A Three Protein-Coding Gene Prognostic Model Predicts Overall Survival in Bladder Cancer Patients

The potential neuro-oncology link of GALR1 protein molecular mechanism in breast cancer: Expression in BT549 and MDA-MB-231 cells and its role in proliferation and migration

The role of GALR1 (mannose bioactive peptide receptor 1) in multiple physiological and pathological processes has attracted much attention, especially in the occurrence and development of cancer. The objective of this study was to examine the expression pattern of GALR1 in BT549 (human breast cancer cells) and MDA-MB-231 (invasive breast cancer cells), and to comprehensively assess its function in cell proliferation and migration, with the aim of uncovering the potential neuro-tumor correlation of GALR1 in cancer. Western blot and real-time quantitative PCR were employed to detect the expression of GALR1 in BT549 and MDA-MB-231 cells. The function of GALR1 was evaluated by cell proliferation assay (e.g., MTT assay) and migration assay (e.g., scratch assay and Transwell migration assay). The expression of GALR1 was down-regulated through RNA interference to investigate its specific role in cell proliferation and migration. The expression of GALR1 was significantly up-regulated in BT549 and MDA-MB-231 cells. Downregulation of GALR1 resulted in a significant decrease in cell proliferation capacity, accompanied by a decrease in migration capacity. Further analysis suggests that GALR1 may act by regulating cell cycle-related proteins and migration-related signaling pathways, such as the PI3K/AKT and MAPK/ERK signaling pathways.

Bladder cancer detection in urine by novel methylation markers

Although cystoscopy is a reliable tool for detecting bladder cancer (BC) in patients with hematuria, it is invasive, costly and often unnecessary since most patients with hematuria do not have BC. Consequently, developing urinary biomarkers for non-invasive BC detection is a major clinical need. While DNA methylation markers hold promise, diagnostic performance can still be improved. We assessed 11 candidate methylation markers for urinary BC detection. Urine samples from 77 primary BC patients and 69 controls were used for marker selection and training, with independent validation conducted on samples from 63 primary BC patients and 71 controls. Samples were self-collected at home, mailed to the hospital and analyzed via quantitative methylation-specific polymerase chain reaction. Marker performance was evaluated through univariable and multivariable logistic regression analyses. Decision curve analysis (DCA) gauged clinical utility by potential cystoscopy reduction. Evaluation identified three most promising markers: NRN1, GALR1, and HAND2. These markers exhibited significantly elevated methylation levels in BC compared to controls in both cohorts (P < 0.001). The combined marker set demonstrated an area under the curve (AUC) of 0.94 at 84% (95% CI: 76-92%) sensitivity and 96% (95% CI: 91-100%) specificity. Validation yielded nearly equivalent accuracy (AUC 0.89, sensitivity 76% (95% CI: 65-86%), specificity 93% (95% CI: 86-99%)). DCA indicated a potential of 20 to 35% reduction in cystoscopies depending on the clinical scenario. The excellent diagnostic potential of our methylation markers for non-invasive BC detection, emphasizes their significance for future diagnostic strategies.

Onco-Ontogeny of Squamous Cell Cancer of the First Pharyngeal Arch Derivatives

Head and neck squamous cell carcinoma (H&NSCC) is an anatomic, biological, and genetic complex disease. It involves more than 1000 genes implied in its oncogenesis; for this review, we limit our search and description to the genes implied in the onco-ontogeny of the derivates from the first pharyngeal arch during embryo development. They can be grouped as transcription factors and signaling molecules (that act as growth factors that bind to receptors). Finally, we propose the term embryo-oncogenesis to refer to the activation, reactivation, and use of the genes involved in the embryo's development during the oncogenesis or malignant tumor invasion and metastasis events as part of an onco-ontogenic inverse process.

