Evaluation of the diagnostic utility of immune microenvironment-related biomarkers in endometriosis using multidimensional transcriptomic data.

PURPOSE: Endometriosis (EMS) is a relatively common gynecological disorder and almost fifty percent of women with EMS suffer from infertility. There are few treatment options for endometriosis, and often recurrences occur following surgery and medication. We aimed to identify potential diagnostic biomarkers for EMS to improve its diagnostic efficiency. METHODS: Differential analysis was utilized to choose EMS-associated abnormal miRNAs (DEMIs) and mRNAs (DEMs). ImmuneAI analysis was to evaluate the levels of immune cells in EMS. Next, the weighted gene co-expression network analysis (WGCNA) was utilized to identify the co-expression modules. Random forest and SVM analyses were used to filter the candidate biomarkers and construct the diagnostic model. qRT-PCR was used to test the expression level of the biomarkers. RESULTS: Based on the different analyses, we obtained 32 DEMIs and 516 DEMs and selected 9 abnormal immune cells whose abundance is abnormal in EMS. Next, we identified five co-expression modules associated with these abnormal immune cells. Then, 176 candidate genes which are both miRNA targets and associated with immune cells and aberrantly expressed in EMS were filtered. Subsequently, random forest analysis selected 11 genes as the diagnostic biomarkers and constructed a diagnostic model by SVM. Finally, we demonstrated that 8 of the 11 genes aberrantly expressed and with better diagnostic efficiency in EMS. CONCLUSIONS: In total, we identified 11 crucial genes regulated by 8 miRNAs that could serve as promising diagnostic biomarkers for EMS, potentially enhancing disease diagnosis with novel factors.

Bioinformatic Analysis Reveals Bone Marrow Kinase as a Potential Diagnostic and Prognostic Biomarker for Multiple Cancer Types.

INTRODUCTION: Bone marrow kinase, or BMX, is alternatively referred to as endothelial tyrosine kinase (Etk). It plays a vital role in the processes of cell proliferation, survival, immune activation, and the modulation of diverse signaling pathways. Since there are few direct comprehensive studies linking BMX role with multiple cancers, this study aimed to utilize bioinformatic tools to conduct a comprehensive analysis of BMX across multiple cancers, assessing its potential role. METHODS: Multiple databases including the Tumor Immune Estimation Resource (TIMER), Gene Expression Profiling Interactive Analysis (GEPIA), and University of Alabama at Birmingham Cancer Data Analysis Portal (UALCAN), have been used to explore BMX expression across different cancers, which has been further validated by using Gene Expression Omnibus (GEO) public datasets. In addition, we used the Kaplan-Meier plotter to estimate overall survival and cBioPortal for genetic alterations analysis. This study accommodates several other analyses like clinical parameters, immune cell infiltration, and DNA promoter methylation profiles to evaluate the general role of BMX in several cancers.  Results: The present investigation revealed that the BMX gene expression was significantly downregulated and could serve as an effective diagnostic biomarker in five types of cancers, namely breast invasive carcinoma (BRCA), colon adenocarcinoma (COAD), lung adenocarcinoma (LUAD), lung squamous cell carcinoma (LUSC), and rectum adenocarcinoma (READ) (all p < 0.05). Detailed analyses revealed notable downregulation of BMX in various clinical parameters such as age, gender, race, and cancer stage (all p < 0.05). To better understand the immunotherapeutic role of BMX, this investigation further examined the immune infiltration which exhibited positive correlations between BMX expression and the infiltration of immunological cells such as B cells, CD8+ T cells, CD4+ T cells, macrophages, neutrophils, and dendritic cells, especially in COAD, LUAD, and LUSC (all p < 0.05). In addition, the present study has demonstrated that diminished BMX gene expression is correlated with an unfavorable prognosis in kidney renal clear cell carcinoma (KIRC), liver hepatocellular carcinoma (LIHC), sarcoma (SARC), and uterine corpus endometrial carcinoma (UCEC); thus BMX gene expression can be used as a prognostic target for these specific cancers. Also, the results showed that the promoter methylation level of BMX was significantly elevated in LUAD and LUSC, whereas it was significantly decreased in BRCA (all p < 0.001). Importantly, our findings of significantly low BMX expression in LUAD and LUSC, along with their methylation profiles suggest that the low expression of BMX across these cancers is due to epigenetic factors. However, genetic alteration analysis revealed that mutations existed in only approximately 2% of the TCGA samples. CONCLUSION: Our study revealed BMX as a diagnostic biomarker in BRCA, COAD, LUAD, LUSC, and READ and a prognostic biomarker in KIRC, LIHC, SARC, and UCEC. Furthermore, epigenetic variables may have a greater impact on BMX expression levels especially in LUAD and LUSC. This study also emphasized the role of BMX in the infiltration of immune cells, such as B cells, CD8+ T cells, CD4+ T cells, macrophages, neutrophils, and dendritic cells, in certain cancers. The BMX expression level highlights the prognostic value and potential therapeutic potential of BMX.

