Immune landscape and prognostic immune-related genes in KRAS-mutant colorectal cancer patients.

BACKGROUND: KRAS gene is the most common type of mutation reported in colorectal cancer (CRC). KRAS mutation-mediated regulation of immunophenotype and immune pathways in CRC remains to be elucidated. METHODS: 535 CRC patients were used to compare the expression of immune-related genes (IRGs) and the abundance of tumor-infiltrating immune cells (TIICs) in the tumor microenvironment between KRAS-mutant and KRAS wild-type CRC patients. An independent dataset included 566 cases of CRC and an in-house RNA sequencing dataset were served as validation sets. An in-house dataset consisting of 335 CRC patients were used to analyze systemic immune and inflammatory state in the presence of KRAS mutation. An immue risk (Imm-R) model consist of IRG and TIICs for prognostic prediction in KRAS-mutant CRC patients was established and validated. RESULTS: NF-κB and T-cell receptor signaling pathways were significantly inhibited in KRAS-mutant CRC patients. Regulatory T cells (Tregs) was increased while macrophage M1 and activated CD4 memory T cell was decreased in KRAS-mutant CRC. Prognosis correlated with enhanced Tregs, macrophage M1 and activated CD4 memory T cell and was validated. Serum levels of hypersensitive C-reactive protein (hs-CRP), CRP, and IgM were significantly decreased in KRAS-mutant compared to KRAS wild-type CRC patients. An immune risk model composed of VGF, RLN3, CT45A1 and TIICs signature classified CRC patients with distinct clinical outcomes. CONCLUSIONS: KRAS mutation in CRC was associated with suppressed immune pathways and immune infiltration. The aberrant immune pathways and immune cells help to understand the tumor immune microenvironments in KRAS-mutant CRC patients.

Roles of RNA m5C modification patterns in prognosis and tumor microenvironment infiltration of diffuse large B-cell lymphoma.

Genetic and epigenetic aberrations display an essential role in the initiation and progression of diffuse large B-cell lymphoma (DLBCL). 5-methylcytosine (m5C), a common RNA modification, regulates various cellular processes and contributes to tumorigenesis and cancer progression. However, m5C alterations in DLBCL remain unclear. Our research constructed an m5C prognostic model utilizing GEO data sets, which can efficiently predict the prognosis of patients with DLBCL, and verified the m5C prognostic model genes by immunohistochemistry analysis. This model was constructed using unsupervised consensus clustering analyses, Least Absolute Shrinkage and Selection Operator (LASSO), and multivariate Cox regression analyses. Based on the expression of m5C genes in the model, patients with DLBCL could be effectively divided into groups with significant survival time differences. The m5C risk-score signature demonstrated a highly significant independent prognostic value. Results from tumor microenvironment analyses revealed that m5C genes altered the infiltration of eosinophils, Tregs, and M2 macrophages. Additionally, they regulated T cell activation by modulating the expression of CTLA4, PDL1, B2M, CD8A, ICOS, and other relevant immune checkpoint expressions. In conclusion, our study presents a robust m5C prognostic model that effectively predicts prognosis in DLBCL. This model may offer a new approach for prognostic stratification and potential therapeutic interventions for patients with DLBCL.

Immune-tumor interaction dictates spatially directed evolution of esophageal squamous cell carcinoma.

