Identification and verification of PTPN3 as a novel biomarker in predicting cancer prognosis, immunity, and immunotherapeutic efficacy.

BACKGROUND: The importance of protein tyrosine phosphatase non-receptor type 3 (PTPN3) in controlling multifaceted tumor cell behaviors throughout cancer development has received widespread attention. Nevertheless, little is known about the biological roles of PTPN3 in drug sensitivity, immunotherapeutic effectiveness, tumor immune microenvironment, and cancer prognosis. METHODS: The Cancer Genome Atlas (TCGA) database's RNAseq data were used to examine the expression of PTPN3 in 33 different cancer types. In addition, immunohistochemistry (IHC) was performed to validate the expression of PTPN3 across various cancer types within our clinical cohorts. The features of PTPN3 alterations were demonstrated throughout the cBioPortal database. This study focused on examining the prognostic and clinicopathological importance of PTPN3 through the acquisition of clinical data from the TCGA database. The investigation of PTPN3's probable role in the tumor immune microenvironment was demonstrated by the application of CIBERSORT, ESTIMATE algorithms, and the TISIDB database. Using Spearman's rank correlation coefficient, the relationships between PTPN3 expression and tumor mutation burden (TMB) and microsatellite instability (MSI) were evaluated. To further investigate the putative biological activities and downstream pathways of PTPN3 in various cancers in humans, Gene Set Enrichment Analysis (GSEA) was carried out. In addition, an examination was conducted to explore the associations between PTPN3 and the effectiveness of PD-1/PD-L1 inhibitors, utilizing data extracted from the GEO database. RESULTS: PTPN3 was abnormally expressed in multiple cancer types and was also strictly associated with the prognosis of cancer patients. IHC was used to investigate and confirm the various expression levels of PTPN3 in various malignancies, including breast cancer, lung cancer, sarcoma, and kidney renal clear cell carcinoma in our clinical cohorts. There is a high correlation between the levels of PTPN3 expression in different cancers and infiltrating immune cells, including mast cells, B cells, regulatory T cells, CD8 + T cells, macrophages, and dendritic cells. Infiltrating immune cells, such as regulatory T cells, CD8 + T cells, macrophages, B cells, dendritic cells, and mast cells, are strongly correlated with PTPN3 expression levels in various tumors. The expression of PTPN3 exhibited a substantial correlation with many immune-related biomolecules and the expression of TMB and MSI in multiple types of cancer. In addition, PTPN3 has demonstrated promise in predicting the therapeutic benefits of PD-1/PD-L1 inhibitors and the susceptibility to anti-cancer medications in the treatment of clinical cancer. CONCLUSIONS: Our findings highlight the importance of PTPN3 as a prognostic biomarker and predictor of immunotherapy success in various forms of cancer. Furthermore, PTPN3 appears to have an important role in modifying the tumor immune microenvironment, highlighting its potential as a promising biomarker for prognosis prediction, immunotherapeutic efficacy evaluation, and identification of immune-related characteristics in diverse cancer types.

Pan-cancer analysis identifies RNF43 as a prognostic, therapeutic and immunological biomarker.

BACKGROUND: RING finger protein 43 (RNF43), an E3 ubiquitin ligase, is a homologous gene mutated in several cancers. However, the pan-cancer panoramic picture of RNF43 and its predictive value for tumor immune phenotypes and immunotherapeutic efficacy are still largely unclear. Our study aims to clarify the functions of RNF43 in predicting the prognosis, immune signature, and immunotherapeutic efficacy in pan-cancer. METHODS: By using RNA-seq, mutation, and clinical data from the TCGA database, the expression levels and prognostic significance of RNF43 in pan-cancer were analyzed. The genetic alteration characteristics of RNF43 were displayed by the cBioPortal database. Gene Set Enrichment Analysis (GSEA) was performed to investigate the potential biological functions and signaling pathways modulated by RNF43 in cancers. The relationship of RNF43 expression with immune cell infiltration, and immune modulators expression was interpreted by the ESTIMATE algorithm, CIBERSORT algorithm, and TISIDB database. The correlations between RNF43, microsatellite instability (MSI), and tumor mutation burden (TMB) were also investigated. Furthermore, the predictive value of RNF43 for immunotherapeutic efficacy and drug sensitivity was further illustrated. Besides, immunohistochemistry (IHC) was employed to validate the expression of the RNF43 in different cancer types by our clinical cohorts, including patients with lung cancer, sarcoma, breast cancer, and kidney renal clear cell carcinoma. RESULTS: The results demonstrated that RNF43 was abnormally expressed in multiple cancers, and RNF43 is a critical prognosis-related factor in several cancers. RNF43 was frequently mutated in several cancers with a high frequency of 4%, and truncating mutation was the most frequent RNF43 mutation type. RNF43 expression was linked to the abundance of several immune cell types, including CD8+ T cells, B cells, and macrophages within the tumor immune microenvironment. Furthermore, RNF43 expression was significantly correlated with the efficacy of anti-PD-1/PD-L1 treatment, and it could predict the sensitivity of various anti-cancer drugs. Finally, IHC explored and validated the different expression levels of RNF43 in different cancers by our clinical samples. CONCLUSION: Our results first present the expression pattern and the mutation signature of RNF43, highlighting that RNF43 is an important prognostic biomarker in pan-cancer. Furthermore, RNF43 seems to be a critical modulator in the tumor immune microenvironment and can function as a promising biomarker for predicting the immunotherapeutic efficacy of anti-PD-1/PD-L1 treatment, and drug sensitivity in cancer treatment.

