Predicting treatment failure in stage III colon cancer patients after radical surgery.

Purpose: The aim to assess treatment failure in patients with stage III colon cancer who underwent radical surgery and was analyzed using the nomogram. Methods: Clinical factors and survival outcomes for stage III colon cancer patients registered in the SEER database from 2018 to 2019 were analyzed, with patients split into training and testing cohorts (7:3 ratio). A total of 360 patients from the First Affiliated Hospital of Longyan served as an external validation cohort. Independent predictors of treatment failure were identified using logistic regression analyses. The nomograms was evaluated by concordance index (C-index), calibration curves, and the area under the curve (AUC), decision curve analysis (DCA) and clinical impact curves (CIC) assessed the clinical utility of nomograms versus TNM staging. Results: The study included 4,115 patients with stage III colon cancer. Multivariate logistic analysis age, tumor site, pT stage, pN stage, chemotherapy, pretreatment CEA levels, number of harvested lymph nodes, perineural invasion and marital status were identified as independent risk factors for treatment failure. The C-indices for the training and testing sets were 0.853 and 0.841. Validation by ROC and calibration curves confirmed the stability and reliability of the model. DCA showed that the net clinical effect of the histogram was superior to that of the TNM staging system, while CIC highlighted the potentially large clinical impact of the model. Conclusions: The developed Nomogram provides a powerful and accurate tool for clinicians to assess the risk of treatment failure after radical surgery in patients with stage III colon cancer.

CDK4 as a Prognostic Marker of Hepatocellular Carcinoma and CDK4 Inhibitors as Potential Therapeutics.

BACKGROUND: The proteins CDK4 and CDK6, which are extremely homologous, control cell cycle entry. For the treatment of breast tumors that include hormone receptors, CDK4 and CDK6 inhibitors have been authorized. The link between CDK4 and liver hepatocellular carcinoma (LIHC), however, has not yet been established. OBJECTIVE: The study aimed to explore the link between CDK4 and LIHC and the effect of CDK4 inhibitors on LIHC. METHOD: In this study, we have evaluated CDK4's prognostic relevance in LIHC using data from The Cancer Genome Atlas (TCGA). The relationship between clinical-pathologic features and CDK4 expression has been evaluated using the Kruskal-Wallis test, the Wilcoxon signed-rank test, and logistic regression. We have analyzed CDK4 and factors related to the prognosis of HCC using the Kaplan-Meier technique and multivariate Cox regression. Gene set enrichment analysis (GSEA) identified CDK4-related critical pathways. To investigate the connections between CDK4 and cancer immune infiltrates, TCGA data were employed in single-sample gene set enrichment analysis (ssGSEA). For functional validation, CDK4 was chosen since it can be inhibited by recognized CDK4/ 6-inhibitors (e.g., abemaciclib). RESULTS: Poorer overall and disease-specific outcomes were linked to high CDK4 expression in HCC patients. GSEA suggested that CDK4 and immune response are closely connected. The amount of Th2 cells infiltrating was positively correlated with CDK4 expression, while the amount of cytotoxic cells infiltrating was negatively correlated, according to ssGSEA. Both in vitro and in vivo, the anti-tumor efficacy of CDK4 inhibitor has been found to be superior to that of sorafenib. CONCLUSION: This study suggests a relationship between CDK4 and immune infiltration and prognosis in HCC. Additionally, a CDK4 inhibitor may have anti-tumor properties against hepatocellular cancer.

Age-Related Effect of Uric Acid on Contrast-Induced Acute Kidney Injury of Patients Undergoing Coronary Angiography.

Background: The association between uric acid (UA) and contrast-induced acute kidney injury (CI-AKI) following coronary angiography (CAG) has been established. However, whether the association would vary with age remained undetermined. Methods: We performed the retrospective analysis based on the Cardio-renal Improvement II study, (ClinicalTrials.gov NCT05050877), which enrolled consecutive patients undergoing coronary angiography in 5 teaching hospitals in China from 2007 to 2020. The primary outcome was CI-AKI defined as the rise of serum creatinine (SCr) ≥ 0.5 mg/dL or 25% compared with the baseline value within 48 hours following CAG. The effect of age on the association between uric acid and CI-AKI was assessed by the logistic regression model. Results: A total of 36,550 patients (mean age 63.08±5.6-year-old, 41.7% men) were included in the study. After adjusting for the confounders, the risk of CI-AKI between each quartile of uric acid was insignificant in the young group. In patients of the middle group, lower UA was associated with a lower risk of CI-AKI while higher UA was associated with a higher risk (Q1 OR: 0.853, 95% CI: 0.734-0.993; Q4 OR: 1.797, 95% CI: 1.547-2.09). In patients of the elder group, lower and higher UA were both associated with a higher risk of CI-AKI (Q1 OR: 1.247, 95% CI: 1.003-1.553; Q4 OR: 1.688, 95% CI: 1.344-2.124). The restricted cubic spline indicated a non-linear association between UA and CI-AKI in middle and elder age groups but a linear association in the young age group. Conclusion: The association between uric acid and CI-AKI vary in patients of different age. Patients with elder age should maintain a middle level of uric acid while patients with middle age should consider a lower level of uric acid to reduce the risk of CI-AKI. The level of UA was an insignificant risk factor for CI-AKI in young patients.

