Title: Involvement of unsaturated fatty acid biosynthesis in CRC progression based on in vitro and in silico studies

A new modality for cholesterol impact tracking in colon cancer development - Raman imaging, fluorescence and AFM studies combined with chemometric analysis

Colorectal cancer (CRC) is the third most common cancer worldwide. Obesity, alcohol consumption, smoking, high consumption of red or processed meat and a diet with low fibre, fruit, and vegetable intake increase CRC risk. Despite advances in surgery (the basic treatment for recovery), chemotherapy, and radiotherapy, CRC remains the second leading cause of cancer-related deaths in the world. Therefore the social importance of this problem stimulates research aimed at developing new tools for rapid CRC diagnosis and analysis of CRC risk factors. Considering the association between the cholesterol level and CRC, we hypothesize that cholesterol spectroscopic and AFM (atomic force microscopy) studies combined with chemometric analysis can be new, powerful tools used to visualize the cholesterol distribution, estimate cholesterol content and determine its influence on the biochemical and nanomechanical properties of colon cells. Our paper presents the analysis of human colon tissues: normal and cancer and human colon single cells normal CCD18-Co and cancer CaCo-2 in the physiological state and CaCo-2 upon mevastatin supplementation. Based on vibrational features we have shown that Raman spectroscopy and imaging allow cholesterol content in human colon tissues and human colon single cells of both types to be tracked and allow the effectiveness of mevastatin in the mevalonate pathway modulation and disruption of the cholesterol level to be proven. All observations have been confirmed by chemometric analysis including principal component analysis (PCA) and partial least squares discriminant analysis (PLSDA). The positive impact of statins on cholesterol content has also been studied by using fluorescence microscopy and atomic force microscopy (AFM). A significant increase in Young modulus as a mechanomarker for CaCo-2 human cancer colon cells upon mevastatin supplementation compared to CCD18-Co human normal colon cells was observed. This paper is one of the first reports about the use of Raman spectroscopic techniques in cholesterol investigations and the first one about cholesterol investigation using Raman spectroscopy (RS) on human cells ex vivo in the context of colon cancer development.

Discovery of new strains for furfural degradation using adaptive laboratory evolution in Saccharomyces cerevisiae

In industrial production, the excessive discharge of furfural can pose harm to soil microorganisms, aquatic animals and plants, as well as humans. Therefore, it is crucial to develop efficient and cost-effective methods for degrading furfural in the environment. Currently, the use of Saccharomyces cerevisiae for furfural degradation in water has shown effectiveness, but there is a need to explore improved efficiency and tolerance in S. cerevisiae for this purpose. In this study, we isolated and evolved highly efficient furfural degradation strains, namely YBA_08 and F60C. These strains exhibited remarkable capabilities, degrading 59% and 99% furfural in the YPD medium after 72 h of incubation, significantly higher than the 31% achieved by the model strain S288C. Through analysis of the efficient degradation mechanism in the evolutionary strain F60C, we discovered a 326% increase in the total amount of NADH and NADPH. This increase likely promotes faster furfural degradation through intracellular aldehyde reductases. Moreover, the decrease in NADPH content led to a 406% increase in glutathione content at the background level, which protects cells from damage caused by reactive oxygen species. Mutations and differential expression related to cell cycle and cell wall synthesis were observed, enabling cell survival in the presence of furfural and facilitating rapid furfural degradation and growth recovery. Based on these findings, it is speculated that strains YBA_08 and F60C have the potential to contribute to furfural degradation in water and the production of furfuryl alcohol, ethanol, and FDCA in biorefinery processes.

Integrative bioinformatics analysis of ACS enzymes as candidate prognostic and diagnostic biomarkers in colon adenocarcinoma

Background and purpose

Acyl-CoA synthetase (ACS) enzymes play an important role in the activation of fatty acids. While many studies have found correlations between the expression levels of ACS enzymes with the progression, growth, and survival of cancer cells, their role and expression patterns in colon adenocarcinoma are still greatly unknown and demand further investigation.