Identification and validation of novel biomarkers associated with immune infiltration for the diagnosis of osteosarcoma based on machine learning.

Objectives: Osteosarcoma is the most common primary malignant tumor in children and adolescents, and the 5-year survival of osteosarcoma patients gained no substantial improvement over the past decades. Effective biomarkers in diagnosing osteosarcoma are warranted to be developed. This study aims to explore novel biomarkers correlated with immune cell infiltration in the development and diagnosis of osteosarcoma. Methods: Three datasets (GSE19276, GSE36001, GSE126209) comprising osteosarcoma samples were extracted from Gene Expression Omnibus (GEO) database and merged to obtain the gene expression. Then, differentially expressed genes (DEGs) were identified by limma and potential biological functions and downstream pathways enrichment analysis of DEGs was performed. The machine learning algorithms LASSO regression model and SVM-RFE (support vector machine-recursive feature elimination) analysis were employed to identify candidate hub genes for diagnosing patients with osteosarcoma. Receiver operating characteristic (ROC) curves were developed to evaluate the discriminatory abilities of these candidates in both training and test sets. Furthermore, the characteristics of immune cell infiltration in osteosarcoma, and the correlations between these potential genes and immune cell abundance were illustrated using CIBERSORT. qRT-PCR and western blots were conducted to validate the expression of diagnostic candidates. Results: GEO datasets were divided into the training (merged GSE19276, GSE36001) and test (GSE126209) groups. A total of 71 DEGs were screened out in the training set, including 10 upregulated genes and 61 downregulated genes. These DEGs were primarily enriched in immune-related biological functions and signaling pathways. After machine learning by SVM-RFE and LASSO regression model, four biomarkers were chosen for the diagnostic nomogram for osteosarcoma, including ASNS, CD70, SRGN, and TRIB3. These diagnostic biomarkers all possessed high diagnostic values (AUC ranging from 0.900 to 0.955). Furthermore, these genes were significantly correlated with the infiltration of several immune cells, such as monocytes, macrophages M0, and neutrophils. Conclusion: Four immune-related candidate hub genes (ASNS, CD70, SRGN, TRIB3) with high diagnostic value were confirmed for osteosarcoma patients. These diagnostic genes were significantly connected with the immune cell abundance, suggesting their critical roles in the osteosarcoma tumor immune microenvironment. Our study provides highlights on novel diagnostic candidate genes with high accuracy for diagnosing osteosarcoma patients.

Ferroptosis-related gene HIC1 in the prediction of the prognosis and immunotherapeutic efficacy with immunological activity.

