Potential Marker Research Articles

TRIP6 a potential diagnostic marker for colorectal cancer with glycolysis and immune infiltration association

Thyroid hormone receptor interactor 6 (TRIP6) it is an adaptor protein belonging to the zyxin family of LIM proteins, participating in signaling events through interactions with various molecules. Despite this, TRIP6's role in colorectal cancer (CRC), particularly its correlation with glucose metabolism and immune cell infiltration, remains unclear. Through the TCGA and GEO databases, we obtained RNA sequencing data to facilitate our in-depth study and analysis of TRIP6 expression. To investigate the prognostic value of TRIP6 in CRC, we also used univariate Cox regression analysis. In addition, this study also covered a series of analyses, including clinicopathological analysis, functional enrichment analysis, glycolysis correlation analysis, immunoinfiltration analysis, immune checkpoint analysis, and angiogenesis correlation analysis, to gain a comprehensive and in-depth understanding of this biological phenomenon. It has been found that TRIP6 expression is significantly upregulated in CRC and correlates with the stage of the disease. Its overexpression portends a worse survival time. Functional enrichment analysis reveals that TRIP6 is associated with focal adhesion and glycolysis. Mechanistically, TRIP6 appears to exert its tumorigenic effect by regulating the glycolysis-related gene GPI. A higher level of expression of TRIP6 is associated with an increase in the number of iDC immune cells and a decrease in the number of Th1 immune cells. Also, TRIP6 may promote angiogenesis in tumor cells by promoting the expression of JAG2. Our study uncovers the upregulation of TRIP6 in CRC, illuminating its prognostic and diagnostic value within this context. Furthermore, we examine the relationship between TRIP6 expression levels, glycolysis, angiogenesis and immune cell infiltration. This underscores its potential as a biomarker for CRC treatment and as a therapeutic target.

Plasma levels of hydrogen sulfide and homocysteine correlate with the efficacy of antidepressant agents and serve as potential diagnostic and therapeutic markers

ObjectiveHydrogen sulfide (H2S) is associated with depressive-like behavior in rodents. We undertook cross-sectional and longitudinal analyses of plasma levels of H2S and its substrate homocysteine (Hcy) in depression and assessed the association of both parameters with psychopathology and cognitive function. MethodsForty-one patients suffering from depression (PSDs) and 48 healthy volunteers were recruited. PSDs were treated for 8 weeks. Analyzable data were collected from all participants for assessment of their psychopathology and cognitive function. Plasma was collected for determination of levels of H2S and Hcy, and data were correlated to determine their potential as plasma biomarkers. ResultsCross-sectional analyses revealed PSDs to have a low plasma H2S level and high Hcy level. Longitudinal analyses revealed that 8 weeks of treatment reversed the changes in plasma levels of H2S and Hcy in PSDs. Plasma levels of H2S and Hcy were associated with psychopathology and cognitive function in depression. The area under the receiver operating characteristic curve (AUC) for a combination of plasma levels of H2S and Hcy and expression of the TNF gene (i.e., H2S–Hcy–TNF) was 0.848 for diagnosing depression and 0.977 for predicting the efficacy of antidepressant agents. ConclusionPlasma levels of H2S and Hcy reflect changes in psychopathology and cognitive function in depression and H2S–Hcy–TNF has the potential to diagnose depression and predict the efficacy of antidepressant medications.

RANK/RANKL axis promotes migration, invasion, and metastasis of osteosarcoma via activating NF-κB pathway

Osteosarcoma (OS) is one of the most prevalent primary bone tumors with a high degree of metastasis and poor prognosis. Epithelial-to-mesenchymal transition (EMT) is a cellular mechanism that contributes to the invasion and metastasis of cancer cells, and OS cells have been reported to exhibit EMT-like characteristics. Our previous studies have shown that the interaction between tumor necrosis factor superfamily member 11 (TNFRSF11A; also known as RANK) and its ligand TNFSF11 (also known as RANKL) promotes the EMT process in breast cancer cells. However, whether the interaction between RANK and RANKL enhances aggressive behavior by inducing EMT in OS cells has not yet been elucidated. In this study, we showed that the interaction between RANK and RANKL increased the migration, invasion, and metastasis of OS cells by promoting EMT. Importantly, we clarified that the RANK/RANKL axis induces EMT by activating the nuclear factor-kappa B (NF-κB) pathway. Furthermore, the NF-κB inhibitor dimethyl fumarate (DMF) suppressed migration, invasion, and EMT in OS cells. Our results suggest that the RANK/RANKL axis may serve as a potential tumor marker and promising therapeutic target for OS metastasis. Furthermore, DMF may have clinical applications in the treatment of lung metastasis in patients with OS.