Experimental approach

The expression data of colon adenocarcinoma samples were downloaded from the Cancer Genome Atlas (TCGA) database. Normalization and differential expression analysis were performed to identify differentially expressed genes (DEGs). Gene set enrichment analysis was applied to identify top enriched genes from ACS enzymes in cancer samples. Gene ontology and protein-protein interaction analyses were performed for the prediction of molecular functions and interactions. Survival analysis and receiver operating characteristic test (ROC) were performed to find potential prognostic and diagnostic biomarkers.

Findings/Results

ACSL6 and ACSM5 genes demonstrated more significant differential expression and LogFC value compared to other ACS enzymes and also achieved the highest enrichment scores. Gene ontology analysis predicted the involvement of top DEGs in fatty acids metabolism, while protein-protein interaction network analysis presented strong interactions between ACSLs, ACSSs, ACSMs, and ACSBG enzymes with each other. Survival analysis suggested ACSM3 and ACSM5 as potential prognostic biomarkers, while the ROC test predicted stronger diagnostic potential for ACSM5, ACSS2, and ACSF2 genes.

Conclusion and implications

Our findings revealed the expression patterns, prognostic, and diagnostic biomarker potential of ACS enzymes in colon adenocarcinoma. ACSM3, ACSM5, ACSS2, and ACSF2 genes are suggested as possible prognostic and diagnostic biomarkers.

Colon cancer transcriptome

Over the last four decades, methodological innovations have continuously changed transcriptome profiling. It is now feasible to sequence and quantify the transcriptional outputs of individual cells or thousands of samples using RNA sequencing (RNA-seq). These transcriptomes serve as a connection between cellular behaviors and their underlying molecular mechanisms, such as mutations. This relationship, in the context of cancer, provides a chance to unravel tumor complexity and heterogeneity and uncover novel biomarkers or treatment options. Since colon cancer is one of the most frequent malignancies, its prognosis and diagnosis seem to be critical. The transcriptome technology is developing for an earlier and more accurate diagnosis of cancer which can provide better protectivity and prognostic utility to medical teams and patients. A transcriptome is a whole set of expressed coding and non-coding RNAs in an individual or cell population. The cancer transcriptome includes RNA-based changes. The combined genome and transcriptome of a patient may provide a comprehensive picture of their cancer, and this information is beginning to affect treatment decision-making in real-time. A full assessment of the transcriptome of colon (colorectal) cancer has been assessed in this review paper based on risk factors such as age, obesity, gender, alcohol use, race, and also different stages of cancer, as well as non-coding RNAs like circRNAs, miRNAs, lncRNAs, and siRNAs. Similarly, they have been examined independently in the transcriptome study of colon cancer.

The role of fatty acid desaturase 2 in multiple tumor types revealed by bulk and single-cell transcriptomes

BACKGROUND

Previous studies have demonstrated the important role of fatty acid desaturase 2 (FADS2) in governing tumorigenesis and tumor metastasis. Although FADS2 is an essential regulator of fatty acid metabolism, its prognostic and immunotherapeutic value remains uncertain.

METHODS

The role of FADS2 was investigated across different types of tumors. Besides, the relationship between FADS2 and survival prognosis, clinicopathologic features, tumor-infiltrating immune cells, immunoregulatory genes, chemokines, chemokines receptor, tumor mutational burden (TMB), and microsatellite instability (MSI) was also explored. FADS2-related genes enrichment analysis was performed to further explore the molecular function of FADS2. Finally, the relationship between FADS2 expression and altered functional states in single-cell levels across different tumor cells was explored.

RESULTS

FADS2 was increased in most tumor tissues. Elevated FADS2 expression was associated with a poor overall survival (OS) and disease-free survival (DFS). FADS2 amplification was germane to worse progress-free survival (PFS). In addition, FADS2 correlated with the majority of tumor-infiltrating immune cells, immunoregulatory genes, and chemokines. Especially, FADS2 expression positively correlated with cancer-associated fibroblast (CAFs) infiltration. Gene Ontology and KEGG analysis demonstrated that FADS2 was involved in the fatty acid metabolic process, arachidonic acid metabolism, RAS, PPAR, and VEGF pathway. FADS2 had a positive relationship with tumor biological behaviors such as inflammation, cell cycle, proliferation, DNA damage, and DNA repair response in single-cell levels.