Background: Hypermethylated in Cancer 1 (HIC1) was originally confirmed as a tumor suppressor and has been found to be hypermethylated in human cancers. Although growing evidence has supported the critical roles of HIC1 in cancer initiation and development, its roles in tumor immune microenvironment and immunotherapy are still unclear, and no comprehensive pan-cancer analysis of HIC1 has been conducted. Methods: HIC1 expression in pan-cancer, and differential HIC1 expression between tumor and normal samples were investigated. Immunohistochemistry (IHC) was employed to validate HIC1 expression in different cancers by our clinical cohorts, including lung cancer, sarcoma (SARC), breast cancer, and kidney renal clear cell carcinoma (KIRC). The prognostic value of HIC1 was illustrated by Kaplan-Meier curves and univariate Cox analysis, followed by the genetic alteration analysis of HIC1 in pan-cancer. Gene Set Enrichment Analysis (GSEA) was conducted to illustrate the signaling pathways and biological functions of HIC1. The correlations between HIC1 and tumor mutation burden (TMB), microsatellite instability (MSI), and the immunotherapy efficacy of PD-1/PD-L1 inhibitors were analyzed by Spearman correlation analysis. Drug sensitivity analysis of HIC1 was performed by extracting data from the CellMiner™ database. Results: HIC1 expression was abnormally expressed in most cancers, and remarkable associations between HIC1 expression and prognostic outcomes of patients in pan-cancer were detected. HIC1 was significantly correlated with T cells, macrophages, and mast cell infiltration in different cancers. Moreover, GSEA revealed that HIC1 was significantly involved in immune-related biological functions and signaling pathways. There was a close relationship of HIC1 with TMB and MSI in different cancers. Furthermore, the most exciting finding was that HIC1 expression was significantly correlated with the response to PD-1/PD-L1 inhibitors in cancer treatment. We also found that HIC1 was significantly correlated with the sensitivity of several anti-cancer drugs, such as axitinib, batracylin, and nelarabine. Finally, our clinical cohorts further validated the expression pattern of HIC1 in cancers. Conclusions: Our investigation provided an integrative understanding of the clinicopathological significance and functional roles of HIC1 in pan-cancer. Our findings suggested that HIC1 can function as a potential biomarker for predicting the prognosis, immunotherapy efficacy, and drug sensitivity with immunological activity in cancers.

Exosomal circRNAs in cancer: Implications for therapy resistance and biomarkers.

Despite the advances in cancer treatment in recent years, the development of resistance to cancer therapy remains the biggest hurdle towards curative cancer treatments. Therefore, investigating the molecular mechanisms underlying cancer therapy resistance is of paramount clinical importance. Circular RNAs (circRNAs), novel members of the noncoding RNA family, are endogenous biomolecules in eukaryotes characterized by a covalently closed loop structure with multiple biological functions. Significantly, circRNAs are abundant and stable in exosomes and can be packaged, secreted and transferred to targeted tumour cells, thereby modulating diverse hallmarks of cancer behaviours, such as proliferation, migration, and immune escape. Notably, a great number of exosomal circRNAs are abnormally expressed during cancer treatment and can mediate cancer therapy resistance through complex mechanisms; therefore, targeting exosomal circRNAs is a promising therapeutic method to reverse therapy resistance. This review aimed to elucidate the mechanisms underlying exosomal circRNAs controlling the resistance of cancer to common therapies, such as chemotherapy, targeted therapy, immunotherapy and radiotherapy, and we also discussed the therapeutic potential of exosomal circRNAs as clinical biomarkers and novel targets in cancer clinical management. We also discussed the prospects and challenges of targeting exosomal circRNAs as a novel therapeutic strategy for reversing cancer therapy resistance.

Genetic variants and phenotype analysis in a five-generation Chinese pedigree with PCDH19 female-limited epilepsy.

Objective: Albeit the gene of PCDH19-FE was ascertained, the correlation of gene mutation, PCDH19 protein structure, and phenotype heterogeneity remained obscure. This study aimed to report a five-generation pedigree of seven female patients of PCDH19-FE and tried to explore whether two variants were correlated with PCDH19 protein structure and function alteration, and PCDH19-FE phenotype. Methods: We analyzed the clinical data and genetic variants of a PCDH19-FE pedigree, to explore the phenotype heterogeneity of PCDH19-FE and underlying mechanisms. In addition to the clinical information of family members, next-generation sequencing was adopted to detect the variant sites of probands with validation by sanger sequencing. And the sanger sequencing was conducted in other patients in this pedigree. The biological conservation analysis and population polymorphism analysis of variants were also performed subsequently. The structure alteration of mutated PCDH19 protein was predicted by AlphaFold2. Results: Based on a five-generation pedigree of PCDH19-FE, missense variants of c.695A>G and c.2760T>A in the PCDH19 gene were found in the heterozygous proband (V:1), which resulted in the change of amino acid 232 from Asn to Ser (p.Asn232Ser) and amino acid 920 from Asp to Glu (p.Asp920Glu) influencing PCDH19 function. The other six females in the pedigree (II:6, II:8, IV:3, IV:4, IV:5, IV:11) exhibited different clinical phenotypes but shared the same variant. Two males with the same variant have no clinical manifestations (III:3, III:10). The biological conservation analysis and population polymorphism analysis demonstrated the highly conservative characteristics of these two variants. AlphaFold2 predicted that the variant, p.Asp920Glu, led to the disappearance of the hydrogen bond between Asp at position 920 and His at position 919. Furthermore, the hydrogen bond between Asp920 and His919 also disappeared when the Asn amino acid mutated to Ser at position 232. Conclusion: A strong genotype-phenotype heterogeneity was observed among female patients with the same genotype in our PCDH19-FE pedigree. And two missense variants, c.695A > G and c.2760T>A in the PCDH19 gene, have been identified in our pedigree. The c.2760T>A variant was a novel variant site probably related to the PCDH19-FE.

