Perceived discrimination, recognized as a chronic psychosocial stressor, has adverse consequences on health. DNA methylation (DNAm) may be a potential mechanism by which stressors get embedded into the human body at the molecular level and subsequently affect health outcomes. However, relatively little is known about the effects of perceived discrimination on DNAm. To identify the DNAm sites across the epigenome that are associated with discrimination, we conducted epigenome-wide association analyses (EWAS) of three discrimination measures (everyday discrimination, race-related major discrimination, and non-race-related major discrimination) in 1,151 participants, including 565 non-Hispanic White, 221 African American, and 365 Hispanic individuals, from the Multi-Ethnic Study of Atherosclerosis (MESA). We conducted both race/ethnicity-stratified analyses as well as trans-ancestry meta-analyses. At false discovery rate of 10%, 7 CpGs and 4 differentially methylated regions (DMRs) containing 11 CpGs were associated with perceived discrimination exposures in at least one racial/ethnic group or in meta-analysis. Identified CpGs and/or nearby genes have been implicated in cellular development pathways, transcription factor binding, cancer and multiple autoimmune and/or inflammatory diseases. Of the identified CpGs (7 individual CpGs and 11 within DMRs), two CpGs and one CpG within a DMR were associated with expression of cis genes NDUFS5, AK1RIN1, NCF4 and ADSSL1. Our study demonstrated the potential influence of discrimination on DNAm and subsequent gene expression.

Ankylosing spondylitis (AS) is a chronic autoimmune disease that primarily affects the axial joints. Immune cells play a key role in the pathogenesis of AS. This study integrated bioinformatics methods with experimental validation to explore the role of natural killer (NK) cells in AS.

Two microarray datasets, GSE25101 and GSE73754, were selected, and the scRNA-seq data were obtained from GSE194315 and Liu's research. Differentially expressed genes (DEGs) and functional enrichment analysis were performed respectively. Weighted gene co-expression network analysis (WGCNA) was conducted to identify key modules of co-expressed genes and genes involved in NK cell function. The diagnostic value of the identified key genes was evaluated using ROC curves, logistic regression analysis, and a nomogram. Real-time PCR (RT-PCR) was used to quantified the expression of genes. Statistical analysis was conducted using the R software package, and a p-value of less than 0.05 was considered statistically significant.

Pathways enrichment analysis revealed the involvement of NK cell-mediated immune pathways and regulation of the innate immune response, indicating the crucial role of innate immunity, especially NK cells, in AS pathogenesis. The construction of a co-expression network revealed that the MElightyellow module was most relevant to the NK cell-mediated immune pathway. IL2RB, CD247, PLEKHF1, EOMES, S1PR5, FGFBP2 from the MElightyellow module were identified as key genes involved in NK cell-mediated immune response and served as potential diagnostic biomarkers for AS, with moderate to high diagnostic values based on AUC values. Further analysis using scRNA-seq profiling revealed the higher expression level of IL2RB, CD247, PLEKHF1, S1PR5, FGFBP2 in NK cells compared to that in other cell types. CD247, PLEKHF1, EOMES, S1PR5, and FGFBP2 were reduced expressed in AS patients as compare to control group verified by scRNA-seq data, CD247, EOMES, FGFBP2, IL2RB and S1PR5 were reduced expressed verified by RT-PCR, and PLEKHF1, S1PR5, and FGFBP2 was upregulated after TNF-α blocker therapy.

The study revealed the potential role of NK cells and identified IL2RB, CD247, PLEKHF1, EOMES, S1PR5, and FGFBP2 as key genes associated with NK cells in the pathogenesis of AS.

PCK2, which encodes mitochondrial phosphoenolpyruvate carboxykinase (PEPCK-M), is upregulated in various cancers. We demonstrated high expression of PEPCK-M in approximately half of triple-negative breast cancers (TNBCs) previously. TNBC is associated with an aggressive phenotype and a high metastasis rate. In this study, we investigated the role of PCK2 in TNBC. PCK2 knockdown suppressed proliferation and mTOR signaling in TNBC cells. In addition, cell invasion/migration ability and the expression of epithelial-to-mesenchymal transition (EMT) markers were positively correlated with PCK2 expression in TNBC cells via regulation of transforming growth factor-β (TGF-β)/SMAD3 signaling. SMAD3 was positively regulated by PCK2 in TNBC cells. Knockdown of SMAD3 in PCK2-overexpressing TNBC cells reduced the expression levels of EMT markers, Snail and Slug, and suppressed cell invasion/migration. In addition, PCK2 knockdown attenuated the stimulatory effect of TGF-β on SMAD3 phosphorylation in TNBC cells. PEPCK-M promotes the protein and mRNA expression of SMAD3 via competitive binding to tripartite motif-containing 67 (TRIM67), an E3 ubiquitin ligase, to reduce SMAD3 ubiquitination, which leads to promoting nuclear translocation of SMAD3 and autoregulation of SMAD3 transcription. Moreover, high PCK2 mRNA expression was significantly associated with poor survival in TNBC patients. In conclusion, our study revealed for the first time that PCK2 activates TGF-β/SMAD3 signaling by regulating the expression and phosphorylation of SMAD3 by inhibiting TRIM67-mediated SMAD3 ubiquitination and promoting the stimulatory effect of TGF-β to promote TNBC invasion. The regulatory effect of PCK2 on mTOR and TGF-β/SMAD3 signaling suggests that PCK2 is a potential therapeutic target for suppressing TNBC progression.

