A novel autophagy-related long non-coding RNAs signature predicting progression-free interval and I-131 therapy benefits in papillary thyroid carcinoma

This study aimed to explore the prognostic and predictive value of autophagy-related lncRNAs in papillary thyroid carcinoma (PTC). The expression data of autophagy-related genes and lncRNAs of the PTC patients were obtained from TCGA database. Autophagy-related-differentially expressed lncRNAs (DElncs) were identified and used to establish the lncRNAs signature predicting patients' progression-free interval (PFI) in the training cohort. Its performance was assessed in the training cohort, validation cohort, and entire cohort. Effects of the signature on I-131 therapy were also explored. We identified 199 autophagy-related-DElncs and constructed a novel six-lncRNAs signature was constructed based on these lncRNAs. This signature had a good predictive performance and was superior to TNM stages and previous clinical risk scores. I-131 therapy was found to be associated with favorable prognosis in patients with high-risk scores but not those with low-risk scores. Gene set enrichment analysis suggested that a series of hallmark gene sets were enriched in the high-risk subgroup. Single-cell RNA sequencing analysis suggested that the lncRNAs were mainly expressed in thyroid cells but not stromal cells. In conclusion, our study constructed a well-performed six-lncRNAs signature to predict PFI and I-131 therapy benefits in PTC.

A cell cycle-related lncRNA signature predicts the progression-free interval in papillary thyroid carcinoma

The cell cycle plays a vital role in tumorigenesis and progression. Long non-coding RNAs (lncRNAs) are key regulators of cell cycle processes. Therefore, understanding cell cycle-related lncRNAs (CCR-lncRNAs) is crucial for determining the prognosis of papillary thyroid carcinoma (PTC). RNA-seq and clinical data of PTC were acquired from The Cancer Genome Atlas, and CCR-lncRNAs were selected based on Pearson's correlation coefficients. According to univariate Cox regression, least absolute shrinkage and selection operator (LASSO), and multivariate Cox regression analyses, a five-CCR-lncRNA signature (FOXD2-AS1, LOC100507156, BSG-AS1, EGOT, and TMEM105) was established to predict the progression-free interval (PFI) in PTC. Kaplan-Meier survival, time-dependent receiver operating characteristic curve, and multivariate Cox regression analyses proved that the signature had a reliable prognostic capability. A nomogram consisting of the risk signature and clinical characteristics was constructed that effectively predicted the PFI in PTC. Functional enrichment analyses indicted that the signature was involved in cell cycle- and immune-related pathways. Furthermore, we also analyzed the correlation between the signature and immune cell infiltration. Finally, we verified the differential expression of CCR-lncRNAs in vitro using quantitative real-time polymerase chain reaction. Overall, the newly developed prognostic risk signature based on five CCR-lncRNAs may become a marker for predicting the PFI in PTC.

Interfering with ITGB1-DT expression delays cancer progression and promotes cell sensitivity of NSCLC to cisplatin by inhibiting the MAPK/ERK pathway

Long non-coding RNA ITGB1-DT is involved in the regulation of cancer growth and metastasis. However, the roles of ITGB1-DT in non-small cell lung cancer (NSCLC) progression and sensitivity to cisplatin has not been elucidated. ITGB1-DT expression in NSCLC tissues, and the relationship between ITGB1-DT expression with NSCLC diagnosis, prognosis, clinicopathological features, and immune cell infiltration were investigated in The Cancer Gene Atlas (TCGA) database. The roles and mechanisms of ITGB1-DT in cell growth, migration, and drug sensitivity of NSCLC cells were explored in the cell model. The prognostic nomograms of ITGB1-DT-related genes were evaluated using bioinformatics. ITGB1-DT was overexpressed in NSCLC. Elevated ITGB1-DT expression was related to the late T stage, N stage, M stage, short overall survival (OS), disease-specific survival (DSS), and progression-free interval (PFI) of NSCLC patients. ITGB1-DT was the independent risk factors for poor prognosis, and had diagnostic value for NSCLC patients. Interfering with the ITGB1-DT expression can inhibit the proliferation, migration, and invasion of A549, H1299, and drug-resistant A549/DDP, possibly due to the inhibition of p38 MAPK and ERK phosphorylation levels. ITGB1-DT expression was correlated with the levels of NSCLC immune infiltration cells, such as the TReg, Th, and NK cells. ITGB1-DT-related gene nomograms were associated with the prognosis, and were expected to evaluate the prognosis of NSCLC patients. In conclusion, inhibition of ITGB1-DT expression delayed the growth and metastasis of NSCLC using the MAPK/ERK signaling mechanism and enhanced the sensitivity of NSCLC to cisplatin drugs. These results indicate that ITGB1-DT might be a biomarker for evaluating the diagnosis and prognosis of NSCLC patients.