Association Between Wisdom and Psychotic-Like Experiences in the General Population: A Cross-Sectional Study.

Introduction: Wisdom has been empirically researched as a complex psychological characteristic that is associated with many mental health outcomes. However, its association with psychotic-like experiences (PLEs) remains unclear. This is the first work to assess wisdom, explore its association with PLEs, and test its moderating effect on the relation between the frequency of PLEs and their associated distress in the general population. Methods: From January 29th to February 5th, 2021, our online self-administered survey recruited 927 participants (ages 14 to 65) from thirteen Chinese provinces. Convenience sampling was employed. We measured wisdom with the 12-item three-dimensional wisdom scale (3D-WS-12) and PLEs with the 15-item positive subscale of the Community Assessment of Psychic Experiences (CAPE-P15). Results: Using the cut-off value of 1.47 in the mean frequency score, we divided our participants into high-PLEs group (188, 22.1%) and low-PLEs group (663, 77.9%). Three-dimensional wisdom score was decreased in the high-PLEs group compared to the low-PLEs group (Kruskal-Wallis t = 59.9, p < 0.001). Wisdom was associated with less frequent PLEs (Spearman's rho = -0.21, p < 0.01) and lower distress related to PLEs (Spearman's rho = -0.28) in the high-PLEs group (all above p < 0.001), which were replicated in the low-PLEs group. Notably, wisdom significantly attenuated the distress associated with PLEs [coefficient = -0.018, Bootstrap 95% CI (-0.029, -0.008)], but only in the low-PLEs group. Conclusion: Our results implicated that wisdom could protect individuals from distressful subclinical psychotic symptoms and wiser individuals have better general mental health.

Comparative Pharmacokinetic Profiles of Puerarin in Rat Plasma by UHPLC-MS/MS after Oral Administration of Pueraria lobata Extract and Pure Puerarin.

Puerarin is the main biologically active isoflavone in Pueraria lobata and has a wide range of biological activities. However, due to its poor water solubility and low oral bioavailability, its clinical applications are restricted. Compared with puerarin, the Pueraria lobata extract (PLE) has better water solubility, lower toxicity, and less side effects. In this study, the pharmacokinetics of orally administered puerarin (100 mg/kg) and PLE (763 mg/kg, equivalent to 100.0 mg/kg of puerarin) to rats was investigated by the UHPLC-MS/MS method. Results showed that when the rats were administered PLE, the area under the concentration-time curve from zero to infinity (AUC 0-inf ) dramatically increased from 219.83 ± 64.37 µg h/L to 462.62 ± 51.74 µg h/L (p < 0.01). The elimination half-time (t 1/2 ) also increased from 1.60 ± 0.38 h to 12.04 ± 5.10 h (p < 0.01). The maximum concentration (C max) of puerarin decreased from 101.64 ± 41.82 ng/mL to 48.64 ± 21.47 ng/mL (p < 0.01), and time to reach the maximum plasma concentration (T max) of puerarin decreased from 1.46 ± 1.08 h to 0.54 ± 0.30 h (p < 0.01). Results indicated that the pharmacokinetics of puerarin in Pueraria lobata may be dramatically different from pure puerarin in the plasma of rat, and oral bioavailability of puerarin may be increased when PLE was administrated to rats.

Circulating Fetuin-A and Risk of All-Cause Mortality in Patients With Chronic Kidney Disease: A Systematic Review and Meta-Analysis.

Background: Investigations on the association of circulating fetuin-A with all-cause mortality risk in patients with chronic kidney disease (CKD) are conflicting. This meta-analysis aimed to provide a comprehensive estimation of the relationship between fetuin-A and all-cause mortality in CKD patients. Methods: A systematic literature search was performed in PubMed, EMBASE, and The Cochrane Library up until 12 December 2018. Hazard risk (HR) and 95% confidence interval (CI) were pooled using random-effect or fixed-effect model models. Results: A total of 13 studies comprising 5,169 CKD patients were included in the meta-analysis. In a comparison of individuals in the bottom third vs. the top third of baseline fetuin-A levels, the pooled multivariate-adjusted HR for the risk of all-cause mortality was 1.92 (95% CI 1.31-2.80), and the significant association was observed only in dialysis patients, but not non-dialysis patients. When fetuin-A was treated as continuous variables, per 0.1 g/L increase of fetuin-A levels was associated with a 8% lower mortality risk in dialysis patients (HR 0.92, 95% CI 0.87-0.97, p = 0.001), but per 0.01 g/L was not. Sensitivity analysis indicated the association was not adjusted by diabetes and inflammation. Conclusion: Lower fetuin-A levels are associated with an increased risk of all-cause mortality independent of diabetes and inflammation in dialysis patients, and there may be a dose-response relationship between them.