Ultrasound Assessment of the Gastrocnemius Muscle as a Potential Tool for Identifying Sarcopenia in Patients with Type 2 Diabetes.

Objective: This study aims to examine the clinical significance of ultrasound evaluation of the gastrocnemius muscle (GM) in identifying sarcopenia in patients with type 2 diabetes (T2D). Methods: One hundred and fifty-three patients with T2D were included in this study. We measured the appendicular skeletal muscle mass index (ASMI), handgrip strength, and 6-meter walking speed. The US-derived muscle thickness (MT), cross-sectional area (CSA), and shear wave ultrasound elastography (SWE) of GM were also measured. We assessed the correlations between clinical indicators and US features. The model for screening sarcopenia was established using stepwise logistic regression. Stepwise linear regression was used to identify a set of variables that jointly estimated ASMI. The model's ability to identify sarcopenia and low muscle mass was assessed by receiver operating characteristic (ROC) curve analysis. Results: The prevalence of sarcopenia in this study was 24.2%. The CSA, MT and SWE values of the patients with sarcopenia were lower than those of patients without sarcopenia (all p < 0.05). ASMI was positively correlated with CSA (r = 0.56, p < 0.001) and MT (r = 0.39, p < 0.001). Handgrip strength was positively correlated with CSA (r = 0.45, p < 0.001), MT (r = 0.25, p < 0.001), and SWE (r = 0.26, p = 0.002). A diagnostic model for sarcopenia was established with a sensitivity of 81.1%, specificity of 75.0%, and an area under the curve (AUC) of 0.800. The estimated ASMI equation was developed and found to have a positive correlation with actual ASMI (r = 0.70, p < 0.001). It was also effective in diagnosing low muscle mass, with an AUC of 0.787 for males and 0.783 for females. Conclusion: Ultrasonographic assessment of the gastrocnemius muscle was found to be a useful and convenient method for detecting sarcopenia in patients with T2D.

Reduced circulating interleukin 35 is associated with enhanced peripheral T cell function in primary biliary cholangitis.

Interleukin 35 (IL-35) mediates immunosuppression of T cells in autoimmune diseases. T cells play an important role in primary biliary cholangitis (PBC) with incompletely elucidated pathogenesis. Thus, we aimed to investigate the role of IL-35 regulation on T cells in PBC patients. Fifty-one PBC patients and 28 controls were enrolled in this study. Plasma IL-35 level was measured. Purified peripheral CD4+ and CD8+ T cells were stimulated with exogenous IL-35 to investigate their functional phenotypes. IL-35-treated CD8+ T cells were cultured with human intrahepatic biliary epithelial cell line to determine the cytotoxicity of CD8+ T cells from PBC patients. Plasma IL-35 concentration was lower in PBC patients and negatively correlated with alkaline phosphatase. CD4+ T cells from PBC patients exhibited elevated transcription factor expressions and cytokine secretion, whereas CD8+ T cells produced increased cytotoxic molecules and cytokines. In vitro IL-35 stimulation suppressed the production of IL-17 and IL-22 by CD4+ T cells from PBC patients. CD8+ T cells treated with IL-35 mediated reduced target cell death in the direct contact co-culture system in PBC patients. This process was accompanied by reduced production of cytotoxic molecules and cytokines and increased expressions of immune checkpoint receptors in CD8+ T cells. Reduced circulating IL-35 might be insufficient to suppress T cell function, leading to the immune dysregulation in PBC patients.

Deciphering complex antibiotic resistance patterns in Helicobacter pylori through whole genome sequencing and machine learning.

Introduction: Helicobacter pylori (H.pylori, Hp) affects billions of people worldwide. However, the emerging resistance of Hp to antibiotics challenges the effectiveness of current treatments. Investigating the genotype-phenotype connection for Hp using next-generation sequencing could enhance our understanding of this resistance. Methods: In this study, we analyzed 52 Hp strains collected from various hospitals. The susceptibility of these strains to five antibiotics was assessed using the agar dilution assay. Whole-genome sequencing was then performed to screen the antimicrobial resistance (AMR) genotypes of these Hp strains. To model the relationship between drug resistance and genotype, we employed univariate statistical tests, unsupervised machine learning, and supervised machine learning techniques, including the development of support vector machine models. Results: Our models for predicting Amoxicillin resistance demonstrated 66% sensitivity and 100% specificity, while those for Clarithromycin resistance showed 100% sensitivity and 100% specificity. These results outperformed the known resistance sites for Amoxicillin (A1834G) and Clarithromycin (A2147), which had sensitivities of 22.2% and 87%, and specificities of 100% and 96%, respectively. Discussion: Our study demonstrates that predictive modeling using supervised learning algorithms with feature selection can yield diagnostic models with higher predictive power compared to models relying on single single-nucleotide polymorphism (SNP) sites. This approach significantly contributes to enhancing the precision and effectiveness of antibiotic treatment strategies for Hp infections. The application of whole-genome sequencing for Hp presents a promising pathway for advancing personalized medicine in this context.

