researchers to perform cancer scRNA-seq data analyses in various dimensions. These enhancements are expected to expand the usability of CancerSCEM 2.0 to a broader range of cancer research and clinical applications, potentially revolutionizing our understanding of cancer mechanisms and treatments., (© The Author(s) 2024. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Microtia is a congenital malformation characterized by underdevelopment of the external ear. While chondrocyte dysfunction has been implicated in microtia, the specific cellular abnormalities remain poorly understood. This study aimed to investigate mitochondrial dysfunction in microtia chondrocytes using single-cell RNA sequencing. Cartilage samples were obtained from patients with unilateral, non-syndromic microtia and healthy controls. Single-cell RNA sequencing was performed using the 10 × Genomics platform. Bioinformatic analyses including cell type identification, trajectory analysis, and gene co-expression network analysis were conducted. Mitochondrial function was assessed through ROS levels, membrane potential, and transmission electron microscopy. Chondrocytes from microtia samples showed lower mitochondrial function scores compared to normal samples. Trajectory analysis revealed more disorganized differentiation patterns in microtia chondrocytes. Mitochondrial dysfunction in microtia chondrocytes was confirmed by increased ROS production, decreased membrane potential, and altered mitochondrial structure. Gene co-expression network analysis identified hub genes associated with mitochondrial function, including SDHA, SIRT1, and PGC1A, which showed reduced expression in microtia chondrocytes. This study provides evidence of mitochondrial dysfunction in microtia chondrocytes and identifies potential key genes involved in this process. These findings offer new insights into the pathogenesis of microtia and may guide future therapeutic strategies., Competing Interests: Declarations. Competing interests: The authors declare no competing interests. Ethics approval and consent to participate: All procedures in this research were approved by the Research Ethics Committee of Shanghai Ninth People’s Hospital. The study followed the Declaration of Helsinki for ethical purposes, and all participants provided written informed consent. Consent for publication: Written informed consent was obtained by the patient., (© 2025. The Author(s).)

Small cell neuroendocrine cervical carcinoma is a highly aggressive tumor characterized by early metastasis, a high recurrence rate, and poor prognosis. This study represents the first instance of single-cell sequencing conducted on small cell neuroendocrine carcinoma of the cervix worldwide. Analysis of gene expression regulatory networks revealed that the transcription factor TFF3 drived up-regulation of ELF3. Furthermore, our findings indicated that the neuroendocrine marker genes and gene regulatory networks associated with small cell neuroendocrine cervical carcinoma differed from those observed in lung, small intestine, and liver neuroendocrine carcinoma within the GEO database, suggesting tissue-specific origins for these malignancies. Overall, this study addresses a significant research in understanding small cell neuroendocrine cervical carcinoma in vivo and provides valuable insights for guiding radiotherapy, chemotherapy, and targeted therapy., Competing Interests: Declarations. Ethics approval and consent to participate: The study was conducted in accordance with the Declaration of Helsinki, and approved by the Ethics Committee of Obstetrics and Gynecology Hospital of Fudan University(2024-113). Informed consent was obtained from all subjects involved in the study. Written informed consent has been obtained from the patient to publish this paper. Consent for publication: Not applicable. Competing interests: The authors declare no conflicts of interest., (© 2024. The Author(s).)

Background: Anti-citrullinated peptide antibodies (ACPA)-negative (ACPA-) rheumatoid arthritis (RA) presents significant diagnostic and therapeutic challenges due to the absence of specific biomarkers, underscoring the need to elucidate its distinctive cellular and metabolic profiles for more targeted interventions., Methods: Single-cell RNA sequencing data from peripheral blood mononuclear cells (PBMCs) and synovial tissues of patients with ACPA- and ACPA+ RA, as well as healthy controls, were analyzed. Immune cell populations were classified based on clustering and marker gene expression, with pseudotime trajectory analysis, weighted gene co-expression network analysis (WGCNA), and transcription factor network inference providing further insights. Cell-cell communication was explored using CellChat and MEBOCOST, while scFEA enabled metabolic flux estimation. A neural network model incorporating key genes was constructed to differentiate patients with ACPA- RA from healthy controls., Results: Patients with ACPA- RA demonstrated a pronounced increase in classical monocytes in PBMCs and C1QChigh macrophages (p < 0.001 and p < 0.05). Synovial macrophages exhibited increased heterogeneity and were enriched in distinct metabolic pathways, including complement cascades and glutathione metabolism. The neural network model achieved reliable differentiation between patients with ACPA- RA and healthy controls (AUC = 0.81). CellChat analysis identified CD45 and CCL5 as key pathways facilitating macrophage-monocyte interactions in ACPA- RA, prominently involving iron-mediated metabolite communication. Metabolic flux analysis indicated elevated beta-alanine and glutathione metabolism in ACPA- RA macrophages., Conclusion: These findings underscore that ACPA-negative rheumatoid arthritis is marked by elevated classical monocytes in circulation and metabolic reprogramming of synovial macrophages, particularly in complement cascade and glutathione metabolism pathways. By integrating single-cell RNA sequencing with machine learning, this study established a neural network model that robustly differentiates patients with ACPA- RA from healthy controls, highlighting promising diagnostic biomarkers and therapeutic targets centered on immune cell metabolism., Competing Interests: The authors declare that this research was conducted without any commercial or financial relationships that could present a potential conflict of interest., (Copyright © 2025 Jiang, Hu, Huang, Ho, Wang and Kang.)

