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Bsacground: Lynch Syndrome (LS) is an inherited cancer syndrome associated with an increased lifetime risk of colorectal cancer (CRC) and characterised by germline mutations in DNA mismatch repair (MMR) genes. Abnormalities in the function of MMR genes lead to errors during DNA replication, including microsatellite instability. Despite regular colonoscopies, up to 15% of LS patients still develop CRC. Gut microbiome, bowel inflammation, the environment and host genetic and epigenetic factors are involved in CRC development. In this sense, the concomitant analysis of stool host microRNA (miRNA) profiles and gut microbiome composition may arise to the identification of specific fecal markers in LS explaining the molecular basis for the development of cancer in these patients. PURPOSE: In the present study, the fecal miRNome and microbiome were characterized in a time progression in an in vivo model using a mismatch repair deficient mice model that recapitulates human LS. The main aim was to evaluate the changes and crosstalk of miRNAs released in the stool by the host and the microbial population residing in the gut during the carcinogenesis process induced in animals. Findings in mice were compared and correlated to data obtained from a cohort of human subjects affected by LS. Methods: We used an in vivo model for LS based on a conditional knockout mouse with the tissue-specific inactivation of Msh2 (Msh2LoxP) in the intestinal mucosa, combining Msh2LoxP allele with the Villin-Cre transgene (VCMsh2LoxP). Stool from mice were collected at different time points (6, 9 and 12 months of age). Small RNA-sequencing (sRNA-seq) and shotgun metagenomics analyses were performed in stool from all samples. In concomitance, we collected 78 stool samples of clinically diagnosed LS subjects, at different follow up time. At the sampling, 36 resulted negative for colorectal adenomas/lesions, 12 were negative but with a previous history of lesions, 23 presented a neoplasia and 6 developed a lesion in the follow-up. Twenty-two stool samples from healthy subjects were used as controls. Results: In mice, preliminary results from sRNA-seq and metagenomics analyses showed several dysregulated miRNAs and differential microbial relative abundances, either between VCMsh2loxP and controls or at different time points. In humans, we identified 41 and 17 miRNAs respectively up- and downregulated in LS subjects who presented a lesion compared to those not having any lesion at follow-up. In the same comparison the metagenomic data showed significantly different microbial abundances, including those of Eubacterium ramulus. Conclusions: This is the first study characterizing the concomitant alterations in microbial composition and host miRNome overtime in relation to the onset of cancerous/precancerous lesions due to LS. Citation Format: Giulia Francescato, Giulio Ferrero, Marc Beltrà, Sonia Tarallo, Giulia Piaggeschi, Carla Di Battista, Antonio Francavilla, Carlijn Bruggeling, Fabio Penna, Barbara Pardini, Paola Costelli, Annemarie Boleij, Alessio Naccarati. Fecal miRNA profiles and gut metagenome composition in Lynch syndrome: results from a mouse model study and human subjects. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3797.

The 8q24 locus is enriched in cancer-associated polymorphisms and, despite containing relatively few protein-coding genes, it hosts the MYC oncogene and other genetic elements connected to tumorigenesis, including microRNAs (miRNAs). Research on miRNAs may provide insights into the transcriptomic regulation of this multiple cancer-associated region.We profiled all miRNAs located in the 8q24 region in 120 colorectal cancer (CRC) patients and 80 controls. miRNA profiling was performed on cancer/non-malignant adjacent mucosa, stool, and plasma extracellular vesicles (EVs), and the results validated with The Cancer Genome Atlas (TCGA) data. To verify if the 8q24-annotated miRNAs altered in CRC were dysregulated in other cancers and biofluids, we evaluated their levels in bladder cancer (BC) cases from the TCGA dataset and in urine and plasma EVs from a set of BC cases and healthy controls.Among the detected mature miRNAs in the region, 12 were altered between CRC and adjacent mucosa (adj. p 0.05). Five and four miRNAs were confirmed as dysregulated in the CRC and BC TCGA dataset, respectively. A co-expression analysis of tumor/adjacent tissue data from the CRC group revealed a correlation between the dysregulated miRNAs and CRC-related genes (PVT1 and MYC) annotated in 8q24 region. miR-30d-5p and miR-151a-3p, altered in CRC tissue, were also dysregulated in stool of CRC patients and urine of BC cases, respectively. Functional enrichment of dysregulated miRNA target genes highlighted terms related to TP53-mediated cell cycle control.Altered expression of 8q24-annotated miRNAs may be relevant for the initiation and/or progression of cancer.