Alpha-L-Fucosidase Has Diagnostic Value in Prostate Cancer With "Gray-Zone PSA" and Inhibits Cancer Progression via Regulating Glycosylation

Background

This study aimed to explore the diagnostic value of alpha-l-fucosidase (AFU) in prostate cancer (PCa) patients with “gray-zone PSA” and to investigate the correlation between AFU expression and clinicopathological characteristics of PCa patients.

Methods

The level of AFU and other necessary clinicopathological variables of patients were retrieved from electronic medical records. The transcriptome profiling and clinical information of PCa patients were obtained from The Cancer Genome Atlas (TCGA) database. The protein level of AFU in tissue was assessed by immunohistochemistry (IHC). All the data were processed by appropriate analysis methods. The p-value of <0.05 was considered statistically significant.

Results

AFU showed ideal diagnostic value for PCa with prostate-specific antigen (PSA) levels ranging from 4 to 10 ng/ml, and its optimal cutoffs were 19.5 U/L. Beyond this, low AFU expression was associated with high pathological grade, T stage and N stage, more postoperative residual tumors, and poor primary therapy outcome, as well as shorter progression-free interval. The Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis illustrated that FUCA1/FUCA2 exerted tumor-suppressive function by regulating the glycosylation.

Conclusions

AFU (<19.5 U/L) could effectively distinguish the PCa from the patients with “gray-zone PSA”, and low expression of AFU was an independent unfavorable predictor for the clinicopathological characteristics of PCa patients.

Progression Risk Assessment of Post-surgical Papillary Thyroid Carcinoma Based on Circular RNA-Associated Competing Endogenous RNA Mechanisms

Background: Accurate risk assessment of post-surgical progression in papillary thyroid carcinoma (PTC) patients is critical. Exploring key differentially expressed mRNAs (DE-mRNAs) regulated by differentially expressed circular RNAs (circRNAs) via the ceRNA mechanism could help establish a novel assessment tool. Methods: ceRNA network was established based on differentially expressed RNAs and correlation analysis. DE-mRNAs within the ceRNA network associated with progression-free interval (PFI) of PTC were identified to construct a prognostic ceRNA regulatory subnetwork. least absolute shrinkage and selection operator (LASSO)-Cox regression was applied to identify hub DE-mRNAs and establish a novel DE-mRNA signature in predicting PFI of PTC. Results: Six hub DE-mRNAs, namely, CLCNKB, FXBO27, FXYD6, RIMS2, SPC24, and CDKN2A, were identified to be most significantly related to the PFI of PTC, and a prognostic DE-mRNA signature was proposed. A nomogram incorporating the DE-mRNA signature and clinical parameters was established to improve the progression risk assessment in post-surgical PTC, which was superior to the American Thyroid Association risk stratification system and distant Metastasis, patient Age, Completeness of resection, local Invasion, and tumor Size (MACIS) score American Joint Committee on Cancer staging system. Conclusions: Based on the circRNA-associated ceRNA RNA mechanism, a DE-mRNA signature and prognostic nomogram was established, which may improve the progression risk assessment in post-surgical PTC.

Survival correlation of immune response in human cancers

Background: The clinical benefit of immune response is largely unknown. We systematically explored the correlation of immune response with patient outcome in human cancers.

Results: The global immune gene signature was primarily located on the plasma membrane with a high gene density at 6p21 and 1q23-1q24. Immune responses varied with a wide range in human cancers. A total of 11 cancer types exhibited significant correlation of immune response with overall survival. Higher immune response was significantly associated with longer overall survival in 7 types and with shorter overall survival in 4 types. In addition, 11 cancer types exhibited significant correlation of immune response with progression-free interval. Higher immune response was significantly associated with longer progression-free interval in 7 types and with shorter progression-free interval in 4 types.