Bisphenol A Negatively Impacts Human Sperm MicroRNA and Protein Profiles

AbstractBisphenol A (BPA), a widely prevalent endocrine disruptor, has detrimental effects on human health and male reproduction. Elevated BPA levels have been linked to reduced sperm quality and production, while paternal exposure may result in poor reproductive outcomes and offspring health. For many years, the effects of BPA exposure in human reproduction were mainly attributed to the deregulation of the hypothalamic–pituitary–gonadal (HPG) axis. In the past decades, other mechanisms of action have been proposed, and studies highlighting epigenetic alterations linked to BPA in sperm emerged. Nevertheless, the impact of BPA on human sperm miRNA and protein profiles and its implications for fertilization and post-fertilization events remain unexplored. This study aimed to investigate the association between BPA concentration in seminal plasma and seminal quality and to examine the alterations in human sperm miRNA and protein expression among men with varying BPA levels in seminal plasma. BPA levels were measured in seminal plasma from 102 Portuguese men, and it was detected in 88% of the samples. No correlation was observed between BPA levels and age or seminal parameters. The small RNA content of 15 normozoospermic samples was evaluated using small RNA sequencing, revealing that 15 miRNAs exhibited a correlation with BPA levels. Gene ontology analysis of their target genes indicated their involvement in embryonic development and response to stress. The proteome of 20 normozoospermic human sperm samples, categorized into four groups based on BPA levels, was accessed by liquid chromatography–mass spectrometry. Data are available via ProteomeXchange with the identifier PXD047280. Sixty-two differentially expressed proteins were identified across groups. The biological processes most affected in samples with higher BPA levels were “protein sumoylation” and “cytoplasmic translation”. The altered miRNAs and proteins identified in spermatozoa from men environmentally exposed to BPA represent potential biological markers of exposure to this endocrine disruptor and may help elucidate cases of idiopathic male infertility, fertilization failure, and abnormal embryo development.

Profiles of subgingival microbiomes and gingival crevicular metabolic signatures in patients with amnestic mild cognitive impairment and Alzheimer’s disease

BackgroundThe relationship between periodontitis and Alzheimer’s disease (AD) has attracted more attention recently, whereas profiles of subgingival microbiomes and gingival crevicular fluid (GCF) metabolic signatures in AD patients have rarely been characterized; thus, little evidence exists to support the oral-brain axis hypothesis. Therefore, our study aimed to characterize both the microbial community of subgingival plaque and the metabolomic profiles of GCF in patients with AD and amnestic mild cognitive impairment (aMCI) for the first time.MethodsThis was a cross-sectional study. Clinical examinations were performed on all participants. The microbial community of subgingival plaque and the metabolomic profiles of GCF were characterized using the 16S ribosomal RNA (rRNA) gene high-throughput sequencing and liquid chromatography linked to tandem mass spectrometry (LC–MS/MS) analysis, respectively.ResultsThirty-two patients with AD, 32 patients with aMCI, and 32 cognitively normal people were enrolled. The severity of periodontitis was significantly increased in AD patients compared with aMCI patients and cognitively normal people. The 16S rRNA gene sequencing results showed that the relative abundances of 16 species in subgingival plaque were significantly correlated with cognitive function, and LC–MS/MS analysis identified a total of 165 differentially abundant metabolites in GCF. Moreover, multiomics Data Integration Analysis for Biomarker discovery using Latent cOmponents (DIABLO) analysis revealed that 19 differentially abundant metabolites were significantly correlated with Veillonella parvula, Dialister pneumosintes, Leptotrichia buccalis, Pseudoleptotrichia goodfellowii, and Actinomyces massiliensis, in which galactinol, sn-glycerol 3-phosphoethanolamine, D-mannitol, 1 h-indole-1-pentanoic acid, 3-(1-naphthalenylcarbonyl)- and L-iditol yielded satisfactory accuracy for the predictive diagnosis of AD progression.ConclusionsThis is the first combined subgingival microbiome and GCF metabolome study in patients with AD and aMCI, which revealed that periodontal microbial dysbiosis and metabolic disorders may be involved in the etiology and progression of AD, and the differential abundance of the microbiota and metabolites may be useful as potential markers for AD in the future.