Serum exosomal miR-200c is a potential diagnostic biomarker for breast cancer.

BACKGROUND: Breast cancer (BC) is one of the most common malignancies in women. Exosomes are widely found in body fluids and carry microRNAs (miRNAs) that reflect the biological properties of the parental cells. Our study aimed to investigate the differential expression of miR-200c in breast cancer serum exosomes and its diagnostic value. METHODOLOGY: miRNA profiles in culture supernatant exosomes of normal mammary epithelial cells MCF-10A and BC cells (MCF-7,MDA-MB-231, MCF-7 Taxol) were examined by miRNA deep sequencing to screen for significantly differentially expressed miRNAs; Transmission electron microscopy (TEM), Nanoparticle tracking analysis (NTA), and Western blot were used to identify exosomes; qPCR was used to detect the expression level of miR-200c in cellular exosomes and serum exosomes; The efficacy of individual and combined tests of each indicator to diagnose BC was evaluated using receiver operating characteristic (ROC) curves. RESULTS: We identified typical exosome features by TEM, NTA and Western blot, indicating successful exosome extraction. Then our miRNA sequencing results and qRT-PCR experiments showed that miR-200c was significantly down-regulated in BC cell exosomes. In addition, we divided the clinical serum samples into two cohorts according to region, and in independent cohort I, the serum exosomal miR-200c levels of BC patients were significantly lower than those of healthy controls. In cohort II, serum exosomal miR-200c expression was significantly lower in the BC group than in the control and benign breast disease (BBD) groups, whereas miR-200c expression in the BBD group was not statistically different from that in the control group. ROC analyses in both independent cohorts confirmed that serum exosomal miR-200c could differentiate between patients with and without breast cancer disease and could be used as an early diagnostic marker for breast cancer disease. CONCLUSION: Serum exosome miR-200c can be used as a potential biomarker for the diagnosis of BC, and combined with conventional serum diagnostic markers AFP, CA125 and CA153 can help to improve diagnostic efficiency.

Pan-Cancer Analysis Reveals Long Non-coding RNA (lncRNA) Embryonic Stem Cell-Related Gene (ESRG) as a Promising Diagnostic and Prognostic Biomarker.

BACKGROUND: Embryonic stem cell-related gene (ESRG; also known as HESRG) is a long non-coding RNA (lncRNA). It is involved in the regulation of human pluripotent stem cells (hPSCs) self-renewal. ESRG gene has the ability to interact with chromatins, different RNA types, and RNA binding proteins (RBP); thus making ESRG be considered an oncogenic lncRNA, where its expression is detected in various tumor tissues. This study aimed to evaluate the prospective diagnostic and prognostic values of ESRG in various human cancers. MATERIALS AND METHODS: The expression of ESRG in various cancers was analyzed using the Gene Expression Profiling Interactive Analysis (GEPIA), Tumor Immune Estimation Resource (TIMER), and University of Alabama at Birmingham Cancer Data Analysis Portal (UALCAN) databases. Moreover, the correlation between the expression of ESRG and clinical pathological parameters was analyzed using UALCAN. The effect of ESRG expression on the survival outcome was evaluated using Kaplan-Meier plotter, UALCAN, GEPIA, and TIMER. The correlation between ESRG expression and immune cell infiltration was studied by TIMER. Additionally, the genetic alterations were investigated cBioportal. Our findings were validated using the GEO2R database. RESULTS: Our results showed ESRG to be significantly up-regulated in colon adenocarcinoma (COAD) and lung squamous cell carcinoma (LUSC) with p<0.001, in addition to rectum adenocarcinoma (READ), and uterine carcinosarcoma (UCEC) with p<0.01. Regarding pathogenic stages, there was a significant upregulation in stages 2, 3, and 4 compared to normal in COAD and stages 1, 2, and 3 for LUSC patients. The combined prognostic analysis showed that the up-regulated expression of ESRG was associated with better survival outcomes in patients with brain lower-grade glioma (LGG). Our results demonstrate a significant negative correlation between ESRG expression and the abundance of CD8+T cells in COAD, READ, LUSC, and UCEC. Additionally, ESRG was mutated in 0.77 (<1%) of the queried samples, and the most prevalent ESRG mutations are deep deletion mutations, followed by amplification. CONCLUSION: Analysis of ESRG across various cancer types elucidated its potential to be used as a diagnostic biomarker in COAD, LUSC, READ, and UCEC and a promising prognostic biomarker in LGG. Our findings provide useful insights for future research.

