Prognostic effect of DNA methylation of BTG2 gene in Chinese hepatocellular carcinoma.

Background: This study aims to develop a prognostic model for overall survival based on potential methylation sites within B-cell translocation gene 2 (BTG2) in Chinese patients with hepatocellular carcinoma (HCC). Methods: This is a retrospective study. The beta values of nine CpG sites and RSEM normalized count values of BTG2 gene were extracted from the Cancer Genome Atlas-Liver Hepatocellular Carcinoma (TCGA-LIHC) (TCGA-LIHC) dataset, with the beta value representing the methylation level by indicating the ratio of the intensity of the methylated bead type to the combined locus intensity. Pyrosequencing was performed to determine the range of methylation values surrounding cg01798157 site in BTG2 gene. A weighted linear model was developed to predict the overall survival (OS). Results: The beta value of cg01798157 was significantly negatively associated with the mRNA expression of BTG2 in the TCGA-LIHC dataset (Spearman's rho = -0.5306, P = 2.27 × 10-27). The methylation level of cg01798157 was significantly associated with OS in the cohort of 51 Chinese HCC patients (Hazard ratio = 0.597, 95% CI: 0.434-0.820, P = 0.001). Multivariate Cox regression analysis identified methylation level of cg01798157, cirrhosis, and microvascular invasion as independent prognostic factors. The prognostic efficiency of death risk score was superior to that of cirrhosis or microvascular invasion alone. Conclusions: The methylation level of cg01798157 in BTG2 may be an epigenetic biomarker in Chinese patients with resectable HCC.

The application of 3D-printed oral stents in intensity-modulated radiotherapy for oropharyngeal cancer and their dosimetric effect on organs at risk.

BACKGROUND: This study investigates the accuracy of 3D-printed dental stents in intensity-modulated radiotherapy (IMRT) for oropharyngeal cancer (OPC) and their dosimetric effects on normal tissues. METHODS: We selected 60 patients with OPC who underwent IMRT in the Department of Oncology, Special Medical Center of Army Medical University. These patients were randomly assigned into 3D-printed oral stent, simple glass bottle, and nonstent groups (20 patients/group). The positioning error was analyzed with the onboard imaging system once a week after 5 fractions of IMRT. The conformity index (CI), homogeneity index (HI), radiation dose of organs at risk (OARs), and oral mucosal reaction were compared among the three groups. RESULTS: No significant difference was observed in the conformity and uniformity of the target dose and the dose received by the spinal cord, larynx, and bilateral parotid glands among the three groups (P > 0.05). Meanwhile, the dose received by the upper cheek, hard palate, and soft palate of patients was significantly lower in the 3D-printed oral stent group than in the nonstent group (P < 0.05) but insignificantly different between the 3D-printed oral stent and simple glass bottle groups (P > 0.05). When compared with the nonstent group, the simple glass bottle group showed a markedly lower dose received by the upper cheek (P < 0.05) and an insignificantly different dose received by the hard palate and soft palate (P > 0.05). According to Common Terminology Criteria for Adverse Events v.5.0, the adverse response rate of the hard palate mucosa was lower in the 3D-printed oral stent group than in the simple glass bottle and nonstent groups (P < 0.05). CONCLUSIONS: For OPC patients undergoing IMRT, the application of 3D-printed oral stents can significantly reduce the exposure dose of the upper cheek and hard palate and decrease the occurrence of adverse events such as oral mucositis although it cannot affect the positioning error.

Machine learning-based signature of necrosis-associated lncRNAs for prognostic and immunotherapy response prediction in cutaneous melanoma and tumor immune landscape characterization.

Background: Cutaneous melanoma (CM) is one of the malignant tumors with a relative high lethality. Necroptosis is a novel programmed cell death that participates in anti-tumor immunity and tumor prognosis. Necroptosis has been found to play an important role in tumors like CM. However, the necroptosis-associated lncRNAs' potential prognostic value in CM has not been identified. Methods: The RNA sequencing data collected from The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression Project (GTEx) was utilized to identify differentially expressed genes in CM. By using the univariate Cox regression analysis and machine learning LASSO algorithm, a prognostic risk model had been built depending on 5 necroptosis-associated lncRNAs and was verified by internal validation. The performance of this prognostic model was assessed by the receiver operating characteristic curves. A nomogram was constructed and verified by calibration. Furthermore, we also performed sub-group K-M analysis to explore the 5 lncRNAs' expression in different clinical stages. Function enrichment had been analyzed by GSEA and ssGSEA. In addition, qRT-PCR was performed to verify the five lncRNAs' expression level in CM cell line (A2058 and A375) and normal keratinocyte cell line (HaCaT). Results: We constructed a prognostic model based on five necroptosis-associated lncRNAs (AC245041.1, LINC00665, AC018553.1, LINC01871, and AC107464.3) and divided patients into high-risk group and low-risk group depending on risk scores. A predictive nomogram had been built to be a prognostic indicator to clinical factors. Functional enrichment analysis showed that immune functions had more relationship and immune checkpoints were more activated in low-risk group than that in high-risk group. Thus, the low-risk group would have a more sensitive response to immunotherapy. Conclusion: This risk score signature could be used to divide CM patients into low- and high-risk groups, and facilitate treatment strategy decision making that immunotherapy is more suitable for those in low-risk group, providing a new sight for CM prognostic evaluation.