Exploration of markers in oxidized rancidity walnut kernels based on lipidomics and volatolomics

Walnut kernels are prone to oxidation and rancidity due to their rich lipid composition, but the existing evaluation indicators are not sensitive enough to promote their industrial development. This study aims to investigate the potential markers in oxidative rancidity walnut kernels using lipidomics and volatolomics. The results showed that the antioxidant capacity of walnut kernels significantly decreased after oxidation, with the decreasing of total phenolic content from 36276.34 mg GAE/kg to 31281.53 mg GAE/kg, the DPPH and ABTS free radical scavenging activity from 89.25% to 73.54%, and 61.69% to 43.73%, respectively. The activities of lipoxygenase (LOX) and lipase (LPS) increased by 6.08-fold and 0.33-fold, respectively. By combining volatolomics and chemometrics methods, it was found that significant differences existed in the content of hexanal, caproic acid, 1-pentanol, (E)-2-octenal, and 2-heptanenal before and after walnut kernel oxidation (VIP > 1). Based on the results of lipidomics, it can be concluded that the above five compounds can serve as characteristic markers for walnut kernel oxidative rancidity, mainly produced through glycerol phospholipid (GPL), glyceride, linoleic acid (LA), and α-linolenic acid (ALA) metabolism pathways. Possible mechanisms of lipid degradation in oxidized walnut kernels were also proposed, providing technical support for the storage, preservation, and high-value utilization of walnut kernels.

Upregulation of serine metabolism enzyme PSAT1 predicts poor prognosis and promotes proliferation, metastasis and drug resistance of clear cell renal cell carcinoma

Serine metabolic reprogramming is known to be associated with oncogenesis and tumor development. The key metabolic enzyme PSAT1 has been identified as a potential prognostic marker for various cancers, but its role in ccRCC remains unkown. In this study, we investigated expression of PSAT1 in ccRCC using the TCGA database and clinical specimens. Our results showed that PSAT1 exhibited lower expression in tumor tissue compared to adjacent normal tissue, but its expression level increased with advancing stages and grades of ccRCC. Patients with elevated expression level of PSAT1 exhibited an unfavorable prognosis. Functional experiments have substantiated that the depletion of PSAT1 shows an effective activity in inhibiting the proliferation, migration and invasion of ccRCC cells, concurrently promoting apoptosis. RNA sequencing analysis has revealed that the attenuation of PSAT1 can diminish tumor resistance to therapeutic drugs. Furthermore, the xenograft model has indicated that the inhibition of PSAT1 can obviously impact the tumorigenic potential of ccRCC and mitigate lung metastasis. Notably, pharmacological targeting PSAT1 by Aminooxyacetic Acid (AOA) or knockdown of PSAT1 increased the susceptibility of sunitinib-resistant cells. Inhibition of PSAT1 increased the sensitivity of drug-resistant tumors to sunitinib in vivo. Collectively, our investigation identifies PSAT1 as an independent prognostic biomarker for advanced ccRCC patients and as a prospective therapeutic target.

A novel sorting method for the enrichment of early human spermatocytes from clinical biopsies

To determine if early spermatocytes can be enriched from a human testis biopsy using fluorescence-activated cell sorting (FACS). Potential surface markers for early spermatocytes were identified using bioinformatics analysis of single-cell RNA-sequenced human testis tissue. Testicular sperm extraction samples from three participants with normal spermatogenesis were digested into single-cell suspensions and cryopreserved. Two to four million cells were obtained from each and sorted by FACS as separate biologic replicates using antibodies for the identified surface markers. A portion from each biopsy remained unsorted to serve as controls. The sorted cells were then characterized for enrichment of early spermatocytes. A laboratory study. Three men with a diagnosis of obstructive azoospermia (age range, 30-40 years). None. Sorted cells were characterized for RNA expression of markers encompassing the stages of spermatogenesis. Sorting markers were validated by their reactivity on human testis formalin-fixed paraffin-embedded tissue. Serine protease 50 (TSP50) and SWI5-dependent homologous recombination repair protein 1 were identified as potential surface proteins specific for early spermatocytes. After FACS sorting, the TSP50-sorted populations accounted for 1.6%-8.9% of total populations and exhibited the greatest average-fold increases in RNA expression for the premeiotic marker stimulated by retinoic acid (STRA8), by 23-fold. Immunohistochemistry showed the staining pattern for TSP50 to be strong in premeiotic undifferentiated embryonic cell transcription factor 1-/doublesex and Mab-3 related transcription factor 1-/STRA8+ spermatogonia as well as SYCP3+/protamine 2- spermatocytes. This work shows that TSP50 can be used to enrich early STRA8-expressing spermatocytes from human testicular biopsies, providing a means for targeted single-cell RNA sequencing analysis and invitro functional interrogation of germ cells during the onset of meiosis. This could enable investigation into details of the regulatory pathways underlying this critical stage of spermatogenesis, previously difficult to enrich from whole tissue samples.