Expression profile of circular RNAs in blood samples of Northern Chinese males with intracerebral hemorrhage shows downregulation of hsa-circ-0090829.

Circular RNAs (circRNAs) are involved in several neurological disorders; however, the mechanisms underlying their involvement remain to be clarified. We attempted to explore the expression profiles of circRNAs and their potential functions and mechanisms in the pathogenesis of intracerebral hemorrhage (ICH) in Northern Chinese males. The microarray results showed that 50 circRNAs were significantly upregulated, while 194 circRNAs were significantly downregulated in ICH patients compared with healthy controls (p < 0.05). After bioinformatics analysis, a circRNA-microRNA-messenger RNA network and a protein-protein interaction network were constructed. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses showed that the neurotrophin signaling pathway, long-term potentiation, and the mitogen-activated protein kinase pathway are potentially implicated in ICH pathophysiology. The quantitative real-time polymerase chain reaction results revealed that hsa-circ-0090829 was significantly downregulated in ICH. The receiver operating characteristic curve analysis showed that the area under the curve of hsa-circ-0090829 between ICH and healthy controls was 0.807. Furthermore, the dual-luciferase assay showed that hsa-circ-0090829 sponged miR-526b-5p. This study reports the altered expression of circRNAs and identifies the potential functions of these circRNAs in ICH. Our results may facilitate further mechanistic research on circRNAs in ICH and provide probable novel diagnostic biomarkers and therapeutic targets for ICH.

Systematic analysis of serum peptidase inhibitor 3 in psoriasis diagnosis and treatment.

BACKGROUND: Psoriasis is a chronic inflammatory skin disease. To date, there are no serum biomarkers for psoriasis that have been validated to diagnose or treat psoriasis. METHODS: Peptidase inhibitor 3 (PI3) levels in serum were measured using chemiluminescence immunoassay (CLIA) in two independent cohorts including healthy controls (HC) and patients diagnosed with chronic urticaria (CU), chronic eczema (CE), systemic lupus erythematosus (SLE), rheumatoid arthritis (RA), psoriatic arthritis (PsA), or psoriasis vulgaris (PV). Receiver operating characteristic (ROC) curve analysis determined the diagnostic performance of PI3 in patients with psoriasis. The correlation between PI3 levels and the Psoriasis Area Severity Index (PASI) score was analyzed using the Spearman correlation method. Additionally, the study evaluated PI3 expression and treatment response of PV patients 12 weeks before and after topical treatment with calcipotriol betamethasone and calcipotriol ointment (T#1) or topical therapy plus PSORI-CM01 granules (T#2). RESULTS: In cohort #1, PI3 levels effectively discriminate PV patients from HC and CU patients, with AUCs of 0.909 and 0.840, respectively. In cohort #2, AUCs for detecting PV patients among HC, CU, CE, SLE, and RA patients were 0.940, 0.926, 0.802, 0.989, and 0.951, respectively. For PsA patients, AUCs were 0.989, 0.986, 0.910, 1.000, and 0.984 compared to HC, CU, CE, SLE, and RA patients, respectively. In both cohorts, PI3 levels correlated significantly with PASI scores in PV patients (cohort #1, r = 0.433; cohort #2, r = 0.634) and PsA patients (cohort #2, r = 0.718). Moreover, univariate logistic regression analyses revealed that PV patients with higher PI3 expression had a significantly higher risk of treatment resistance, with an odds ratio of 3.45 [95% confidence interval (CI) 1.54, 7.74, p = 0.003]. Finally, PI3 levels decreased nearly 35-fold more in the responder than in the non-responder group before and after treatment. CONCLUSIONS: Serological PI3 is a reliable biomarker for PV diagnosis and may have the potential to predict and monitor the progression of PV before and after treatment. Key Points • This study validated PI3's diagnostic performance in two independent psoriasis cohorts using CLIA. • PI3 expression is significantly correlated with the psoriasis severity and with patients who benefited from the treatments. • Serological PI3 is a reliable biomarker for psoriasis diagnosis and may have the potential to monitor the psoriasis progression with and without treatments.

