VEGFA and VEGFR2 RNAscope determination in gastric cancer

Whole Exome Sequencing Study Suggests an Impact of FANCA, CDH1 and VEGFA Genes on Diffuse Gastric Cancer Development

Gastric cancer (GC) is one of the most common cancer types in the world with a high mortality rate. Hereditary predisposition for GC is not fully elucidated so far. The aim of this study was identification of possible new candidate genes, associated with the increased risk of gastric cancer development. Whole exome sequencing (WES) was performed on 18 DNA samples from adenocarcinoma specimens and non-tumor-bearing healthy stomach tissue from the same patient. Three pathogenic variants were identified: c.1320+1G>A in the CDH1 gene and c.27_28insCCCAGCCCCAGCTACCA (p.Ala9fs) of the VEGFA gene were found only in the tumor tissue, whereas c.G1874C (p.Cys625Ser) in the FANCA gene was found in both the tumor and normal tissue. These changes were found only in patients with diffuse gastric cancer and were absent in the DNA of healthy donors.

Screening ssDNA Aptamers Against Human Vascular Endothelial Factor 165 via Semirational Design

As a valid tumor marker, vascular endothelial growth factor 165 (VEGF165) is an effective therapeutic target for anticancer treatments. Aptamers hold great promise for the development of anti-VEGF strategies. In this study, anti-VEGF165 ssDNA aptamers were screened using a semirational design and a multilevel screening strategy. Recombinant human VEGF165 protein was used as a target for the construction of an ssDNA virtual aptamer library with ssDNA that had one sole secondary structure. After silicon-assisted prescreening, circular dichroism and isothermal titration calorimetry were used to further screen for candidates. Three aptamers (nos. 524, 529, and 64) with one sole secondary and tertiary structure, showing a high affinity for VEGF165, were identified. The K_D values obtained using surface plasmon resonance analysis were 36.3, 288, and 79.3 nM for aptamers 524, 529, and 64, respectively. Cytological tests revealed that the three aptamers inhibit rhVEGF165-induced proliferation of HUVECs. Specifically, aptamer 529 had the strongest inhibitory effect (nearly 100% inhibition). The screening strategy used in our study showed improved screening efficiency relative to other methods and resulted in aptamers with one sole conformation. The aptamers had an advantage in ensuring the uniqueness of aptamer targeting. This semirational design and multilevel screening strategy provide a reference for the screening of other aptamers.

RNAscope for VEGF-A Detection in Human Tumor Bioptic Specimens

Different pro-angiogenic factors, such as vascular endothelial growth factor-A (VEGF-A), have been related to microvascular density, clinicopathologic factors, and poor prognosis in many tumors. VEGF-A binds its receptor 2 (VEGFR2) to induce neo-angiogenesis, a constant hallmark of tumor initiation and progression. Based on VEGF-A/VEGFR2 relevance in tumor angiogenesis, several inhibitors were developed. However, the clinical benefits of anti-angiogenic therapies are limited because tumors activate different mechanisms of drug resistance.The need for understanding tumor biology, limitation or failure of anti-angiogenic therapies, and the demand for a personalized therapeutic approach has boosted the search for robust biomarkers for patient stratification as responder or non-responder to anti-VEGF therapies.This chapter presents a detailed protocol to perform chromogenic VEGF-A mRNA detection and quantification in human tumor bioptic specimens using RNAscope technology and RNA-in situ hybridization (ISH) algorithm. RNAscope for VEGF-A detection, even for small amounts, is compatible with precious clinical samples and diagnostic laboratory workflows.

The Inhibitory Effect and Mechanism of Ferula akitschkensis Volatile Oil on Gastric Cancer

Ferula akitschkensis volatile oil (FAVO) has a good inhibitory activity on gastric cancer cell proliferation, but the mechanism of action is not yet clear. In this study, we tested the antigastric cancer efficacy and mechanism of FAVO using both in vivo and in vitro models. The results showed that FAVO effectively inhibited the proliferation, migration, and invasion of human gastric cancer SGC-7901 cells, the formation of small tubules of human umbilical vein endothelial cells as well as zebrafish intersegmental vessel and intestinal vein angiogenesis. In vivo experiments showed that FAVO significantly delayed the growth of SGC-7901 tumor-bearing nude mice and induced higher serum IL-2 and IFN-γ and reduced serum IL-6. Western blot results showed that FAVO reduced the expression of HIF-2α, VEGF, VEGFR2, P-VEGFR2, Akt, and P-Akt in SGC-7901 cells with CoCl2 induced hypoxia. We further clarified the main chemical components of FAVO through GC-MS analysis. In summary, FAVO may inhibit tumor growth and angiogenesis via inhibiting the HIF-2α/VEGF signaling pathway.