Immune depletion of the methylated phenotype of colon cancer is closely related to resistance to immune checkpoint inhibitors.

Background: Molecular typing based on single omics data has its limitations and requires effective integration of multiple omics data for tumor typing of colorectal cancer (CRC). Methods: Transcriptome expression, DNA methylation, somatic mutation, clinicopathological information, and copy number variation were retrieved from TCGA, UCSC Xena, cBioPortal, FireBrowse, or GEO. After pre-processing and calculating the clustering prediction index (CPI) with gap statistics, integrative clustering analysis was conducted via MOVICS. The tumor microenvironment (TME) was deconvolved using several algorithms such as GSVA, MCPcounter, ESTIMATE, and PCA. The metabolism-relevant pathways were extracted through ssGSEA. Differential analysis was based on limma and enrichment analysis was carried out by Enrichr. DNA methylation and transcriptome expression were integrated via ELMER. Finally, nearest template or hemotherapeutic sensitivity prediction was conducted using NTP or pRRophetic. Results: Three molecular subtypes (CS1, CS2, and CS3) were recognized by integrating transcriptome, DNA methylation, and driver mutations. CRC patients in CS3 had the most favorable prognosis. A total of 90 differentially mutated genes among the three CSs were obtained, and CS3 displayed the highest tumor mutation burden (TMB), while significant instability across the entire chromosome was observed in the CS2 group. A total of 30 upregulated mRNAs served as classifiers were identified and the similar diversity in clinical outcomes of CS3 was validated in four external datasets. The heterogeneity in the TME and metabolism-related pathways were also observed in the three CSs. Furthermore, we found CS2 tended to loss methylations while CS3 tended to gain methylations. Univariate and multivariate Cox regression revealed that the subtypes were independent prognostic factors. For the drug sensitivity analysis, we found patients in CS2 were more sensitive to ABT.263, NSC.87877, BIRB.0796, and PAC.1. By Integrating with the DNA mutation and RNA expression in CS3, we identified that SOX9, a specific marker of CS3, was higher in the tumor than tumor adjacent by IHC in the in-house cohort and public cohort. Conclusion: The molecular subtypes based on integrated multi-omics uncovered new insights into the prognosis, mechanisms, and clinical therapeutic targets for CRC.

Plasma exo-hsa_circRNA_0056616: A potential biomarker for lymph node metastasis in lung adenocarcinoma.

Background: To investigate the relationship between CXCR4-related circular RNAs (circRNAs) in exosomes and lymph node metastasis of lung adenocarcinoma. Methods: Totally 41 lung adenocarcinoma tissues (21 with lymph node metastasis and 20 without) were collected. Expression of CXCR4 protein was detected by western blotting analysis. A stable PC9/CXCR4-shRNA and PC14/CXCR4-shRNA knockdown lung adenocarcinoma cell lines were established and subjected to functional assays (cell proliferation, colony formation, migration and invasion) for phenotype changes. Exo-hsa-circRNAs (has-circRNAs in exosomes) were detected in vivo and in vitro. The diagnostic value of differentially expressed exo-has-circRNAs was evaluated. Results: Expression levels of CXCR4 were higher in patients with lymph node metastasis than in those without (P = 0.001). Silencing CXCR4 expression in PC9 and PC14 cell lines with short hairpin RNA could effectively abolish colony formation frequency, proliferation rate, migration rate, and the number of invasive cells (all P < 0.001). Exo_circRNA_0056616 was detected in both PC-9/CXCR4-shRNA cells and lung adenocarcinoma plasma at significantly higher levels than in the corresponding control (P < 0.001). When a receiver operating characteristic (ROC) curve for plasma exo-hsa_circRNA_0056616 levels and diagnosis of lymph node metastasis of lung adenocarcinoma was generated, a cutoff value of 0.394 was identified with an area under the curve of 0.812 (95% confidence interval 0.720-0.903), a sensitivity of 0.792, and specificity of 0.810. Conclusions: Taken together, our findings suggested that CXCR4 was higher in the lung adenocarcinoma tissues with lymph node metastasis. Higher plasma levels of exo-hsa_circRNA_0056616 in these patients also suggest that this circRNA represents a potential biomarker for lymph node metastasis predictor in lung adenocarcinoma.