DNA methylation is a DNA modification playing an important role in several diseases, including cancer. The gold-standard technique for measuring DNA methylation is Bisulfite Sequencing (BS). The treatment with bisulfite alters the sequence of DNA making the analysis of BS data computationally difficult. There are many tools for analysing BS data but the choice of which to use is difficult due to the extensive biological and technical variability of the data. Synthetic and real datasets can be exploited to evaluate the tool performance and to obtain an accurate data analysis. Today, Sherman is the only available tool to generate BS synthetic datasets. However, this tool does not report any information about the methylated cytosines. For this purpose, in this paper we present MethyIFASTQ, an easy-to-use bioinformatics tool that generates synthetic bisulfite datasets in FASTQ format. MethylFASTQ works in parallel manner using producer-consumer approach. It returns: i) a complete dataset in FASTQ format simulating the results of a BS experiment ii) a report file storing the information about the methylation level of the dataset (i.e. methylated cytosines). First, we test MethylFASTQ performances with an increasing number of concurrent processes and we report the comparison of MethylFASTQ with respect to Sherman tool. Then, we also describe an application of synthetic datasets generated with our tool and we use them as input for two bisulfite mapping and methylation calling tools. Finally, we propose MethylFASTQ as a tool to generate synthetic bisulfite sequencing data.

Nowadays, next generation sequencing is closer to clinical application in the field of oncology. Indeed, it allows the identification of tumor-specific mutations acquired during cancer development, progression and resistance to therapy. In parallel with an evolving sequencing technology, novel computational approaches are needed to cope with the requirement of a rapid processing of sequencing data into a list of clinically-relevant genomic variants. Since sequencing data from both tumors and their matched normal samples are not always available (unmatched data), there is a need of a computational pipeline leading to variants calling in unmatched data. Despite the presence of many accurate and precise variant calling algorithms, an efficient approach is still lacking. Here, we propose a parallel pipeline (ParallNormal) designed to efficiently identify genomic variants from whole- exome sequencing data, in absence of their matched normal. ParallNormal integrates well-known algorithms such as BWA and GATK, a novel tool for duplicate removal (DuplicateRemove), and the FreeBayes variant calling algorithm. A re-engineered implementation of FreeBayes, optimized for execution on modern multi-core architectures is also proposed. ParallNormal was applied on whole-exome sequencing data of pancreatic cancer samples without considering their matched normal. The robustness of ParallNormal was tested using results of the same dataset analyzed using matched normal samples and considering genes involved in pancreatic carcinogenesis. Our pipeline was able to confirm most of the variants identified using matched normal data.

Trichoderma gamsii T6085 is a promising beneficial isolate whose effects consist of growth inhibition of the main agents causing Fusarium head blight, reduction of mycotoxin accumulation, competition for wheat debris, and reduction of the disease in both the lab and the field. Here, we present the first genome assembly of a T. gamsii isolate, providing a useful platform for the scientific community.

Trichoderma harzianum T6776 is a promising beneficial isolate whose effects consist of growth promotion, positive response of photosynthetic activity, hormonal signaling, and carbon partitioning in tomato, coupled with biocontrol of plant pathogens. Here, we present the first genome assembly of T6776, providing a useful platform for the scientific community.

For their stability and detectability faecal microRNAs represent promising molecules with potential clinical interest as non-invasive diagnostic and prognostic biomarkers. However, there is no evidence on how stool miRNA profiles change according to an individual’s age, sex, and body mass index (BMI) or how lifestyle habits influence the expression levels of these molecules. We explored the relationship between the stool miRNA levels and common traits (sex, age, BMI, and menopausal status) or lifestyle habits (physical activity, smoking status, coffee, and alcohol consumption) as derived by a self-reported questionnaire, using small RNA-sequencing data of samples from 335 healthy subjects. We detected 151 differentially expressed miRNAs associated with one variable and 52 associated with at least two. Differences in miR-638 levels were associated with age, sex, BMI, and smoking status. The highest number of differentially expressed miRNAs was associated with BMI (n = 92) and smoking status (n = 84), with several miRNAs shared between them. Functional enrichment analyses revealed the involvement of the miRNA target genes in pathways coherent with the analysed variables. Our findings suggest that miRNA profiles in stool may reflect common traits and lifestyle habits and should be considered in relation to disease and association studies based on faecal miRNA expression.