Locally advanced rectal cancer (LARC) is treated with neoadjuvant chemo-radiotherapy (nCRT) followed by surgery. A minority of patients show complete response (CR) to nCRT and may avoid surgery and its functional consequences. Instead, most patients show non-complete response (non-CR) and may benefit from additional treatments to increase CR rates. Reliable predictive markers are lacking. Aim of this study was to identify novel signatures predicting nCRT responsiveness. We performed a combined analysis of tumor-associated microbiome and immune gene expression profiling of diagnostic biopsies from 70 patients undergoing nCRT followed by rectal resection, including 16 with CR and 54 with non-CR. Findings were validated by an independent cohort of 49 patients, including 7 with CR and 42 with non-CR. Intratumoral microbiota significantly differed between CR and non-CR groups at genus and species level. Colonization by bacterial species of Ruminococcus genera was consistently associated with CR, whereas abundance of Fusobacterium, Porhpyromonas, and Oscillibacter species predicted non-CR. Immune gene profiling revealed a panel of 59 differentially expressed genes and significant upregulation of IFN-gamma and -alpha response in patients with CR. Integrated microbiome and immune gene profiling analysis unraveled clustering of microbial taxa with each other and with immune cell-related genes and allowed the identification of a combined signature correctly identifying non-CRS in both cohorts. Thus, combined intratumoral microbiome-immune profiling improves the prediction of response to nCRT. Correct identification of unresponsive patients and of bacteria promoting responsiveness might lead to innovative therapeutic approaches based on gut microbiota pre-conditioning to increase nCRT effectiveness in LARC.

Renal fibrosis is a critical factor in chronic kidney disease progression, with limited diagnostic and therapeutic options. Emerging evidence suggests RNA-binding proteins (RBPs) are pivotal in regulating cellular mechanisms underlying fibrosis.

Utilizing an extensive GEO dataset (175 renal fibrosis and 99 normal kidney samples), we identified and validated key RBPs through integrated bioinformatics and machine learning approaches, including lasso and logistic regression models. Differentially expressed genes were analyzed for pathway enrichment using Gene Ontology and KEGG. Single-cell RNA sequencing delineated cell-specific RBP expression, and a murine unilateral ureteral obstruction (UUO) model provided experimental validation.

A diagnostic model incorporating five RBPs (FKBP11, DCDC2, COL6A3, PLCB4, and GNB5) achieved high accuracy (AUC = 0.899) and robust external validation. These RBPs are implicated in immune-mediated pathways such as cytokine signaling and inflammatory responses. Single-cell analysis highlighted their expression in specific renal cell populations, underscoring functional diversity. Immunofluorescence linked FKBP11 with macrophage infiltration, suggesting its potential as a therapeutic target.

his study identifies novel RBPs associated with renal fibrosis, advancing the understanding of its pathogenesis and offering actionable biomarkers and therapeutic targets. The integration of bioinformatics and machine learning emphasizes their translational potential in kidney care.

To unravel distinct patterns of metagenomic surveillance and respiratory microbiota between Mycoplasma pneumoniae (M. pneumoniae) P1-1 and P1-2 and to explore the impact of the COVID-19 pandemic on epidemiological features, we conducted a multicentre retrospective study which spanned 90,886 pneumonia patients, among which 3164 cases M. pneumoniae were identified. Our findings revealed a concurrent outbreak of M. pneumoniae, with the positivity rate rising sharply to 9.62% from July 2023, compared to the 0.16% to 4.06% positivity rate observed during the 2020-2022 COVID-19 pandemic. P1-1 had a higher odds ratio of co-detecting opportunistic pathogens. However, no significant differences were observed in the co-detection odds ratio between children and other age groups in P1-2. This study is the first to demonstrate differences in relative abundance, diversity of respiratory microbiota and co-detection rate of opportunistic pathogen between M. pneumoniae P1-1 and P1-2. Through bronchoalveolar lavage (BAL) metagenomic and host transcriptomic analyses, we identified variations in co-detection rates of M. pneumoniae P1-1 genotype with opportunistic pathogens like S. pneumoniae, alterations in respiratory microbiota composition, lung inflammation, and disruption of ciliary function. Consistent with the results of host transcriptome, we found that P1-1 infections were associated with significantly higher rates of requiring respiratory support and mechanical ventilation compared to P1-2 infections (Fisher's exact test, p-value = 0.035/0.004). Our study provides preliminary evidence of clinical severity between M. pneumoniae strains, underscoring the need for ongoing research and development of targeted therapeutic strategies.