CONCLUSIONS

FADS2 can serve as a potential prognostic and immunotherapeutic biomarker for multiple tumors, revealing new insights and evidence for cancer treatment.

Emerging roles of polyunsaturated fatty acid synthesis pathway in colorectal cancer

The development of colorectal cancer typically involves the accumulated influences of genetic alterations, medical issues, lifestyle, and diet. Dietary fatty acids appear to affect the tumorigenesis and progression of colorectal cancer. Despite conflicting results, the current consensus on the effects of very long-chain polyunsaturated fatty acids on colorectal cancer is that low levels of eicosapentaenoic acid and docosahexaenoic acid, and high levels of arachidonic acid are associated with an increased risk of colorectal cancer. Altered levels of arachidonic acid in membrane phospholipids can change the levels of prostaglandin E₂, which affect the biological activities of cancer cells in multiple stages. Arachidonic acid and other very long-chain polyunsaturated fatty acids can affect tumorigenesis in prostaglandin E₂-independent manners as well, including stabilization of β-catenine, ferroptosis, ROS generation, regulation of transcription factors, and de novo lipogenesis. Recent studies have revealed an association between the activities of enzymes synthesizing very long-chain polyunsaturated fatty acids and tumorigenesis and cancer progression, although the mechanisms are still unknown. In this study, PUFA effects on tumorigenesis, the endogenous very long-chain polyunsaturated fatty acid synthesis pathway, metabolites of arachidonic acid and their effects on tumorigenesis and progression of CRC, and current knowledge that supports the association of the enzymes involved in the polyunsaturated fatty acid synthesis pathway with colorectal cancer tumorigenesis and progression are reviewed.

Prognostic significance and immune landscape of a fatty acid metabolism-related gene signature in colon adenocarcinoma

Background: Fatty acid metabolism (FAM), as a hallmark of caner, plays important roles in tumor initiation and carcinogenesis. However, the significance of fatty acid metabolism-related genes in colon adenocarcinoma (COAD) are largely unknown. Methods: RNA sequencing data and clinical information were downloaded from the Cancer Genome Atlas (TCGA) cohort. Univariate and multivariate Cox regression analyses were utilized to construct a fatty acid metabolism-related gene signature. Kaplan-Meier survival and receiver operating characteristic (ROC) analyses were used to verify the performance of this signature. GEO datasets were applied to validate the signature. Maftools package was utilized to analyze the mutation profiles of this signature. Correlation between the risk signature and stemness scores was compared by RNA stemness score (RNAss). Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) and gene set variation analysis (GSVA) were performed to explore the potential functions and signaling pathways. Immune landscape of the signature was explored by analyzing different immune cells infiltration, immune functions and microsatellite instability. A nomogram was constructed by combining the risk signature and multiple clinical factors. Expression levels and prognostic values of the risk genes were revealed in the cancer genome atlas and GEO databases. Moreover, the expression the risk genes were measured in cell lines using real time quantitative PCR (qRT-PCR). Results: Eight fatty acid metabolism-related genes (CD36, ENO3, MORC2, PTGR1, SUCLG2, ELOVL3, ELOVL6 and CPT2) were used to construct a risk signature. This signature demonstrated better prognostic value than other clinicopathological parameters, with AUC value was 0.734 according to the cancer genome atlas database. There was negative correlation between the riskscore and RNA stemness score. The patients in the high-risk group demonstrated higher infiltration of M0 macrophages, and less infiltration of activated CD4 memory T cells and Eosinophils. There were more MSI patients in the high-risk group than those in the low-risk group (38% vs. 30%). The risk scores of patients in the MSI group were slightly higher than those in the microsatellite stability group. Gene ontology, kyoto encyclopedia of genes and genomes and gene set variation analysis enrichment analyses showed that several metabolism-related functions and signaling pathways were enriched. A nomogram showed good predictive capability of the signature. Moreover, qRT-PCR revealed upregulated expression of ENO3, MORC2, SUCLG2 and ELOVL6, and downregulated expression of CPT2 in all examined colon adenocarcinoma cell lines. Conclusion: This study provided novel insights into a fatty acid metabolism-related signature in the prognosis an immune landscape of colon adenocarcinoma patients.

