Development and validation of a novel prognostic signature based on m6A/m5C/m1A-related genes in hepatocellular carcinoma

BACKGROUND

RNA methylation modification plays an important role in cancers. This study sought to examine the association between m6A/m5C/m1A-related genes and hepatocellular carcinoma (HCC).

METHODS

Gene expression and clinical data of HCC patients were obtained from the TCGA database. Unsupervised consensus clustering was performed according to the expression of m6A/m5C/m1A-related genes in HCC. The relationships among prognosis, clinicopathological features and molecular subtypes were analyzed. Least absolute shrinkage and selection operator (LASSO) regression analysis was used to establish the m6A/m5C/m1A-related gene prognostic signature. Furthermore, the prognostic signature was validated based on the ICGC dataset. RT‒qPCR was used to detect the expression of the model genes in HCC. Clinicopathological features, functional enrichment, gene mutations, immune cell infiltration, and immunotherapy response in different risk groups were analyzed. A nomogram based on risk score and stage was constructed to predict HCC patient prognosis.

RESULTS

Two m6A/m5C/m1A-related molecular subtypes were identified in HCC, and the prognosis of cluster C1 was worse than that of cluster C2 (p < 0.001). Highly expressed genes in cluster C1 are significantly correlated with G3-4, T3-4, stage III-IV (p < 0.05). An m6A/m5C/m1A-related prognostic signature was established and validated. The RT‒qPCR results showed that the risk signature genes were significantly upregulated in liver cancer tissue (p < 0.05). The prognosis of HCC patients in the high-risk group was worse than that of those in the low-risk group (p < 0.05). Multivariate Cox analysis indicated that the risk score was an independent factor predicting prognosis in HCC patients. ssGSEA revealed that the risk score correlated with the tumor immune microenvironment in HCC. Gene mutation analysis showed that the tumor mutation burden of patients in the high-risk group was much higher (p < 0.05), and the prognosis of HCC patients with high risk scores and high mutation burden was the worst (p = 0.007). A nomogram combining risk scores with clinicopathological features showed performed well in predicting HCC prognosis.

CONCLUSIONS

The m6A/m5C/m1A-related genes could predict the prognosis and tumor microenvironment features of HCC and can be important biomarkers relevant to the immunotherapy response.

A modified melanoma-molGPA scoring model: assessment of survival after and efficacy of different radiotherapy modalities in patients with melanoma brain metastases

PURPOSE

Patients with malignant melanoma brain metastases (MBMs) have poor prognoses. For MBMs, the Melanoma-molGPA is the most widely used predictive score, but its predictive value remains uncertain in patients fully treated with radiotherapy. We identified MBMs prognostic factors and modified the prognostic scoring model.

METHODS

We retrospectively analyzed patients diagnosed with MBMs between December 2010 and November 2021 for prognostic factors influencing overall survival (OS) by univariate and multivariate analyses. Nomogram plots were based on Cox regression modeling. We evaluated overall survival (OS) using Kaplan-Meier survival curves and log-rank tests.

RESULTS

The median OS (mOS) was 7.9 months. On multivariate analysis, BRAF mutation status (p < 0.001), number of brain metastases (BM) (p < 0.001), presence of liver metastases (p < 0.001), brain metastases with a midline shift (p = 0.003), Karnofsky Performance Score (p = 0.02), and lymphocyte-to-monocyte ratio (p < 0.0001) were independent OS predictors. These were incorporated into a modified risk-stratification model. Overall, whole-brain radiotherapy (WBRT) did not significantly affect mOS (mOS, 6.89 vs. 8.83 months; p = 0.07). After risk stratification using our model, WBRT resulted in no significant survival benefit in the low-risk group (mOS 10.07 vs. 13.1 months; p = 0.71) but significantly worse prognosis in the high-risk group (mOS, 2.37 vs. 6.92 months; p = 0.026).

CONCLUSION

We propose a modified model that accurately distinguishes the prognosis of patients with MBMs and guides decision-making for radiotherapy. Based on this novel model, WBRT should be cautiously selected for high-risk patients.