JOURNAL/nrgr/04.03/01300535-202512000-00030/figure1/v/2025-01-31T122243Z/r/image-tiff Studies have shown that vascular dysfunction is closely related to the pathogenesis of Alzheimer's disease. The middle temporal gyrus region of the brain is susceptible to pronounced impairment in Alzheimer's disease. Identification of the molecules involved in vascular aberrance of the middle temporal gyrus would support elucidation of the mechanisms underlying Alzheimer's disease and discovery of novel targets for intervention. We carried out single-cell transcriptomic analysis of the middle temporal gyrus in the brains of patients with Alzheimer's disease and healthy controls, revealing obvious changes in vascular function. CellChat analysis of intercellular communication in the middle temporal gyrus showed that the number of cell interactions in this region was decreased in Alzheimer's disease patients, with altered intercellular communication of endothelial cells and pericytes being the most prominent. Differentially expressed genes were also identified. Using the CellChat results, AUCell evaluation of the pathway activity of specific cells showed that the obvious changes in vascular function in the middle temporal gyrus in Alzheimer's disease were directly related to changes in the vascular endothelial growth factor (VEGF)A-VEGF receptor (VEGFR) 2 pathway. AUCell analysis identified subtypes of endothelial cells and pericytes directly related to VEGFA-VEGFR2 pathway activity. Two subtypes of middle temporal gyrus cells showed significant alteration in AD: endothelial cells with high expression of Erb-B2 receptor tyrosine kinase 4 (ERBB4 high ) and pericytes with high expression of angiopoietin-like 4 (ANGPTL4 high ). Finally, combining bulk RNA sequencing data and two machine learning algorithms (least absolute shrinkage and selection operator and random forest), four characteristic Alzheimer's disease feature genes were identified: somatostatin ( SST ), protein tyrosine phosphatase non-receptor type 3 ( PTPN3 ), glutinase ( GL3 ), and tropomyosin 3 ( PTM3 ). These genes were downregulated in the middle temporal gyrus of patients with Alzheimer's disease and may be used to target the VEGF pathway. Alzheimer's disease mouse models demonstrated consistent altered expression of these genes in the middle temporal gyrus. In conclusion, this study detected changes in intercellular communication between endothelial cells and pericytes in the middle temporal gyrus and identified four novel feature genes related to middle temporal gyrus and vascular functioning in patients with Alzheimer's disease. These findings contribute to a deeper understanding of the molecular mechanisms underlying Alzheimer's disease and present novel treatment targets.

Endoplasmic reticulum stress (ERS) has been implicated in the pathogenesis of various cancers, including colon cancer, by regulating tumor cell survival, growth, and immune response. However, the specific genes involved in ERS that could serve as prognostic markers in colon cancer remain underexplored. This study aims to identify and validate endoplasmic reticulum stress related genes (ERSRGs) in colon cancer that correlate with patient prognosis, thereby enhancing the understanding of ERS in oncological outcomes and potential therapeutic targeting. We utilized bioinformatics analyses to identify ERSRGs from publicly available colon cancer datasets. Differential expression analysis and survival analysis were performed to assess the prognostic significance of these genes. Validation was conducted through quantitative real-time PCR (RT-qPCR) on selected colon cancer cell lines. Our study identified nine ERS related genes (ASNS, ATF4, ATF6B, BOK, CLU, DDIT3, MANF, SLC39A14, TRAF2) involved in critical pathways including IL-12, PI3K-AKT, IL-7, and IL-23 signaling, and linked to 1-, 3-, and 5-year survival of patients with colon cancer. A multivariate Cox model based on these ERS related genes demonstrated significant prognostic power. Further, TRAF2 strong correlated with immune cells infiltration, suggesting its potential roles in modulating immune responses in the tumor microenvironment. The RT-qPCR validation confirmed the differential expression of these genes in human colon cancer cell lines versus human normal colonic epithelial cell line. The identified ERSRGs could serve as valuable prognostic markers and may offer new insights into the therapeutic targeting of ERS in colon cancer.

JOURNAL/nrgr/04.03/01300535-202510000-00031/figure1/v/2024-11-26T163120Z/r/image-tiff Aminoglycosides are a widely used class of antibacterials renowned for their effectiveness and broad antimicrobial spectrum. However, their use leads to irreversible hearing damage by causing apoptosis of hair cells as their direct target. In addition, the hearing damage caused by aminoglycosides involves damage of spiral ganglion neurons upon exposure. To investigate the mechanisms underlying spiral ganglion neuron degeneration induced by aminoglycosides, we used a C57BL/6J mouse model treated with kanamycin. We found that the mice exhibited auditory deficits following the acute loss of outer hair cells. Spiral ganglion neurons displayed hallmarks of pyroptosis and exhibited progressive degeneration over time. Transcriptomic profiling of these neurons showed significant upregulation of genes associated with inflammation and immune response, particularly those related to the NLRP3 inflammasome. Activation of the canonical pyroptotic pathway in spiral ganglion neurons was observed, accompanied by infiltration of macrophages and the release of proinflammatory cytokines. Pharmacological intervention targeting NLRP3 using Mcc950 and genetic intervention using NLRP3 knockout ameliorated spiral ganglion neuron degeneration in the injury model. These findings suggest that NLRP3 inflammasome-mediated pyroptosis plays a role in aminoglycoside-induced spiral ganglion neuron degeneration. Inhibition of this pathway may offer a potential therapeutic strategy for treating sensorineural hearing loss by reducing spiral ganglion neuron degeneration.

