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Gilbert, H.

Publications and source records attributed to Gilbert, H..

9 recordsLinked to original sources

Inflammatory Stromal Aging in Ulcerative Colitis and Colitis-Associated Cancer

ABSTRACTUlcerative colitis is a chronic inflammatory bowel disease that can progress from dysplasia to cancer. Inflammatory responses are critical drivers in this process, typically triggered by epithelial lesions and the ensuing infiltration of microbiota into the interstitial layer. Here, we focus on the pro-inflammatory state of the interstitial fibroblasts, which promotes immune infiltration and augments disease progression. The study aims to provide a mechanistic link how fibroblasts of the colitis-associated microenvironment integrate inflammatory signals, microbial infiltration and cellular memory. To this end, we investigated a large number of primary colon fibroblasts obtained from normal, colitis and colon cancer samples using a range of in vitro approaches and an in vivo co-inoculation cancer model. mRNA sequencing analysis identified that the disease-associated fibroblasts are exhibit a cellular inflammatory status, which involves the injury-induced senescence pathway. Using CXCL8, a potent chemokine upregulated in colitis and cancer colon fibroblasts, as a paradigm, this inflammatory status is triggered by the activation of the NF{kappa}B signaling via immune-derived cytokines (TNF, IL-1{beta}), bacterial signals (LPS) and the microbiome itself using mycoplasma as a paradigm. Finally, iPSC reprogramming studies indicate that fibroblasts from ulcerative colitis retain an epigenetic memory that sustains elevated CXCL8 expression. Together, our findings demonstrate that the senescence associated secretory phenotype of colon fibroblasts is a robust indicator for inflammation-driven colon tumorigenesis.

cancer biology↗

Daily feeding rhythms may play a role in the genetic variability of feed efficiency in growing pigs

AO_SCPLOWBSTRACTC_SCPLOWImproving feed efficiency in pigs is essential for reducing production costs and environmental impacts. This study examines the influence of circadian feeding rhythms and genetic polymorphisms on feed efficiency variability using two pig lines divergently selected for Residual Feed Intake (RFI) over ten generations. Feeding behavior was monitored using automatic concentrate dispensers, recording 6,494,097 visits from 3,824 pigs to analyze meal frequency, duration, and diurnal patterns. LRFI pigs ate less frequently, with larger meals and longer durations, they exhibited two distinct feeding peaks: one around 8:00 AM and a higher one at 5:00 PM and they consumed more feed during the diurnal period and less at night. HRFI pigs showed a smoother, less rhythmic feeding behavior with increased nocturnal intake. The differences between the two RFI lines became more pronounced as the number of generations of selection increased, suggesting a genetic basis. Feeding behaviors, including intake during the two main diurnal peaks, were found to be heritable (heritability estimates: 0.30-0.40) and genetic correlations were observed between feed intake and RFI, especially for intake between the two peaks. Then, we investigated the evolution of allele frequencies of single nucleotide polymorphisms (SNPs) in DNA sequences surrounding 10 core clock genes (ARNTL, CLOCK, CRY1, CRY2, NPAS2, NR1D1, PER1, PER2, PER3, RORA) along generations of selection. SNPs with significant frequency changes were mapped to regulatory regions and transposable elements, especially in HRFI line, suggesting potential functional impacts on circadian regulation. These results underscore the role of feeding behavior and genetic variation in feed efficiency, offering insights for breeding programs aimed at improving metabolic efficiency and sustainability in pig production.

zoology↗

Investigating the dynamics of heat acclimation in pig through transcriptome analysis of blood samples

This study aimed to investigate the dynamics of gene expression in pigs during heat stress (HS), focusing on both short-term (STHA) and long-term (LTHA) heat acclimation phases. A total of 12 castrated males were exposed to thermoneutral temperatures (24{degrees}C) for 14 days (TN) and then to a constant temperature of 30{degrees}C for 21 days. Rectal temperature measurements indicated a biphasic thermoregulatory response, with an initial peak followed by acclimation. Using whole blood transcriptome analysis at seven time points between day 5 before the initiation of HS challenge and day 13 post HS. A total of 525 genes were differentially expressed during the STHA (day 0-day 2) phase. A switch in the expression of most genes was observed around 20 hours after HS. Functional pathway enrichment analysis identified through shape-based clustering revealed the activation of the immune system, especially mediated through toll-like receptor signaling pathways. The LTHA phase (day 2-day 13) revealed 985 differentially expressed genes, with pathways associated with various metabolisms, including mitochondrial fatty acid beta-oxidation, and electron transport, ATP synthesis, and heat production by uncoupling proteins. Interestingly, oxidative phosphorylation was predicted to be activated during the LTHA, particularly in Complex V, whereas other complexes showed mixed regulation. Comparative pathway analysis indicated distinct metabolic adaptations between STHA and LTHA, with up-regulation of glucose and lipid metabolism in late STHA and down-regulation of lipid metabolism during LTHA. This study contributes to a better understanding of the time course of adaptation mechanisms in pigs to HS, underlying a coordinated regulation during STHA involving several stress-specific mechanisms (via the HSP) and metabolic variation to help pigs achieve homeothermy.

