Personalized targeted therapy prescription in colorectal cancer using algorithmic analysis of RNA sequencing data

Bioinformatic and clinical experimental assay uncovers resistance and susceptibility mechanisms of human glioblastomas to temozolomide and identifies new combined and individual survival biomarkers outperforming MGMT promoter methylation

Background

Glioblastoma (GBM) is the most aggressive and lethal central nervous system (CNS) tumor. The treatment strategy is mainly surgery and/or radiation therapy, both combined with adjuvant temozolomide (TMZ) chemotherapy. Historically, methylation of MGMT gene promoter is used as the major biomarker predicting individual tumor response to TMZ.

Objectives

This research aimed to analyze genes and molecular pathways of DNA repair as biomarkers for sensitivity to TMZ treatment in GBM using updated The Cancer Genome Atlas (TCGA) data and validate the results on experimental datasets.

Methods

Survival analysis of GBM patients under TMZ therapy and hazard ratio (HR) calculation were used to assess all putative biomarkers on World Health Organization CNS5 reclassified TCGA project collection of molecular profiles and experimental multicenter GBM patient cohort. Pathway activation levels were calculated for 38 DNA repair pathways. TMZ sensitivity pathway was reconstructed using a human interactome model built using pairwise interactions extracted from 51,672 human molecular pathways.

Results

We found that expression/activation levels of seven and six emerging gene/pathway biomarkers served as high-quality positive (HR < 0.61) and negative (HR > 1.63), respectively, patient survival biomarkers performing better than MGMT methylation. Positive survival biomarkers were enriched in the processes of ATM-dependent checkpoint activation and cell cycle arrest whereas negative-in excision DNA repair. We also built and characterized gene pathways which were informative for GBM patient survival following TMZ administration (HR 0.18-0.44, p < 0.0009; area under the curve 0.68-0.9).

Conclusion

In this study, a comprehensive analysis of the expression of 361 DNA repair genes and activation levels of 38 DNA repair pathways revealed 13 potential survival biomarkers with increased prognostic potential compared to MGMT methylation. We algorithmically reconstructed the TMZ sensitivity pathway with strong predictive capacity in GBM.

Novel regimens and treatment strategies in neoadjuvant therapy for colorectal cancer: A systematic review

Objective

The objective of this systematic review was to describe novel regimens and treatment strategies in neoadjuvant therapy for colorectal cancer (CRC). The aim was to summarize the current advancements in neoadjuvant chemotherapy (NACT) for CRC, including the use of cytotoxic drugs, targeted treatments, and immunotherapy. The analysis aimed to provide insights into the potential benefits and drawbacks of these novel approaches and highlight the need for further research to optimize NACT use in CRC and improve patient outcomes.

Methods

From October 20, 2023, to December 10, 2023, a comprehensive literature search was conducted across multiple databases, including PubMed, Ovid, Web of Science, the Cochrane Library, Cumulative Index to Nursing and Allied Health Literature, Embase, and Scopus. Studies addressing the use of and treatment strategies for CRC and neoadjuvant therapies were included. Screening was conducted in two steps, initially by title and abstract and then by full-text articles. English-language articles were considered, while preprints, non-English publications, and articles published as grey literature were excluded from the study. A total of 85 studies were selected for further analysis after screening and filtering.

Results

After filtering out duplicates and items that were irrelevant to our research query from the initial database search's 510 results, 397 unique articles were found. Eighty-five studies were chosen for additional analysis after the articles underwent two rounds of screening.

Conclusion

The review concluded that neoadjuvant therapy for CRC has evolved beyond conventional approaches and holds promise for improving patient outcomes. Future prospects for advancing neoadjuvant approaches are promising, with ongoing clinical trials investigating the refinement of strategies, identification of predictive biomarkers, and optimization of patient selection. The adoption of novel regimens, precision medicine, and immunotherapy offers opportunities to redefine treatment paradigms and enhance patient care in CRC.

Targeted Inhibitors of EGFR: Structure, Biology, Biomarkers, and Clinical Applications

Members of the EGFR family of tyrosine kinase receptors are major regulators of cellular proliferation, differentiation, and survival. In humans, abnormal activation of EGFR is associated with the development and progression of many cancer types, which makes it an attractive target for molecular-guided therapy. Two classes of EGFR-targeted cancer therapeutics include monoclonal antibodies (mAbs), which bind to the extracellular domain of EGFR, and tyrosine kinase inhibitors (TKIs), which mostly target the intracellular part of EGFR and inhibit its activity in molecular signaling. While EGFR-specific mAbs and three generations of TKIs have demonstrated clinical efficacy in various settings, molecular evolution of tumors leads to apparent and sometimes inevitable resistance to current therapeutics, which highlights the need for deeper research in this field. Here, we tried to provide a comprehensive and systematic overview of the rationale, molecular mechanisms, and clinical significance of the current EGFR-targeting drugs, highlighting potential candidate molecules in development. We summarized the underlying mechanisms of resistance and available personalized predictive approaches that may lead to improved efficacy of EGFR-targeted therapies. We also discuss recent developments and the use of specific therapeutic strategies, such as multi-targeting agents and combination therapies, for overcoming cancer resistance to EGFR-specific drugs.

Application of artificial intelligence in colorectal cancer screening by colonoscopy: Future prospects (Review)

Colorectal cancer (CRC) has become a severe global health concern, with the third‑high incidence and second‑high mortality rate of all cancers. The burden of CRC is expected to surge to 60% by 2030. Fortunately, effective early evidence‑based screening could significantly reduce the incidence and mortality of CRC. Colonoscopy is the core screening method for CRC with high popularity and accuracy. Yet, the accuracy of colonoscopy in CRC screening is related to the experience and state of operating physicians. It is challenging to maintain the high CRC diagnostic rate of colonoscopy. Artificial intelligence (AI)‑assisted colonoscopy will compensate for the above shortcomings and improve the accuracy, efficiency, and quality of colonoscopy screening. The unique advantages of AI, such as the continuous advancement of high‑performance computing capabilities and innovative deep‑learning architectures, which hugely impact the control of colorectal cancer morbidity and mortality expectancy, highlight its role in colonoscopy screening.

Algorithmically Reconstructed Molecular Pathways as the New Generation of Prognostic Molecular Biomarkers in Human Solid Cancers

Individual gene expression and molecular pathway activation profiles were shown to be effective biomarkers in many cancers. Here, we used the human interactome model to algorithmically build 7470 molecular pathways centered around individual gene products. We assessed their associations with tumor type and survival in comparison with the previous generation of molecular pathway biomarkers (3022 "classical" pathways) and with the RNA transcripts or proteomic profiles of individual genes, for 8141 and 1117 samples, respectively. For all analytes in RNA and proteomic data, respectively, we found a total of 7441 and 7343 potential biomarker associations for gene-centric pathways, 3020 and 2950 for classical pathways, and 24,349 and 6742 for individual genes. Overall, the percentage of RNA biomarkers was statistically significantly higher for both types of pathways than for individual genes (p < 0.05). In turn, both types of pathways showed comparable performance. The percentage of cancer-type-specific biomarkers was comparable between proteomic and transcriptomic levels, but the proportion of survival biomarkers was dramatically lower for proteomic data. Thus, we conclude that pathway activation level is the advanced type of biomarker for RNA and proteomic data, and momentary algorithmic computer building of pathways is a new credible alternative to time-consuming hypothesis-driven manual pathway curation and reconstruction.