Comparative analysis of phytochemical profile and antioxidant and anti-inflammatory activity of four Gentiana species from the Qinghai-Tibet Plateau

Ethnopharmacological relevanceGentiana species, known as the traditional Tibetan medicine “Bangjian,” have been integral to clinical practice for millennia. Despite their longstanding use, our understanding of the variation in chemical constituents and bioactive effects among different species is limited. Aim of the studyIn the present study, we aimed to assess the differences in chemical profiles and bioactivities among four Gentiana species (G. veitchiorum, G. trichotoma, G. crassuloides, and G. squarrosa) and explore potential bioactive markers. Materials and methodsThe chemical composition of the four Gentiana species was analyzed using UPLC-QE-Orbitrap-MS. The antioxidant activity of the extracts was compared through DPPH, ABTS, and reducing power assays. The anti-inflammatory activity was evaluated by measuring the inhibitory effects on lipopolysaccharide-induced secretion of nitric oxide (NO), interleukin-6 (IL-6), and tumor necrosis factor-alpha (TNF-α) by RAW264.7 macrophages. Additionally, compounds strongly correlated with anti-inflammatory and antioxidant activities were identified through spectrum–effect relationship analysis. ResultsA total of 50 compounds were identified across the four Gentiana species. In vitro antioxidant assays demonstrated DPPH and ABTS scavenging abilities and reducing power within the concentration range of 62.5–2000 μg/mL. All four species inhibited the production of NO, IL-6, and TNF-α in RAW264.7 cells. Spectrum–effect relationship analysis revealed that gentiascabraside A, gentiatibetine, tachioside, lutonarin, and isotachioside were associated with the highest antioxidant activity; and swertiamarin, tarennoside, eleganoside C, and alpigenoside were associated with the highest anti-inflammatory activity. ConclusionsThis study presents, for the first time, the chemical profiles and bioactivities of G. trichotoma, G. crassuloides, and G. squarrosa, which were comprehensively compared with those of G. veitchiorum. The findings provide novel insights to understand the traditional use and/or expand the current use of Gentiana species. Additionally, this research highlights the potential of Gentiana species as natural sources of antioxidants and anti-inflammatory agents, suggesting promising applications in tea production or medicinal contexts in the near future.

Effectiveness of Ya-Samarn-Phlae in diabetic wound healing: Evidence from in vitro studies and a multicenter randomized controlled clinical trial

Ethnopharmacological relevanceYa-Samarn-Phlae (YaSP) has traditionally been widely used in southern Thailand for treating chronic and infected wounds, including diabetic foot ulcers. However, there are only a limited number of clinical studies supporting the use of this polyherbal formulation. Therefore, the present work aims to provide clinical evidence to support the application of YaSP, prepared according to a standardized traditional procedure (T-YaSP). Additionally, its potential chemical markers and wound healing-related biological activities were examined. Materials and methodsThe in vitro wound healing-related biological activities of YaSP ethanol extract and T-YaSP, including antibacterial activity against Staphylococcus epidermidis, inhibition and eradication of staphylococcal biofilm, anti-inflammatory effects, and enhancement of human dermal fibroblast migration in scratch wounds, were examined using well-established protocols. The chemical profiles of the ethanol extract of YaSP and T-YaSP were compared, and with promising chemical markers, arecoline, alpha-mangostin, and curcumin were selected and quantified using the HPLC method. A prospective, multicenter, randomized, controlled, parallel-group study was conducted over 12 weeks to evaluate the efficacy of the YaSP solution as an adjunct therapy, combined with standard wound care, for diabetic ulcers compared to standard treatment. ResultsThe YaSP extract reduces NO production and can scavenge NO radicals in LPS-induced RAW 264.7 macrophage cells. Additionally, in a scratch assay, this extract and one of its herbal components, Curcuma longa, enhance the migration of human dermal fibroblasts. T-YaSP, containing 2.412 ± 0.002 mg/g of arecoline, 2.399 ± 0.005 mg/g of curcumin, and 0.017 ± 0.000 mg/g of α-mangostin, has shown the ability to inhibit the development and eradicate the mature biofilm of S. epidermidis. The use of T-YaSP as an adjunct therapy led to a significantly higher proportion of patients achieving healing within six weeks compared to the standard treatment group (36%/9 patients vs. 4%/1 patient; p = 0.013). After 12 weeks, 19 out of 25 patients in the T-YaSP group experienced complete healing, whereas only four patients in the standard treatment group achieved complete wound healing (76% in the T-YaSP group vs. 16% in the control group; p < 0.001). ConclusionThe results presented here represent the first randomized controlled trial to demonstrate the effectiveness of the traditional polyherbal solution, T-YaSP, which exhibits a wide range of wound healing-related activities. Utilizing T-YaSP as an adjunctive treatment resulted in a significant improvement in the number of type 2 diabetic patients achieving complete healing. However, to explore and utilize YaSP further, conducting a double-blind, randomized controlled trial with a larger population is necessary.