Main Conclusion: Small RNA sequencing analysis in two chickpea genotypes, JG 62 (Fusarium wilt-susceptible) and WR 315 (Fusarium wilt-resistant), under Fusarium wilt stress led to identification of 544 miRNAs which included 406 known and 138 novel miRNAs. A total of 115 miRNAs showed differential expression in both the genotypes across different combinations. A miRNA, Car-miR398 targeted copper chaperone for superoxide dismutase (CCS) that, in turn, regulated superoxide dismutase (SOD) activity during chickpea-Foc interaction. Fusarium wilt (FW) of chickpea (Cicer arietinum L.) caused by Fusarium oxysporum f. sp. ciceris (Foc) is a destructive soil-borne disease that severely reduces the chickpea yield and quality globally. In the present study, we have investigated microRNAs and the microRNA/target gene crosstalk involved in chickpea resistance to FW. The control and stress samples from two genotypes, JG 62 (FW-susceptible) and WR 315 (FW-resistant), collected at 10 days post-inoculation (dpi), were selected for small RNA sequencing. A total of 12 libraries were constructed and sequenced using Illumina HiSeq 2500 platform. The sequencing and in silico analyses revealed the identification of 544 miRNAs which included 406 known and 138 novel miRNAs. A total of 50 miRNAs were physically co-localized with Foc-resistance QTLs present on chromosome 2 (also known as Foc hotspot). A total of 115 miRNAs showed differential expression in both the genotypes across different combinations. Prediction and functional annotation of miRNA targets revealed their role in transcription regulation, disease resistance, defense response, metabolism, etc. Ten miRNAs and their targets were validated using poly(A)-based qRT-PCR in two genotypes grown under lab and field conditions. Many miRNAs and their targets showed genotype-specific expression. The expression profiling also highlighted, both, similar and different expression patterns for the same sets of miRNA and mRNA at different stages of Foc infection. A high correlation in expression patterns of the miRNAs and their targets in lab- and field-grown plant samples was observed. Interestingly, Car-miR398 targeted copper chaperone for superoxide dismutase (CCS) that, in turn, regulated superoxide dismutase (SOD) activity during chickpea-Foc interaction. The cleavage site in targets was mapped for three miRNAs by analyzing publicly available degradome data for chickpea. The study, for the first time, provides novel insights into microRNA-mediated regulation of resistance and susceptibility mechanisms in chickpea against FW and opens up avenues for the development of the wilt-resistant cultivars in chickpea., Competing Interests: Declarations. Competing interest: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2024. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

Background: Undifferentiated carcinoma (UC) is a rare subtype of pancreatic cancer distinguished from UC with osteoclast-like giant cells (UC-OGC) in 2019, affecting interpretation of literature that does not distinguish these subtypes. We sought to identify translationally relevant differences between these 2 variants and compared with pancreatic ductal adenocarcinoma., Methods: We characterized clinical and multiomic differences between UC (n = 32) and UC-OGC (n = 15) using DNA sequencing, RNA sequencing, and multiplex immunofluorescence and compared these findings with pancreatic ductal adenocarcinoma., Results: Characteristics at diagnosis were similar between UC and UC-OGC, though the latter was more resectable (P = .009). Across all stages, median overall survival was shorter for UC than for UC-OGC (0.4 years vs 10.8 years, respectively; P = .003). This shorter survival was retained after stratification by resection, albeit without statistical significance (1.8 years vs 11.9 years, respectively; P = .08). In a subset of patients with available tissue, the genomic landscape was similar among UC (n = 9), UC-OGC (n = 5), and pancreatic ductal adenocarcinoma (n = 159). Bulk RNA sequencing was deconvoluted and, along with multiplex immunofluorescence in UC (n = 13), UC-OGC (n = 5), and pancreatic ductal adenocarcinoma (n = 16), demonstrated statistically significantly increased antigen-presenting cells, including M2 macrophages and natural killer cells, and decreased cytotoxic and regulatory T cells in UC and UC-OGC vs pancreatic ductal adenocarcinoma. Findings were similar between UC and UC-OGC , except for decreased regulatory T cells in UC-OGC (P = .04)., Conclusions: In this series, UC was more aggressive than UC-OGC, with these variants having more antigen-presenting cells and fewer regulatory T cells than pancreatic ductal adenocarcinoma, suggesting potential for immune-modulating therapies in the treatment of these pancreatic cancer subtypes., (© The Author(s) 2024. Published by Oxford University Press.)

