HMGA1 Has Predictive Value in Response to Chemotherapy in Gastric Cancer

RNA-binding protein expression based machine learning model predicts metastasis and treatment outcome of testicular cancer

BACKGROUND

RNA-binding proteins (RBPs) are key regulators of cellular transcription and are associated with the occurrence and development of diseases.

OBJECTIVE

This study aimed to validate the biological characteristics and clinical value of RBPs in testicular cancer, and then construct prediction models for testicular cancer metastasis and treatment outcome.

METHODS

RNA sequencing data from 150 testicular tumors and 6 normal tissues were obtained from the cancer genome atlas (TCGA). Additionally, RNA sequencing data from 165 normal testicular tissues were downloaded from the genotype-tissue expression (GTEx) portal. The chemotherapy sensitivity of testicular tumor was evaluated based on the genomics of drug sensitivity in cancer (GDSC) and cancer therapeutics response portal (CTRP) databases. RNA sequencing data was analyzed and predicted for tumor metastasis and treatment outcomes through machine learning models such as artificial neural networks (ANN), random forests (RF), support vector machines (SVM), and logistic regression models (LR).

RESULTS

A RBP risk-score model was developed with the genes: GAPDH, APOBEC3G, KRT18, NOSIP, KCTD12, ENO1, HMGA1, LDHB, ANXA2, ELOVL6, TCF7, BICD1. Those biomarkers were enriched in growth factor activity, hormone receptor binding, and cell killing signaling pathway. Risk-score model can predict the progress free interval (PFI), disease free interval (DFI), and metastasis status of patients with testicular cancer. Patients with high risk-score tumor had an increased tumor infiltrating M2 macrophage, and were more likely to progress after anti-PD-L1 immunotherapy. High risk patients seemed to benifit more from cisplatin-based chemotherapy, but less from bleomycin chemotherapy. Machine learning models basing on RBPs were able to predict tumor metastasis and the effects of chemotherapy and radiotherapy. ANN model achieved the highest accuracy in predicting tumor lymph node metastasis and radiotherapy sensitivity.

CONCLUSION

RBP signature genes can serve as biomarkers for testicular cancer and play a role in predicting tumor metastasis and therapeutic efficacy.

FOSL1 drives the malignant progression of pancreatic cancer cells by regulating cell stemness, metastasis and multidrug efflux system

BACKGROUND

Targeted therapy is an effective strategy for the treatment of advanced and metastatic pancreatic cancer, one of the leading causes for cancer-related death worldwide. To address the limitations of existing targeted drugs, there is an urgently need to find novel targets and therapeutic strategies. Transcription factor FOS like 1 (FOSL1) is a potential therapeutic target for challenging pancreatic cancer, which contributes to the malignant progression and poor gnosis of pancreatic cancer. High mobility group A1 (HMGA1) is a nonhistone chromatin structural protein that contributes to malignant progression and poor prognosis of cancer.

METHODS

Human FOSL1 complete RNA, shRNA against FOSL1 and shRNA against HMGA1 lentiviral recombination vectors were used to overexpress FOSL1 and knock down FOSL1 and HMGA1. RNA sequencing, Q-PCR and Western blots were used to investigate the mechanism of FOSL1 in regulating the proliferation of pancreatic cancer cells. The relationship between FOSL1 and HMGA1 were analyzed by co-immunoprecipitation Mass spectrometry, Q-PCR of chromatin immunoprecipitation and Western blots. The regulation of FOSL1 and HMGA1 in the invasion and migration, stemness, and multidrug efflux system were determined by transwell assay, sphere formation assay, immunofluorescence, Q-PCR and Western blots.

RESULTS

We found that FOSL1 promoted the proliferation and progression of pancreatic cancer by trigging stemness, invasion and metastasis, and drug resistance. HMGA1 was a key downstream target regulated by FOSL1 at the transcriptional level and directly interacted with FOSL1. Knockdown of HMGA1 inhibited the proliferation of pancreatic cancer cells by regulating the expression of genes related to stemness, epithelial-mesenchymal transition and multidrug efflux system. Targeted inhibition of FOSL1 and HMGA1 expression significantly inhibited the proliferation of pancreatic cancer cells.

CONCLUSION

FOSL1 promote the malignant progression of pancreatic cancer by promoting HMGA1 expression. Targeting FOSL1 and HMGA1 in monotherapy or combination therapy is a promising strategy for the treatment of advanced and metastasis pancreatic cancer.