Esophageal squamous cell carcinoma (ESCC) is a poor-prognostic cancer type with extensive intra- and inter-patient heterogeneity in both genomic variations and tumor microenvironment (TME). However, the patterns and drivers of spatial genomic and microenvironmental heterogeneity of ESCC remain largely unknown. Here, we generated a spatial multi-omic atlas by whole-exome, transcriptome, and methylome sequencing of 507 tumor samples from 103 patients. We identified a novel tumor suppressor PREX2, accounting for 22% of ESCCs with frequent somatic mutations or hyper-methylation, which promoted migration and invasion of ESCC cells in vitro. Analysis of the TME and quantification of subclonal expansion indicated that ESCCs undergo spatially directed evolution, where subclones mostly originated from the tumor center but had a biased clonal expansion to the upper direction of the esophagus. Interestingly, we found upper regions of ESCCs often underwent stronger immunoediting with increased selective fitness, suggesting more stringent immune selection. In addition, distinct TMEs were associated with variable genomic and clinical outcomes. Among them, hot TME was associated with high immune evasion and subclonal heterogeneity. We also found that immunoediting, instead of CD8+ T cell abundance, acts as an independent prognostic factor of ESCCs. Importantly, we found significant heterogeneity in previously considered potential therapeutic targets, as well as BRCAness characteristics in a subset of patients, emphasizing the importance of focusing on heterogeneity in ESCC targeted therapy. Collectively, these findings provide novel insights into the mechanisms of the spatial evolution of ESCC and inform precision therapeutic strategies.

Weighted gene co-expression network analysis identifies the prognosis-related models of left- and right-sided colon cancer.

Left-sided colon cancer (LC) and right-sided colon cancer (RC) are 2 essentially different diseases, and the potential mechanisms regulating them remain unidentified. In this study, we applied weighted gene co-expression network analysis (WGCNA) to confirm a yellow module, mainly enriched in metabolism-related signaling pathways related to LC and RC. Based on the RNA-seq data of colon cancer in The Cancer Genome Atlas (TCGA) and GSE41258 dataset with their corresponding clinical information, a training set (TCGA: LC: n = 171; RC: n = 260) and a validation set (GSE41258: LC: n = 94; RC: n = 77) were divided. Least absolute shrinkage and selection operator (LASSO) penalized COX regression analysis identified 20 prognosis-related genes (PRGs) and helped constructed 2 risk (LC-R and RC-R) models in LC and RC, respectively. The model-based risk scores accurately performed in risk stratification for colon cancer patients. The high-risk group of the LC-R model showed associations with ECM-receptor interaction, focal adhesion, and PI3K-AKT signaling pathway. Interestingly, the low-risk group of the LC-R model showed associations with immune-related signaling pathways like antigen processing and presentation. On the other hand, the high-risk group of the RC-R model showed enrichment for cell adhesion molecules and axon guidance signaling pathways. Furthermore, we identified 20 differentially expressed PRGs between LC and RC. Our findings provide new insights into the difference between LC and RC, and uncover the potential biomarkers for the treatment of LC and RC.

Integrated multi-omics profiling yields a clinically relevant molecular classification for esophageal squamous cell carcinoma.

Integrated molecular analysis of human cancer has yielded molecular classification for precise management of cancer patients. Here, we analyzed the whole genomic, epigenomic, transcriptomic, and proteomic data of 155 esophageal squamous cell carcinomas (ESCCs). Multi-omics analysis led to the classification of ESCCs into four subtypes: cell cycle pathway activation, NRF2 oncogenic activation, immune suppression (IS), and immune modulation (IM). IS and IM cases were highly immune infiltrated but differed in the type and distribution of immune cells. IM cases showed better response to immune checkpoint blockade therapy than other subtypes in a clinical trial. We further developed a classifier with 28 features to identify the IM subtype, which predicted anti-PD-1 therapy response with 85.7% sensitivity and 90% specificity. These results emphasize the clinical value of unbiased molecular classification based on multi-omics data and have the potential to further improve the understanding and treatment of ESCC.

Modified Frailty Index Independently Predicts Postoperative Pulmonary Infection in Elderly Patients Undergoing Radical Gastrectomy for Gastric Cancer.