JOURNAL/nrgr/04.03/01300535-202507000-00028/figure1/v/2024-09-09T124005Z/r/image-tiff Alzheimer's disease is characterized by deposition of amyloid-β, which forms extracellular neuritic plaques, and accumulation of hyperphosphorylated tau, which aggregates to form intraneuronal neurofibrillary tangles, in the brain. The NLRP3 inflammasome may play a role in the transition from amyloid-β deposition to tau phosphorylation and aggregation. Because NLRP3 is primarily found in brain microglia, and tau is predominantly located in neurons, it has been suggested that NLRP3 expressed by microglia indirectly triggers tau phosphorylation by upregulating the expression of pro-inflammatory cytokines. Here, we found that neurons also express NLRP3 in vitro and in vivo, and that neuronal NLRP3 regulates tau phosphorylation. Using biochemical methods, we mapped the minimal NLRP3 promoter and identified FUBP3 as a transcription factor regulating NLRP3 expression in neurons. In primary neurons and the neuroblastoma cell line Neuro2A, FUBP3 is required for endogenous NLRP3 expression and tau phosphorylation only when amyloid-β is present. In the brains of aged wild-type mice and a mouse model of Alzheimer's disease, FUBP3 expression was markedly increased in cortical neurons. Transcriptome analysis suggested that FUBP3 plays a role in neuron-mediated immune responses. We also found that FUBP3 trimmed the 5' end of DNA fragments that it bound, implying that FUBP3 functions in stress-induced responses. These findings suggest that neuronal NLRP3 may be more directly involved in the amyloid-β-to-phospho-tau transition than microglial NLRP3, and that amyloid-β fundamentally alters the regulatory mechanism of NLRP3 expression in neurons. Given that FUBP3 was only expressed at low levels in young wild-type mice and was strongly upregulated in the brains of aged mice and Alzheimer's disease mice, FUBP3 could be a safe therapeutic target for preventing Alzheimer's disease progression.

In vitro maturation (IVM) of oocytes is a vital aspect of assisted reproductive technology (ART), and its proper application can enhance reproductive efficiency. However, owing to the scarcity of research on the IVM of yak oocytes, its application in yak breeding remains underexplored. Therefore, in this study, we conducted high-throughput mRNA sequencing of immature and mature yak oocytes, which revealed transcriptomic changes during the IVM process in this unique high-altitude domesticated animal. Transcriptomic analysis also identified the histone methyltransferase SET domain-containing 2 (SETD2) as a key factor associated with post-translational modifications during oocyte maturation. To determine the role of SETD2 in oocytes, we employed the SETD2 inhibitor EZM0414 during oocyte maturation. Inhibition of SETD2 resulted in a significant reduction in histone methylation levels, lower oocyte maturation rate in vitro, and suppression of maternal mRNAs degradation suppression (P < 0.05). These findings indicated that SETD2 modulates oocyte maturation by regulating histone methylation and maternal mRNAs degradation. Furthermore, suppression of SETD2 markedly reduced the expression of oocyte secretion-related proteins (TSG6 and GDF9) and cumulus expansion-related protein (PTGS2), demonstrating that oocyte secretion and cumulus expansion were positively correlated with SETD2. Overall, our findings establish SETD2 as an essential regulator of yak oocyte maturation via histone methylation and maternal mRNAs degradation.

Intervertebral disc degeneration (IVDD) is a significant contributor to lower back pain (LBP), affecting approximately 80 % of the global population. The RalA inhibitor BQU57 plays a role in various cellular functions; however, its impact on nucleus pulposus cell (NPC) degeneration remains unclear.

This study employed a combination of bioinformatics analysis and experimental validation to investigate the role of RalA in IVDD and its inhibitor BQU57 in its therapeutic potential. Gene expression datasets from the GEO database were analyzed to identify genes associated with IVDD, and clinical intervertebral disc samples were collected to validate the upregulation of RalA in degenerated discs. In vivo and in vitro assessments were conducted to evaluate the effects of BQU57 on the extracellular matrix (ECM) metabolism and apoptosis of nucleus pulposus (NP) cells.

Elevated expression of RalA was observed in degenerated intervertebral discs from IVDD patients, and its expression was correlated with disease severity. Further mechanistic studies revealed that the RalA inhibitor BQU57 could balance ECM metabolism and apoptosis, potentially through the activation of the NF-κB signaling pathway.

RalA plays a significant role in the pathogenesis of IVDD, and it may serve as a novel therapeutic target for IVDD. BQU57 demonstrates potential as an effective small molecule drug for the prevention and treatment of IVDD.

Tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) is a potential cancer therapeutic that induces apoptosis in cancer cells while sparing the non-malignant cells in preclinical models. However, its efficacy in clinical trials has been limited, suggesting unknown mechanisms modulating TRAIL activity in patients. We hypothesized that TRAIL treatment elicits transcriptional changes in triple negative breast cancer (TNBC) cells that alter the immune milieu. RNAseq analysis of MDA-MB-231 cells along with validation in additional cell lines demonstrated that TRAIL induced cytokines such as CXCLs 1, 2, 3, 8,11 and IL-6, which are known to modify neutrophil function. Mechanistically, TRAIL dependent induction of the cytokines was predominantly mediated by death receptor 5, caspase-8 and the non-canonical NFKB2 pathway. These cytokines produced by TRAIL-treated TNBC cells enhanced chemotaxis of normal human donor isolated neutrophils. Using TNBC xenograft models, TRAIL induced activation of NFkB2 pathway, cytokine production and increased neutrophil recruitment into the tumors. Moreover, preincubation of neutrophils in supernatants from TRAIL-treated TNBC cells significantly impaired neutrophil function as measured by reduced respiratory burst and cytotoxic effect against TNBC cells. Transcriptomic analysis of neutrophils incubated with either TRAIL alone or supernatant of TRAIL-treated TNBC cells revealed increased expression of inflammatory cytokines, immune modulatory genes, immune checkpoint genes, and genes implicated in delayed neutrophil apoptosis. Functional studies showed that these neutrophils suppress T cell proliferation and augment Treg suppressive phenotype. Collectively, our study demonstrates a novel role of TRAIL-induced NFKB2-dependent cytokine production that promotes neutrophil chemotaxis and neutrophil-mediated immune suppression.