Identifying Potential miRNA Biomarkers for Gastric Cancer Diagnosis Using Machine Learning Variable Selection Approach

Aim: This study aimed to accurately identification of potential miRNAs for gastric cancer (GC) diagnosis at the early stages of the disease. Methods: We used GSE106817 data with 2,566 miRNAs to train the machine learning models. We used the Boruta machine learning variable selection approach to identify the strong miRNAs associated with GC in the training sample. We then validated the prediction models in the independent sample GSE113486 data. Finally, an ontological analysis was done on identified miRNAs to eliciting the relevant relationships. Results: Of those 2,874 patients in the training the model, there were 115 (4%) patients with GC. Boruta identified 30 miRNAs as potential biomarkers for GC diagnosis and hsa-miR-1343-3p was at the highest ranking. All of the machine learning algorithms showed that using hsa-miR-1343-3p as a biomarker, GC can be predicted with very high precision (AUC; 100%, sensitivity; 100%, specificity; 100% ROC; 100%, Kappa; 100) using with the cut-off point of 8.2 for hsa-miR-1343-3p. Also, ontological analysis of 30 identified miRNAs approved their strong relationship with cancer associated genes and molecular events. Conclusion: The hsa-miR-1343-3p could be introduced as a valuable target for studies on the GC diagnosis using reliable biomarkers.

Characterization of neuroendocrine regulation- and metabolism-associated molecular features and prognostic indicators with aid to clinical chemotherapy and immunotherapy of patients with pancreatic cancer

The worldwide prevalence of pancreatic cancer has been rising in recent decades, and its prognosis has not improved much. The imbalance of substance and energy metabolism in tumour cells is among the primary causes of tumour formation and occurrence, which is often controlled by the neuroendocrine system. We applied Cox and LASSO regression analysis to develop a neuroendocrine regulation- and metabolism-related prognostic risk score model with three genes (GSK3B, IL18 and VEGFA) for pancreatic cancer. TCGA dataset served as the training and internal validation sets, and GSE28735, GSE62452 and GSE57495 were designated as external validation sets. Patients classified as the low-risk population (category, group) exhibited considerably improved survival duration in contrast with those classified as the high-risk population, as determined by the Kaplan-Meier curve. Then, we combined all the samples, and divided them into three clusters using unsupervised clustering analysis. Unsupervised clustering, t-distributed stochastic neighbor embedding (t-SNE), and principal component analysis (PCA) were further utilized to demonstrate the reliability of the prognostic model. Moreover, the risk score was shown to independently function as a predictor of pancreatic cancer in both univariate and multivariate Cox regression analyses. The results of gene set enrichment analysis (GSEA) illustrated that the low-risk population was predominantly enriched in immune-associated pathways. "ESTIMATE" algorithm, single-sample GSEA (ssGSEA) and the Tumor Immune Estimation Resource (TIMER) database showed immune infiltration ratings were enhanced in the low-risk category in contrast with the high-risk group. Tumour immune dysfunction and exclusion (TIDE) database predicted that immunotherapy for pancreatic cancer may be more successful in the high-risk than in the low-risk population. Mutation analysis illustrated a positive link between the tumour mutation burden and risk score. Drug sensitivity analysis identified 44 sensitive drugs in the high- and low-risk population. GSK3B expression was negatively correlated with Oxaliplatin, and IL18 expression was negatively correlated with Paclitaxel. Lastly, we analyzed and verified gene expression at RNA and protein levels based on GENPIA platform, HPA database and quantitative real-time PCR. In short, we developed a neuroendocrine regulation- and metabolism-associated prognostic model for pancreatic cancer that takes into account the immunological microenvironment and drug sensitivity.