Purpose: Previous studies have reported divergent sexual responses to aging; however, specific variations in gene expression between aging males and females and their potential association with age-related retinal diseases remain unclear. This study collected data from public databases and developed a comprehensive comparison of retina between aging females and males., Methods: Single-cell RNA (scRNA) and bulk RNA sequencing data of the aging retina from females and males in public databases were utilized for integrated analysis to investigate sex-biased expression in retina. Additionally, in vitro experiments were conducted on individuals with retinitis pigmentosa (RP) to validate the sex difference in degenerative retina., Results: Bulk RNA analysis revealed sex-biased expression of specific genes in retina of aging individuals, with immune pathway-related genes exhibiting higher expression in females compared to males. The scRNA analysis demonstrated that sex-biased gene expression was cell-type specific in aging retina. Furthermore, susceptibility genes for age-related macular degeneration and RP exhibited variation across different cell types and sexes. Cell-to-cell communication unveiled an increased interaction associated with TGFB1, CCL7, and VEGFA in Müller glia, microglia, and astrocytes of female retina. Notably, we observed female-biased chemokine expression in microglia contributing to heightened susceptibility to immune inflammation in female retina. Finally, we confirmed a more pronounced inflammatory response during degeneration in female rd10 mouse retina compared to males., Conclusions: This study provides a comprehensive comparison of retina between females and males in healthy aging human retina and highlights the significance of sex as an influential factor in retinal diseases.

Small-cell neuroendocrine cancer (SCNEC) of the uterine cervix is an exceedingly rare, highly aggressive tumor with an extremely poor prognosis. The cellular heterogeneity, origin, and tumorigenesis trajectories of SCNEC of the cervix remain largely unclear. We performed single-cell RNA sequencing and whole-exome sequencing on tumor tissues and adjacent normal cervical tissues from two patients diagnosed with SCNEC of the cervix. Here, we provide the first comprehensive insights into the cellular composition, HPV infection-related features, and gene expression profiles of SCNEC of the cervix at single-cell resolution. Correlation analyses suggested that SCNEC of the cervix may originate from squamous epithelial cells, and this observation was validated with bulk RNA-seq data from external cervical neuroendocrine cancer. Furthermore, sex-determining region Y-box 2 (SOX2), a key transcription factor that functions in direct neural differentiation, was located in the copy number gain region and highly expressed in neuroendocrine tumor cells from both patients. Notable, the distributions of the HPV-infected epithelium and SOX2 highly expressed epithelium were consistent with each other. Therefore, we supposed that high-risk HPV infection and amplification of SOX2 in the squamous epithelium may contribute to the progression of small-cell neuroendocrine tumorigenesis in the cervix., (© 2025 Wiley Periodicals LLC.)

Previous studies in sports science suggested that regular exercise has a positive impact on human health. However, the effects of endurance sports and their underlying mechanisms are still not completely understood. One of the main debates regards the modulation of immune dynamics in high-intensity exercise. As part of the "Run 4 Science" project in Verona, Italy, we conducted a single-cell RNA sequencing analysis on half-marathon amateur runners to investigate the transcriptional dynamics of peripheral blood mononuclear cells following endurance exercise. Blood samples were collected from four participants before and after running a half-marathon to carry out a comprehensive transcriptomic analysis of immune cells at the single-cell level. Our analysis revealed significant alterations in the transcriptional profiles following endurance physical exercise. Modulations in myeloid cells suggested the activation of stress response (6 related pathways, p < 0.04) and pathways related to viral processes (4 related pathways, p < 0.03), while in lymphoid cells they hinted to a shift towards immune activation (24 related pathways, p < 0.01). Additionally, transcriptional changes in platelets point to an activation of the coagulation process (5 related pathways, p < 0.005). Single-cell data was also analyzed following a pseudo-bulk approach (i.e., simulating a bulk RNAseq experiment) to gain further biological insights. Our findings suggest that a pseudo-bulk analysis could offer complementary findings to classical single-cell analysis methods and demonstrate that endurance physical exercise, such as running a half-marathon, induces substantial changes in the transcriptional dynamics of immune cells. These insights contribute to a better understanding of the immune modulation mediated by endurance exercise and may inform future training routines or nutritional guidelines based on individual gene expression levels., (© 2025 The Author(s). Scandinavian Journal of Medicine & Science In Sports published by John Wiley & Sons Ltd.)