Search Results (125)

Background/Objective: Exertional rhabdomyolysis (ER) is primarily driven by mechanical stress on muscles during strenuous or unaccustomed exercise, often exacerbated by environmental factors like heat and dehydration. While the general cellular pathway involving energy depletion and calcium overload is understood in horse ER models, the underlying mechanisms specific to the ER are not universally known within humans. This study aimed to evaluate whether patients with ER exhibited transcriptional signatures that were significantly different from those of healthy individuals. Methods: This study utilized RNA sequencing on skeletal muscle samples from 19 human patients with ER history, collected at a minimum of six months after the most recent ER event, and eight healthy controls to investigate the transcriptomic landscape of ER. To identify any alterations in biological processes between the case and control groups, functional pathway analyses were conducted. Results: Functional pathway enrichment analyses of differentially expressed genes revealed strong suppression of mitochondrial function. This suppression included the “aerobic electron transport chain” and “oxidative phosphorylation” pathways, indicating impaired energy production. Conversely, there was an upregulation of genes associated with adhesion and extracellular matrix-related pathways, indicating active restoration of muscle function in ER cases. Conclusions: The study demonstrated that muscle tissue exhibited signs of suppressed mitochondrial function and increased extracellular matrix development. Both of these facilitate muscle recovery within several months after an ER episode. Full article

Background: Extremely premature neonates are at increased risk for respiratory complications, often resulting in recurrent hospitalizations during early childhood. Early identification of preterm infants at highest risk of respiratory hospitalizations could enable targeted preventive interventions. While clinical and demographic factors offer some prognostic value, integrating transcriptomic data may improve predictive accuracy. Objective: To determine whether early-life gene expression profiles can predict respiratory-related hospitalizations within the first four years of life in extremely preterm neonates. Methods: We conducted a retrospective cohort study of 58 neonates born at <32 weeks’ gestational age, using publicly available transcriptomic data from peripheral blood samples collected on days 5, 14, and 28 of life. Random forest models were trained to predict unplanned respiratory readmissions. Model performance was evaluated using sensitivity, specificity, positive predictive value, negative predictive value, and area under the receiver operating characteristic curve (AUC). Results: All three models, built using transcriptomic data from days 5, 14, and 28, demonstrated strong predictive performance (AUC = 0.90), though confidence intervals were wide due to small sample size. We identified 31 genes and eight biological pathways that were differentially expressed between preterm neonates with and without subsequent respiratory readmissions. Conclusions: Transcriptomic data from the neonatal period, combined with machine learning, accurately predicted respiratory-related rehospitalizations in extremely preterm neonates. The identified gene signatures offer insight into early biological disruptions that may predispose preterm neonates to chronic respiratory morbidity. Validation in larger, diverse cohorts is needed to support clinical translation. Full article

Background: The N⁶-methyladenosine (m⁶A) modification of eukaryotic mRNA is the most prevalent of such epigenetic modifications and has recently been identified as a potential player in the pathogenesis and progression of hepatocellular carcinoma (HCC). With the increasing emergence of immunotherapy in the treatment of HCC, we have evaluated the potential of m⁶A-related genes in predicting overall survival and the therapeutic efficacy of immunotherapy in HCC patients. Methods: We employed transcriptomic data from TCGA-LIHC and GSE76427, comprising a total of 485 HCC patients, as the training set. Based on 23 recognized m⁶A regulators, we performed clustering analysis on HCC patients. The intersecting differentially expressed genes (DEGs) among subtypes were used in least absolute shrinkage and selection operator (LASSO) Cox and multivariate Cox regression analyses to construct the risk model. For the quantification of a risk model of HCC patients, a risk score was developed and correlated with clinical and immunological parameters. Furthermore, a single-cell transcriptomic atlas was used to analyze the relationship between model genes and immune cell subpopulations. Mechanistic studies included in vitro assays to validate the association between the m⁶A-related gene ANLN and the progression of HCC. Results: Internal (TCGA and GEO) and external validation (ICGC) suggested that an 8-gene risk score provides an accurate and stable prognostic assessment for HCC. Furthermore, the high-risk score, characterized by elevated TP53 mutation frequency, tumor mutation burden (TMB), and tumor stem cell characteristics indicated a poor prognosis. The prognostic signature was associated with immune cell infiltration in HCC. Those patients with a high-risk score had lower immune tolerance with a better prediction of the efficacy of immunotherapy. The risk model helps to assess and predict the response and prognosis of HCC patients to immune checkpoint inhibitors (ICIs). Additionally, single-cell RNA sequencing data revealed that the high-risk group had a higher proportion of T cells and fewer immunosuppressive T cells, potentially correlating with a better response to immunotherapy. Finally, in vitro experiments showed that ANLN, an m⁶A-related gene, promoted the proliferation and migration of HCC cells. Conclusions: In this study, we identified and validated an m⁶A gene signature consisting of eight genes that can be used to predict prognosis and immunotherapy efficacy in HCC patients. Full article