Whole exome sequencing analysis of canine urothelial carcinomas without BRAF V595E mutation: Short in-frame deletions in BRAF and MAP2K1 suggest alternative mechanisms for MAPK pathway disruption

Molecular profiling studies have shown that 85% of canine urothelial carcinomas (UC) harbor an activating BRAF V595E mutation, which is orthologous to the V600E variant found in several human cancer subtypes. In dogs, this mutation provides both a powerful diagnostic marker and a potential therapeutic target; however, due to their relative infrequency, the remaining 15% of cases remain understudied at the molecular level. We performed whole exome sequencing analysis of 28 canine urine sediments exhibiting the characteristic DNA copy number signatures of canine UC, in which the BRAF V595E mutation was undetected (UDV595E specimens). Among these we identified 13 specimens (46%) harboring short in-frame deletions within either BRAF exon 12 (7/28 cases) or MAP2K1 exons 2 or 3 (6/28 cases). Orthologous variants occur in several human cancer subtypes and confer structural changes to the protein product that are predictive of response to different classes of small molecule MAPK pathway inhibitors. DNA damage response and repair genes, and chromatin modifiers were also recurrently mutated in UDV595E specimens, as were genes that are positive predictors of immunotherapy response in human cancers. Our findings suggest that short in-frame deletions within BRAF exon 12 and MAP2K1 exons 2 and 3 in UDV595E cases are alternative MAPK-pathway activating events that may have significant therapeutic implications for selecting first-line treatment for canine UC. We developed a simple, cost-effective capillary electrophoresis genotyping assay for detection of these deletions in parallel with the BRAF V595E mutation. The identification of these deletion events in dogs offers a compelling cross-species platform in which to study the relationship between somatic alteration, protein conformation, and therapeutic sensitivity.

Mortality prediction models after radical cystectomy for bladder tumour: A systematic review and critical appraisal

INTRODUCTION

To identify risk-predictive models for bladder-specific cancer mortality in patients undergoing radical cystectomy and assess their clinical utility and risk of bias.

METHODS

Systematic review (CRD42021224626:PROSPERO) in Medline and EMBASE (from their creation until 31/10/2021) was screened to include articles focused on the development and internal validation of a predictive model of specific cancer mortality in patients undergoing radical cystectomy. CHecklist for critical Appraisal and data extraction for systematic Reviews of prediction Modelling Studies (CHARMS) and Prediction model Risk Of Bias ASsessment Tool (PROBAST) were applied.

RESULTS

Nineteen observational studies were included. The main predictors were sociodemographic variables, such as age (18 studies, 94.7%) and sex (17, 89.5% studies), tumour characteristics (TNM stage (18 studies, 94.7%), histological subtype/grade (15 studies, 78.9%), lymphovascular invasion (10 studies, 52.6%) and treatment with chemotherapy (13 studies, 68.4%). C-index values were presented in 14 studies. The overall risk of bias assessed using PROBAST led to 100% of studies being classified as high risk (the analysis domain was rated to be at high risk of bias in all the studies), and 52.6% showed low applicability. Only 5 studies (26.3%) included an external validation and 2 (10.5%) included a prospective study design.

CONCLUSIONS

Using clinical predictors to assess the risk of bladder-specific cancer mortality is a feasibility alternative. However, the studies showed a high risk of bias and their applicability is uncertain. Studies should improve the conducting and reporting, and subsequent external validation studies should be developed.

The Galaninergic System: A Target for Cancer Treatment

The aim of this review is to show the involvement of the galaninergic system in neuroendocrine (phaeochromocytomas, insulinomas, neuroblastic tumors, pituitary tumors, small-cell lung cancer) and non-neuroendocrine (gastric cancer, colorectal cancer, head and neck squamous cell carcinoma, glioma) tumors. The galaninergic system is involved in tumorigenesis, invasion/migration of tumor cells and angiogenesis, and this system has been correlated with tumor size/stage/subtypes, metastasis and recurrence rate. In the galaninergic system, epigenetic mechanisms have been related with carcinogenesis and recurrence rate. Galanin (GAL) exerts both proliferative and antiproliferative actions in tumor cells. GAL receptors (GALRs) mediate different signal transduction pathways and actions, depending on the particular G protein involved and the tumor cell type. In general, the activation of GAL1R promoted an antiproliferative effect, whereas the activation of GAL2R induced antiproliferative or proliferative actions. GALRs could be used in certain tumors as therapeutic targets and diagnostic markers for treatment, prognosis and surgical outcome. The current data show the importance of the galaninergic system in the development of certain tumors and suggest future potential clinical antitumor applications using GAL agonists or antagonists.