Olfactory deficit: a potential functional marker across the Alzheimer's disease continuum.

Alzheimer's disease (AD) is a prevalent form of dementia that affects an estimated 32 million individuals globally. Identifying early indicators is vital for screening at-risk populations and implementing timely interventions. At present, there is an urgent need for early and sensitive biomarkers to screen individuals at risk of AD. Among all sensory biomarkers, olfaction is currently one of the most promising indicators for AD. Olfactory dysfunction signifies a decline in the ability to detect, identify, or remember odors. Within the spectrum of AD, impairment in olfactory identification precedes detectable cognitive impairments, including mild cognitive impairment (MCI) and even the stage of subjective cognitive decline (SCD), by several years. Olfactory impairment is closely linked to the clinical symptoms and neuropathological biomarkers of AD, accompanied by significant structural and functional abnormalities in the brain. Olfactory behavior examination can subjectively evaluate the abilities of olfactory identification, threshold, and discrimination. Olfactory functional magnetic resonance imaging (fMRI) can provide a relatively objective assessment of olfactory capabilities, with the potential to become a promising tool for exploring the neural mechanisms of olfactory damage in AD. Here, we provide a timely review of recent literature on the characteristics, neuropathology, and examination of olfactory dysfunction in the AD continuum. We focus on the early changes in olfactory indicators detected by behavioral and fMRI assessments and discuss the potential of these techniques in MCI and preclinical AD. Despite the challenges and limitations of existing research, olfactory dysfunction has demonstrated its value in assessing neurodegenerative diseases and may serve as an early indicator of AD in the future.

Pan-cancer analysis predicts CANT1 as a potential prognostic, immunologic biomarker

BackgroundCANT1, calcium-activated nucleotidase 1, was reported to be upregulated in certain tumors. However, the function mechanism of CANT1 in pan-cancer is still unclear. MethodsWe utilized the Cancer Genome Atlas Program (TCGA) and UALCAN databases to analyze CANT1 expression at the level of mRNA, protein, and promoter methylation in pan-cancer, and the cBioportal database to study the frequency of gene changes for CANT1. Wilcoxon test was applied to discuss the correlation between CANT1 and clinicopathological features in different tumor types. The prognosis of CANT1 in pan-cancer was discussed by Cox regression. Spearman analysis was applied to discuss the relationship of CANT1 with tumor mutation burden(TMB), microsatellite instability(MSI), immune cell infiltration, and immune checkpoints. The association between CANT1 expression and drug sensitivity for pan-cancer was investigated by the GSCALite database. In addition, we collected 40 cases of lung adenocarcinoma (LUAD) and adjacent normal tissues for immunohistochemical staining and investigated the relationship between CANT1 and clinicopathology and prognosis in LUAD. Finally, the molecular pathways involved in CANT1-related genes in LUAD were analyzed by gene set enrichment analysis(GSEA). ResultsThe CANT1 mRNA level was significant higher in 14 tumors, and CANT1 protein level was significant higher in 7 tumors compared with normal tissues. CANT1 expression was linked with the T stage, N stage, and pathological stage in some tumors, and overexpression CANT1 was associated with adverse overall survival(OS) and disease-specific survival(DSS) in kidney renal papillary cell carcinoma(KIRP), brain lower grade glioma(LGG), and LUAD. By Spearman correlation analysis, the results showed that CANT1 had a positive correlation with TMB and MSI in bladder urothelial carcinoma(BLCA), breast invasive carcinoma(BRCA), esophageal carcinoma(ESCA), LGG, and sarcoma(SARC). Furthermore, CANT1 was related to immune cell infiltration and immune checkpoints in several cancers. Drug sensitivity analysis suggested that CANT1 was inversely linked with three drugs. Immunohistochemical staining analysis showed that CANT1 expression was higher in LUAD than in normal tissues, and was related to N stage and pathological stage. Survival curves showed that CANT1 overexpression had poor OS and DSS. Time-dependent ROC curves revealed that the 1-year, 5-year, and 10-year OS and DSS in LUAD were above 0.5. CANT1-related genes in LUAD mainly participated in the pathway of dorso ventral axis formation, small cell lung cancer, DNA replication, O-glycan biosynthesis, and cell cycle. ConclusionCANT1 is considered a potential marker for prognosis in several tumors, and a promising target for tumor immunological treatment.