Tumor development is mainly marked by the gradual transformation of cells that acquire capacities such as sustained growth signaling, evasion of growth suppression, resistance to cell death, and induction of angiogenesis, achieving replicative immortality and activating invasion and metastasis. How different epigenetic alterations like m¹A, m⁵C, and m⁶A contribute to tumor development is a field that still needs to be investigated. The immune modulators, CD70, CD80, and TIGIT, mainly regulate T-cell activation and consequently the immune evasion of tumors. Here, we explored the presence and the potential consequences of RNA modifications in these regulators in pan-cancer. Our findings highlight the critical role of the m⁶A, m⁵C, and m¹A in regulating CD70, CD80, and TIGIT across multiple solid tumors. By combining epitranscriptomics data with functional enrichment and survival modeling, we show that RNA modification enzymes not only modulate immune-related gene expression but also serve as potential biomarkers for patient prognosis. By constructing a robust four-gene prognostic signature involving YTHDF3, RBM15B, IGF2BP2, and TRMT61A, we demonstrate that RNA modification profiles can accurately stratify patients into risk groups with distinct overall survival outcomes. The performance of this model across eight cancer types underscores the translational promise of epitranscriptomic markers in both mechanistic understanding and personalized oncology. Altogether, our study bridges the gap between the mechanistic regulation of immune checkpoints and their clinical utility, offering novel insights into how the epitranscriptome can be leveraged to improve cancer prognosis and potentially enhance immunotherapeutic strategies. Full article

The spectrin family genes play critical roles in cytoskeletal organization and cellular integrity, yet their evolutionary and functional significance in non-classical model organisms remains poorly explored. Here, we systematically identified and characterized spectrin family genes in the silkworm Bombyx mori. Genome-wide analysis identified 17 predicted spectrin genes, which were integrated into eight optimized members through transcriptome-guided structural refinement. Multi-species genomic analysis revealed 8, 23, and 24 spectrin family genes in Drosophila melanogaster, Mus musculus, and Homo sapiens, respectively. Phylogenetic analysis revealed conserved clades across insects and mammals, with gene family expansions in vertebrates. Spatiotemporal expression profiling demonstrated ubiquitous expression of these genes during silkworm development. Population genomic analyses detected strong selection signatures in BmTrio during domestication and implicated BmBeta_spc as a candidate gene for silk yield enhancement in Chinese-improved strains (CHN-I). Expression profiles of parental strains and F₁ offspring from a commercial hybrid cross (Jingsong × Haoyue) revealed BmBeta_spc expression correlating with heterosis in silk yield traits. This study elucidates the characterization and functional relevance of silkworm spectrin genes, providing insights into their roles in domestication and breeding. Full article