Integrated computational analysis reveals HOX genes cluster as oncogenic drivers in head and neck squamous cell carcinoma

Alterations in homeobox (HOX) gene expression are involved in the progression of several cancer types including head and neck squamous cell carcinoma (HNSCC). However, regulation of the entire HOX cluster in the pathophysiology of HNSCC is still elusive. By using different comprehensive databases, we have identified the significance of differentially expressed HOX genes (DEHGs) in stage stratification and HPV status in the cancer genome atlas (TCGA)-HNSCC datasets. The genetic and epigenetic alterations, druggable genes, their associated functional pathways and their possible association with cancer hallmarks were identified. We have performed extensive analysis to identify the target genes of DEHGs driving HNSCC. The differentially expressed HOX cluster-embedded microRNAs (DEHMs) in HNSCC and their association with HOX-target genes were evaluated to construct a regulatory network of the HOX cluster in HNSCC. Our analysis identified sixteen DEHGs in HNSCC and determined their importance in stage stratification and HPV infection. We found a total of 55 HNSCC driver genes that were identified as targets of DEHGs. The involvement of DEHGs and their targets in cancer-associated signaling mechanisms have confirmed their role in pathophysiology. Further, we found that their oncogenic nature could be targeted by using the novel and approved anti-neoplastic drugs in HNSCC. Construction of the regulatory network depicted the interaction between DEHGs, DEHMs and their targets genes in HNSCC. Hence, aberrantly expressed HOX cluster genes function in a coordinated manner to drive HNSCC. It could provide a broad perspective to carry out the experimental investigation, to understand the underlying oncogenic mechanism and allow the discovery of new clinical biomarkers for HNSCC.

Low Levels of TRIM28-Interacting KRAB-ZNF Genes Associate with Cancer Stemness and Predict Poor Prognosis of Kidney Renal Clear Cell Carcinoma Patients

Simple Summary

This is the first report investigating the involvement of TRIM28-interacting KRAB-ZNFs in kidney cancer progression. We demonstrate a significant negative association between KRAB-ZNFs and cancer stemness followed by an attenuated immune-suppressive response and reveal the prognostic role for several KRAB-ZNFs. Our findings may help better understand the molecular basis of kidney cancer and ultimately pave the way to more appropriate prognostic tools and novel therapeutic strategies directly eradicating the dedifferentiated compartment of the tumor.

Abstract

Krüppel-associated box zinc finger (KRAB-ZNF) proteins are known to regulate diverse biological processes, such as embryonic development, tissue-specific gene expression, and cancer progression. However, their involvement in the regulation of cancer stemness-like phenotype acquisition and maintenance is scarcely explored across solid tumor types, and to date, there are no data for kidney renal clear cell cancer (KIRC). We have harnessed The Cancer Genome Atlas (TCGA) and the Gene Expression Omnibus (GEO) database transcriptomic data and used several bioinformatic tools (i.e., GEPIA2, GSCALite, TISIDB, GSEA, CIBERSORT) to verify the relation between the expression and genomic alterations in KRAB-ZNFs and kidney cancer, focusing primarily on tumor dedifferentiation status and antitumor immune response. Our results demonstrate a significant negative correlation between KRAB-ZNFs and kidney cancer dedifferentiation status followed by an attenuated immune-suppressive response. The transcriptomic profiles of high KRAB-ZNF-expressing kidney tumors are significantly enriched with stem cell markers and show a depletion of several inflammatory pathways known for favoring cancer stemness. Moreover, we show for the first time the prognostic role for several KRAB-ZNFs in kidney cancer. Our results provide new insight into the role of selected KRAB-ZNF proteins in kidney cancer development. We believe that our findings may help better understand the molecular basis of KIRC.

An interactive nomogram based on clinical and molecular signatures to predict prognosis in multiple myeloma patients

Although novel drugs and treatments have been developed and improved, multiple myeloma (MM) is still recurrent and difficult to cure. In the present study, the magenta module containing 400 hub genes was determined from the training dataset of GSE24080 through weighted gene co-expression network analysis (WGCNA). Then, using the least absolute shrinkage and selection operator (Lasso) analysis, a fifteen-gene signature was firstly selected and the predictive performance for overall survival (OS) was favorable, which was identified by Receiver Operating Characteristic (ROC) curves. The risk score model was constructed based on survival-associated fifteen genes from the Lasso model, which classified MM patients into high-risk and low-risk groups. Areas under the curve (AUC) of ROC curve and log-rank test showed that the high-risk group was correlated to the dismal survival outcome of MM patients, which was also identified in testing dataset of GSE9782. The calibration plot, the AUC value of the ROC curve and Concordance-index showed that the interactive nomogram with risk score could favorably predict the probability of multi-year OS of MM patients. Therefore, it may help clinicians make a precise therapeutic decision based on the easy-to-use tool of the nomogram.