Type I interferons (IFNs-I), a group of pleiotropic cytokines, critically modulate host response in various inflammatory diseases. However, the role of the IFN-I pathway in periodontitis remains largely unknown. In this report, we describe that the IFN-β levels in the gingival crevicular fluid of human subjects were negatively associated with periodontitis and clinical gingival inflammation. Disruption of IFN-I signaling worsened alveolar bone resorption in a ligature-induced periodontitis murine model. Deficiency of the IFN-I pathway resulted in an exaggerated inflammatory response in myeloid cells and drastically increased the interleukin-17 (IL-17)-mediated neutrophil recruitment in the gingiva. We further identified that the myeloid lineage-specific IFN-I response was essential in safeguarding against periodontal inflammation by suppressing the IL-17-producing γδ T cells in gingiva. IFN-I signaling also directly repressed osteoclastogenesis in monocytes, which are precursor cells for osteoclasts. Therefore, our findings demonstrate that an integral myeloid-specific IFN-I pathway protects against bone loss by keeping the IL-17-neutrophil axis in check and directly inhibiting osteoclast formation in periodontitis.

Far-upstream element-binding protein 3 (FUBP3) was identified at actively transcribing HIV promoters through chromatin affinity purification and mass spectrometry. Known for regulating cellular processes such as transcription and translation by binding to DNAs and RNAs, FUBP3's role in HIV transcriptional regulation was previously unrecognized. This study reveals that FUBP3 enhances HIV-1 transcriptional activation by interacting with Tat and trans-activation response (TAR)-RNA, critical for boosting viral transcription through recruitment of activating factors that promote RNA polymerase II (RNAPII) elongation. Transcriptomic analysis, chromatin immunoprecipitation, and biochemical assays demonstrated that FUBP3 associates with and stabilizes TAR-RNA, in a Tat-dependent manner, and enhances Tat steady-state levels via interaction with Tat's basic domain. Suppressing FUBP3 decreased HIV-1 transcription and altered expression of host genes linked to T cell activation and inflammation, underscoring its broad regulatory impact. Additionally, FUBP3 was enriched at active promoters, confirming its role in transcriptional regulation at specific genomic locations. These findings highlight FUBP3's critical role in the HIV-1 life cycle and suggest its potential as a therapeutic target in HIV-1 infection. Additionally, this study expands our understanding of FUBP3's functions in oncogenic and inflammatory pathways.

Human adipose-derived mesenchymal stem cells (hAD-MSCs) have garnered significant interest as a viable alternative source of stem cells for applications in bone tissue engineering due to their high and ease availability. At present, the limited studies on potential epigenetic regulatory mechanism in hAD-MSCs greatly hinders its clinical application in bone repair. Histone acetylation has been identified as a critical regulator of the osteogenic differentiation of mesenchymal stem cells (MSCs), with increased levels of histone acetylation sites frequently correlating with enhanced osteogenic differentiation. However, their specific roles in MSCs osteogenesis remain unclear. In this study, we observed a significant up-regulation of H3K18 acetylation (H3K18ac) during the osteogenic induction of hAD-MSCs. This modification was notably enriched in the promoter regions of genes associated with osteogenesis, thereby facilitating osteogenic differentiation. Furthermore, the treatment of histone acetyltransferases p300 inhibitor A-485 in hAD-MSCs resulted in a reduction of H3K18 acetylation levels during the osteogenic differentiation, which corresponded with a diminished osteoblast phenotype and function. These results indicated that p300-mediated acetylation of H3K18 enhances the osteogenic differentiation of hAD-MSCs. It provides a novel insight into understanding the mechanism of osteogenic differentiation of hAD-MSCs and promoting its application in bone tissue engineering.

Reactive astrocytes are associated with Alzheimer's disease (AD), and several AD genetic risk variants are associated with genes highly expressed in astrocytes. However, the contribution of genetic risk within astrocytes to cellular processes relevant to the pathogenesis of AD remains ill-defined. Here, we present a resource for studying AD genetic risk in astrocytes using a large collection of induced pluripotent stem cell (iPSC) lines from deeply phenotyped individuals with a range of neuropathological and cognitive outcomes. IPSC lines from 44 individuals were differentiated into astrocytes followed by unbiased molecular profiling using RNA sequencing and tandem mass tag-mass spectrometry. We demonstrate the utility of this resource in examining gene- and pathway-level associations with clinical and neuropathological traits, as well as in analyzing genetic risk and resilience factors through parallel analyses of iPSC-astrocytes and brain tissue from the same individuals. Our analyses reveal that genes and pathways altered in iPSC-derived astrocytes from individuals with AD are concordantly dysregulated in AD brain tissue. This includes increased levels of prefoldin proteins, extracellular matrix factors, COPI-mediated trafficking components and reduced levels of proteins involved in cellular respiration and fatty acid oxidation. Additionally, iPSC-derived astrocytes from individuals resilient to high AD neuropathology show elevated basal levels of interferon response proteins and increased secretion of interferon gamma. Correspondingly, higher polygenic risk scores for AD are associated with lower levels of interferon response proteins in astrocytes. This study establishes an experimental system that integrates genetic information with a matched iPSC lines and brain tissue data from a large cohort of individuals to identify genetic contributions to molecular pathways affecting AD risk and resilience.