Clear cell renal cell carcinoma (ccRCC) is distinguished by metabolic irregularities and unique immunological profiles. Nevertheless, the comprehensive examination of immune and metabolic attributes within the tumor microenvironment of ccRCC remains inadequately elucidated. In this study, we identified two distinct molecular subtypes (C1 and C2) of ccRCC using the non-negative matrix factorization (NMF) algorithm. Utilizing univariate and least absolute shrinkage and selection operator (LASSO) Cox regression analyses, we developed a prognostic signature comprising eight immune- and metabolism-related genes (IMRGs) associated with the tumor microenvironment. The validation of this signature was performed using both testing and entire datasets. A nomogram was developed using IMRGs prognostic signature and various clinical parameters, including age and TNM stage. We also performed the in vitro experiments to validate the carcinogenic role of PYCR1 in ccRCC cells. Subtype C1 exhibited a more favorable prognosis and higher levels of immune cell infiltration compared to subtype C2. The AUCs of the nomogram at 1-, 3-, and 5-year intervals (AUC = 0.874, 0.820, and 0.794) were slightly higher than those of the IMRGs signature alone (AUC = 0.773, 0.755, and 0.764). The association between risk score and immune checkpoint expressions, immunophenoscore (IPS), and microsatellite instability (MSI) collectively predicted treatment efficacy accurately. Additionally, in vitro experiments confirmed the involvement of PYCR1 in promoting the aggressive behaviors of ccRCC cells, as evidenced by reduced proliferation, invasion, and enhanced apoptosis upon PYCR1 knockdown. In conclusion, the IMRGs signature shows promise in predicting prognostic risk, assessing the effectiveness of immunotherapy, and tailoring treatment for ccRCC patients. Full article

Alkane-oxidizing bacteria play a crucial role in the global carbon cycle. Rhodococcus species are well-known hydrocarbon degraders, distinguished by the harboring of multiple homologs of AlkB family alkane monooxygenases. Although different types of rhodococcal AlkBs have been described, the overall picture of their diversity remains unclear, leaving gaps in the current classification. We conducted a phylogenetic analysis of all AlkBs identified in Rhodococcus (sensu lato) and examined the genomic context of the corresponding genes. The sequence clustering was well aligned with genomic neighborhoods, allowing both features to be used as criteria for proposing AlkB types that form distinct phylogenetic groups and have characteristic genomic contexts. Our approach allowed us to revise the classification of previously described AlkBs, identifying eight types on their basis, and to propose three new ones. Alkane monooxygenases whose genes are co-localized with rubredoxin genes can be considered a generalized AlkBR type, the most common among all Rhodococcus. In the AlkB0 type, which is a paralog of AlkBR, violations of conservativity in known alkane monooxygenase signature motifs were found. Our findings provide a more consistent classification framework for rhodococcal AlkB that prevents the over-reporting of “novel” types and contributes to a deeper understanding of alkane monooxygenase diversity. Full article

Leishmania (Leishmania) infantum chagasi infections range from asymptomatic (AS) to severe visceral leishmaniasis (VL). One of the manifestations is an atypical non-ulcerated cutaneous leishmaniasis (NUCL), which occurs in some locations of Central America with few cases of VL. We conducted a transcriptomic analysis of cell-mediated immunity (CMI) on blood samples from NUCL, AS, VL patients from Amapala, Honduras, and healthy controls. RNA-seq revealed a similar perturbation of gene expression in NUCL and AS. Eight gene signatures of CMI were found in NUCL involved in CD8⁺ T lymphocyte infiltration, reactive oxygen species generation, PD-1 receptor ligand, inflammasome assembly, chemotaxis, complement receptor and suppressor immune cell infiltration. NUCL was distinguished from VL by its up-regulation of differently expressed genes (DEGs) related to T lymphocyte exhaustion, adhesion and transmigration of leukocytes, and down-regulation of oxidative stress genes. In contrast, VL exhibited up-regulated DEGs involved in antigen cross-presentation, and similar to VL from Brazil, down-regulated DEGs involved in innate immunity. Corroborating the transcriptome findings, both the Leishmanin skin test, and the immunopathology of NUCL skin lesion defined NUCL as a proinflammatory condition, intermediate between the AS and VL clinical outcomes. That condition may be the underlying element for the benign nature of the NUCL. Full article

