CAR-NK Cells for Cancer Therapy: Molecular Redesign of the Innate Antineoplastic Response

Functional identification and prediction of lncRNAs in esophageal cancer

Esophageal cancer is a highly lethal malignancy with poor prognosis, and the identification of molecular biomarkers is crucial for improving diagnosis and treatment. Long non-coding RNAs (lncRNAs) have been shown to play important roles in the development and progression of esophageal cancer. However, due to the time cost of biological experiments, only a small number of lncRNAs related to esophageal cancer have been discovered. Currently, computational methods have emerged as powerful tools for identifying and characterizing lncRNAs, as well as predicting their potential functions. Therefore, this article proposes a transformer-based method for identifying esophageal cancer-related lncRNAs. Experimental results show that the AUC and AUPR of this method are superior to other comparison methods, with an AUC of 0.87 and an AUPR of 0.83, and the identified lncRNA targets are closely associated with esophageal cancer. We focus on the role of esophageal cancer-related lncRNAs in the immune microenvironment, and fully explore the functions of the target genes regulated by lncRNAs. Enrichment analysis shows that the predicted target genes are related to multiple pathways involved in the occurrence, development, and prognosis of esophageal cancer. This not only demonstrates the effectiveness of the method but also indicates the accuracy of the prediction results.

Natural killer cells modified with a Gpc3 aptamer enhance adoptive immunotherapy for hepatocellular carcinoma

INTRODUCTION

Natural killer cells can attack cancer cells without prior sensitization, but their clinical benefit is limited owing to their poor selectivity that is caused by the lack of specific receptors to target tumor cells. In this study, we aimed to endow NK cells with the ability to specifically target glypican-3+ tumor cells without producing cell damage or genetic alterations, and further evaluated their therapeutic efficiency.

METHODS

NK cells were modified with a Gpc3 DNA aptamer on the cell surface via metabolic glycoengineering to endow NK cells with specific targeting ability. Then, the G-NK cells were evaluated for their specific targeting properties, cytotoxicity and secretion of cytokines in vitro. Finally, we investigated the therapeutic efficiency of G-NK cells against glypican-3+ tumor cells in vivo.

RESULTS

Compared with NK cells modified with a random aptamer mutation and unmodified NK cells, G-NK cells induced significant apoptosis/necrosis of GPC3+ tumor cells and secreted cytokines to preserve the intense cytotoxic activities. Moreover, G-NK cells significantly suppressed tumor growth in HepG2 tumor-bearing mice due to the enhanced enrichment of G-NK cells at the tumor site.

CONCLUSIONS

The proposed strategy endows NK cells with a tumor-specific targeting ability to enhance adoptive therapeutic efficiency in GPC3+ hepatocellular carcinoma.

Mechanism of breast cancer immune microenvironment in prognosis of heart failure

The treatment of breast cancer can potentially impose a burden on the heart, leading to an increased risk of heart failure. Studies have shown that more than half of breast cancer patients die from non-tumor-related causes, with cardiovascular disease (CVD) being the leading cause of death. However, the underlying mechanism linking breast cancer prognosis and heart failure remains unclear. To investigate this, we conducted an analysis where we compared the differentially expressed genes (DEGs) in early and advanced breast cancer with genes associated with heart failure. This analysis revealed 18 genes that overlapped between the two conditions, with 15 of them being related to immune function. This suggests that immune pathways may play a role in the prognosis of breast cancer patients with heart failure. Using gene expression data from 1260 breast cancer patients, we further examined the impact of these 15 genes on survival time. Additionally, through enrichment analysis, we explored the functions and pathways associated with these genes in relation to breast cancer and heart failure. By constructing a transformer model, we discovered that the expression patterns of these 15 genes can accurately predict the occurrence of heart failure. The model achieved an AUC of 0.86 and an AUPR of 0.91. Moreover, through analysis of single-cell sequencing data from breast cancer patients undergoing PD-1 treatment and experiencing heart failure, we identified a significant number of cell-type-specific genes that were shared between both diseases. This suggests that changes in gene expression in immune cells following breast cancer treatment may be associated with the development of heart failure.