Mir-150-5p distinguishes acute pulmonary embolism, predicts the occurrence of pulmonary arterial hypertension, and regulates ox-LDL-induced endothelial cell injury.

BACKGROUND: Acute pulmonary embolism (APE) is a major type of venous thromboembolism (VTE) with a high risk of mortality and disability. There is a lack of biomarkers for APE to indicate deteriorating development and predict adverse outcomes. This study evaluated the significance of miR-150-5p in APE aiming to explore a novel potential biomarker for APE. METHODS: The study enrolled APE (n = 137) and deep wein thrombosis (DVT, n = 67) patients and collected plasma samples from all study subjects. The expression of miR-150-5p was analyzed by PCR and its significance in screening APE and pulmonary arterial hypertension (PAH) was assessed by receiver operating curve (ROC) and logistic analyses. The study established oxidized low-density lipoprotein (ox-LDL)-induced human venous endothelial cells (HUVECs). Through cell transfection combined with cell counting kit-8 (CCK8), flow cytometry, and enzyme-linked immunosorbent assay (ELISA), the effect of miR-150-5p on ox-LDL-induced HUVEC injury was evaluated. RESULTS: Significant downregulation of miR-150-5p was observed in the plasma of APE patients compared with DVT patients (P < 0.0001). The plasma miR-150-5p levels in APE patients occurred PAH was much lower than in patients without PAH (P < 0.0001). Reducing miR-150-5p distinguished APE patients from DVT patients (AUC = 0.912) and was identified as a risk factor for the occurrence of PAH in APE patients (OR = 0.385, P = 0.010). In HUVECs, oxidized low-density lipoprotein (ox-LDL) caused inhibited cell proliferation, enhanced apoptosis, increased pro-inflammatory cytokines, reactive oxygen species (ROS), malondialdehyde (MDA), and decreased superoxide dismutase (SOD). Overexpressing miR-150-5p could promote proliferation, inhibit apoptosis, and alleviate inflammation and oxidative stress of ox-LDL-treated HUVECs. CONCLUSIONS: Downregulated plasma miR-150-5p served as a diagnostic biomarker for APE and predicted the predisposition of PAH in APE patients. Overexpressing miR-150-5p could alleviate ox-LDL-induced endothelial cell injury in HUVECs.

Serum levels of stearic and dihomo-γ-linolenic acids can be used to diagnose cervical cancer and cervical intraepithelial neoplasia.

Despite widespread cervical cancer (CC) screening programs, low participation has led to high morbidity and mortality rates, especially in developing countries. Because early-stage CC often has no symptoms, a non-invasive and convenient diagnostic method is needed to improve disease detection. In this study, we developed a new approach for differentiating both CC and cervical intraepithelial neoplasia (CIN)2/3, a precancerous lesion, from healthy individuals by exploring CC fatty acid metabolic reprogramming. Analysis of public datasets suggested that various fatty acid metabolizing enzymes were expressed at higher levels in CC tissues than in normal tissues. Correspondingly, 11 free fatty acids (FFAs) showed significantly different serum levels in CC patient samples compared with healthy donor samples. Nine of these 11 FFAs also displayed significant alterations in CIN2/3 patients. We then generated diagnostic models using combinations of these FFAs, with the optimal model including stearic and dihomo-γ-linolenic acids. Receiver operating characteristic curve analyses suggested that this diagnostic model could detect CC and CIN2/3 more accurately than using serum squamous cell carcinoma antigen level. In addition, the diagnostic model using FFAs was able to detect patients regardless of clinical stage or histological type. Overall, the serum FFA diagnostic model developed in this study could be a powerful new tool for the non-invasive early detection of CC and CIN2/3.

Genetic variants in FCGR2A, PTPN2, VDR as predictive signatures of aggressive phenotypes in cerebral cavernous malformation.