Background/Objectives: Colorectal cancer (CRC) arises from the epithelial lining of the colon or rectum, often following a progression from benign adenomatous polyps to malignant carcinoma. Screening modalities such as colonoscopy, faecal immunochemical tests (FIT), and FIT-DNA are critical for early detection and prevention, but non-invasive methods lack sensitivity to polyps and early CRC. Chromosome conformations (CCs) are potent epigenetic regulators of gene expression. We have previously developed an epigenetic assay, EpiSwitch^®®, that employs an algorithmic-based CCs analysis. Using EpiSwitch^®® technology, we have shown the presence of cancer-specific CCs in peripheral blood mononuclear cells (PBMCs) and primary tumours of patients with melanoma and prostate cancer. EpiSwitch^®®-based commercial tests are now available to diagnose prostate cancer with 94% accuracy (PSE test) and response to immune checkpoint inhibitors across 14 cancers with 85% accuracy (CiRT test). Methods/Results/Conclusions: Using blood samples collected from n = 171 patients with CRC, n = 44 patients with colorectal polyps and n = 110 patients with a ‘clear’ colonoscopy we performed whole Genome DNA screening for CCs correlating to CRC diagnosis. Our findings suggest the presence of two eight-marker CC signatures (EpiSwitch^®® NST) in whole blood that allow diagnosis of CRC and precancerous polyps, respectively. Independent validation cohort testing demonstrated high accuracy in identifying colorectal polyps and early versus late stages of CRC with an exceptionally high sensitivity of 79–90% and a high positive prediction value of 60–84%. Linking the top diagnostic CCs to nearby genes, we have built pathways maps that likely underline processes contributing to the pathology of polyp and CRC progression, including TGFβ, cMYC, Rho GTPase, ROS, TNFa/NFκB, and APC. Full article

Background/Objectives: Astroblastoma is a rare glial neoplasm more frequent in young female patients, with unclear clinical behaviors and outcomes. The diagnostic molecular alteration is a rearrangement of the Meningioma 1 (MN1) gene. MicroRNAs (miRNAs) are important gene expression regulators with strong implications in biological processes. Here, we investigated microRNA expression, regulation, and biological processes correlated to target genes of deregulated miRNAs in MN1-altered astroblastoma. Methods: A cohort of 14 tumor samples, histologically classified as astroblastoma, was retrospectively collected and analyzed through their DNA methylation profiles. MiRNA expression profiles were then detected on MN1-altered astroblastomas (n = 8) and normal brain controls (n = 2) by Nanostring technology and validated by RT-qPCR; then, the expression of deregulated miRNAs was correlated with clinical-pathological characteristics. Subsequently, the methylation status of promoters of deregulated miRNAs was investigated through a methylation profiling microarray. Finally, bioinformatics analysis was conducted to explore the biological processes (BPs) and target genes of differentially expressed miRNAs. Results: Eight MN-altered astroblastoma were identified. Thirty-nine miRNAs were deregulated in tumor samples compared to normal brain tissue. Downregulated microRNAs exhibited an association with an increased risk of recurrence. The promoter methylation status was investigated in 32/39 miRNAs: 14/32 were epigenetically deregulated. None of them were genetically regulated. Conclusions: MN1-altered astroblastomas have an miRNA expression signature that identifies specific BPs and pathways. Our findings suggested that the involved pathways could be associated with clinical and pathological characteristics of MN1-altered astroblastomas. Also, the biology of this rare tumor could have potential implications on prognostic markers and therapy. Full article