Study of Shanxi aged vinegar by non-targeted metabolomics techniques and antioxidant activity characteristics

The quality and flavor of Shanxi Aged Vinegar (SAV) are closely related to its aging time. In this study, for the first time, UPLC-Q-TOF/MS combined with non-targeted metabolomics techniques were employed to analyze SAV samples from 5 different years. The antioxidant activities were evaluated using ABTS and DPPH assays. The non-targeted metabolomics results identified a total of 99 metabolites, among which 24 were significantly associated with the aging time of SAV and were identified as potential markers of vintage, including key components such as organic acids, amino acids, and polyphenols. They contribute significantly to the unique flavor and nutritional value of SAV. Specifically, in SAV aged for 10 years, the contents of citric acid, L-malic acid, L-glutamic acid, protocatechuic acid, and hydroferulic acid were significantly higher than in other vintages. The results of ABTS and DPPH antioxidant activities indicated a positive correlation between the antioxidant activity of SAV and its aging time. Among the 12 identified polyphenols, chlorogenic acid may be the primary contributor to the antioxidant results of SAV. This study provides important references for further exploration of the health value and antioxidant mechanisms of SAV.

MicroRNAs in spermatogenesis dysfunction and male infertility: clinical phenotypes, mechanisms and potential diagnostic biomarkers.

Infertility affects approximately 10-15% of couples worldwide who are attempting to conceive, with male infertility accounting for 50% of infertility cases. Male infertility is related to various factors such as hormone imbalance, urogenital diseases, environmental factors, and genetic factors. Owing to its relationship with genetic factors, male infertility cannot be diagnosed through routine examination in most cases, and is clinically called 'idiopathic male infertility.' Recent studies have provided evidence that microRNAs (miRNAs) are expressed in a cell-or stage-specific manner during spermatogenesis. This review focuses on the role of miRNAs in male infertility and spermatogenesis. Data were collected from published studies that investigated the effects of miRNAs on spermatogenesis, sperm quality and quantity, fertilization, embryo development, and assisted reproductive technology (ART) outcomes. Based on the findings of these studies, we summarize the targets of miRNAs and the resulting functional effects that occur due to changes in miRNA expression at various stages of spermatogenesis, including undifferentiated and differentiating spermatogonia, spermatocytes, spermatids, and Sertoli cells (SCs). In addition, we discuss potential markers for diagnosing male infertility and predicting the varicocele grade, surgical outcomes, ART outcomes, and sperm retrieval rates in patients with non-obstructive azoospermia (NOA).

Comprehensive analysis of the potential pathogenesis of COVID-19 infection and liver cancer.

A growing number of clinical examples suggest that coronavirus disease 2019 (COVID-19) appears to have an impact on the treatment of patients with liver cancer compared to the normal population, and the prevalence of COVID-19 is significantly higher in patients with liver cancer. However, this mechanism of action has not been clarified. To investigate the disease relevance of COVID-19 in liver cancer. Gene sets for COVID-19 (GSE180226) and liver cancer (GSE87630) were obtained from the Gene Expression Omnibus database. After identifying the common differentially expressed genes (DEGs) of COVID-19 and liver cancer, functional enrichment analysis, protein-protein interaction network construction and screening and analysis of hub genes were performed. Subsequently, the validation of the differential expression of hub genes in the disease was performed and the regulatory network of transcription factors and hub genes was constructed. Of 518 common DEGs were obtained by screening for functional analysis. Fifteen hub genes including aurora kinase B, cyclin B2, cell division cycle 20, cell division cycle associated 8, nucleolar and spindle associated protein 1, etc., were further identified from DEGs using the "cytoHubba" plugin. Functional enrichment analysis of hub genes showed that these hub genes are associated with P53 signalling pathway regulation, cell cycle and other functions, and they may serve as potential molecular markers for COVID-19 and liver cancer. Finally, we selected 10 of the hub genes for in vitro expression validation in liver cancer cells. Our study reveals a common pathogenesis of liver cancer and COVID-19. These common pathways and key genes may provide new ideas for further mechanistic studies.

Early results of the integrative epigenomic-transcriptomic landscape of colorectal adenoma and cancer.

Aberrant methylation is common during the initiation and progression of colorectal cancer (CRC), and detecting these changes that occur during early adenoma (ADE) formation and CRC progression has clinical value. To identify potential DNA methylation markers specific to ADE and CRC. Here, we performed SeqCap targeted bisulfite sequencing and RNA-seq analysis of colorectal ADE and CRC samples to profile the epigenomic-transcriptomic landscape. Comparing 22 CRC and 25 ADE samples, global methylation was higher in the former, but both showed similar methylation patterns regarding differentially methylated gene positions, chromatin signatures, and repeated elements. High-grade CRC tended to exhibit elevated methylation levels in gene promoter regions compared to those in low-grade CRC. Combined with RNA-seq gene expression data, we identified 14 methylation-regulated differentially expressed genes, of which only AGTR1 and NECAB1 methylation had prognostic significance. Our results suggest that genome-wide alterations in DNA methylation occur during the early stages of CRC and demonstrate the methylation signatures associated with colorectal ADEs and CRC, suggesting prognostic biomarkers for CRC.