The characterization of gene sets is a recurring task in computational biology. Identifying specific properties of a hit set compared to a reference set can reveal biological roles and mechanisms, and can lead to the prediction of new hits. However, collecting the features to evaluate can be time consuming, and implementing an informative but compact graphical representation of the multiple comparisons can be challenging, particularly for bench scientists. Here, I present Qarles (quick characterization of large sets of genes), a web server that annotates Saccharomyces cerevisiae gene sets by querying a database of 31 features widely used by the yeast community and that identifies their specific properties, providing publication-ready figures and reliable statistics. Qarles has a deliberately simple user interface with all the functionality in a single web page and a fast response time to facilitate adoption by the scientific community. Qarles provides a rich and compact graphical output, including up to five gene set comparisons across 31 features in a single dotplot, and interactive boxplots to enable the identification of outliers. Qarles can also predict new hit genes by using a random forest trained on the selected features. The web server is freely available at https://qarles.org.

Fibroblasts are important components in the tumor microenvironment and can affect tumor progression and metastasis. However, the roles of genetic variants of the fibroblast-related genes (FRGs) in the prognosis of non-small-cell lung cancer (NSCLC) patients have not been reported. Therefore, we investigated the associations between 26,544 single nucleotide polymorphisms (SNPs) in 291 FRGs and survival of NSCLC patients from the Prostate, Lung, Colorectal, and Ovarian (PLCO) Cancer Screening Trial. In Cox regression multivariable analysis, we found that 661 SNPs were associated with NSCLC overall survival (OS). Then we validated these SNPs in another independent replication dataset of 984 patients from the Harvard Lung Cancer Susceptibility (HLCS) Study. Finally, we identified two independent SNPs (i.e., FER rs7716388 A>G and SULF1 rs11785839 G>C) that remained significantly associated with NSCLC survival with hazards ratios (HRs) of 0.87 (95% confidence interval [CI] = 0.77-0.98, p = 0.018) and 0.88 (95% CI = 0.79-0.99, p = 0.033), respectively. Combined analysis for these two SNPs showed that the number of protective alleles was associated with better OS and disease-specific survival. Expression quantitative trait loci analysis indicated that the FER rs7716388 G allele was associated with the up-regulation of FER mRNA expression levels in lung tissue. Our results indicated that these two functional SNPs in the FRGs may be prognostic biomarkers for the prognosis of NSCLC patients, and the possible mechanism may be through modulating the expression of their corresponding genes.

The incidence of thyroid cancer (TC) increases year by year. It is necessary to construct a prognostic model for risk stratification and management of TC patients. Glutamine metabolism is essential for tumor progression and the tumor microenvironment. The present study aimed to develop a predictive model for TC using a glutamine metabolism gene set. Differentially expressed genes in cells with high glutamine metabolism levels from single cell RNA‑sequencing data were compared with genes differentially expressed between normal and TC tissues from The Cancer Genome Atlas Program data. Through Boruta feature selection methods and multivariate Cox regression, six crucial genes were identified for a risk‑scoring system to develop a prognostic model. The role of each gene was verified in TC cells in vitro. A risk‑scoring system was developed according to the glutamine gene set to forecast the overall survival of TC patients. This risk score could stratify TC patients and minimize unnecessary surgeries and invasive treatments. In addition, signal induced proliferation associated 1 like 2 (SIPA1L2), an important gene in the prognostic model, knockdown in TPC‑1 and BCPAP cell lines enhanced TC cell proliferation, migration and invasion. A risk model was developed based on a glutamine metabolism gene set. The model has reference values for TC stratification.

Osteosarcoma, the most prevalent malignant bone tumor in adolescents, is characterized by its aggressiveness and tendency to metastasize. Despite the advancements in treatment that have improved survival rates for localized cases, metastatic osteosarcoma remains challenging to treat due to the limited efficacy of current therapies and the severe side effects of chemotherapy. Epithelial-mesenchymal transition (EMT) is a key factor in osteosarcoma metastasis, and the miR-194/215 cluster, which is upregulated in osteosarcoma, promotes this process. This study sought to investigate natural compounds that could counteract the miR-194/215 cluster's effects and inhibit osteosarcoma metastasis. By analyzing miRNA databases and clinical data, a signature gene set for the miR-194/215 cluster was established, and the LINCS database was screened to find natural compounds with antagonistic effects. Icariside II, an active component of Epimedium, was identified as a potential inhibitor and was shown to reduce the migration and invasion of osteosarcoma cells in vitro and lung metastasis in vivo. The study utilized various techniques, including Gene Set Enrichment Analysis (GSEA), Drug Affinity Responsive Target Stability (DARTS), Cellular Thermal Shift Assay (CETSA), molecular docking, and enzyme activity assays, to identify phosphoglycerate kinase 1 (PGK1) as the target protein of Icariside II. It was found that Icariside II competitively inhibits PGK1 by binding to its ADP binding pocket, reducing its activity and thus antagonizing the miR-194/215 cluster's promotion of EMT in metastatic osteosarcoma. The results suggest that Icariside II could be a promising therapeutic agent for metastatic osteosarcoma, providing new targets and strategies for clinical treatment.