BACKGROUND: Pulmonary infection is one of the most common postoperative complications after radical gastrectomy for gastric cancer (GC) and is associated with a poorer prognosis. This study aimed to investigate potential predictive factors for pulmonary infection in elderly GC patients. METHODS: This study retrospectively enrolled 346 elderly GC patients undergoing elective radical gastrectomy between January 2017 and December 2020. Pulmonary infection within postoperative 30 days was set as the primary observational endpoint. The baseline demographic, clinicopathological, and laboratory data were compared between patients with or without pulmonary infection. ROC curves were plotted to evaluate the cut-off and predictive values of factors. Binary univariate and multivariate logistic regression analyses were employed to determine risk factors for postoperative pulmonary infection. RESULTS: Of the enrolled 346 patients, pulmonary infection was observed in 51 patients within postoperative 30 days, with an incidence of 14.7%. mFI was a significant predictor for pulmonary infection by ROC curve analysis (AUC: 0.770, P < 0.001). Moreover, preoperative mFI was the only independent risk factor for pulmonary infection (OR: 2.72, 95% CI: 2.02-3.31, P = 0.011) by univariate and multivariate logistic regression analyses. CONCLUSION: Our study indicates that mFI independently predicts pulmonary infection in elderly GC patients.

Prognostic role and clinical significance of C-reactive protein-lymphocyte ratio in colorectal cancer.

Systemic inflammatory response (SIRS) can be used as a potential prognostic marker in patients with colorectal cancer (CRC). The purpose of this study was to examine the predictive role of the C-reactive protein (CRP)-lymphocyte ratio (CLR) in the prognosis of CRC. We retrospectively analyzed the data of CRC patients who underwent surgery from 2004 to 2019. The clinicopathological characteristics and follow-up records were analyzed. According to a cutoff value of CLR, the patients were divided into the high and low groups. Kaplan-Meier curves and Cox proportional hazards regression model were applied to assess the overall survival (OS). Clinicopathological characteristics analysis showed that gender, age, BMI, lymphocyte count, tumor location, left- and right-sided CRC, differentiation, T stage, M stage, TNM stage, carcinoembryonic antigen (CEA), CLR, CRP, and microsatellite status were found to differ significantly between the high and low CLR groups. Kaplan-Meier curves revealed that the high CLR group had a shorter OS, and the elderly or right-sided CRC patients faced a worse prognosis. Multivariate analysis suggested that age (hazard ratio [HR]:1.011, P = 0.003), differentiation (HR:1.331, P = 0.000), TNM stage (HR:2.425, P = 0.000), CEA (HR:1.001, P = 0.025), CLR (HR:1.261, P = 0.014) were significant independent prognostic factors for OS. Subgroup analysis demonstrated that females or patients not receiving postoperative adjuvant chemotherapy with high CLR might suffer a worse prognosis. Overall, CLR can be applied as a promising prognostic marker in CRC patients and has great potential in guiding clinical work.

CDCA7 Facilitates Tumor Progression by Directly Regulating CCNA2 Expression in Esophageal Squamous Cell Carcinoma.

BACKGROUND: CDCA7 is a copy number amplified gene identified not only in esophageal squamous cell carcinoma (ESCC) but also in various cancer types. Its clinical relevance and underlying mechanisms in ESCC have remained unknown. METHODS: Tissue microarray data was used to analyze its expression in 179 ESCC samples. The effects of CDCA7 on proliferation, colony formation, and cell cycle were tested in ESCC cells. Real-time PCR and Western blot were used to detect the expression of its target genes. Correlation of CDCA7 with its target genes in ESCC and various SCC types was analyzed using GSE53625 and TCGA data. The mechanism of CDCA7 was studied by chromatin immunoprecipitation (ChIP), luciferase reporter assays, and rescue assay. RESULTS: The overexpression of CDCA7 promoted proliferation, colony formation, and cell cycle in ESCC cells. CDCA7 affected the expression of cyclins in different cell phases. GSE53625 and TCGA data showed CCNA2 expression was positively correlated with CDCA7. The knockdown of CCNA2 reversed the malignant phenotype induced by CDCA7 overexpression. Furthermore, CDCA7 was found to directly bind to CCNA2, thus promoting its expression. CONCLUSIONS: Our results reveal a novel mechanism of CDCA7 that it may act as an oncogene by directly upregulating CCNA2 to facilitate tumor progression in ESCC.

Profiles of alternative splicing events in the diagnosis and prognosis of Gastric Cancer.