Identifying the Mechanisms of Rosa Roxburghii Tratt on Treating Gastric Cancer: Combining the Targetable Screening From the Cancer Genome Atlas With Network Pharmacology

The Chinese herbal medicine Rosa roxburghii Tratt (RRT) is widely used in the treatment of malignant tumors, including gastric cancer (GC), but its pharmacological mechanism remains unclear. The purpose of this research was to identify the mechanisms of RRT on treating GC by using network pharmacology and molecular docking, combined with the analysis of differential expressed genes in GEO gene chips and TCGA database. We first defined the effective components of RRT and their potential targets for the treatment of GC, and identified core targets according to the topology analysis by constructing a protein-protein interaction network. Furthermore, molecular docking was used to verify the docking between the core active ingredients and the key targets. The results showed that the effect of RRT may be closely associated with multiple signal pathways, including pathways in cancer, phosphatidylinositol 3-kinase-AKT serine/threonine kinase (PI3K-Akt), tumor necrosis factor (TNF), hypoxia-inducible factor 1 (HIF-1), and mitogen-activated protein kinase (MAPK). It is suggested that RRT may play an effect by regulating hypoxia, improving the tumor microenvironment, inhibiting inflammatory reactions and promoting apoptosis. The mechanism of RRT in the treatment of GC is revealed here for the first time based on network pharmacology analysis, which may provide a new direction for further exploration of the mechanisms of RRT in the treatment of GC and a new perspective for research on anti-tumor drugs.

First-in-human DR5 PET reveals insufficient DR5 expression in patients with gastrointestinal cancer

BACKGROUND

Death receptor 5 (DR5) is a promising therapeutic target for cancer therapy. However, many clinical trials of DR5 agonists failed to show significant therapeutic efficacy in patients with cancer. The study aimed to investigate the feasibility of using ⁸⁹Zr-CTB006 positron emission tomography (PET) for noninvasive imaging of DR5 expression in preclinical models and patients with gastrointestinal (GI) cancers.

METHODS

Balb/c, Sp2/0 xenograft and patient-derived tumor xenograft were employed for micro-PET/CT imaging in vivo. In the clinical study, patients with GI cancers planning to undergo surgical operation were enrolled and underwent ¹⁸F-FDG and ⁸⁹Zr-CTB006 PET/CT. The tumor tissues were obtained through surgical operation and DR5 expression levels were confirmed by RNAscope.

RESULTS

Preclinical studies showed that ⁸⁹Zr-CTB006 PET could specifically detect DR5 expression levels in vivo. Twenty-one patients, including nine gastric cancers and 12 colorectal cancers, were enrolled. The biodistribution showed high uptake in the liver and spleen and low uptake in the brain, lung and muscle with an acceptable whole-body dosimetry of 0.349 mSv/MBq. Strikingly, the adrenal glands maintained stable high uptake over the entire examination in all patients. The tumor lesions showed different levels of uptake of ⁸⁹Zr-CTB006 with a mean maximum standardized uptake value (SUV_max) of 6.63±3.29 (range 1.8-13.8). Tumor tissue was obtained from 18 patients, and ⁸⁹Zr-CTB006 uptake in patients with RNAscope scores of 3-4 was significantly higher than that in patients with scores of 0-2. An SUV_max of 9.3 at 48 hours and 6.3 at 72 hours could be used to discriminate the DR5 expression status of tumors both with a sensitivity and specificity of 100% and 92.9%, respectively.

CONCLUSIONS

⁸⁹Zr-CTB006 PET/CT is capable of detecting DR5 expression in cancer patients and is a promising approach to screen patients with DR5 overexpression.

miR-29a-3p inhibits endometrial cancer cell proliferation, migration and invasion by targeting VEGFA/CD C42/PAK1

Background

This study aimed to investigate the mechanism of miR-29a-3p in regulating endometrial cancer (EC) progression.

Methods

A total of 72 EC patients were enrolled. EC cells were transfected. Cells proliferation, cloning ability, migration and invasion were researched by MTT assay, colony formation experiment, cell scratch test and Transwell experiment respectively. Dual-luciferase reporter assay was performed. Xenograft experiment was conducted using nude mice. miR-29a-3p, VEGFA, CDC42, PAK1 and p-PAK1 expression in cells/tissues was investigated by qRT-PCR and Western blot.

Results

miR-29a-3p expression was aberrantly reduced in EC patients, which was associated with poor outcome. miR-29a-3p inhibited EC cells proliferation, cloning formation, migration and invasion (P <  0.05 or P <  0.01 or P <  0.001). miR-29a-3p inhibited CDC42/PAK1 signaling pathway activity in EC cells (P <  0.01). VEGFA expression was directly inhibited by miR-29a-3p. miR-29a-3p suppressed EC cells malignant phenotype in vitro and growth in vivo by targeting VEGFA/CDC42/PAK1 signaling pathway (P < 0.05 or P < 0.01).