According to the Humane Society, 25 to 40 percent of pet dogs in the United States are adopted from animal shelters. Shelter dogs can harbor bacterial, viral, fungal, and protozoal pathogens, posing risks to canine and human health. These bacterial pathogens may also carry antibiotic resistance genes (ARGs), serving as a reservoir for antimicrobial resistance (AMR) transmission. This study aimed to utilize whole metagenome sequencing (WMS) to screen for microbial pathogens and assess the resistome in healthy shelter dogs. Fecal samples from 58 healthy shelter dogs across 10 shelters in Kentucky, Tennessee, and Virginia were analyzed using WMS. Genomic DNA was extracted, and bioinformatics analyses were performed to identify pathogens and ARGs. The WMS detected 53 potentially zoonotic or known pathogens including thirty-eight bacterial species, two protozoa, five yeast species, one nematode, four molds, and three viruses. A total of 4560 ARGs signatures representing 182 unique genes across 14 antibiotic classes were detected. Tetracycline resistance genes were most abundant (49%), while β-lactam resistance genes showed the highest diversity with 75 unique ARGs. ARGs were predominantly detected in commensal bacteria; however, nearly half (18/38, 47.4%) of known bacterial pathogens detected in this study carried ARGs for resistance to one or more antibiotic classes. This study provides evidence that healthy shelter dogs carry a diverse range of zoonotic and antibiotic-resistant pathogens, posing a transmission risk through fecal shedding. These findings highlight the value of WMS for pathogen detection and AMR surveillance, informing therapeutic and prophylactic strategies to mitigate the transmission of pathogens among shelter dog populations and the risk associated with zoonoses. Full article

Foam cell formation is a hallmark of atherosclerosis, yet the cellular complexity within foam cells in human plaques remains unexplored. Here, we integrate published single-cell RNA-sequencing, spatial transcriptomic, and chromatin accessibility sequencing datasets of human atherosclerotic lesions across eight distinct studies. Through this large-scale integration of patient-derived information, we identified foamy macrophages enriched for genes characteristic of the foamy signature. We further re-clustered the foamy macrophages into five unique subsets with distinct potential functions: (i) pro-foamy macrophages, exhibiting relatively high inflammatory and adhesive properties; (ii) phagocytic foamy macrophages, specialized in efferocytosis; (iii) high-efflux foamy macrophages marked by high NR1H3 expression; (iv) mature foamy macrophages prone to programmed cell death; and (v) synthetic subset. Trajectory analysis elucidated a bifurcated differentiation cell fate from pro-foam macrophages toward either the programmed death (iv) or synthetic (v) phenotype. The existence of these foamy macrophage subsets was validated by immunostaining. Moreover, these foamy macrophage subsets exhibited strong potential ligand–receptor interactions. Finally, we conducted Mendelian randomization analyses to identify a possible causal relationship between key regulatory genes along the programmed death pathway in foamy macrophages and atherosclerotic diseases. This study provides a high-resolution map of foam cell diversity and a set of potential key regulatory genes in atherosclerotic plaques, offering novel insights into the multifaceted pathophysiology underlying human atherosclerosis. Full article

Background/Objectives: Schlafen12 (SLFN12) is an intermediate human Schlafen protein shown to correlate with survivability in triple-negative breast cancer (TNBC). SLFN12 causes differential expressions of significant cancer genes, but how they change in response to chemotherapy remains unknown. Our aim is to identify the effect of chemotherapy on genes that improve TNBC outcomes and other SLFN family members following SLFN12 knockout or overexpression. Methods: We overexpressed SLFN12 using a lentiviral vector and knocked out SLFN12 (AdvShSLFN12) using a hairpin adenovirus in MDA-MB-231 TNBC cells. Cells were treated with camptothecin, paclitaxel, zoledronic acid, or carboplatin to evaluate the SLFN12 signature cancer genes associated with improved TNBC outcomes using qPCR. Additionally, cells were treated alone and in combination with AdvShSLFN12, IFN-α2 (known SLFN12 stimulator), carboplatin, and paclitaxel. After treatment, the viable cell numbers were analyzed utilizing a colorimetric crystal violet assay for cell viability. Results: The SLFN family and SLFN12 cancer signature gene mRNA expressions were analyzed by RT-qPCR. Treating SLFN12-overexpressing TNBC cells with chemotherapy agents resulted in the differential expressions of eight cancer-related genes. Notably, GJB3 was downregulated following treatment with each chemotherapeutic drug. Inducing SLFN12 with IFN-α2 resulted in decreased cell viability and increased SLFN12 mRNA levels following treatment with paclitaxel or carboplatin. Conclusions: These results suggest that SLFN12 overexpression significantly affects the expressions of genes driving phenotypic changes in response to chemotherapy and influences additional SLFN family members following IFN-α2 treatment. This may contribute to improving the survival of patients with SLFN12 overexpression. Additionally, patient SLFN12 levels can be used as a factor when pursuing personalized chemotherapy treatments. Full article