Background: Gastric cancer (GC) is a heterogeneous disease, and alternative splicing (AS) is a powerful universal transcriptional regulatory mechanism that contributes to the occurrence and development of cancer. However, the systematic analysis of AS events in GC is lacking; therefore, further studies are needed. Methods: Genome-wide analysis of AS events was performed using RNA-Seq data to evaluate the difference between GC and adjacent tissues at the AS level. Prognostic signatures based on differentially expressed alternative splicing (DEAS) events and a correlation network between DEAS and genes were built. Results: We identified 48,141 AS events, of which 2325 showed differential expression patterns. The parental genes before DEAS events play an essential role in regulating GC-related processes such as ribosome (FDR < 0.0001) and thermogenesis (FDR = 0.0002). There were 76 survival-associated DEAS cases. Stratifying patients according to the percent spliced in index value of six types of splicing patterns formed significant Kaplan-Meier curves in the overall survival analysis. A prognostic feature based on DEAS performed well for stratification in patients with GC. Conclusion: The present study will enrich our understanding regarding the distinction of GC and provide a generous amount of biomarkers and potential targets for the treatment of GC.

Serum C-Reactive Protein-to-Body Mass Index Ratio Predicts Overall Survival in Patients With Resected Colorectal Cancer.

BACKGROUND AND PURPOSE: Systemic inflammation and nutritional status have been shown to be associated with the prognosis of colorectal cancer. The purpose of this study was to evaluate the impact of the serum C-reactive protein-to-body mass index ratio on the prognosis of patients with curatively resected colorectal cancer. METHODS: We conducted a retrospective analysis of a database of 2,471 eligible patients with colorectal cancer who underwent curative resection at our hospital between 2004 and 2019. The optimal cut-off for CPR-to-BMI ratio was determined using maximally selected rank statistics. Patients were divided into 2 groups according to the cut-off value of the serum C-reactive protein-to-body mass index ratio. Kaplan-Meier curves and Cox regression analysis were used to compare overall survival. A two-sided P-value < 0.05 was considered statistically significant. RESULTS: The proportion of patients with a high C-reactive protein-to-body mass index ratio increased with increasing age, male sex, right-sided colon cancer, poorly differentiated tumors, advanced-stage disease, local/distant metastases, tumor-node-metastasis stage, and microsatellite instability. In subgroup analysis according to tumor-node-metastasis stage, the overall survival of the high C-reactive protein-to-body mass index ratio group was significantly shorter than that of the low C-reactive protein-to-body mass index ratio group (P < 0.001). Multivariate analysis identified age, differentiation, tumor-node-metastasis stage, carcinoembryonic antigen level, and the C-reactive protein-to-body mass index ratio as independent poor prognostic factors for overall survival. CONCLUSIONS: The C-reactive protein-to-body mass index ratio predicts the prognosis of patients with curatively resected colorectal cancer and is an independent risk factor for overall survival in patients with colorectal cancer.

A Novel Nomogram for Individually Predicting of Vascular Invasion in Gastric Cancer.

PURPOSE: Vascular invasion (VI) is associated with recurrence and is an indicator of poor prognosis in gastric cancer (GC). Pre-operative identification of VI may guide the selection of the optimal surgical approach and assess the requirement for neoadjuvant therapy. METHODS: A total of 271 patients were retrospectively collected and randomly allocated into the training and validation datasets. The least absolute shrinkage and selection operator regression model was used to select potentially relevant features, and multivariable logistic regression analysis was used to develop the nomogram. RESULTS: The nomogram consisted of pre-operative serum complement C3 levels, duration of symptoms, pre-operative computed tomography stage, abdominal distension and undifferentiated carcinoma. The nomogram provided good calibration for both the training and the validation set, with area under the curve values of 0.792 and 0.774. Decision curve analysis revealed that the nomogram was clinically useful. CONCLUSION: The present study constructed a nomogram for the pre-operative prediction of VI in patients with GC. The nomogram may aid the identification of high-risk patients and aid the optimization of pre-operative decision-making.