Conclusion

miR-29a-3p inhibits EC cells proliferation, migration and invasion by targeting VEGFA/CDC42/PAK1 signaling pathway.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12885-021-08506-z.

In situ c-KIT mRNA quantification of canine cutaneous mast cell tumours and its relationship to prognostic factors

Cutaneous mast cell tumours (MCTs) are the most frequent malignant skin tumours in dogs. Mutations in the c-KIT proto-oncogene are correlated with the pathogenesis and aggressiveness of MCTs. To date, studies have focused on c-KIT mutations and KIT protein localization, with a general lack of mRNA-level analyses. In this study, c-KIT mRNA expression was investigated in canine MCTs by RNA in situ hybridization (RNA-ISH). Furthermore, we evaluated associations between c-KIT mRNA expression and the histological grade, KIT immunohistochemical staining pattern and other clinicopathological parameters. c-KIT mRNA expression was observed in all MCT samples, appearing as clusters of dots in the cytoplasm of neoplastic cells. A significant correlation was detected between c-KIT mRNA expression (quantified according to the H-score and the percentage of positive cells) and the histological grade (determined using two-and three-tier grading systems; P < .05). We also found a significant positive correlation (all P < .05) between c-KIT mRNA expression and the proliferation indices (mitotic index, Ki-67, and Ag67). However, no significant associations with c-KIT expression from RNA-ISH were found with respect to different KIT staining patterns. Overall, these results demonstrate that c-KIT mRNA expression might be an additional tool for measuring the c-KIT status in canine cutaneous MCTs and could serve as a potential prognostic factor. Further studies should evaluate the prognostic significance of c-KIT mRNA expression in a large and uniform cohort of canine MCTs.

Circular RNA 0047905 acts as a sponge for microRNA4516 and microRNA1227-5p, initiating gastric cancer progression

Several lines of evidence suggest that circular RNAs (circRNAs) play important roles in oncogenesis and tumor progression. However, our knowledge of the role of circRNAs in gastric cancer (GC) remains limited. We investigated the possibility that circular RNA 0047905 (circRNA0047905) might act as a tumor promoter in the pathogenesis of gastric cancer by profiling miRNA expression in GC tissues and paired noncancerous mucosa tissues using miRNA microarrays. Next, a ceRNA network was constructed according to common miRNAs binding circRNAs and mRNAs. Mechanistically, we demonstrated that circRNA0047905 directly binds miR4516 and miR1227-5p, relieving suppression for targets SERPINB5 and MMP11. We observed that down-regulated circRNA0047905 expression in gastric cancer cells inhibited Akt/CREB signaling pathway activation. RNA scope in situ hybridization revealed expression of circRNA0047905 in GC. Our data suggest that circRNA0047905 is a promising target for GC diagnosis and therapy.

PD-L1 expression and association with malignant behavior in pheochromocytomas/paragangliomas

The immunosuppressive effect of the programmed death (PD)-1/PD-L1 pathway plays an important role in the treatment of a variety of tumors, such as lung and breast cancer, but there is little literature about PD-1/PD-L1 in pheochromocytomas/paragangliomas (PCCs/PGLs). We explored the relationship of PD-L1 and malignant behavior in 77 cases of PCC/PGL using immunohistochemistry (IHC) to assess protein expression and RNAscope to detect mRNA expression in 20 cases. The IHC data showed that 59.74% of the PCCs/PGLs expressed PD-L1, and the extent of expression was highly correlated with Ki-67 (P = .019) and hypertension (P = .013) but not with age, sex, tumor size, capsular invasion, tumor necrosis, relapse/distant metastasis, secretion of noradrenaline/adrenaline/dopamine, or diabetes mellitus. In addition, we found an excellent correlation of PD-L1 mRNA and protein expression with a κ coefficient of 0.828, and further stratification of the IHC and RNAscope findings showed high consistency (Pearson coefficient 0.753). The correlation of PD-L1 and Ki-67 indicated that PD-L1 could be considered a malignant proliferation biomarker for PCCs/PGLs, which would be a putative biomarker for anti-PD-L1 therapies.