Multi-omics immune regulatory mechanisms in lung adenocarcinoma metastasis and survival time

Lung adenocarcinoma (LUAD) is the most common type of lung cancer. Despite previous research on immune mechanisms and related molecules in LUAD, the specific regulatory mechanisms of these molecules in the immune microenvironment remain unclear. Furthermore, the impact of regulatory genes or RNA on LUAD metastasis and survival time is yet to be understood. To address these gaps, we collected a substantial amount of data, including 17,226 gene expression profiles from 1,018 samples, 370,640 methylation sites from 461 samples, and 248 miRNAs from 513 samples. Our aim was to explore the genes, miRNAs, and methylation sites associated with LUAD progression. Leveraging the regulatory functions of miRNAs and methylation sites, we identified target and regulated genes. Through the utilization of LASSO and survival analysis, we pinpointed 22 key genes that play pivotal roles in the immune regulatory mechanism of LUAD. Notably, the expression levels of these 22 genes demonstrated significant discriminatory power in predicting LUAD patient survival time. Additionally, our deep learning model accurately predicted distant metastasis in LUAD patients using the expression levels of these genes. Further pathway enrichment analysis revealed that these 22 genes are significantly enriched in pathways closely linked to LUAD progression. Through Immune Infiltration Assay, we observed that T cell CD4 memory resting, monocytes, and macrophages.M2 were the three most abundant cell types in the immune microenvironment of LUAD. These cells are known to play crucial roles in tumor growth, invasion, and metastasis. Single-cell data analysis further validated the functional significance of these genes, indicating their involvement not only in immune cells but also in epithelial cells, showcasing significant differential expression. Overall, this study sheds light on the regulatory mechanisms underlying the immune microenvironment of LUAD by identifying key genes associated with LUAD progression. The findings provide insights into potential prognostic markers and therapeutic targets.

Molecular characterization of colorectal adenoma and colorectal cancer via integrated genomic transcriptomic analysis

Introduction

Colorectal adenoma can develop into colorectal cancer. Determining the risk of tumorigenesis in colorectal adenoma would be critical for avoiding the development of colorectal cancer; however, genomic features that could help predict the risk of tumorigenesis remain uncertain.

Methods

In this work, DNA and RNA parallel capture sequencing data covering 519 genes from colorectal adenoma and colorectal cancer samples were collected. The somatic mutation profiles were obtained from DNA sequencing data, and the expression profiles were obtained from RNA sequencing data.

Results

Despite some similarities between the adenoma samples and the cancer samples, different mutation frequencies, co-occurrences, and mutually exclusive patterns were detected in the mutation profiles of patients with colorectal adenoma and colorectal cancer. Differentially expressed genes were also detected between the two patient groups using RNA sequencing. Finally, two random forest classification models were built, one based on mutation profiles and one based on expression profiles. The models distinguished adenoma and cancer samples with accuracy levels of 81.48% and 100.00%, respectively, showing the potential of the 519-gene panel for monitoring adenoma patients in clinical practice.

Conclusion

This study revealed molecular characteristics and correlations between colorectal adenoma and colorectal cancer, and it demonstrated that the 519-gene panel may be used for early monitoring of the progression of colorectal adenoma to cancer.

Emerging Targeted Therapies for HER2-Positive Breast Cancer

Breast cancer is the most common cancer in women and the leading cause of death. HER2 overexpression is found in approximately 20% of breast cancers and is associated with a poor prognosis and a shorter overall survival. Tratuzumab, a monoclonal antibody directed against the HER2 receptor, is the standard of care treatment. However, a third of the patients do not respond to therapy. Given the high rate of resistance, other HER2-targeted strategies have been developed, including monoclonal antibodies such as pertuzumab and margetuximab, trastuzumab-based antibody drug conjugates such as trastuzumab-emtansine (T-DM1) and trastuzumab-deruxtecan (T-DXd), and tyrosine kinase inhibitors like lapatinib and tucatinib, among others. Moreover, T-DXd has proven to be of use in the HER2-low subtype, which suggests that other HER2-targeted therapies could be successful in this recently defined new breast cancer subclassification. When patients progress to multiple strategies, there are several HER2-targeted therapies available; however, treatment options are limited, and the potential combination with other drugs, immune checkpoint inhibitors, CAR-T cells, CAR-NK, CAR-M, and vaccines is an interesting and appealing field that is still in development. In this review, we will discuss the highlights and pitfalls of the different HER2-targeted therapies and potential combinations to overcome metastatic disease and resistance to therapy.