Pre-vaccination transcriptomic profiles of immune responders to the MUC1 peptide vaccine for colon cancer prevention

Introduction

Self-antigens abnormally expressed on tumors, such as MUC1, have been targeted by therapeutic cancer vaccines. We recently assessed in two clinical trials in a preventative setting whether immunity induced with a MUC1 peptide vaccine could reduce high colon cancer risk in individuals with a history of premalignant colon adenomas. In both trials, there were immune responders and non-responders to the vaccine.

Methods

Here we used PBMC pre-vaccination and 2 weeks after the first vaccine of responders and non-responders selected from both trials to identify early biomarkers of immune response involved in long-term memory generation and prevention of adenoma recurrence. We performed flow cytometry, phosflow, and differential gene expression analyses on PBMCs collected from MUC1 vaccine responders and non-responders pre-vaccination and two weeks after the first of three vaccine doses.

Results

MUC1 vaccine responders had higher frequencies of CD4 cells pre-vaccination, increased expression of CD40L on CD8 and CD4 T-cells, and a greater increase in ICOS expression on CD8 T-cells. Differential gene expression analysis revealed that iCOSL, PI3K AKT MTOR, and B-cell signaling pathways are activated early in response to the MUC1 vaccine. We identified six specific transcripts involved in elevated antigen presentation, B-cell activation, and NF-κB1 activation that were directly linked to finding antibody response at week 12. Finally, a model using these transcripts was able to predict non-responders with accuracy.

Discussion

These findings suggest that individuals who can be predicted to respond to the MUC1 vaccine, and potentially other vaccines, have greater readiness in all immune compartments to present and respond to antigens. Predictive biomarkers of MUC1 vaccine response may lead to more effective vaccines tailored to individuals with high risk for cancer but with varying immune fitness.

Incidence of Gastric Adenocarcinoma in Those With Gastric Atrophy: A Systematic Review

Gastric atrophy (GA), or atrophic gastritis, is a pre-neoplastic lesion of gastric cancer (GC). It is part of the Correa cascade, which culminates in intestinal-type gastric adenocarcinoma. The cascade posits that intestinal-type gastric adenocarcinoma develops along a defined pathway of pre-neoplastic stages. The cascade begins with chronic gastritis, most commonly caused by Helicobacter pylori (H. pylori) infection, and proceeds through GA, gastric intestinal metaplasia (GIM), both complete and incomplete, dysplasia, both low and high-grade, and culminating in intestinal-type gastric adenocarcinoma. Attempts in Europe have been made to identify patients at risk of developing GC and target them with surveillance oesophagogastroduodenoscopy (OGD). However, there remains uncertainty about GA's risk of developing into GC. This poses issues in terms of guiding the need for and determining intervals for surveillance OGDs, which are a costly form of surveillance. As such, we attempted to gather all available studies assessing the risk of GC developing from GA, which is the first step in the Correa cascade. This study was a comprehensive systematic review of published papers, reported per the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) statement. This systematic review, which included a substantial 25,455 patients across 18 studies, found that the relative risk (RR) of GC in those with GA, using standardised incidence ratios as a measure of RR, was 15.1, with a 95% confidence interval ranging from 13.5 to 16.9. We conclude that GA does increase the risk of developing GC, and this risk may be higher than previously appreciated. Further large-scale studies are needed in Western cohorts of patients to precisely define this risk and guide the need for surveillance programs. These future studies must be standardised to account for H. pylori status, the topographical distribution of the GA, and the methods for assessing the degree of GA.

Pre-vaccination transcriptomic profiles of immune responders to the MUC1 peptide vaccine for colon cancer prevention

Self-antigens abnormally expressed on tumors, such as MUC1, have been targeted by therapeutic cancer vaccines. We recently assessed in two clinical trials in a preventative setting whether immunity induced with a MUC1 peptide vaccine could reduce high colon cancer risk in individuals with a history of premalignant colon adenomas. In both trials, there were immune responders and non-responders to the vaccine. Here we used PBMC pre-vaccination and 2 weeks after the first vaccine of responders and non-responders selected from both trials to identify early biomarkers of immune response involved in long-term memory generation and prevention of adenoma recurrence. We performed flow cytometry, phosflow, and differential gene expression analyses on PBMCs collected from MUC1 vaccine responders and non-responders pre-vaccination and two weeks after the first of three vaccine doses. MUC1 vaccine responders had higher frequencies of CD4 cells pre-vaccination, increased expression of CD40L on CD8 and CD4 T-cells, and a greater increase in ICOS expression on CD8 T-cells. Differential gene expression analysis revealed that iCOSL, PI3K AKT MTOR, and B-cell signaling pathways are activated early in response to the MUC1 vaccine. We identified six specific transcripts involved in elevated antigen presentation, B-cell activation, and NF-kB1 activation that were directly linked to finding antibody response at week 12. Finally, a model using these transcripts was able to predict non-responders with accuracy. These findings suggest that individuals who can be predicted to respond to the MUC1 vaccine, and potentially other vaccines, have greater readiness in all immune compartments to present and respond to antigens. Predictive biomarkers of MUC1 vaccine response may lead to more effective vaccines tailored to individuals with high risk for cancer but with varying immune fitness.

