The thymus, a central lymphoid organ in animals, serves as the site for T cell development, differentiation and maturation, vital to adaptive immunity. The thymus is critical for maintaining tissue homeostasis to protect against tumors and tissue damage. An overactive or prolonged immune response can lead to oxidative stress from increased production of reactive oxygen species. Heat stress induces oxidative stress and overwhelms the natural antioxidant defense mechanisms. This study’s objectives were to investigate the protective properties of astaxanthin against heat-induced oxidative stress and apoptosis in the chicken thymus, by comparing the growth performance and gene signaling pathways among three groups: thermal neutral, heat stress, and heat stress with astaxanthin. The thermal neutral temperature was 21–22 °C, and the heat stress temperature was 32–35 °C. Both heat stress groups experienced reduced growth performance, while the astaxanthin-treated group showed a slightly lesser decline. The inflammatory response and antioxidant defense system were activated by the upregulation of the NF-kB, NFE2L2, PPARα, cytoprotective capacity, and apoptotic gene pathways during heat stress compared to the thermal neutral group. However, expression levels showed no significant differences between the thermal neutral and heat stress with antioxidant groups, suggesting that astaxanthin may mitigate inflammation and oxidative stress damage.

The gastrointestinal tract has a pivotal role in nutrient absorption, immune function, and overall homeostasis. The ileum segment of the small intestine plays respective roles in nutrient breakdown and absorption. The purpose of this study was to investigate the impact of heat-induced oxidative stress and the potential mitigating effects of an astaxanthin antioxidant treatment on the ileum of broilers. By comparing the growth performance and gene expression profiles among three groups—thermal neutral, heat stress, and heat stress with astaxanthin—thermal neutral temperature conditions of 21–22 °C and heat stress temperature of 32–35 °C, this research aims to elucidate the role of astaxanthin in supporting homeostasis and cellular protection in the ileum. Results showed both treatments under heat stress experienced reduced growth performance, while the group treated with astaxanthin showed a slightly lesser decline. Results further showed the astaxanthin treatment group significantly upregulated in the cytoprotective gene expression for HSF2, SOD2, GPX3, and TXN, as well as the upregulation of epithelial integrity genes LOX, CLDN1, and MUC2. In conclusion, our experimental findings demonstrate upregulation of cytoprotective and epithelial integrity genes, suggesting astaxanthin may effectively enhance the cellular response to heat stress to mitigate oxidative damage and contribute to cytoprotective capacity.

Background: Lung cancer, particularly non-small cell lung cancer (NSCLC), accounts for about 85% of all lung cancer cases and remains a major global health challenge. Traditional diagnostic methods, such as chest X-rays and low-dose CT scans, have limitations, including high false-positive rates, radiation risks, and the invasiveness of tissue biopsies. This study aims to develop a non-invasive liquid biopsy approach for early NSCLC diagnosis. Methods: We developed a machine-learning model to analyze small RNA sequencing data from 1446 tissue samples to identify a diagnostic tRNA signature. This signature was independently validated using the in-house data of 233 plasma exosome samples. Diagnostic performance was assessed using Area Under the Curve (AUC) metrics. Signature tRNAs were then evaluated across various clinical and demographic variables, with further survival analysis and functional studies to explore the molecular role of the signature tRNAs. Results: We identify a robust six-tRNA signature with strong diagnostic performance, achieving AUC values of 0.97 in discovery, 0.96 in hold-out validation, and 0.84 in independent validation. The signature effectively distinguishes cancerous from benign samples (AUC = 0.85) and consistently performs across clinical and demographic variables, with AUC values exceeding 0.80, particularly for early-stage lung cancer diagnosis. Additionally, three signature tRNAs demonstrate prognostic value for independent survival prediction. Functional studies suggest potential regulatory roles of specific tRNAs and their associated fragments in tumor metabolism pathways. Conclusions: This research underscores the diagnostic power of tRNA signature for NSCLC liquid biopsy and provides epigenetic insights that enhance our understanding of oncogenic molecular pathophysiology.