The microbiome types of colorectal tissue are potentially associated with the prognosis of patients with colorectal cancer

As the second leading cause of cancer worldwide, colorectal cancer (CRC) is associated with a poor prognosis. Although recent studies have explored prognostic markers in patients with CRC, whether tissue microbes carry prognostic information remains unknown. Here, by assessing the colorectal tissue microbes of 533 CRC patients, we found that Proteobacteria (43.5%), Firmicutes (25.3%), and Actinobacteria (23.0%) dominated the colorectal tissue microbiota, which was different from the gut microbiota. Moreover, two clear clusters were obtained by clustering based on the tissue microbes across all samples. By comparison, the relative abundances of Proteobacteria and Bacteroidetes in cluster 1 were significantly higher than those in cluster 2; while compared with cluster 1, Firmicutes and Actinobacteria were more abundant in cluster 2. In addition, the Firmicutes/Bacteroidetes ratios in cluster 1 were significantly lower than those in cluster 2. Further, compared with cluster 2, patients in cluster 1 had relatively poor survival (Log-rank test, p = 0.0067). By correlating tissue microbes with patient survival, we found that the relative abundance of dominant phyla, including Proteobacteria, Firmicutes, and Bacteroidetes, was significantly associated with survival in CRC patients. Besides, the co-occurrence network of tissue microbes at the phylum level of cluster 2 was more complicated than that of cluster 1. Lastly, we detected some pathogenic bacteria enriched in cluster 1 that promote the development of CRC, thus leading to poor survival. In contrast, cluster 2 showed significant increases in the abundance of some probiotics and genera that resist cancer development. Altogether, this study provides the first evidence that the tissue microbiome of CRC patients carries prognostic information and can help design approaches for clinically evaluating the survival of CRC patients.

Discussion of tumor mutation burden as an indicator to predict efficacy of immune checkpoint inhibitors: A case report

There are many treatment options for advanced lung cancer, among which immunotherapy has developed rapidly and benefited a lot of patients. However, immunotherapy can only benefit a subgroup of patients, and how to select patients suitable for this therapy is critical. Tumor mutation burden (TMB) is one of the important reference indicators for immune checkpoint inhibitors (ICIs). However, there are many factors influencing the usage of this indicator, which will lead to considerable consequences if not treated well. In this study, we performed a case study on a male advanced lung squamous cell carcinoma patient of age 83. The patient suffered from “cough and sputum”, and did chest CT scans on 24 October 2018, which showed “a mass-like mass in the anterior segment of the right lung upper lobe, about 38mm×28mm”. He was treated with systemic chemotherapy; however, the tumor was still under progression. Although PD-L1 was not tested in gene testing, he had a TMB value of 10.26 mutations/Mb with a quantile value 88.63%. Thus, “toripalimab injection” was added as immunotherapy and the size of the lesion decreased. In summary, we adopted a clinical case as the basis to explore the value and significance of TMB in immunotherapy in this study. We hope that more predictive molecular markers will be discovered, which will bring more treatment methods for advanced lung cancer.

Alternative CAR Therapies: Recent Approaches in Engineering Chimeric Antigen Receptor Immune Cells to Combat Cancer

For nearly three decades, chimeric antigen receptors (CARs) have captivated the interest of researchers seeking to find novel immunotherapies to treat cancer. CARs were first designed to work with T cells, and the first CAR T cell therapy was approved to treat B cell lymphoma in 2017. Recent advancements in CAR technology have led to the development of modified CARs, including multi-specific CARs and logic gated CARs. Other immune cell types, including natural killer (NK) cells and macrophages, have also been engineered to express CARs to treat cancer. Additionally, CAR technology has been adapted in novel approaches to treating autoimmune disease and other conditions and diseases. In this article, we review these recent advancements in alternative CAR therapies and design, as well as their mechanisms of action, challenges in application, and potential future directions.

A Systematic Framework for Identifying Prognostic Genes in the Tumor Microenvironment of Colon Cancer

As one of the most common cancers of the digestive system, colon cancer is a predominant cause of cancer-related deaths worldwide. To investigate prognostic genes in the tumor microenvironment of colon cancer, we collected 461 colon adenocarcinoma (COAD) and 172 rectal adenocarcinoma (READ) samples from The Cancer Genome Atlas (TCGA) database, and calculated the stromal and immune scores of each sample. We demonstrated that stromal and immune scores were significantly associated with colon cancer stages. By analyzing differentially expressed genes (DEGs) between two stromal and immune score groups, we identified 952 common DEGs. The significantly enriched Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) terms for these DEGs were associated with T-cell activation, immune receptor activity, and cytokine–cytokine receptor interaction. Through univariate Cox regression analysis, we identified 22 prognostic genes. Furthermore, nine key prognostic genes, namely, HOXC8, SRPX, CCL22, CD72, IGLON5, SERPING1, PCOLCE2, FABP4, and ARL4C, were identified using the LASSO Cox regression analysis. The risk score of each sample was calculated using the gene expression of the nine genes. Patients with high-risk scores had a poorer prognosis than those with low-risk scores. The prognostic model established with the nine-gene signature was able to effectively predict the outcome of colon cancer patients. Our findings may help in the clinical decisions and improve the prognosis for colon cancer.