METTL3 regulates N6-methyladenosine modification of ANGPTL3 mRNA and potentiates malignant progression of stomach adenocarcinoma

BACKGROUND

N6-methyladenosine (m6A) is associated with mammalian mRNA biogenesis, decay, translation and metabolism, and also contributes greatly to gastrointestinal tumor formation and development. Therefore, the specific mechanisms and signaling pathways mediated by methyltransferase-like 3 (METTL3), which catalyzes the formation of m6A chemical labeling in stomach adenocarcinoma (STAD), are still worth exploring.

METHODS

Quantitative real-time PCR (qRT-PCR) was constructed to detect the expression of METTL3 in gastric cancer cell lines and patient tissues. The biological function of METTL3 was investigated in vitro/in vivo by Cell Counting Kit-8, colony formation assay, Transwell assay and nude mouse tumorigenesis assay. Based on the LinkedOmics database, the genes co-expressed with METTL3 in the TCGA STAD cohort were analyzed to clarify the downstream targets of METTL3. Methylated RNA immunoprecipitation-qPCR (MeRIP-qPCR) and RNA stability analysis were employed to explore the mechanism of METTL3 in gastric cancer progression.

RESULTS

We analyzed TCGA data and found that METTL3 was frequently elevated in STAD, and demonstrated that METTL3 was present at high levels in clinical STAD tissues and cells. High METTL3 expression was more likely to have advanced TNM tumors and distant metastasis. On the other hand, METTL3 silencing effectively impeded the higher oncogenic capacity of AGS and HGC27 cells in vivo and in vitro, as reflected by slowed cell growth and diminished migration and invasion capacities. Continued mining of the TCGA dataset identified the co-expression of angiopoietin-like 3 (ANGPTL3) and METTL3 in STAD. Lower level of ANGPTL3 was related to increased level of METTL3 in STAD samples and shorter survival times in STAD patients. ANGPTL3 enrichment limited the growth and metastasis of STAD cells. Besides, ANGPTL3 mRNA levels could be decreased by METTL3-dominated m6A modifications, a result derived from a combination of MeRIP-qPCR and RNA half-life experiments. Importantly, the inhibitory effect of METTL3 silencing on cancer could be reversed to some extent by ANGPTL3 inhibition.

CONCLUSIONS

Overall, our findings suggested that METTL3 functioned an oncogenic role in STAD by reducing ANGPTL3 expression in an m6A-dependent manner. The discovery of the METTL3-ANGPTL3 axis and its effect on STAD tumor growth will contribute to further studies on the mechanisms of gastric adenocarcinoma development.

Cellular Transcriptomics of Carboplatin Resistance in a Metastatic Canine Osteosarcoma Cell Line

Osteosarcoma prognosis has remained unchanged for the past three decades. In both humans and canines, treatment is limited to excision, radiation, and chemotherapy. Chemoresistance is the primary cause of treatment failure, and the trajectory of tumor evolution while under selective pressure from treatment is thought to be the major contributing factor in both species. We sought to understand the nature of platinum-based chemotherapy resistance by investigating cells that were subjected to repeated treatment and recovery cycles with increased carboplatin concentrations. Three HMPOS-derived cell lines, two resistant and one naïve, underwent single-cell RNA sequencing to examine transcriptomic perturbation and identify pathways leading to resistance and phenotypic changes. We identified the mechanisms of acquired chemoresistance and inferred the induced cellular trajectory that evolved with repeated exposure. The gene expression patterns indicated that acquired chemoresistance was strongly associated with a process similar to epithelial–mesenchymal transition (EMT), a phenomenon associated with the acquisition of migratory and invasive properties associated with metastatic disease. We conclude that the observed trajectory of tumor adaptability is directly correlated with chemoresistance and the phase of the EMT-like phenotype is directly affected by the level of chemoresistance. We infer that the EMT-like phenotype is a critical component of tumor evolution under treatment pressure and is vital to understanding the mechanisms of chemoresistance and to improving osteosarcoma prognosis.