Despite significant progress in understanding the molecular basis of colorectal cancer (CRC), the precise mechanisms driving its development and progression remain poorly defined. This gap limits the identification of novel therapeutic targets and the development of effective early detection methods. N6-methyladenosine (m6A) has merged as a key role in CRC pathogenesis. But research on mRNA methylation in CRC remains sparse. We aimed to address the roles of m6A modifications in CRC and to understand how mRNA methylation contributes to CRC development and progression. We obtained a comprehensive mapping of altered m6 peaks within mRNAs using Methylated RNA Immunoprecipitation Sequencing (MeRIP-seq) from 34 CRC samples and 34 adjacent normal tissue samples and dissect molecular mechanisms of identified key CRC gene(s). By integrating these data, we identified differentially expressed mRNAs with altered m6A levels. Further analysis identified 119 overlapping peaks with both significantly altered RNA methylation and expression levels. Finally, we analyzed the relationship between m6A-regulated gene expression and Immune infiltrates using CRC patient-derived PBMC samples. Additionally, we established a subcutaneous xenograft tumor model to explore the role of SIM2 in CRC progression. Our comprehensive analysis of 68 fresh-frozen CRC samples identified 119 overlapping m6A peaks across 77 genes, classified based on m6A and mRNA expression changes. Survival analyses revealed a signature of m6A-modified genes with prognostic potential. These methylated genes were significant associated with immune cell profiles in the tumor microenvironment and immune checkpoints regulation, highlighting m6A as a promising immunotherapeutic target for CRC. SIM2 emerged as a key candidate, exhibiting elevated m6A and RNA expression levels in tumors and Macrophage M2 cells. NTMT1 (a writer) and YTHDF1 (a reader) were identified as pivotal regulators of m6A modifications in the 5'-UTR of SIM2 mRNA, emphasizing their role in CRC progression. Silencing methylated SIM2 significantly suppressed tumor growth, suggesting its potential as a therapeutic target. Our integrative analyses provide a valuable resource for unraveling the molecular landscape of CRC. These finding offer new insight for advancing diagnostic precision and refining prognostic and therapeutic strategies for CRC.

This study describes the development of a resource module that is part of a learning platform named ‘NIGMS Sandbox for Cloud-based Learning’ https://github.com/NIGMS/NIGMS-Sandbox. The overall genesis of the Sandbox is described in the editorial NIGMS Sandbox at the beginning of this Supplement. This module is designed to facilitate interactive learning of whole-genome bisulfite sequencing (WGBS) data analysis utilizing cloud-based tools in Google Cloud Platform, such as Cloud Storage, Vertex AI notebooks and Google Batch. WGBS is a powerful technique that can provide comprehensive insights into DNA methylation patterns at single cytosine resolution, essential for understanding epigenetic regulation across the genome. The designed learning module first provides step-by-step tutorials that guide learners through two main stages of WGBS data analysis, preprocessing and the identification of differentially methylated regions. And then, it provides a streamlined workflow and demonstrates how to effectively use it for large datasets given the power of cloud infrastructure. The integration of these interconnected submodules progressively deepens the user’s understanding of the WGBS analysis process along with the use of cloud resources. Through this module, we can enhance the accessibility and adoption of cloud computing in epigenomic research, speeding up the advancements in the related field and beyond. This manuscript describes the development of a resource module that is part of a learning platform named ``NIGMS Sandbox for Cloud-based Learning'' https://github.com/NIGMS/NIGMS-Sandbox. The overall genesis of the Sandbox is described in the editorial NIGMS Sandbox [1] at the beginning of this Supplement. This module delivers learning materials on the analysis of bulk and single-cell ATAC-seq data in an interactive format that uses appropriate cloud resources for data access and analyses.