Evaluation of the ability of fatty acid metabolism signature to predict response to neoadjuvant chemoradiotherapy and prognosis of patients with locally advanced rectal cancer

Neoadjuvant chemoradiotherapy (nCRT) is widely used to treat patients with locally advanced rectal cancer (LARC), and treatment responses vary. Fatty acid metabolism (FAM) is closely associated with carcinogenesis and cancer progression. In this study, we investigated the vital role of FAM on the gut microbiome and metabolism in the context of cancer. We screened 34 disease-free survival (DFS)-related, FAM-related, and radiosensitivity-related genes based on the Gene Expression Omnibus database. Subsequently, we developed a five-gene FAM-related signature using the least absolute shrinkage and selection operator Cox regression model. The FAM-related signature was also validated in external validation from Fujian Cancer Hospital for predicting nCRT response, DFS, and overall survival (OS). Notably, patients with a low-risk score were associated with pathological complete response and better DFS and OS outcomes. A comprehensive evaluation of the tumor microenvironment based on the FAM-related signature revealed that patients with high-risk scores were closely associated with activating type I interferon response and inflammation-promoting functions. In conclusion, our findings indicate the potential ability of FAM to predict nCRT response and the prognosis of DFS and OS in patients with LARC.

Delayed postoperative radiotherapy might improve the long-term prognosis of locally advanced esophageal squamous cell carcinoma

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Postoperative radiotherapy timing for esophageal cancer remains to be determined.

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Delayed postoperative radiotherapy (>48 days) provides better survival benefit.

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Postoperative radiotherapy following 2–4 chemotherapy cycles achieved best survival.

Objective

There is no consensus on the optimal timing of postoperative radiotherapy (PORT) for locally advanced esophageal squamous cell carcinoma (ESCC). We aimed to determine whether the timing of PORT affects the long-term prognosis of ESCC, and plotted nomograms to predict survival.

Methods

We retrospectively analyzed 351 ESCC patients who underwent radical surgery and PORT. Receiver operating characteristic curves were used to estimate the optimal cutoff point of the time interval between surgery and PORT. Cox proportional hazards regression was used to identify prognostic predictors. Overall survival (OS) and progression-free survival (PFS) were predicted using nomograms.

Results

The median follow-up was 53 months (range: 3–179 months). Compared to early PORT, PORT at >48 days after surgery was associated with better OS (adjusted hazard ratio [HR]: 1.406, p = 0.037) and PFS (adjusted HR: 1.475, p = 0.018). In the chemotherapy subgroup, incorporation of chemotherapy timing into the analysis suggested that 2–4 chemotherapy cycles followed by PORT was the optimal treatment schedule as compared to 0–1 chemotherapy cycle followed by PORT and concurrent chemoradiotherapy (5-year PFS: 65.9% vs. 51.0% vs. 50.1%; p = 0.049). The nomograms for OS and PFS were superior to the TNM classification (concordance indices: 0.721 vs. 0.626 and 0.716 vs. 0.610, respectively).

Conclusions

Delayed PORT (>48 days) provides better survival benefit than early PORT among ESCC patients. PORT following 2–4 chemotherapy cycles might lead to the best survival rate. The nomogram plotted in this study effectively predicted survival and may help guide treatment.

Prognostic factors and treatment comparison in small cell neuroendocrine carcinoma of the uterine cervix based on population analyses

Objective

We aimed to assess the impact of the treatment modality on the outcome of small cell neuroendocrine cervical carcinoma (SCNEC) using the Surveillance Epidemiology and End Results (SEER) database.

Methods

Patients from the SEER program between 1981 and 2014 were identified. Significant factors for cancer‐specific survival (CSS) and overall survival (OS) were analyzed using the Kaplan‐Meier survival and Cox regression methods.

Results

A total of 503 SCNEC patients were identified. The 5‐year CSS and OS were 36.6% and 30.6%, respectively. The International Federation of Gynecology and Obstetrics (FIGO) stage I to IV distributions was 189 (37.6%), 108 (21.5%), 95 (18.9%), and 111 patients (22.0%), respectively. Within the patients with known treatment strategies, 177 (45.9%) were treated with radical surgery and 209 (54.1%) underwent primary radiotherapy. Local treatment strategies were independent prognostic factor for CSS and OS. The 5‐year CSS for radical surgery and primary radiotherapy was 50.0% and 27.9%, respectively (P < .001). The 5‐year OS for those who received radical surgery and primary radiotherapy was 57.8%, and 29.6%, respectively (P < .001). In FIGO stage I SCNEC, patients treated with radical surgery had superior CSS (P = .001) and OS (P = .003) than those with primary radiotherapy. However, in FIGO stage II and III SCNEC, there were no differences in CSS and OS with respect to different local treatment strategies. Our results also found that the addition of brachytherapy impacted OS in the FIGO stage III SENCE (P = .002). The 5‐year CSS and OS of patients with FIGO IV were only 11.7% and 7.1%, respectively.

Conclusions

SCNEC is a rare disease with aggressive clinical behavior. The findings indicate that radical surgery should be suggested for early‐stage SCNEC and combining radiation therapy with brachytherapy should be suitable for patients with advanced stage.