Risk assessment of psychiatric complications in infectious diseases: CALCulation of prognostic indices on example of COVID-19.

Factors such as coronavirus neurotropism, which is associated with a massive increase in pro-inflammatory molecules and neuroglial reactivity, along with experiences of intensive therapy wards, fears of pandemic, and social restrictions, are pointed out to contribute to the occurrence of neuropsychiatric conditions. The aim of this study is to evaluate the role of COVID-19 inflammation-related indices as potential markers predicting psychiatric complications in COVID-19. A total of 177 individuals were examined, with 117 patients from a temporary infectious disease ward hospitalized due to COVID-19 forming the experimental group and 60 patients from the outpatient department showing signs of acute respiratory viral infection comprising the validation group. The PLR index (platelet-to-lymphocyte ratio) and the CALC index (comorbidity + age + lymphocyte + C-reactive protein) were calculated. Present State Examination 10, Hospital Anxiety and Depression Scale, and Montreal Cognitive Assessment were used to assess psychopathology in the sample. Regression and Receiver operating characteristic (ROC) analysis, establishment of cutoff values for the COVID-19 prognosis indices, contingency tables, and comparison of means were used. The presence of multiple concurrent groups of psychopathological symptoms in the experimental group was associated (R² = 0.28, F = 5.63, p < 0.001) with a decrease in the PLR index and a simultaneous increase in CALC. The Area Under Curve (AUC) for the cutoff value of PLR was 0.384 (unsatisfactory). For CALC, the cutoff value associated with an increased risk of more psychopathological domains was seven points (sensitivity = 79.0%, specificity = 69.4%, AUC = 0.719). Those with CALC > 7 were more likely to have disturbances in orientation (χ² = 13.6; p < 0.001), thinking (χ² = 7.07; p = 0.008), planning ability (χ² = 3.91; p = 0.048). In the validation group, an association (R²McF = 0.0775; p = 0.041) between CALC values exceeding seven points and the concurrent presence of pronounced anxiety, depression, and cognitive impairments was demonstrated (OR = 1.52; p = 0.038; AUC = 0.66). In patients with COVID-19, the CALC index may be used for the risk assessment of primary developed mental disturbances in the context of the underlying disease with a diagnostic threshold of seven points.

A mandatory practice in type 2 diabetes mellitus to maintain quality of life

Nepalese owing to modern lifestyle and processed food are racially at an elevated risk of acquiring central obesity-related insulin resistance (IR) and thus Type 2 diabetes mellitus (T2DM) and Diabetic Kidney Disease (DKD). Low birth weight in utero and later becoming obese risks the development of T2DM. In a total of eighty-four newly diagnosed treatment-naive Nepalese T2DMs, incidence of IR, percentage beta-cell function (%BCF) and percentage insulin sensitivity (%IS) were determined using Homeostatic Model Assessment 2 (HOMA2-IR). Association of HOMA2-IR with albuminuria, kidney function, hs-CRP, fatty liver, fatty pancreas, several anthropometric and biochemical parameters were analyzed. Among the eighty-four T2DMs, fifty-four agreeing regular follow-ups were prescribed a low-carbohydrate diet (&amp;#60;130gm/day). At 6 months, their glycemic controls were monitored. From 84 newly diagnosed T2DMs, 56 (66.7%) were insulin resistant and 28(33.3%) insulin-sensitive on HOMA2-IR. There was a significant association of HOMA2-IR with albuminuria and declining kidney function (p=0.006 and 0.034 respectively) and most of them were at reversible stages. Waist circumference (WC), waist-hip ratio (WHR), lipid profile ratios, fatty liver and fatty pancreas were elucidated as potential markers for IR. The IS group (ISG) had significantly inadequate %BCF (p=0.001) but high %IS (p&amp;#60;0.001) has healthier WHR (p=0.001) and lipid profile ratios which are opposite to IR group (IRG). 13 ISG had raised hs-CRP and 15 normal and 21 IRG had normal hs-CRP and 35 raised. At 6 months, the IRG achieved significantly better postprandial glycemic goals (p=0.04) and significant improvement in WC and WHR (p=0.008 and 0.03 respectively) with a low-carbohydrate diet as compared to ISG. Severe insulin resistance and IR-associated DKD, fatty liver and fatty pancreas are highly prevalent from the time of diagnosis of T2DM in the Nepalese population. Thus inspecting for IR and its consequences mandatorily at diagnosis and applying precision therapies like adjustments in the quality and quantity of staple food carbohydrates significantly improves IR-related parameters and glycemia.