Identification of a novel interplaying loop of PPARγ and respective lncRNAs are involved in colorectal cancer progress

Long noncoding RNAs (lncRNAs) as regulatory molecules play important roles in early treatment and diagnosis of cancers. Considering the role of PPARγ in colorectal cancer (CRC) as a tumor suppressor, the GEO database was used to identify candidate genes that affect the activation of PPARγ protein in CRC cell lines. Then were selected 5 genes containing PPARγ response element (PPRE) in up to 4000 bp upstream and were affected by PPARγ protein activation in HT-29 colon cancer cell line using UCSC database. Expression meta-analysis was applied to map the expression network between candidate genes and all known lncRNAs through expression correlation and lncRNAs that correlated with a greater number of candidate genes (R > 0.5, P.value < 0.001). Moreover, were selected 3 lncRNAs as lncRNAs affected by PPARγ protein activation. Next, the expression levels of candidate genes and lncRNAs were evaluated using RT-qPCR in HT-29 cell line. Results showed a significant increase (FDR <0.05) in the expression level of 5 candidate genes and lncRNAs LINC01133, MBNL1-AS, LOC100288911 after treatment with pioglitazone as PPARγ ligand compared to the untreated group in HT-29 cells. Although additional tests are needed to confirm bioinformatics predictions, it can be concluded that increased expression of PPARγ may increase genes and lncRNAs expression. In summary, this study could be suggested identifying lncRNAs affected by PPARγ activation could be a new strategy in understanding the function and activity of PPARγ in colon cancer.

Direct Support Professionals’ Perspectives on using Technology to help support Adults with Autism Spectrum Disorder: A Mixed-Methods Study (Preprint)

BACKGROUND

Documentation is a critical responsibility for direct support professionals (DSPs) who work with adults with autism spectrum disorder (ASD); however, it contributes significantly to their workload. Targeted efforts must be made to mitigate the burden of necessary data collection and documentation, which contributes to high DSP turnover rates and poor job satisfaction.

OBJECTIVE

This mixed methods study aimed to explore how technology could assist DSPs who work with adults with ASD and prioritize aspects of technology that would be most useful for future development efforts.

METHODS

In the first study, 15 DSPs who worked with adults with ASD participated in 1 of the 3 online focus groups. The topics included daily tasks, factors that would influence the adoption of technology, and how DSPs would like to interact with technologies to provide information about their clients. Responses were thematically analyzed across focus groups and ranked by salience. In the second study, 153 DSPs across the United States rated the usefulness of technology features and data entry methods and provided qualitative responses on their concerns regarding the use of technology for data collection and documentation. Quantitative responses were ranked based on their usefulness across participants, and rank-order correlations were calculated between different work settings and age groups. The qualitative responses were thematically analyzed.

RESULTS

In study 1, participants described difficulties with paper-and-pencil data collection, noted benefits and concerns about using technology instead, identified benefits and concerns about particular technology features, and specified work-environment factors that impact data collection. In study 2, participants rated multiple features of technology as useful, with the highest usefulness percentages endorsed for task views (ie, by shift, client, and DSP), logging completed tasks, and setting reminders for specific tasks. Participants also rated most data entry methods (eg, typing on a phone or tablet, typing on a keyboard, and choosing from options on a touch screen) as useful. Rank-order correlations indicated that the usefulness of technology features and data entry methods differed across work settings and age groups. Across both studies, DSPs cited some concerns with technology, such as confidentiality, reliability and accuracy, complexity and efficiency, and data loss from technology failure.

CONCLUSIONS

Understanding the challenges faced by DSPs who work with adults with ASD, and their thoughts about using technology to meet those challenges, represents an essential first step toward developing technology solutions that can increase DSPs' effectiveness and job satisfaction. The survey results indicate that technology innovations should incorporate multiple features to account for different needs across DSPs, settings, and age groups. Future research should explore barriers to adopting data collection and documentation tools and elicit input from agency directors, families, and others interested in reviewing data about adults with ASD.