Prolyl hydroxylase domain 3 influences the radiotherapy efficacy of pancreatic cancer cells by targeting hypoxia-inducible factor-1α

Purpose

Pancreatic cancer is characterized by a hypoxic microenvironment and resistance to most currently available treatment modalities. Prolyl hydroxylase domain 3 (PHD3) is a rate-limiting enzyme that regulates the degradation of hypoxia-inducible factors (HIFs) and is deregulated in pancreatic cancer cells. Whether such alteration of PHD3 expression contributes to the sustained growth and radioresistance of pancreatic cancer cells remains largely unknown.

Materials and methods

PHD3 was overexpressed in pancreatic cancer Mia-paca2 cells via lentiviral expression. Cell cycle progression and apoptosis were assayed by flow cytometry. HIF-1α, EGFR, and PHD3 protein expression was assessed by Western blotting. Cell survival was determined in a colony formation assay.

Results

PHD3 overexpression suppressed HIF-1α protein expression and EGFR phosphorylation and enhanced the 2 Gy irradiation-mediated reductions in HIF-1α and phosphorylated (p)-EGFR under either normoxic or hypoxic conditions. PHD3 overexpression inhibited the growth and colony formation of Mia-paca2 cells in response to irradiation under either normoxic or hypoxic conditions. PHD3 overexpression exacerbated irradiation-induced apoptosis, with a greater effect under hypoxia than normoxia. Cell cycle distribution analysis demonstrated that PHD3 overexpression resulted in further shortened S phase and lengthened G2/M phase in response to irradiation.

Conclusion

PHD3 expression may contribute to the radiotherapy efficacy of pancreatic cancer cells and serve as a novel biomarker for improving radiotherapy efficacy in pancreatic cancer.

Prognostic value of vascular endothelial growth factor receptor 1 and class III β-tubulin in survival for non-metastatic rectal cancer

AIM

To assess the long-term prognostic value of vascular endothelial growth factor receptor 1 (VEGFR1) and class III β-tubulin (TUBB3) mRNA expression in non-metastatic rectal cancer.

METHODS

A total of 75 consecutive patients with non-metastatic rectal cancer from March 2004 to November 2008 were analyzed retrospectively at our institute. The mRNA expressions of VEGFR1 and TUBB3 were detected by multiplex branched DNA liquid-chip technology. The Cutoff Finder application was applied to determine cutoff point of mRNA expression. SPSS software version 22.0 was used for analysis.

RESULTS

The median follow-up was 102.7 mo (range, 6-153.6). The χ2 and Fisher's exact tests showed that VEGFR1 expression was related to lymph node metastasis (P = 0.013), while no relationships between TUBB3 and clinicopathological features were observed. Univariate analysis showed that T stage, lymph node metastasis, tumor differentiation, VEGFR1 and TUBB3 mRNA expression were correlated to overall survival (OS) (P = 0.048, P = 0.003, P = 0.052, P = 0.003 and P = 0.015, respectively). Also, lymph node metastasis and VEGFR1 expression independently influenced OS by multivariate analysis (P = 0.027 and P = 0.033). VEGFR1 expression was positively correlated with TUBB3 (P = 0.024). The patients with low expression of both TUBB3 and VEGFR1 presented a better OS (P = 0.003). In addition, the receiver operating characteristic analysis suggested that the combination of lymph node metastasis and VEGFR1 had a more favorable prognostic value (P < 0.001).

CONCLUSION

VEGFR1 expression and lymph node metastasis independently and jointly affect survival. Moreover, low expression of VEGFR1 and TUBB3 presented a better OS in patients with non-metastatic rectal cancer, which might serve as a potential prognostic factor.

Survival benefit of re-irradiation in esophageal Cancer patients with Locoregional recurrence: a propensity score-matched analysis

BACKGROUND

To investigate the treatment failure pattern and factors influencing locoregional recurrence of esophageal squamous cell carcinoma (ESCC) and examine patient survival with re-irradiation (re-RT) after primary radiotherapy.

METHODS

We retrospectively analyzed 87 ESCC patients treated initially with radiotherapy. Failure patterns were classified into regional lymph node recurrence only (LN) and primary failure with/without regional lymph node recurrence (PF). Patients received either re-RT or other treatments (non-re-RT group). Baseline covariates were balanced by a propensity score model. Overall survival (OS) and toxicities were assessed as outcomes.