The mutual interactions among Helicobacter pylori, chronic gastritis, and the gut microbiota: a population-based study in Jinjiang, Fujian.

Helicobacter pylori (H. pylori) is a type of bacteria that infects the stomach lining, and it is a major cause of chronic gastritis (CG). H. pylori infection can influence the composition of the gastric microbiota. Additionally, alterations in the gut microbiome have been associated with various health conditions, including gastrointestinal disorders. The dysbiosis in gut microbiota of human is associated with the decreased secretion of gastric acid. Chronic atrophic gastritis (CAG) and H. pylori infection are also causes of reduced gastric acid secretion. However, the specific details of how H. pylori infection and CG, especially for CAG, influence the gut microbiome can vary and are still an area of ongoing investigation. The incidence of CAG and infection rate of H. pylori has obvious regional characteristics, and Fujian Province in China is a high incidence area of CAG as well as H. pylori infection. We aimed to characterize the microbial changes and find potential diagnostic markers associated with infection of H. pylori as well as CG of subjects in Jinjiang City, Fujian Province, China. Enrollment involved sequencing the 16S rRNA gene in fecal samples from 176 cases, adhering to stringent inclusion and exclusion criteria. For our study, we included healthy volunteers (Normal), individuals with chronic non-atrophic gastritis (CNAG), and those with CAG from Fujian, China. The aim was to assess gut microbiome dysbiosis based on various histopathological features. QIIME and LEfSe analyses were performed. There were 176 cases, comprising 126 individuals who tested negative for H. pylori and 50 who tested positive defined by C14 urea breath tests and histopathological findings in biopsies obtained through endoscopy. CAG was also staged by applying OLGIM system. When merging the outcomes from 16S rRNA gene sequencing results, there were no notable variations in alpha diversity among the following groups: Normal, CNAG, and CAG; OLGIM I and OLGIM II; and H. pylori positive [Hp (+)] and H. pylori negative [Hp (-)] groups. Beta diversity among different groups show significant separation through the NMDS diagrams. LEfSe analyses confirmed 2, 3, and 6 bacterial species were in abundance in the Normal, CNAG, and CAG groups; 26 and 2 species in the OLGIM I and OLGIM II group; 22 significant phylotypes were identified in Hp (+) and Hp (-) group, 21 and 1, respectively; 9 bacterial species exhibited significant differences between individuals with CG who were Hp (+) and those who were Hp (-). The study uncovered notable distinctions in the characteristics of gut microbiota among the following groups: Normal, CNAG, and CAG; OLGIM I and OLGIM II; and Hp (+) and Hp (-) groups. Through the analysis of H. pylori infection in CNAG and CAG groups, we found the gut microbiota characteristics of different group show significant difference because of H. pylori infection. Several bacterial genera could potentially serve as diagnostic markers for H. pylori infection and the progression of CG.

Neoadjuvant chemo- or chemo-radiation-therapy of pancreatic ductal adenocarcinoma differentially shift ECM composition, complement activation, energy metabolism and ribosomal proteins of the residual tumor mass.

Pancreatic ductal adenocarcinoma (PDAC) is a highly lethal cancer, often diagnosed at stages that dis-qualify for surgical resection. Neoadjuvant therapies offer potential tumor regression and improved resectability. Although features of the tumor biology (e.g., molecular markers) may guide adjuvant therapy, biological alterations after neoadjuvant therapy remain largely unexplored. We performed mass spectrometry to characterize the proteomes of 67 PDAC resection specimens of patients who received either neoadjuvant chemo (NCT) or chemo-radiation (NCRT) therapy. We employed data-independent acquisition (DIA), yielding a proteome coverage in excess of 3500 proteins. Moreover, we successfully integrated two publicly available proteome datasets of treatment-naïve PDAC to unravel proteome alterations in response to neoadjuvant therapy, highlighting the feasibility of this approach. We found highly distinguishable proteome profiles. Treatment-naïve PDAC was characterized by enrichment of immunoglobulins, complement and extracellular matrix (ECM) proteins. Post-NCT and post-NCRT PDAC presented high abundance of ribosomal and metabolic proteins as compared to treatment-naïve PDAC. Further analyses on patient survival and protein expression identified treatment-specific prognostic candidates. We present the first proteomic characterization of the residual PDAC mass after NCT and NCRT, and potential protein candidate markers associated with overall survival. We conclude that residual PDAC exhibits fundamentally different proteome profiles as compared to treatment-naïve PDAC, influenced by the type of neoadjuvant treatment. These findings may impact adjuvant or targeted therapy options.