HMGA1 Regulates the Expression of Replication-Dependent Histone Genes and Cell-Cycle in Breast Cancer Cells

Breast cancer (BC) is the primary cause of cancer mortality in women and the triple-negative breast cancer (TNBC) is the most aggressive subtype characterized by poor differentiation and high proliferative properties. High mobility group A1 (HMGA1) is an oncogenic factor involved in the onset and progression of the neoplastic transformation in BC. Here, we unraveled that the replication-dependent-histone (RD-HIST) gene expression is enriched in BC tissues and correlates with HMGA1 expression. We explored the role of HMGA1 in modulating the RD-HIST genes expression in TNBC cells and show that MDA-MB-231 cells, depleted of HMGA1, express low levels of core histones. We show that HMGA1 participates in the activation of the HIST1H4H promoter and that it interacts with the nuclear protein of the ataxia-telangiectasia mutated locus (NPAT), the coordinator of the transcription of the RD-HIST genes. Moreover, we demonstrate that HMGA1 silencing increases the percentage of cells in G0/G1 phase both in TNBC and epirubicin resistant TNBC cells. Moreover, HMGA1 silencing causes an increase in epirubicin IC₅₀ both in parental and epirubicin resistant cells thus suggesting that targeting HMGA1 could affect the efficacy of epirubicin treatment.

Expression, tumor immune infiltration, and prognostic impact of HMGs in gastric cancer

Background

In the past decade, considerable research efforts on gastric cancer (GC) have been expended, however, little advancement has been made owing to the lack of effective biomarkers and treatment options. Herein, we aimed to examine the levels of expression, mutations, and clinical relevance of HMGs in GC to provide sufficient scientific evidence for clinical decision-making and risk management.

Methods

GC samples were obtained from The Cancer Genome Atlas (TCGA). University of California Santa Cruz (UCSC) XENA, Human Protein Atlas (HPA), Gene Expression Profiling Interactive Analysis (GEPIA), Kaplan-Meier Plotter, cBioPortal, GeneMANIA, STRING, LinkedOmics, and DAVID databases were employed. The "ggplot2" package in the R software (×64 3.6.3) was used to thoroughly analyze the effects of HMGs. qRT-PCR was performed to assess HMG levels in GC cell lines.

Results

A total of 375 GC tissues and 32 paraneoplastic tissues were analyzed. The levels of HMGA1, HMGA2, HMGB1, HMGB2, HMGB3, HMGN1, HMGN2, and HMGN4 expression were increased in GC tissues relative to normal gastric tissues. HMGA1, HMGA2, HMGB1, HMGB2, and HMGB3 were highly expressed in GC cell lines. The OS was significantly different in the group showing low expressions of HMGA1, HMGA2, HMGB1, HMGB2, HMGB3, HMGN2, HMGN3, and HMGN5. There was a significant difference in RFS between the groups with low HMGA2, HMGB3, and high HMGN2 expression. The levels of HMGA2, HMGB3, and HMGN1 had a higher accuracy for prediction to distinguish GC from normal tissues (AUC value > 0.9). HMGs were tightly associated with immune infiltration and tumor immune escape and antitumor immunity most likely participates in HMG-mediated oncogenesis in GC. GO and KEGG enrichment analyses showed that HMGs played a vital role in the cell cycle pathway.

Conclusions

Our results strongly suggest a vital role of HMGs in GC. HMGA2 and HMGB3 could be potential markers for prognostic prediction and treatment targets for GC by interrupting the cell cycle pathway. Our findings might provide renewed perspectives for the selection of prognostic biomarkers among HMGs in GC and may contribute to the determination of the optimal strategy for the treatment of these patients.

LINC00665: An Emerging Biomarker for Cancer Diagnostics and Therapeutics

Long intergenic noncoding RNA 00665 (LINC00665) is located on human chromosome 19q13.12. LINC00665 was upregulated in eighteen cancers and downregulated in two cancers. LINC00665 not only inhibits 25 miRNAs but also directly affects the stability of ten protein-coding genes. Notably, LINC00665 also encodes a micro-peptide CIP2A-BP that promotes triple-negative breast cancer progression. LINC00665 can participate in five signaling pathways to regulate cancer progression, including the Wnt/β-catenin signaling pathway, TGF-β signaling pathway, NF-κB signaling pathway, PI3K/AKT signaling pathway, and MAPK signaling pathway. Aberrant expression of LINC00665 in breast cancer, gastric cancer, and hepatocellular carcinoma can be used for disease diagnosis. In addition, aberrant expression of LINC00665 is closely associated with clinicopathological features and poor prognosis of various cancers. LINC00665 is closely associated with the effects of anticancer drugs, including gefitinib and cisplatin in non-small cell lung cancer, gemcitabine in cholangiocarcinoma, and cisplatin-paclitaxel in breast cancer. This work systematically summarizes the diagnostic and prognostic values of LINC00665 in various tumors, and comprehensively analyzes the molecular regulatory mechanism related to LINC00665, which is expected to provide clear guidance for future research.