Background: While miRNAs are increasingly recognized for their role in tumorigenesis, their involvement in head and neck cancer (HNC) remains insufficiently explored. Additionally, the carcinogenic mechanisms of areca nut, a major habitual carcinogen in Southeast Asia, are not well understood. Methods and results: This study adopts a systematic approach to identify miRNA profiles associated with areca nut-induced HNC. Using miRNA microarray analysis, we identified 292 miRNAs dysregulated in areca nut-treated HNC cells, with 136 upregulated and 156 downregulated. Bioinformatic analysis of the TCGA-HNSC dataset uncovered a set of 692 miRNAs relevant to HNC development, comprising 449 overexpressed and 243 underexpressed in tumor tissues. Integrating these datasets, we defined a signature of 84 miRNAs, including 39 oncogenic miRNAs (OncomiRs) and 45 tumor-suppressive miRNAs (TsmiRs), highlighting their pivotal role in areca nut-induced carcinogenesis. MultiMiR analysis identified 740 genes cross-regulated by eight hub TsmiRs, significantly impacting key cancer-related pathways (p53, PI3K-AKT, MAPK, and Ras) and critical oncogenic processes. Moreover, we validated miR-499a-5p as a vital regulator, demonstrating its ability to mitigate areca nut-induced cancer progression by reducing cell migration, invasion, and chemoresistance. Conclusions: Thus, this miRNA signature addresses a crucial gap in understanding the molecular underpinnings of areca nut-induced carcinogenesis and offers a promising platform for clinical applications in risk assessment, diagnosis, and prognosis of areca nut-associated malignancies. Full article

Non-small cell lung cancer (NSCLC), representing 85% of lung cancer cases, is characterized by its heterogeneity and progression through distinct stages. This study applied Weighted Gene Co-expression Network Analysis (WGCNA) to explore the molecular mechanisms of NSCLC and identify potential therapeutic targets. Gene expression data from the GEO database were analyzed across four NSCLC stages (NSCLC1, NSCLC2, NSCLC3, and NSCLC4), with the NSCLC2 dataset selected as the reference for module preservation analysis. WGCNA identified eight highly preserved modules—Cyan, Yellow, Red, Dark Turquoise, Turquoise, White, Purple, and Royal Blue—across datasets, which were enriched in key pathways such as “Cell cycle” and “Pathways in cancer”, involving processes like cell division and inflammatory responses. Hub genes, including PLK1, CDK1, and EGFR, emerged as critical regulators of tumor proliferation and immune responses. Estrogen receptor ESR1 was also highlighted, correlating with improved survival outcomes, suggesting its potential as a prognostic marker. Signature-based drug repurposing analysis identified promising therapeutic candidates, including GW-5074, which inhibits RAF and disrupts the EGFR–RAS–RAF–MEK–ERK signaling cascade, and olomoucine, a CDK1 inhibitor. Additional candidates like pinocembrin, which reduces NSCLC cell invasion by modulating epithelial-mesenchymal transition, and citalopram, an SSRI with anti-carcinogenic properties, were also identified. These findings provide valuable insights into the molecular underpinnings of NSCLC and suggest new directions for therapeutic strategies through drug repurposing. Full article