OBJECTIVE: The biological behavior of Cerebral Cavernous Malformation (CCM) is still controversial, lacking a clear-cut signature for a mechanistic explanation of lesion aggressiveness. In this study, we evaluated the predictive capacity of genetic variants concerning the aggressive behavior of CCM and their implications in biological processes. METHODS: We genotyped the variants in VDRrs7975232, VDRrs731236, VDRrs11568820, PTPN2rs72872125 and FCGR2Ars1801274 genes using TaqMan Genotyping Assays in a cohort study with 103 patients, 42 of whom had close follow-up visits for 4 years, focusing on 2 main aspects of the disease: (1) symptomatic events, which included both intracranial bleeding or epilepsy, and (2) the onset of symptoms. The genotypes were correlated with the levels of several cytokines quantified in peripheral blood, measured using the x-MAP method. RESULTS: We report a novel observation that the PTPN2rs72872125 CT and the VDRrs7975232 CC genotype were independently associated with an asymptomatic phenotype. Additionally, PTPN2rs72872125 CC genotype and serum level of GM-CSF could predict a diagnostic association with symptomatic phenotype in CCM patients, while the FCGR2Ars1801274 GG genotype could predict a symptomatic event during follow-up. The study also found a correlation between VDRrs731236 AA and VDRrs11568820 CC genotype to the time to the first symptomatic event. CONCLUSIONS: These genetic markers could pave the way for precision medicine strategies for CCM, enhancing patient outcomes by enabling customized therapeutic approaches.

Identification and evaluation of a serum microRNA panel to diagnose colorectal cancer patients.

Screening plays a crucial role in the early detection of colorectal cancer, greatly reducing mortality rates. The objective of this study was to identify a non-invasive diagnostic method utilizing serum microRNA expression for the diagnosis of colorectal cancer patients. The study consisted of three stages. In the first stage, 129 patients with colorectal cancer and 129 normal subjects were recruited as the training set for the development of a blood miRNA panel. The second stage involved recruiting 200 patients from each group as the validation cohort. Finally, a blinded study was conducted in the third stage, with 260 patients recruited to determine the predictive value of our miRNA panel. Serum samples were prospectively collected from colorectal cancer patients and normal subjects between 2017 and 2021 at Queen Mary Hospital in Hong Kong. Quantitative PCR was utilized to detect the serum levels of candidate microRNAs, and a multiple linear regression model was employed to formulate a serum microRNA panel for diagnosing colorectal cancer patients. The performance of the panel was evaluated using ROC analysis. Our study showed that the values of three pairs of serum microRNAs, namely miR-106b-5p/miR-1246, miR-106b-5p/miR-16 and miR-106b-5p/miR-21-5p, exhibited statistically significant differences between colorectal cancer patients and normal subjects. A serum microRNA panel formulated from these three pairs of microRNAs demonstrated high accuracy in diagnosing colorectal cancer patients from normal subjects, with an AUC of approximately 0.9. The serum miRNA test proved to be a feasible and promising non-invasive biomarker for the diagnosis of colorectal cancer patients in comparison to normal subjects.

The kappa free light chains index is an accurate diagnostic biomarker for paediatric multiple sclerosis.

BACKGROUND: Multiple sclerosis (MS) may occur before the age of 18. Differentiation between paediatric MS (PedMS) and other demyelinating syndromes (ODSs) is challenging. In adult with MS, the kappa free light chain (KFLC) index has proven to be a reliable marker of intrathecal Ig synthesis. OBJECTIVE: To assess the diagnostic value of the KFLC index in a cohort of patients with paediatric-onset, inflammatory disorders of the CNS. METHODS: We included 73 patients and divided them into four groups: PedMS (n = 16), ODS (n = 17), encephalitis and/or inflammatory epilepsy (EE, n = 15), and controls without inflammatory CNS diseases (n = 25). The KFLC index was calculated and compared with the results of the oligoclonal bands determination. RESULTS: The KFLC index was higher in the PedMS group (median (interquartile range (IQR)): 150.9 (41.02-310.6)) than in the ODS (3.37 (2.22-8.11)), the EE (5.53 (2.31-25.81)) and the control group (3.41 (2.27-5.08)), respectively. The best KFLC index cut-off for differentiating between patients with PedMS and controls was 6.83 (sensitivity: 100%; specificity: 92%). A KFLC index over 93.77 indicated that the patient is very likely to have PedMS (sensitivity: 68%; specificity: 100%). CONCLUSION: The KFLC index is a reliable tool for the diagnosis of MS in a paediatric population.

The potential of circulating microRNAs as novel diagnostic biomarkers of COVID-19: a systematic review and meta-analysis.