Proteomics provides individualized options of precision medicine for patients with gastric cancer.

While precision medicine driven by genome sequencing has revolutionized cancer care, such as lung cancer, its impact on gastric cancer (GC) has been minimal. GC patients are routinely treated with chemotherapy, but only a fraction of them receive the clinical benefit. There is an urgent need to develop biomarkers or algorithms to select chemo-sensitive patients or apply targeted therapy. Here, we carried out retrospective analyses of 1,020 formalin-fixed, paraffin-embedded GC surgical resection samples from 5 hospitals and developed a mass spectrometry-based workflow for proteomic subtyping of GC. We identified two proteomic subtypes: the chemo-sensitive group (CSG) and the chemo-insensitive group (CIG) in the discovery set. The 5-year overall survival of CSG was significantly improved in patients who had received adjuvant chemotherapy after surgery compared with those who received surgery only (64.2% vs. 49.6%; Cox P-value=0.002), whereas no such improvement was observed in CIG (50.0% vs. 58.6%; Cox P-value=0.495). We validated these results in an independent validation set. Further, differential proteome analysis uncovered 9 FDA-approved drugs that may be applicable for targeted therapy of GC. A prospective study is warranted to test these findings for future GC patient care.

Preoperative neutrophil-lymphocyte ratio, an independent risk factor for postoperative cognitive dysfunction in elderly patients with gastric cancer.

AIM: This study aimed to investigate the potential risk factors for postoperative cognitive dysfunction (POCD) in elderly patients with gastric cancer (GC) after radical gastrectomy. METHODS: In total, 221 elderly patients with GC who were scheduled to undergo selective radical gastrectomy in our hospital were enrolled in this study. To define early POCD, the neuropsychological assessment was carried out 1 day before surgery and 7 days after surgery. Receiver operating characteristic curve analysis was carried out to evaluate the predicative and cut-off values of risk factors, including neutrophil-lymphocyte ratio (NLR) for early POCD. The univariate and multivariate logistic regression analyses were performed to investigate risk factors for early POCD. RESULTS: Of the 221 enrolled elderly patients with GC, 42 were identified as early POCD with an incidence of 19.0% (42 of 221). Receiver operating characteristic curve analysis indicated that NLR was a significant predictor for POCD with a cut-off value of 2.50 and an area under the curve of 0.711 (95% confidence interval: 0.624-0.798, P < 0.001). Preoperative NLR (≥2.50) was the only independent risk factor associated with POCD (odds ratio: 2.44, 95% confidence interval: 1.52-3.68, P = 0.013) by the multivariate logistic regression analysis. CONCLUSIONS: Preoperative NLR level was an independent risk factor for POCD in elderly patients with GC undergoing curative resection. Geriatr Gerontol Int 2020; 20: 927-931.

[Preliminary Application of Body Surface Theodolitic Puncture Localization Method in Thoracoscopic Surgery of Pulmonary Ground-glass Nodules].

BACKGROUND: How to locate pulmonary ground-glass nodules in thoracoscopic surgery is an important clinical topic in minimally invasive thoracic surgery. There is no unified localization method at present. This study intends to investigate the accuracy and security of body surface theodolitic puncture localization method in video-assisted thoracoscopic surgery for pulmonary ground-glass nodules. METHODS: The clinical data of 41 patients from August 2018 to December 2019 were analyzed retrospectively, including 28 males and 13 females. After anesthesia, the patient was located by body surface theodolitic puncture, and then partial lobectomy was performed under video-assisted thoracoscopy. The distance from the nodule to the marked suture and the distance from the nodule to the incisal margin were measured, and the accuracy of localization, the rate of complication and the success rate of surgical resection were calculated. RESULTS: A total of 51 nodules in 41 patients were located by body surface theodolitic puncture localization method. The accuracy rate was 96.1%, and the average location time was 8.3 min. Puncture bleeding occurred in 5 cases (12.2%), all of which were successfully stopped by video-assisted thoracoscopy, and there were no other complications. All patients underwent thoracoscopic partial lobectomy, including 33 cases of anatomical segmentectomy and 8 cases of wedge lobectomy. All the patients in operation process smoothly. The distance between nodule and incisal margin was measured, and all specimens were more than 2 cm, reaching a safe distance. The success rate of surgical resection was 100.0%. CONCLUSIONS: In video-assisted thoracoscopic surgery for ground glass nodules of lung, the body surface theodolitic puncture localization method can be accurate, safe and simple.