Promotor methylation status of MAPK4 is a novel epigenetic biomarker for prognosis of recurrence in patients with thymic epithelial tumors.

BACKGROUND: The prognosis of thymic epithelial tumors (TETs) currently relies on the commonly adopted WHO classification and Masaoka staging system, which cannot reflect the undefined biological behaviors limiting them as prognostic factors. METHODS: In this study, we first identified 40 genes and 179 genes, respectively that were epigenetically upregulated and silenced, corresponding to a total of 509 functionally methylated CpG sites between thymomas and thymic carcinomas by using the TCGA dataset. RESULTS: The methylation ß-values of cg20068620 in MAPK4 and cg18770944 in USP51 were significantly associated with recurrence-free survival (RFS). In the independent validation cohort, only WHO classification and methylation ß-values of cg20068620 in MAPK4 were independent prognostic factors for RFS in Chinese patients with TETs. A linear weighted model including these two factors was used to calculate the recurrence risk score (RRS). Time-dependent ROC curve analysis revealed that RRS was overwhelmingly superior to WHO classification for predicting 3-, 5-, and 10-year RFS and Masaoka stage for 3- and 5-year RFS. CONCLUSIONS: These results suggested that the methylation site cg20068620 in MAPK4 can improve the accuracy of the WHO classification alone regarding the prognostic value of TETs recurrence.

A CTL/M2 macrophage-related four-gene signature predicting metastasis-free survival in triple-negative breast cancer treated with adjuvant radiotherapy.

PURPOSE: This study aimed to develop and validate a prognostic model for metastasis-free survival (MFS) based on genes that may functionally interact with cytotoxic T lymphocytes (CTLs) and M2 macrophages in patients with triple-negative breast cancer (TNBC) who underwent adjuvant radiotherapy. METHODS: The transcriptional and phenotypic profiles of TNBC and other breast cancer subtypes were downloaded from gene expression omnibus (GEO). The abundance of infiltrated immune cells was evaluated through CIBERSORTx or MCP-counter. A weighted linear model, the score for MFS (SMFS), was developed using the least absolute shrinkage and selection operator (LASSO) in GSE58812 and validated in GSE2034 and GSE12276. The biological implication of the SMFS was explored by evaluating its associations with TNBC molecular subtypes and other radiosensitivity- or immune-related signatures. RESULTS: A model consisting of the PCDH12/ELP3, PCDH12/MSRA, and FAM160B2/MSRA gene expression ratios with non-zero coefficients finally selected by LASSO was developed using GSE58812. In GSE2034 (treatment with adjuvant radiotherapy), the SMFS was significantly associated with MFS in TNBC patients (hazard ratio (HR) = 8.767, 95% confidence interval (CI) 1.856-41.408, P = 0.006) and, to a lesser extent, in non-TNBC patients (HR = 2.888, 95% CI 1.076-7.750, P = 0.035). However, the interaction of subtype (TNBC vs non-TNBC) and the SMFS tended to be significant (Pinteraction = 0.081). In contrast, the SMFS was not significantly associated with MFS in either TNBC patients (P = 0.499) or non-TNBC patients (P = 0.536) in GSE12276 (treatment without radiotherapy). Among the four TNBC molecular subtypes, the c1 and c4 subtypes exhibited higher CTL infiltration and lower SMFS values than the c2 and c3 subtypes. In addition, the SMFS was positively correlated with the abundance of endothelial cells (r = 0.413, P < 0.001). CONCLUSION: The proposed model has the potential to predict MFS in TNBC patients after adjuvant radiotherapy, and the SMFS may represent a measurement of tumor immune suppression.

Co-Occurring Alteration of NOTCH and DDR Pathways Serves as Novel Predictor to Efficacious Immunotherapy in NSCLC.

Although immune checkpoint inhibitors (ICIs) have shown remarkable benefit for treatment of advanced non-small lung cancer (NSCLC), only a minority of patients can achieve durable responses and the most patients produce an ultra-rapid progressive disease. Here, we collected the availably published datasets and mined the determinants of response to immunotherapy on pathway levels. One hundred six NSCLC patients treated with immunotherapy were combined from Rizvi et al. and Hellman et al. studies (whole exon sequencing). Two independent validation datasets consisted of the MSKCC cohort (targeted sequencing) and data by Anagnostou and colleagues (whole exon sequencing). The Cancer Genome Atlas (TCGA) somatic mutation and gene expression data were applied to explore the immunobiology features. In the first combined cohort, we detected NOTCH pathway altered in 71% patients with durable clinical benefit (DCB) while only 36% among no durable benefit (NDB) (p = 0.005). Compared to NDB group, co-occurrence of NOTCH and at least two DDR (co-DDR) pathway was discovered in DCB group and contributed to a prolonged progression-free survival (PFS) [22.1 vs 3.6 months, p < 0.0001, HR, 0.34, 95% confidence interval (CI), 0.2-0.59]. In two independent datasets, co-occurrence of NOTCH+/co-DDR+ was also validated to be a better immunotherapy efficacy [Cohort 2: 13 vs 6 months, p = 0.034, HR, 0.55, 95% CI, 0.31-0.96; Cohort 3: 21 vs 11 months, p = 0.067, HR, 0.45, 95% CI, 0.18-1.1]. By analyzing TCGA cohort, we found patients with coexisting NOTCH+/co-DDR+ pathway had a higher TMB, more infiltration of CD4+T cells. Overall, co-occurrence of NOTCH and co-DDR pathway reflect a better immunotherapy efficacy in advanced NSCLC. This genomic predictor show promise in stratifying patients that suit for immunotherapy for future clinical practice.