INTRODUCTION: The COVID-19 pandemic has caused an unprecedented health threat globally, necessitating innovative and efficient diagnostic approaches for timely identification of infected individuals. Despite few emerging reports, the clinical utility of circulating microRNAs (miRNAs) in early and accurate diagnosis of COVID-19 is not well-evidenced. Hence, this meta-analysis aimed to explore the diagnostic potential of circulating miRNAs for COVID-19. The protocol for this study was officially recorded on PROSPERO under registration number CRD42023494959. METHODS: Electronic databases including Embase, PubMed, Scopus, and other sources were exhaustively searched to recover studies published until 16th January, 2024. Pooled specificity, sensitivity, positive likelihood ratio (PLR), negative likelihood ratio (NLR), diagnostic ratio (DOR), positive predictive value (PPV), negative predictive value (NPV), and area under the curve (AUC) were computed from the metadata using Stata 14.0 software. Risk of bias appraisal of included articles was carried out using Review Manager (Rev-Man) 5.3 package through the modified QUADAS-2 tool. Subgroup, heterogeneity, meta-regression and sensitivity analyses were undertaken. Publication bias and clinical applicability were also evaluated via Deeks' funnel plot and Fagan nomogram (scattergram), respectively. RESULT: A total of 43 studies from 13 eligible articles, involving 5175 participants (3281 COVID-19 patients and 1894 healthy controls), were analyzed. Our results depicted that miRNAs exhibit enhanced pooled specificity 0.91 (95% CI: 0.88-0.94), sensitivity 0.94 (95% CI: 0.91-0.96), DOR of 159 (95% CI: 87-288), and AUC values of 0.97 (95% CI: 0.95-0.98) with high pooled PPV 96% (95% CI: 94-97%) and NPV 88% (95% CI: 86-90%) values. Additionally, highest diagnostic capacity was observed in studies involving larger sample size (greater than 100) and those involving the African population, demonstrating consistent diagnostic effectiveness across various specimen types. Notably, a total of 12 distinct miRNAs were identified as suitable for both exclusion and confirmation of COVID-19 cases, denoting their potential clinical applicability. CONCLUSION: Our study depicted that miRNAs show significantly high diagnostic accuracy in differentiating COVID-19 patients from healthy counterparts, suggesting their possible use as viable biomarkers. Nonetheless, thorough and wide-ranging longitudinal researches are necessary to confirm the clinical applicability of miRNAs in diagnosing COVID-19.

Paired box proteins as diagnostic biomarkers for endocervical adenocarcinoma.

In this editorial, we commented on the article by Akers et al published in the recent issue of the World Journal of Clinical Cases. We focused specifically on the role of the transcription factor paired box protein 8 (PAX8) belonging to the family PAX in the carcinogenesis of a gynecologic tumor, endocervical adenocarcinoma, arising from the tissue of mesonephric origin, and the potential diagnostic value for the same type of neoplasms. The global vaccination program of human papillomavirus (HPV) has dramatically reduced the incidence of cervical cancer, including cases of adenocarcinoma. The type of adenoid epithelial origin has a lower frequency of HPV detection but tends to be more aggressive and fatal. Cases of endocervical adenocarcinoma occurring in females of menopause age have been described in the 2023 volume of the World Journal of Clinical Cases and in our study recently published in Oncol Lett. The histopathological findings and immunohistochemical assays showed that the lesions had glandular morphology, and the specimens in these two reports were immunohistochemically positive for the transcription factor PAX8, albeit that they had opposing expression profiles of tumor suppressor p16 and estrogen receptor and the presence of the HPV genome. The presence of a mucin protein, MUC 5AC, as revealed in both studies suggested target molecules for the diagnosis of mucinous adenoid type of uterine tumor and other histological origins. The clinical outcome was unfavorable due to metastasis and recurrence. This prompted the improvement of the antitumor modality, with the introduction of precise targeting therapy. Mucin has now been reported to be the therapeutic target for adenocarcinomas.

Aging-related biomarkers for the diagnosis of Parkinson's disease based on bioinformatics analysis and machine learning.