The availability of high-dimensional transcriptomic datasets is increasing at a tremendous pace, together with the need for suitable computational tools. Clustering and dimensionality reduction methods are popular go-to methods to identify basic structures in these datasets. At the same time, different topic modeling techniques have been developed to organize the deluge of available data of natural language using their latent topical structure. This paper leverages the statistical analogies between text and transcriptomic datasets to compare different topic modeling methods when applied to gene expression data. Specifically, we test their accuracy in the specific task of discovering and reconstructing the tissue structure of the human transcriptome and distinguishing healthy from cancerous tissues. We examine the properties of the latent space recovered by different methods, highlight their differences, and their pros and cons across different tasks. We focus in particular on how different statistical priors can affect the results and their interpretability. Finally, we show that the latent topic space can be a useful low-dimensional embedding space, where a basic neural network classifier can annotate transcriptomic profiles with high accuracy.

Platinum-based combination chemotherapy remains the backbone of first-line treatment for patients with advanced epithelial ovarian cancer (EOC). While most patients initially respond well to the treatment, patients with relapse ultimately develop platinum resistance. This study identified FLYWCH-type zinc finger-containing protein 1 (FLYWCH1) as an important regulator in the resistance development process. We showed that the loss of FLYWCH1 promotes platinum resistance in EOC cells, and the low FLYWCH1 expression is correlated with poor prognosis of EOC patients. In platinum-sensitive cells, FLYWCH1 colocalizes with H3K9me3, but this association is significantly reduced when cells acquire resistance. The suppression of FLYWCH1 induces gene expression changes resulting in the deregulation of pathways associated with resistance. In line with its connection to H3K9me3, FLYWCH1 induces gene silencing in a synthetic reporter assay and the suppression of FLYWCH1 alters H3K9me3 at promoter regions and repeat elements. The loss of FLYWCH1 leads to the derepression of LTR and Alu repeats, thereby increasing transcriptional plasticity and driving the resistance development process. Our data highlight the importance of FLYWCH1 in chromatin biology and acquisition of platinum resistance through transcriptional plasticity and propose FLYWCH1 as a potential biomarker for predicting treatment responses in EOC patients.

Acute wounds present a significant clinical challenge due to delayed healing, which is often exacerbated by elevated levels of reactive oxygen species (ROS). These high ROS concentrations hinder the natural healing process, leading to prolonged recovery and increased risk of complications. W-GA nanodots, synthesized via a simple coordination method, have emerged as promising solutions, demonstrating multifunctional enzymatic activity that effectively scavenges ROS. To explore the underlying mechanisms of ROS-induced oxidative stress, we conducted RNA sequencing on macrophages exposed to H2O2. The results revealed significant regulation of key stress response pathways, including substantial upregulation of the "p53 signaling pathway" and the "HIF-1 signaling pathway," both of which are essential for cellular adaptation to oxidative stress. By alleviating oxidative stress, W-GA nanodots not only accelerate wound repair but also improve overall healing outcomes. Notably, RNA sequencing of animal tissue samples revealed that W-GA nanodots activate the "Wnt signaling pathway," further promoting wound healing. These findings underscore the potential of W-GA nanodots as a novel therapeutic strategy for enhancing wound healing and treating oxidative stress-related conditions, positioning them as promising candidates for future clinical applications in wound care and inflammatory diseases.

Malignant melanoma is a highly aggressive tumor originating from the pigment producing cells, the melanocytes. It accounts for the majority of skin cancer related deaths worldwide. This is often due to the development of therapy resistance or tumor dormancy, eventually resulting in tumor relapse by yet undefined mechanisms. Tumor dormancy is thought to be mediated by the cellular microenvironment and models taking this factor into account are urgently needed. We 3D bioprinted melanoma cells in the hydrogels Cellink Bioink (CIB) or Matrigel (MG), each as a substitute of the extracellular matrix, and, thereby, induced a quiescent or a proliferative phenotype of the melanoma cell lines, respectively. RNA-Seq with subsequent comprehensive bioinformatical and molecular analyses assigned CIB-cultured cells to a predominantly mesenchymal and Matrigel-cultured cells to a more mitotic phenotype, emphasizing the CIB model as a suitable platform for the investigation of dormancy under consideration of the microenvironment. Melanoma cells in CIB 3D culture reflect a quiescent and migratory active cell state e.g. by revealing significant downregulation of genes associated with replication and cell cycle progression in this setting. Using this model system, we identified the mechanosensory gene FHL2 as one early sensor of changes in the ECM and suggest a FHL2-p21/AP-1 axis contributing to the dormant phenotype of melanoma cells in CIB.

TLR7 stimulation of T-bet+CD11c+IgD-CD27- double-negative 2 (DN2) B cells is crucial for autoantibody formation in systemic lupus erythematosus (SLE). Here, we show that administration of IL-4 for five weeks significantly reduced autoantibodies and T-bet+CD11c+ IgD- B cells in autoimmune BXD2 mice treated with R848, a TLR7 agonist. Single-cell transcriptomics analysis indicates that following two doses of in vivo administration, IL-4 redirected development toward follicular, CD23+ germinal center (GC), and DN4-like memory B cells compared to treatment with R848 alone. While IL-4 enhanced genes related to antigen processing and presentation, it also suppressed R848-induced Ki67+ GC B cells in vivo. In vitro stimulation of SLE patient B cells with a DN2 polarizing cocktail revealed that IL-4 reduced the expression of interferon response and DN2 signature genes, promoting a population of CD23+T-bet- DN4 B population. These findings suggest that developmental reprogramming by IL-4 counteracts TLR7-promoted DN2 and GC B cells in SLE.