systems biology↗

Genetic and heat-stress related environmental influences on pig whole-blood gene expression levels

BackgroundGene expression levels are affected by genetics and environmental effects. However, quantification of the influence of genetics and environmental effects on gene expression remains limited, especially in farm animals. Here, the relative influence of genetic and heat-related environmental variations on gene expression levels was investigated in pigs, using a backcross herd of diverse heat adaptation levels. Backcross animals were raised in either a tropical or temperate environment. Animals raised in temperate environment were subjected to an experimental heat stress at the end of their growth. ResultsWe identified 1,967 differentially expressed genes (DEGs) between pigs raised in the tropical (n = 181) and temperate (n = 180) facilities, and 472 DEGs throughout a 3 weeks experimental heat stress. Transcriptome-wide association (TWAS) study identified 139 associations between gene expression levels and thermoregulation/production traits. We detected 6,014 expression quantitative trait loci (eQTLs) associated with the expression level of 3,297 genes. Genetic variance was estimated to explain 36.3% of gene expression variance on average, and was the main source of variance for 27.7% of transcripts. Most eQTLs found are located in proximal regions (cis-eQTLs) and few within distal regions (trans-eQTLs) to their assigned genes. A trans-eQTL hotspot highlighted a hematopoietic mechanism driven by GPATCH8. An integration of GWAS and TWAS pointed to TMCO1 and ZNF184 as candidate genes for backfat thickness. ConclusionsThis study provides a better understanding of the impact of climate, heat stress and genetic influences on the pig whole blood transcriptome.

genomics↗

Guiding eQTL mapping and genomic prediction of gene expression in three pig breeds with tissue-specific epigenetic annotations from early development

Gene expression is a dynamic phenotype influenced by tissue-specific regulatory mechanisms, which can modulate expression directly or indirectly through cis or trans factors. Identifying genetic variants in these regulatory regions can improve both expression quantitative trait locus (eQTL) mapping and gene expression prediction. Whole genome sequences offer the possibility for enhanced eQTL mapping accuracy, but detecting causal variants remains challenging. Here, we evaluate the potential added-value of integrating tissue-specific epigenetic annotations, such as chromatin accessibility and methylation status, into within-breed genomic predictions of expression for three pig breeds. Functional annotations from early developmental stages improved eQTL mapping interpretability as shown by the enrichment of trait-relevant QTLs. However, despite the use of functional annotations, predictions across breeds remain challenging due to differences in genetic architectures. Our work contributes to the understanding of gene expression regulation in livestock and highlights the value of functional annotations, despite continued challenges for predictions across breeds. HighlightsO_LIMatched whole-genome sequences and expressions reveal transcriptional regulatory variants. C_LIO_LIEarly epigenetic marks can guide transcriptome prediction and eQTL mapping. C_LIO_LIAnnotation-guided models can enhance the interpretability of eQTL mapping. C_LIO_LIPorting predictions across pig breeds remains challenging even with annotations. C_LIO_LIA case study linked IGF2 liver eQTLs with annotations and cholesterol QTLs. C_LI

genomics↗

Stronger transcriptomic response to feed intake in the duodenum of pig with high feed efficiency from a divergent selection experiment

Feed efficiency is a trait of interest in pigs as it contributes to lowering the ecological and economical costs of pig production. A divergent genetic selection experiment from a Large White pig population was performed for 10 generations, leading to pig lines with relative low-(LRFI, more efficient) and high-(HRFI, less efficient) residual feed intake (RFI). Feeding behaviour and metabolic differences have been previously reported between the two lines. We hypothesised that part of these differences could be related to differential sensing and absorption of nutrients in the proximal intestine. Here we investigated the duodenum transcriptome and DNA methylation profiles comparing overnight fasting with ad libitum feeding in LRFI and HRFI pigs (n=24). We identified 1,106 differentially expressed genes between the two lines, notably affecting pathways of the transmembrane transport activity and related to mitosis or chromosome separation. The LRFI line showed a greater transcriptomic response to feed intake, with 2,222 differentially expressed genes before and after a meal, as compared to 61 differentially expressed genes in the HRFI line. Feed intake affected genes from both anabolic and catabolic pathways in the pig duodenum, such as rRNA production and autophagy. We noted that several nutrient transporter and tight junction genes were differentially expressed between lines and/or by short term feed intake. We also identified 409 differentially methylated regions in the duodenum mucosa between the two lines, while this epigenetic mark was less affected by feeding. However most of the differentially expressed genes were not associated with proximal changes in DNA methylation profiles. Altogether, our findings highlighted that the genetic selection for feed efficiency in pigs changed the transcriptome profiles of the duodenum, and notably its response to feed intake, suggesting key roles for this proximal gut segment in mechanisms underlying feed efficiency.

genomics↗

Genetic relationships between efficiency traits and gut microbiota traits in growing pigs fed a conventional or a high fiber diet