Parkinson's disease (PD) is a multifactorial disease that lacks reliable biomarkers for its diagnosis. It is now clear that aging is the greatest risk factor for developing PD. Therefore, it is necessary to identify novel biomarkers associated with aging in PD. In this study, we downloaded aging-related genes from the Human Ageing Gene Database. To screen and verify biomarkers for PD, we used whole-blood RNA-Seq data from 11 PD patients and 13 healthy control (HC) subjects as a training dataset and three datasets retrieved from the Gene Expression Omnibus (GEO) database as validation datasets. Using the limma package in R, 1435 differentially expressed genes (DEGs) were found in the training dataset. Of these genes, 29 genes were found to occur in both DEGs and 307 aging-related genes. By using machine learning algorithms (LASSO, RF, SVM, and RR), Venn diagrams, and LASSO regression, four of these genes were determined to be potential PD biomarkers; these were further validated in external validation datasets and by qRT-PCR in the peripheral blood mononuclear cells (PBMCs) of 10 PD patients and 10 HC subjects. Based on the biomarkers, a diagnostic model was developed that had reliable predictive ability for PD. Two of the identified biomarkers demonstrated a meaningful correlation with immune cell infiltration status in the PD patients and HC subjects. In conclusion, four aging-related genes were identified as robust diagnostic biomarkers and may serve as potential targets for PD therapeutics.

Data-driven analysis that integrates bioinformatics and machine learning uncovers PANoptosis-related diagnostic genes in early pediatric septic shock.

Objectives: Sepsis is one of the leading causes of death for children worldwide. Additionally, refractory septic shock is one of the most significant groups that contributes to a high death rate. The interaction of pyroptosis, apoptosis, and necroptosis results in a unique inflammatory cell death mechanism known as PANoptosis. An increasing amount of evidence suggests that PANoptosis can be brought on by several stimuli, including cytokine storms, malignancy, and bacterial or viral infections. The goal of this study is to improve the diagnostic significance of the PANoptosis-related gene signature in early pediatric septic shock. Design and methods: We examined children with septic shock from the GSE66099 discovery cohort and looked at differentially expressed genes (DEGs). To filter the important modules, weighted gene co-expression network analysis (WCGNA) was employed. In the end, random forest analysis and the least absolute shrinkage and selection operator (LASSO) were used to determine the PANoptosis diagnostic signature genes. To determine the PANoptosis signature genes, we also found four validation cohorts: GSE26378, GSE26440, GSE8121, and GSE13904. The area under the curve (AUC) of the receiver operating characteristic curves (ROCs), along with sensitivity, specificity, positive predictive value, and negative predictive value, were used to assess the diagnostic efficacy of these signature genes. Results: From GSE66099, 1142 DEGs in total were tested. Following the WGCNA clustering of the data into 16 modules, the MEgrey module showed a significant correlation with pediatric septic shock (p < 0.0001). Following the use of LASSO and random forest algorithms to identify the PANoptosis-related signature genes, which include ANXA3, S100A9, TXN, CLEC5A, and TMEM263. These signature genes' receiver operating characteristic curves (ROCs) were confirmed in the external dataset from GSE26378, GSE26440, GSE8121, and GSE13904, and were 0.994 (95 % CI 0.987-0.999), 0.987 (95 % CI 0.974-0.997), 0.957 (95 % CI 0.927-0.981), 0.974 (95 % CI 0.954-0.988), 0.897 (95 % CI 0.846-0.941), respectively. Conclusion: In summary, the discovery of PANoptosis genes, ANXA3, S100A9, TXN, CLEC5A, and TMEM263 proved to be quite helpful in the early detection of pediatric septic shock patients. These early results, which need to be further confirmed in basic and clinical research, are extremely important for understanding immune cell infiltration in the pathophysiology of pediatric septic shock.

Identification of autoantibodies as potential non-invasive biomarkers for intrahepatic cholangiocarcinoma.

Intrahepatic cholangiocarcinoma (iCCA) presents a challenging diagnosis due to its nonspecific early clinical manifestations, often resulting in late-stage detection and high mortality. Diagnosing iCCA is further complicated by its limited accuracy, often necessitating multiple invasive procedures for precise identification. Despite carbohydrate antigen 19-9 (CA19-9) having been investigated and employed for iCCA diagnosis, it demonstrates modest diagnostic performance. Consequently, the identification of novel biomarkers with improved sensitivity and specificity remains an imperative yet formidable task. Autoantibodies, as early indicators of the immune response against cancer, offer a promising avenue for enhancing diagnostic accuracy. Our study aimed to identify non-invasive blood-based autoantibody biomarkers capable of distinguishing iCCA patients from healthy individuals (CTRs). We profiled autoantibodies in 26 serum samples (16 iCCAs and 10 CTRs) using protein microarrays containing 1622 functional proteins. Leveraging machine learning techniques, we identified a signature composed of three autoantibody biomarkers (NDE1, PYCR1, and VIM) in conjunction with CA19-9 for iCCA detection. This combined signature demonstrated superior diagnostic performance with an AUC of 96.9%, outperforming CA19-9 alone (AUC: 83.8%). These results suggest the potential of autoantibody biomarkers to develop a complementary non-invasive diagnostic utility for routine iCCA screening.