Complete tissue recovery following traumatic injury remains a major clinical challenge. While tissue adhesives show promise for managing traumatic injuries, developing materials with robust wet adhesion and high biocompatibility remains difficult. Decellularized extracellular matrix (ECM)-derived materials are widely utilized in tissue engineering due to their superior biocompatibility and bioactivity. In this study, a wet adhesive is developed by functionalizing ECM with dopamine. The resulting ECM-dopamine exhibits strong wet adhesion and excellent biocompatibility. Furthermore, ECM-dopamine can be engineered into a drug delivery platform for small agents and macromolecules. Solid lipid nanoparticles (SLNs) are incorporated into ECM-dopamine to enable sustained release of small molecules. The ECM-dopamine-SLN system ensures sustained drug release for at least one week upon adhesion to target tissues. ECM-dopamine-SLN loaded with antimicrobials accelerates wound healing and promotes angiogenesis by modulating the inflammatory response in a mouse skin excision model. Additionally, ECM-dopamine can deliver bioactive macromolecules to injured tissue. ECM-dopamine loaded with insulin-like growth factor-1 promotes skeletal muscle regeneration in a mouse volumetric muscle loss model, likely through the modulation of M2-like macrophage polarization. The dual functionality of ECM-dopamine as both a wet adhesive and a drug delivery platform offers significant potential for regenerative medicine applications.

Aberrant increases in osteoclast formation and/or activity are the underlying cause of bone loss in a variety of osteolytic diseases. Fatty acid synthase (Fasn)-mediated de novo lipogenesis (DNL) is one of the major lipid metabolic pathways and has been shown to play critical roles in diverse physiological and pathological processes. However, little is known about its role in osteoclastogenesis. Here, we investigate the direct role of DNL in osteoclastogenesis and its therapeutic potential in osteolytic diseases. We found that Fasn expression and DNL levels are upregulated during receptor activator of nuclear factor-κB ligand (RANKL)-induced osteoclastogenesis. Inhibition of Fasn by shRNA knockdown or its pharmacological inhibitors (ASC40 and trans-C75) impairs osteoclast differentiation in vitro. Mechanistically, pharmacological inhibition of Fasn suppresses RANKL-induced c-Fos/NFATc1 expression and thus osteoclastogenesis partly by disrupting STAT3 palmitoylation, while promoting ROS scavenging to impair mitogen-activated protein kinase (MAPK) signaling. Finally, the therapeutic potential of ASC40 for the treatment of osteolytic bone loss is tested in two mouse models of osteolytic diseases, i.e. ovariectomy (OVX)-induced osteoporosis and titanium nanoparticle-induced calvarial osteolysis. The results show that ASC40 significantly attenuates bone loss and osteoclastogenesis in both models. In conclusion, our results demonstrate that Fasn-mediated DNL is a novel positive regulator of osteoclastogenesis and may serve as a promising therapeutic target for the treatment of osteoclast-driven osteolytic bone diseases.

Hepatocyte organoids (HOs) hold significant potential for constructing bioartificial liver construction, toxicology research, and liver failure therapies. However, challenges such as difficulties in induced pluripotent stem cells (iPSCs) harvest and differentiation, safety concerns of tumor-derived matrices, and limited primary cell regulation hinder clinical applications. In this study, we developed a non-tumor-derived decellularized extracellular matrix (dECM) system with tunable mechanical properties and viscoelasticity to enhance stem cell proliferation and organoid functionality using thrombospondin-1 (THBS1). Nanoindentation and transcriptomic analysis revealed that THBS1 mediates adaptation and remodeling between organoids and ECM proteins, exhibiting native tissue-like viscoelasticity and up-regulated reprogramming transcriptional factors KLF4 and SOX2 via the YAP/TAZ pathway. Transplanting HOs presenting reprogramming effects into a 70 % hepatectomy model demonstrated improved liver regeneration, underscoring the potential of the THBS1-based dynamic ECM system in organoids manipulation and liver regeneration.

Genetic studies have revealed hundreds of loci associated with bone-related phenotypes, including bone mineral density (BMD) and fracture risk. However, translating discovered loci into effective new therapies remains challenging. We review success stories including PCSK9-related drugs in cardiovascular disease and evidence supporting the use of human genetics to guide drug discovery, while highlighting advances in artificial intelligence and machine learning with the potential to improve target discovery in skeletal biology. These strategies are poised to improve how we integrate diverse data types, from genetic and electronic health records data to single-cell profiles and knowledge graphs. Such emerging computational methods can position bone genomics for a future of more precise, effective treatments, ultimately improving the outcomes for patients with common and rare skeletal disorders.

Publicly accessible expression data produced by large consortium projects like TCGA and GTEx are increasing in number and size at an unprecedented rate. Their utility cannot be underestimated given the diversity of valuable tools widely used to interrogate these data and the many discoveries of biological and clinical significance already garnered from these datasets. However, there remain undiscovered ways to mine these rich resources and a continuing need to provide researchers with easily accessible and user-friendly applications for complex or bespoke analyses. We introduce TRanscriptome ANalysis of StratifiEd CohorTs (TRANSECT), a bioinformatics application automating the stratification and subsequent differential expression analysis of cohort data to provide further insights into gene regulation. TRANSECT works by defining two groups within a cohort based on disparate expression of a gene or a gene set and subsequently compares the groups for differences in global expression. Akin to reverse genetics minus the inherent requirement of in vitro or in vivo perturbations, cell lines or model organisms and all the while working within natural physiological limits of expression, TRANSECT compiles information about global transcriptomic change and functional outcomes. TRANSECT is freely available as a command line application or online at https://transect.au.