RESULTS

The median follow-up time was 87 months. Thirty-nine patients received re-RT. Failure pattern and re-RT were independent prognostic factors for OS (P = 0.040 and 0.015) by Cox multivariate analysis. Re-RT with concomitant chemotherapy showed no survival benefit over re-RT alone (P = 0.70). No differences in characteristics were found between the groups by Chi-square tests after propensity score matching. The Cox model showed that failure pattern and re-RT were prognostic factors with hazard ratios (HR) of 0.319 (P = 0.025) and 0.375 (P = 0.002), respectively, in the matched cohort. Significant differences in OS were observed according to failure pattern (P = 0.004) and re-RT (P < 0.001). In the re-RT and non-re-RT groups, 9.09% and 3.03% of patients experienced tracheoesophageal fistulas, and 15.15% and 3.03% of patients developed pericardial/pleural effusion, respectively (P > 0.05). The incidence of radiation pneumonitis was higher in the re-RT group (24.24% vs. 6.06%, P = 0.039), but no cases of pneumonia-related death occurred.

CONCLUSIONS

Re-RT improved long-term survival in patients with locoregional recurrent ESCC. Despite a high incidence of radiation pneumonitis, toxicities were tolerable.

High-biologically effective dose palliative radiotherapy for a tumor thrombus might improve the long-term prognosis of hepatocellular carcinoma: a retrospective study

Background

This study aimed to highlight the type of tumor thrombus and identify the prognostic factors influencing the long-term survival outcomes in patients with hepatocellular carcinoma (HCC) having a tumor thrombus. A tumor thrombus in HCC is associated with poor prognosis.

Methods

Eighty patients diagnosed with HCC having a tumor thrombus between May 2006 and April 2014 were enrolled in this study. Age, gender, clinical characteristics, laboratory findings, Child-Pugh classification, performance status (ECOG), types of tumor thrombi, radiotherapy method, biologically effective dose (BED), and primary treatment method were analyzed to identify the prognostic factors associated with the overall survival (OS) rates. Statistical analyses were performed using SPSS version 19.0.

Results

The median follow-up duration was 24 months (range 6–90). The 1-, 3-, and 5-year OS rates of the patients were 77.6%, 37.6%, and 18.8%, respectively. On univariate analysis, gender, radiotherapy method, BED, types of tumor thrombi, Child-Pugh classification, ECOG, and total bilirubin were associated with OS (P < 0.001, P = 0.001, P = 0.016, P = 0.003, P < 0.001, P < 0.001, P = 0.039, respectively). The prognostic factors for OS in multi-variate analyses were gender (P < 0.001), BED (P = 0.044), Child Pugh classification (P = 0.020), performance status (ECOG) (P = 0.004), and types of tumor thrombi (P = 0.001). The median OS for the high-BED group was better than that for the low-BED groups (42 months vs. 19 months, P = 0.016).

Conclusions

Gender, BED, performance status (ECOG), Child-Pugh classification, and types of tumor thrombi seemed to affect OS, and a stepwise decrease in survival was observed with the types of tumor thrombi ranging from I to IV. High-BED palliative radiotherapy might improve the long-term outcomes for patients with HCC having a tumor thrombus.

Radiation-Guided Peptide Delivery in a Mouse Model of Nasopharyngeal Carcinoma

Purpose. This study aimed to evaluate the characteristics of the HVGGSSV peptide, exploring radiation-guided delivery in a mouse model of nasopharyngeal carcinoma. Methods. Mice with CNE-1 nasopharyngeal carcinoma were assigned to two different groups treated with Cy7-NHS and Cy7-HVGGSSV, respectively. Meanwhile, each mouse received a single dose of 3 Gy radiation. Biological distribution of the recombinant peptide was assessed on an in vivo small animal imaging system. Results. The experimental group showed maximum fluorescence intensity in irradiated tumors treated with Cy7-labeled HVGGSSV, while untreated (0 Gy) control tumors showed lower intensity levels. Fluorescence intensities of tumors in the right hind limbs of experimental animals were 7.84 × 10⁷ ± 1.13 × 10⁷, 1.35 × 10⁸ ± 2.66 × 10⁷, 4.05 × 10⁸ ± 1.75 × 10⁷, 5.57 × 10⁸ ± 3.47 × 10⁷, and 9.26 × 10⁷ ± 1.73 × 10⁷ photons/s/cm² higher compared with left hind limb values at 1, 2, 15, 24, and 48 h, respectively. Fluorescence intensities of tumor in the right hind limbs of the experimental group were 1.66 × 10⁸ ± 1.71 × 10⁷, 1.51 × 10⁸ ± 3.23 × 10⁷, 5.38 × 10⁸ ± 1.96 × 10⁷, 5.89 × 10⁸ ± 3.57 × 10⁷, and 1.62 × 10⁸ ± 1.69 × 10⁷ photons/s/cm² higher compared with control group values at 1, 2, 15, 24, and 48 h, respectively. Fluorescence was not specifically distributed in the control group. Compared with low fluorescence intensity in the heart, lungs, and tumors, high fluorescence distribution was found in the liver and kidney at 48 h. Conclusions. HVGGSSV was selectively bound to irradiated nasopharyngeal carcinoma, acting as a targeting transport carrier for radiation-guided drugs that are mainly metabolized in the kidney and liver.