Methods: The Ingenuity Knowledge Base and human genome assembly GRCh38 were used to annotate the immune gene signature by cellular components and genomic coordinates, respectively. We devised an mRNA-based metric of pre-existing immune conditions by using the gene signature, and calculated the metric for 10,062 The Cancer Genome Atlas tumor samples across 32 different cancer types. The Kaplan-Meier method was used to evaluate the overall survival and progression-free interval differences between dichotomic groups stratified by the median metric for each cancer type.

Conclusions: Immune responses have different impacts on patient outcome in different human cancers. Prospective verification is needed before the findings can be applied for clinical trial development.

Identification of a Five-Gene Signature and Establishment of a Prognostic Nomogram to Predict Progression-Free Interval of Papillary Thyroid Carcinoma

Background: The incidence of papillary thyroid carcinoma (PTC) is high and increasing worldwide. Although prognosis is relatively good, it is important to select the minority of patients with poorer prognosis to avoid side effects associated with unnecessary over-treatment in low-risk patients; this requires accurate prognostic predictions. Materials and Methods: Six PTC expression datasets were obtained from the gene expression omnibus (GEO) database. Level 3 mRNA expression and clinicopathological data were obtained from The Cancer Genome Atlas Thyroid Cancer (TCGA-THCA) database. Through integrated analysis of these datasets, highly reliable differentially-expressed genes (DEGs) between tumor and normal tissue were identified and lasso Cox regression was applied to identify DEGs related to the progression-free interval (PFI) and to establish a prognostic gene signature. The performance of a five-gene signature was evaluated based on a Kaplan-Meier curve, receiver operating characteristic (ROC), and Harrell's concordance index (C-index). Multivariate Cox regression analysis was used to identify factors associated with PTC prognosis. Finally, a prognostic nomogram was established based on the TCGA-THCA dataset. Results: A novel five-gene signature was established to predict the PTC PFI, which included PLP2, LYVE1, FABP4, TGFBR3, and FXYD6, and the ROC curve and C-index showed good performance in both training and validation datasets. This could classify patients into high- and low-risk groups with distinct PFIs and differentiate PTC tumors from normal tissue. Univariate Cox regression revealed that this signature was an independent prognostic factor for PTC. The established nomogram, incorporating the prognostic gene signature and clinical parameters, was able to predict the PFI with high efficiency. The gene signature-based nomogram was superior to the American Thyroid Association (ATA) risk stratification to predict PTC PFI. Conclusions: Our study identified a five-gene signature and established a prognostic nomogram, which were reliable in predicting the PFI of PTC; this could be beneficial for individualized treatment and medical decision making.

Retrospective evaluation of toceranib phosphate (Palladia®) use in the treatment of gastrointestinal stromal tumors of dogs

Background

Gastrointestinal stromal tumors (GISTs) are uncommon intestinal neoplasms in the dog. Literature regarding adjunctive therapy for GISTs in dogs is sparse. High‐risk GISTs in humans respond to tyrosine kinase inhibition in the adjuvant setting.

Objectives

To review cases of toceranib phosphate use in dogs with GISTs and provide initial assessment of possible biological activity. A secondary aim was to evaluate patient and tumor characteristics for possible prognostic value.

Animals

Twenty‐seven dogs with confirmed GISTs based on histopathology and immunohistochemistry treated with toceranib.

Methods

Retrospective study in which cases of toceranib use in dogs with GIST were solicited using the American College of Veterinary Internal Medicine Oncology and Small Animal Internal Medicine listservs.

Results

Five of 7 dogs with gross disease experienced clinical benefit (71%; 3 complete responses, 1 partial response, 1 stable disease). These included 2 dogs with durable responses after toceranib discontinuation. Median progression‐free interval (PFI) in dogs with gross disease was 110 weeks (range, 36‐155 weeks). Median PFI in dogs with microscopic disease was 67 weeks (range, 9‐257 weeks). Metastasis at diagnosis (P = 0.04) and high mitotic index (P < 0.001) were associated with shorter PFI in toceranib‐treated dogs.