BRD4 expression and its regulatory interaction with miR-26a-3p, DLG5-AS1, and JMJD1C-AS1 lncRNAs in gastric cancer progression.

Gastric cancer remains a significant health challenge despite advancements in diagnosis and treatment. Early detection is critical to reducing mortality, necessitating the investigation of molecular mechanisms underlying gastric cancer progression. This study focuses on BRD4 expression and its correlation with miR-26a-3p, DLG5-AS1, and JMJD1C-AS1 lncRNAs in gastric cancer. Analysis of The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) datasets revealed significant upregulation of BRD4 in gastric cancer tissues compared to normal tissues, correlating negatively with miR-26a-3p and positively with DLG5-AS1 and JMJD1C-AS1 lncRNAs. Quantitative RT-PCR confirmed these findings in 25 gastric cancer tissue samples and 25 normal samples. BRD4's overexpression was associated with reduced survival rates and older patient age. MiR-26a-3p, a known tumor suppressor, showed decreased expression in gastric cancer tissues, with ROC analysis suggesting it, alongside BRD4, as a potential diagnostic biomarker. Additionally, bioinformatics predicted miR-26a-3p's interaction with BRD4 mRNA. Upregulated lncRNAs DLG5-AS1 and JMJD1C-AS1 likely act as competing endogenous RNAs, sponging miR-26a-3p, thus promoting BRD4 dysregulation. These lncRNAs have not been previously studied in gastric cancer. The findings propose a novel BRD4/lncRNA/miRNA regulatory axis in gastric cancer, highlighting the potential of BRD4, DLG5-AS1, and JMJD1C-AS1 as biomarkers for early diagnosis. Further studies with larger sample sizes and in vivo and in vitro experiments are needed to elucidate this regulatory mechanism's role in gastric cancer progression.

Comprehensive pan-cancer analysis of ZNF337 as a potential diagnostic, immunological, and prognostic biomarker.

BACKGROUND: Zinc Finger Protein 337 (ZNF337) is a novel Zinc Finger (ZNF) protein family member. However, the roles of ZNF337 in human cancers have not yet been investigated. METHODS: In this study, with the aid of TCGA databases, GTEx databases, and online websites, we determined the expression levels of ZNF337 in pan-cancer and its potential value as a diagnostic and prognostic marker for pan-cancer and analyzed the relationship between ZNF337 expression and immune cell infiltration and immune checkpoint genes. We then focused our research on the potential of ZNF337 as a biomarker for diagnostic and prognostic in KIRC (kidney renal clear cell carcinoma) and validated in the E-MTAB-1980 database. Moreover, the expression of ZNF337 was detected through qRT-PCR and Western blotting (WB). CCK-8 experiment, colony formation experiment, and EDU experiment were performed to evaluate cell proliferation ability. Wound healing assay and transwell assay were used to analyze its migration ability. The qRT-PCR and WB were used to detect the expression of ZNF337 in tumor tissues and paracancerous tissues of KIRC patients. RESULTS: The pan-cancer analysis revealed that abnormal ZNF337 expression was found in multiple human cancer types. ZNF337 had a high diagnostic value in pan-cancer and a significant association with the prognosis of certain cancers, indicating that ZNF337 may be a valuable prognostic biomarker for multiple cancers. Further analysis demonstrated that the expression level of ZNF337 displayed significant correlations with cancer-associated fibroblasts, immune cell infiltration, and immune checkpoint genes in many tumors. Additionally, ZNF337 was observed to have a high expression in KIRC. Its expression was significantly associated with poor prognosis [overall survival (OS), disease-specific survival (DSS)], age, TNM stage, histologic grade, and pathologic stage. The high ZNF337 expression was associated with poor prognosis in the E-MTAB-1980 validation cohort. The in vitro experiments suggested that the expression of ZNF337 in KIRC tumor tissues was higher than in adjacent tissues, and ZNF337 knockdown inhibited the proliferation and migration of KIRC cells, whereas overexpression of ZNF337 had the opposite effects. CONCLUSIONS: ZNF337 might be an important prognostic and immunotherapeutic biomarker for pan-cancer, especially in KIRC.