A Combined Epithelial Mesenchymal Transformation and DNA Repair Gene Panel in Colorectal Cancer With Prognostic and Therapeutic Implication.

BACKGROUND: Epithelial mesenchymal transformation (EMT) and DNA repair status represent intrinsic features of colorectal cancer (CRC) and are associated with patient prognosis and treatment responsiveness. We sought to develop a combined EMT and DNA repair gene panel with potential application in patient classification and precise treatment. METHODS: We comprehensively evaluated the EMT and DNA repair patterns of 1,652 CRC patients from four datasets. Unsupervised clustering was used for classification. The clinical features, genetic mutation, tumor mutation load, and chemotherapy as well as immunotherapy sensitivity among different clusters were systematically compared. The least absolute shrinkage and selection operator regression method was used to develop the risk model. RESULTS: Three distinct CRC clusters were determined. Clustet1 was characterized by down-regulated DNA repair pathways but active epithelial markers and metabolism pathway and had intermediate prognosis. Clustet2 was characterized by down-regulated both epithelial markers and DNA repair pathways and had poor outcome. Clustet3 presented with activation of DNA repair pathway and epithelial markers had favorable prognosis. Clustet1 might benefit form chemotherapy and Clustet3 had a higher response rate to immunotherapy. An EMT and DNA repair risk model related to prognosis and treatment response was developed. CONCLUSIONS: This work developed and validated a combined EMT and DNA repair gene panel for CRC classification, which may be an effective tool for survival prediction and treatment guidance in CRC patients.

[Jinleng method is effective and safe for the treatment of oligospermia and asthenospermia].

OBJECTIVE: The Jinleng method is based on the principle of lowered temperature and diathermic action on the testis. The aim of this study is to investigate the effect and safety of the Jinleng method on oligospermia and asthenospermia. METHODS: We treated 39 infertile males with oligospermia or asthenospermia with Jinleng underpants (Jinleng method) bid for 3 months, observed the changes in the sperm parameters of the patients after the treatment and recorded the pregnancy outcomes of their wives. RESULTS: Of the 36 patients who accomplished the treatment, 31 showed significantly improvement in semen volume, sperm concentration, forward sperm motility, total sperm motility, total sperm count and total motile sperm count (P < 0.05), with an effectiveness rate of 86.1%. Five of the patients wives achieved pregnancy in the 2-month follow-up. Adverse effects were found in none of the patients. CONCLUSION: Jinleng method is effective and safe for the treatment of infertile males with oligospermia and asthenospermia.

Systematic profiling of alternative splicing events and splicing factors in left- and right-sided colon cancer.

Left- and right-sided colon cancer (LC and RC) differ substantially in their molecular characteristics and prognoses, and are thus treated using different strategies. We systematically analyzed alternative splicing (AS) events and splicing factors in LC and RC. RNA-seq data were used for genome-wide profiling of AS events that could distinguish LC from RC. The Exon Skip splicing pattern was more common in RC, while the Retained Intron pattern was more common in LC. The AS events that were upregulated in RC were enriched for genes in the axon guidance pathway, while those that were upregulated in LC were enriched for genes in immune-related pathways. Prognostic models based on differentially expressed AS events were built, and a prognostic signature based on these AS events performed well for risk stratification in colon cancer patients. A correlation network of differentially expressed AS events and differentially expressed splicing factors was constructed, and RBM25 was identified as the hub gene in the network. In conclusion, large differences in AS events may contribute to the phenotypic differences between LC and RC. The differentially expressed AS events reported herein could be used as biomarkers and treatment targets for colon cancer.