Identification of low-density lipoprotein receptor class A domain containing 4 (LDLRAD4) as a prognostic indicator in primary gastrointestinal stromal tumors.

BACKGROUND: There is an urgent clinical need to select the patients with resectable gastrointestinal stromal tumors (GISTs) who can benefit from adjuvant treatment after complete resection based on disease recurrence risk stratification. We hypothesized that integrating biomarkers into available risk assessment tools may improve the precision of GIST prognostic predictions. METHODS: Candidate genes that may cause GIST progression were identified using the Gene Expression Omnibus dataset GSE20708. Quantitative Real-time was used to confirm the prognostic value of the candidate genes for recurrence-free survival (RFS) in a cohort of 94 patients. RESULTS: Thirty-seven differentially expressed genes between localized tumors and metastatic primary tumors were found; 14 (37.8%) were upregulated and 23 (62.2%) were downregulated in the latter tumors. Low-density lipoprotein receptor class A domain containing 4 (LDLRAD4) was selected for further prognostic analysis. Although LDLRAD4 mRNA expression was not associated with recurrence risk grades as determined by the revised NIH consensus criteria, multivariate Cox regression analysis showed that LDLRAD4 expression (hazard ratio [HR] = 4.403, 95% confidence interval [CI]: 1.822-10.641, P = 0.001), tumor size (HR = 1.174, 95% CI: 1.027-1.342, P = 0.019) and tumor location (HR = 6.291, 95% CI: 1.128-35.080, P = 0.036) were independent prognostic factors for RFS in patients with resectable GISTs. Moreover, the RFS model constructed by these three factors may effectively predict GIST prognosis within the first 2 postsurgical years. CONCLUSION: Our study identifies LDLRAD4 as a suitable prognostic marker for GISTs. The integration of biomarkers into risk assessment tools may improve the precision of GIST prognostic predictions.

The predictive value of pre- and post-induction chemotherapy plasma EBV DNA level and tumor volume for the radiosensitivity of locally advanced nasopharyngeal carcinoma.

This study was dedicated to investigate the predictive value of pre- and post-induction chemotherapy plasma EBV (Epstein-Barr Virus) DNA level and tumor volume for the radiosensitivity of locally advanced NPC. 129 previously untreated locally advanced NPC patients were enrolled. Plasma EBV-DNA copy number and tumor volume was detected before and after induction chemotherapy. The tumor volume was also measured after radiotherapy. Among 129 patients, 98 were positive for EBV DNA. The residual gross target volume of the primary tumor (GTVnx) and GTVnd after radiotherapy was positively correlated with post-induction chemotherapy EBV copy number (rho=0.357, P<0.001; rho=0.356, P<0.001, respectively). Univariate logistic regression analyses showed that the AUC of ROC curves of post-induction chemotherapy tumor volume, tumor regression rate before and after induction chemotherapy, post-induction EBV copy number, EBV decrease rate for predicting no residual nasopharyngeal tumor were 0.859, 0.782, 0.678 and 0.657, respectively. Multivariate logistic analyses showed that T stage, post-induction chemotherapy EBV copy number and tumor volume were independent predictors for no residual nasopharyngeal tumor after radiotherapy. The changes in plasma EBV DNA and tumor volume during treatment could be used to predict the sensitivity of locally advanced NPC patients in response to intensity-modulated radiation therapy (IMRT).

Iodine-125 seed implantation in the treatment of sacrococcygeal chordoma: a case report.

The objective of this was to summarize the efficacy and safety of iodine-125 seed implantation in the treatment of sacrococcygeal chordoma. CT-guided implantation of radioactive iodine-125 seed was applied in treating a patient with sacrococcygeal chordoma. The incidence of complications was recorded and the results were evaluated and analyzed, to compare the postoperative complications and recurrence rate of sacrococcygeal chordoma. The patient was followed up to 15 months after operation. The minimum peripheral dose was 180 Gy, and 8 months after the implantation, the tumor mass was reduced significantly. There was no serious complications detected during the follow-up period. Radioactive iodine-125 seed implantation can improve the target volume dose, with the high doses of radioactive iodine-125 seed, the tumor, which was refractory and insensitive to chemotherapy and radiotherapy, can be effectively controlled and complications are less than surgical treatment. However, the long-term efficacy of this treatment needs further follow-up.