Radiotherapy Combined With Androgen Deprivation for Bone Oligometastases After Primary Curative Radiotherapy for Prostate Cancer: A Retrospective Study

To evaluate the effects and toxicity of radiotherapy (RT) combined with androgen deprivation (AD) for bone oligometastases after primary curative RT for prostate cancer (PCa).We retrospectively analyzed 30 consecutively treated PCa patients with bone oligometastases from April 2005 to July 2014. All patients underwent RT combined with AD for oligometastatic bones after curative RT for PCa. Measured outcomes included overall survival (OS) rate, local control (LC), progression-free survival (PFS), pain relief, and toxicities. Statistical analysis was performed with SPSS17.0.The median follow-up was 32.5 months (range, 0.6-50.3). The 3-year PFS and OS rates were 22.8% (95% CI, 13.4-37.5%) and 69% (95% CI, 51.7-81.1%), respectively. The number of bone oligometastases and RT schedule were found to be significantly associated with OS on univariate analysis (P < 0.05, respectively). The 3-year OS for patients with 1 and >1 metastases was 78.8% versus 42.2%, respectively (P = 0.037). The long-course RT was associated with better 3-year OS compared with short-course (76.4% vs 44.1%, P = 0.03). A total of 15 (83.3%, 15/18) patients achieved pain relief. No grade 3 toxicity was observed.Long-course RT combined with ADT was effective and well-tolerated in PCa patients with bone oligometastases after curative RT for PCa. Further randomized controlled trials are needed to corroborate the findings.

Long-term follow-up and prognostic factors for advanced thymic carcinoma

The aim of this study was to evaluate the long-term survival outcomes in patients with advanced thymic carcinoma and identify prognostic factors influencing the survival. We retrospectively analyzed 90 consecutive patients with pathologically confirmed advanced thymic carcinoma (Masaoka III and IV) in our institute, from December 2000 to 2012. Age, sex, clinical characteristics, laboratory findings, Masaoka and tumor node metastasis staging, pathologic grade, and treatment modalities were analyzed to identify prognostic factors associated with the progress-free survival (PFS) and the overall survival (OS) rates. Statistical analysis was conducted using SPSS, version 19.0 (SPSS, Inc, Chicago, IL). A total of 73 (81.1%) male and 17 (18.9%) female patients participated in the study. The median follow-up time was 75 months (range, 20-158 months). The 5-year PFS and OS rates were 23.6% (95% confidence interval [CI], 14.6%-33.8%) and 35.7% (95% CI, 25.1%-46.4%), respectively. The multivariate Cox regression model analysis showed that factors improving the PFS were the normal lactate dehydrogenase (LDH) level (P<0.001), Masaoka III stage (P=0.028), and radiotherapy (RT) (P<0.001). The LDH (P<0.001), T stage (P<0.001), and the pathologic grade (P=0.047) were independently prognostic of OS. Long-term follow-up of the advanced thymic carcinoma showed poor outcomes of PFS and OS. LDH, Masaoka stage, and RT affected the PFS, and LDH, T stage, and pathologic grade seemed to affect the OS. Establishing a better staging system for predicting outcomes would be warranted.

The effects of the shape and size of the clinical target volume on the planning target volume margin

PURPOSE

To investigate the impact of clinical target volume (CTV) shape and size on CTV to planning target volume (PTV) margin expansion.

METHODS AND MATERIALS

Using numerical integration methods, margins accounting for random errors and systematic errors were calculated for CTVs of different shapes and sizes. We use k(r-95) and k(s-95) to represent the coefficients, for random errors and systematic errors, respectively, that ensure that every point of the CTV receives ≥95% of the prescribed dose.

RESULTS

The part of the margin accounting for random errors depends on CTV shape and size; generally, a convex part of a CTV would have a larger margin than a concave part. However, the part of the margin accounting for systematic errors is independent of CTV shape and size.

CONCLUSIONS

CTV shape and size should be considered when generating a PTV. For a complex CTV, the margins of the various parts of the CTV are different and related to local forms.