Intestinal microbiota alterations by dietary exposure to chemicals from food cooking and processing. Application of data science for risk prediction

NLP for computational insights into nutritional impacts on colorectal cancer care

Colorectal cancer (CRC) is one of the most prominent cancers globally, with its incidence rising among younger adults due to improved screening practices. However, existing algorithms for CRC prediction are frequently trained on datasets that primarily reflect older persons, thus limiting their usefulness in more diverse populations. Additionally, the part of nutrition in CRC deterrence and management is gaining significant attention, although computational approaches to analyzing the impact of diet on CRC remain underdeveloped. This research introduces the Nutritional Impact on CRC Prediction Framework (NICRP-Framework), which combines Natural Language Processing (NLP) techniques with Adaptive Tunicate Swarm Optimized Large Language Models (ATSO-LLMs) to present important insights into the part of the diet in CRC care across diverse populations. The colorectal cancer dietary and lifestyle dataset, encompassing >1000 participants, is collected from multiple regions and sources. The dataset includes structured and unstructured data, including textual descriptions of food ingredients. These descriptions are processed using standardization techniques, such as stop word removal, lowercasing, and punctuation elimination. Relevant terms are then extracted and visualized in a word cloud. The dataset also contained an imbalanced binary CRC outcome, which is rebalanced utilizing the random oversampling. ATSO-LLMs are employed to analyze the processed dietary data, identifying key nutritional factors and forecasting CRC and non-CRC phenotypes based on dietary patterns. The results show that combining NLP-derived features with ATSO-LLMs significantly enhances prediction accuracy (98.4 %), sensitivity (97.6 %) specificity (96.9 %) and F1-Score (96.2 %), with minimal misclassification rates. This framework represents a transformative advancement in life science by offering a new, data-driven approach to understanding the nutritional determinants of CRC, empowering healthcare professionals to make more precise predictions and adapted dietary interventions for diverse populations.

Conjugated therapeutic proteins as a treatment for bacteria which trigger cancer development

In recent years, an increasing amount of research has focused on the intricate and complex correlation between bacterial infections and the development of cancer. Some studies even identified specific bacterial species as potential culprits in the initiation of carcinogenesis, which generated a great deal of interest in the creation of innovative therapeutic strategies aimed at addressing both the infection and the subsequent risk of cancer. Among these strategies, there has been a recent emergence of the use of conjugated therapeutic proteins, which represent a highly promising avenue in the field of cancer therapeutics. These proteins offer a dual-targeting approach that seeks to effectively combat both the bacterial infection and the resulting malignancies that may arise because of such infections. This review delves into the landscape of conjugated therapeutic proteins that have been intricately designed with the purpose of specifically targeting bacteria that have been implicated in the induction of cancer.

Microbiota and other detrimental metabolites in colorectal cancer

Increasing scientific evidence demonstrates that gut microbiota plays an essential role in the onset and development of Colorectal cancer (CRC). However, the mechanisms by which these microorganisms contribute to cancer development are complex and far from completely clarified. Specifically, the impact of gut microbiota-derived metabolites on CRC is undeniable, exerting both protective and detrimental effects. This paper examines the effects and mechanisms by which important bacterial metabolites exert detrimental effects associated with increased risk of CRC. Metabolites considered include heterocyclic amines and polycyclic aromatic hydrocarbons, heme iron, secondary bile acids, ethanol, and aromatic amines. It is necessary to delve deeper into the mechanisms of action of these metabolites in CRC and identify the microbiota members involved in their production. Furthermore, since diet is the main factor capable of modifying the intestinal microbiota, conducting studies that include detailed descriptions of dietary interventions is crucial. All this knowledge is essential for developing precision nutrition strategies to optimise a protective intestinal microbiota against CRC.

Host-microbiota interactions and oncogenesis: Crosstalk and its implications in etiology

A number of articles have discussed the potential of microbiota in oncogenesis. Several of these have evaluated the modulation of microbiota and its influence on cancer development. Even in recent past, a plethora of studies have gathered in order to understand the difference in microbiota population among different cancer and normal individuals. Although in majority of studies, microbiota mediated oncogenesis has been primarily attributed to the inflammatory mechanisms, there are several other ways through which microbiota can influence oncogenesis. These relatively less discussed aspects including the hormonal modulation through estrobolome and endobolome, production of cyclomodulins, and lateral gene transfer need more attention of scientific community. We prepared this article to discuss the role of microbiota in oncogenesis in order to provide concise information on these relatively less discussed microbiota mediated oncogenesis mechanisms.

What we know about protein gut metabolites: Implications and insights for human health and diseases

Gut microbiota is a complex ecosystem of symbiotic bacteria that contribute to human metabolism and supply intestinal metabolites, whose production is mainly influenced by the diet. Dietary patterns characterized by a high intake of protein promotes the growth of proteolytic bacteria's, which produce metabolites from undigested protein fermentation. Microbioal protein metabolites can regulate immune, metabolic and neuronal responses in different target organs. Metabolic pathways of these compounds and their mechanisms of action on different pathologies can lead to the discovery of new diagnostic techniques, drugs and the potential use as functional ingredients in food. This review discusses the potential mechanisms by which amino acid catabolism is involved in microbial protein metabolites. In addition, results from several studies on the association of products from the intestinal metabolism of indigestible proteins and the state of health or disease of the host are revised.

Elucidation of the conformational dynamics and assembly of Argonaute-RNA complexes by distinct yet coordinated actions of the supplementary microRNA

Argonaute (AGO) proteins, the core of RNA-induced silencing complex, are guided by microRNAs (miRNAs) to recognize target RNA for repression. The miRNA-target RNA recognition forms initially through pairing at the seed region while the additional supplementary pairing can enhance target recognition and compensate for seed mismatch. The extension of miRNA lengths can strengthen the target affinity when pairing both in the seed and supplementary regions. However, the mechanism underlying the effect of the supplementary pairing on the conformational dynamics and the assembly of AGO-RNA complex remains poorly understood. To address this, we performed large-scale molecular dynamics simulations of AGO-RNA complexes with different pairing patterns and miRNA lengths. The results reveal that the additional supplementary pairing can not only strengthen the interaction between miRNA and target RNA, but also induce the increased plasticity of the PAZ domain and enhance the domain connectivity among the PAZ, PIWI, N domains of the AGO protein. The strong community network between these domains tightens the mouth of the supplementary chamber of AGO protein, which prevents the escape of target RNA from the complex and shields it from solvent water attack. Importantly, the inner stronger matching pairs between the miRNA and target RNA can compensate for weaker mismatches at the edge of supplementary region. These findings provide guidance for the design of miRNA mimics and anti-miRNAs for both clinical and experimental use and open the way for further engineering of AGO proteins as a new tool in the field of gene regulation.