Conclusions and Clinical Importance

Biological activity of toceranib is evident in dogs with gross disease. Metastasis of GIST at diagnosis, as well as high tumor mitotic index, was associated with shorter PFI in toceranib‐treated dogs. Larger studies are needed to define postsurgical risk and refine the use of toceranib in dogs with gross and microscopic GIST.

An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics

For a decade, The Cancer Genome Atlas (TCGA) program collected clinicopathologic annotation data along with multi-platform molecular profiles of more than 11,000 human tumors across 33 different cancer types. TCGA clinical data contain key features representing the democratized nature of the data collection process. To ensure proper use of this large clinical dataset associated with genomic features, we developed a standardized dataset named the TCGA Pan-Cancer Clinical Data Resource (TCGA-CDR), which includes four major clinical outcome endpoints. In addition to detailing major challenges and statistical limitations encountered during the effort of integrating the acquired clinical data, we present a summary that includes endpoint usage recommendations for each cancer type. These TCGA-CDR findings appear to be consistent with cancer genomics studies independent of the TCGA effort and provide opportunities for investigating cancer biology using clinical correlates at an unprecedented scale.

An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics

For a decade, The Cancer Genome Atlas (TCGA) program collected clinicopathologic annotation data along with multi-platform molecular profiles of more than 11,000 human tumors across 33 different cancer types. TCGA clinical data contain key features representing the democratized nature of the data collection process. To ensure proper use of this large clinical dataset associated with genomic features, we developed a standardized dataset named the TCGA Pan-Cancer Clinical Data Resource (TCGA-CDR), which includes four major clinical outcome endpoints. In addition to detailing major challenges and statistical limitations encountered during the effort of integrating the acquired clinical data, we present a summary that includes endpoint usage recommendations for each cancer type. These TCGA-CDR findings appear to be consistent with cancer genomics studies independent of the TCGA effort and provide opportunities for investigating cancer biology using clinical correlates at an unprecedented scale.

Liposomal doxorubicin: Effective treatment for pediatric desmoid fibromatosis

Efficacy of liposomal doxorubicin (LD) in treating desmoid fibromatosis (DF) in children has not been well evaluated. This retrospective case series examines five children with progressive DF, treated with LD. We report progression-free intervals (PFIs) and radiographic as well as clinical responses for each medication received. LD was well tolerated, with an average 4.5% reduction in tumor size and median PFI of 29 months. Treatment with LD conferred the longest PFI of all medical therapies pursued. Thus, LD is an important treatment option for DF in pediatrics.

Redistribution of resistance and sensitivity to platinum during the observation period following treatment of epithelial ovarian cancer

The standard postoperative chemotherapy for epithelial ovarian cancer is a combination therapy including platinum and taxanes. The aim this study was to investigate the degree of platinum sensitivity in patients with relapsed epithelial ovarian cancer according to the treatment-free interval (TFI) and the histological tumor type. The medical records of 405 patients diagnosed with stage III/IV ovarian cancer, including 107 patients who relapsed after attaining a clinical complete response with first-line treatment, were retrospectively reviewed. The degree of platinum sensitivity was assessed by comparing the progression-free survival (PFS) following the second-line treatment. In patients with serous/endometrioid adenocarcinoma who were treated with platinum following relapse, there were significant differences in the PFS between the following groups of patients: those who relapsed within 6 months and those who relapsed between 6 and 12 months; those who relapsed between 6 and 12 months and those who relapsed between 12 and 18 months; and those who relapsed between 12 and 18 months and those who relapsed after 18 months. By contrast, in patients with clear cell/mucinous adenocarcinoma who were treated with platinum following a relapse, there were no significant differences in the PFS between patients who relapsed within 6 months and those who relapsed between 6 and 12 months, while there were significant differences in the PFS between those who relapsed between 6 and 12 months and those who relapsed after 12 months. With regard to the patients who relapsed after 12 months, the PFS of those with clear cell/mucinous adenocarcinoma was significantly shorter compared with the PFS of those with serous/endometrioid adenocarcinoma. Therefore, we considered it justified to classify patients with clear cell/mucinous adenocarcinoma who relapsed within 12 months as platinum-resistant and those who relapsed after 12 months as platinum-sensitive.