Comparative Analysis of the Transcriptome of Latent Autoimmune Diabetes in Adult (LADA) Patients from Eastern China.

Latent autoimmune diabetes in adults (LADA) is characterized as a slow-progressing form of autoimmune diabetes. LADA resembles some phenotypes of type 1 diabetes (T1D) and type 2 diabetes (T2D), frequently leading to misdiagnosis and inappropriate therapeutic strategies. Understanding its transcriptome profiles aids in revealing the detailed molecular mechanisms of LADA and its therapy. In the present study, we performed RNA-seq analysis of LADA patients from Eastern China and showed that LADA exhibited 277 differentially expressed genes (DEGs) with 199 upregulated and 78 downregulated. Gene ontology and KEGG pathway enrichment analysis revealed that these DEGs were mainly related to immune function and cell death and growth. Furthermore, a comparison of DEGs in LADA with those in T1D and T2D identified from the online databases showed that there are very few overlapped genes between LADA and T1D or T2D, confirming LADA to be a distinct type of diabetes from T1D or T2D. In summary, our comprehensive analysis may aid in the understanding and treatment of LADA patients in Eastern China.

Comparison of Serum MicroRNA21 and Tumor Markers in Diagnosis of Early Non-Small Cell Lung Cancer.

OBJECTIVE: To compare the clinical value of serum microRNA21 (miR21) and other tumor markers in early diagnosis of non-small cell lung cancer (NSCLC). METHODS: Serums carcinoembryonic antigen (CEA), cytokeratin 19 fragment (CYFRA21-1), neuron-specific enolase (NSE), and miR21 were detected in 50 NSCLC cases and 60 healthy control individuals. RESULTS: Average serums miR21, CEA, NSE, and CYFRA21-1 levels were significantly higher in the case group than in control group (P < 0.01). Analysis of areas under the receiver operating characteristic (ROC) curve (AUC) revealed that CEA had the highest diagnostic efficiency for NSCLC. Serums miR21 and CYFRA21-1 levels were significantly lower at TNM stages I-II than stages III-IV (P < 0.05). Further, logistic multivariate regression analysis showed that the incidence of early NSCLC (TNM stages I-II) was correlated with serums CYFRA21-1 (OR = 1.076) and miR21 (OR = 2.473) levels (P < 0.05). By AUC analysis, miR21 had the highest diagnostic efficiency for early NSCLC, and single or combined detection of serums CYFRA21-1 and miR21 levels showed improved diagnostic efficiency for joint detection of both markers. CONCLUSIONS: Serum miR21 could serve as an important marker for auxiliary diagnosis of early NSCLC, while joint detection of serums miR21 and CYFRA21-1 levels could improve diagnostic efficiency.

Serum fetuin-A concentrations are positively associated with serum VEGF levels in patients with newly diagnosed type 2 diabetes.

Fetuin-A was considered to be involved in pathogenesis of type 2 diabetes. On the other hand, higher vascular endothelial growth factor (VEGF) expression is associated with diabetes and its vascular complications, but the mechanisms leading to higher VEGF levels are still not clear. To the best of our knowledge, there are no data to show the associations between fetuin-A and VEGF in patients with type 2 diabetes. Therefore, the aim of this study is to investigate the relationship between serum fetuin-A concentrations and serum VEGF levels in patients with type 2 diabetes. We recruited 345 patients with newly diagnosed type 2 diabetes. Serum fetuin-A concentrations and serum VEGF levels were measured using enzyme-linked immunosorbent assay (ELISA) method. In this study, there was a significant positive correlation between serum fetuin-A concentrations and serum VEGF levels (r=0.223, P<0.001), and the correlation remained significant even after adjustment for other confounding factors in the multivariate regression model (ß=0.151, P=0.006). Mantel-Haenszel (M-H) stratified analysis showed that the degree of association of high concentrations of fetuin-A with high levels of VEGF is higher than that with low levels of VEGF (odds ratio of M-H [ORM-H], 2.938; 95% confidence interval [CI], 1.896-4.553). In addition, this study showed that both fetuin-A and VEGF were positively associated with fasting plasma glucose (FPG), glycated hemoglobin A1c (HbA1c) and C-reactive protein (CRP). These data suggested that serum fetuin-A concentrations were positively associated with serum VEGF levels in patients with newly diagnosed type 2 diabetes.