In pigs, the gut microbiota composition plays a major role in the process of digestion, but is influenced by many external factors, especially diet. To be used in breeding applications, genotype by diet interactions on microbiota composition have to be quantified, as well as their impact on genetic covariances with feed efficiency (FE) and digestive efficiency (DE) traits. This study aimed at determining the impact of an alternative diet on variance components of microbiota traits (genera and alpha diversity indices), and estimating genetic correlations between microbiota and efficiency traits for pigs fed a conventional (CO) or a high fiber (HF) diet. Fecal microbes of 812 full-siblings fed a CO diet and 752 pigs fed the HF diet were characterized at 16 weeks of age by sequencing the V3-V4 region of the 16S rRNA gene. A total of 231 genera were identified. Digestibility coefficients of nitrogen, organic matter and energy were predicted analyzing the same fecal samples with near infrared spectrometry. Daily feed intake, feed conversion ratio, residual feed intake and average daily gain (ADG) were also recorded. The 71 genera with less than 20% of zeros were retained for genetic analyses. Heritability (h2) of microbiota traits were similar between diets (from null to 0.38 {+/-} 0.12 in the CO diet and to 0.39 {+/-} 0.12 in the HF diet). Only three out of the 24 genera and two alpha diversity indices with significant h2 in both diets had genetic correlations across diets significantly different from 0.99 (P < 0.05), indicating limited genetic by diet interactions for these traits. When both diets were analyzed jointly, 59 genera had h2 significantly different from zero. Based on the genetic correlations between these genera and ADG, FE and DE traits, three groups of genera could be identified. A group of 29 genera was favorably correlated with DE and FE traits, 14 genera were unfavorably correlated with DE traits, and the last group of 16 genera had correlations close to zero with production traits. However, genera favorably correlated with DE and FE traits were unfavorably correlated with ADG, and vice versa. Alpha diversity indices had correlation patterns similar to the first group. In the end, genetic by diet interactions on gut microbiota composition of growing pigs were limited in this study. Based on this study, microbiota-based traits could be used as proxies to improve FE and DE in growing pigs.

genetics↗

A genome-wide epistatic network underlies the molecular architecture of continuous color variation of body extremities: a rabbit model

Deciphering the molecular architecture of coat coloration for a better understanding of the biological mechanisms underlying pigmentation still remains a challenge. We took advantage of a rabbit French experimental population in which both a pattern and a gradient of coloration from white to brown segregated within the himalayan phenotype. The whole experimental design was genotyped using the high density Affymetrix(R) AxiomOrcun SNP Array and phenotyped into 6 different groups ordered from the lighter to the darker. Genome-wide association analyses pinpointed an oligogenic determinism, under recessive and additive inheritance, involving genes already known in melanogenesis (ASIP, KIT, MC1R, TYR), and likely processed pseudogenes linked to ribosomal function, RPS20 and RPS14. We also identified (i) gene-gene interactions through ASIP:MC1R affecting light cream/beige phenotypes while KIT:RPS responsible of dark chocolate/brown colors and (ii) a genome-wide epistatic network involving several others coloration genes such as POT1 or HPS5. Finally, we determined the recessive inheritance of the English spotting phenotype likely involving a copy number variation affecting at least the end of the coding sequence of the KIT gene. Our analyses of coloration as a continuous trait allowed us to go beyond much of the established knowledge through the detection of additional genes and gene-gene interactions that may contribute to the molecular architecture of the coloration phenotype. Moreover, the characterization of a network including genes that contribute to melanogenesis and pigmentation, two processes affected in various human disorders, shows the potential interest of our rabbit model for transversal studies.

genetics↗

Identification of genomic regions affecting production traits in pigs divergently selected for feed efficiency

BackgroundFeed efficiency is a major driver of the sustainability of pig production systems. Understanding biological mechanisms underlying these agronomic traits is an important issue whether for environment and farms economy. This study aimed at identifying genomic regions affecting residual feed intake (RFI) and other production traits in two pig lines divergently selected for RFI during 9 generations (LRFI, low RFI; HRFI, high RFI). ResultsWe built a whole dataset of 570,447 single nucleotide polymorphisms (SNPs) in 2,426 pigs with records for 24 production traits after both imputation and prediction of genotypes using pedigree information. Genome-wide association studies (GWAS) were performed including both lines (Global-GWAS) or each line independently (LRFI-GWAS and HRFI-GWAS). A total of 54 chromosomic regions were detected with the Global-GWAS, whereas 37 and 61 regions were detected in LRFI-GWAS and HRFI-GWAS, respectively. Among those, only 15 regions were shared between at least two analyses, and only one was common between the three GWAS but affecting different traits. Among the 12 QTL detected for RFI, some were close to QTL detected for meat quality traits and 9 pinpointed novel genomic regions for some harbored candidate genes involved in cell proliferation and differentiation processes of gastrointestinal tissues or lipid metabolism-related signaling pathways. Detection of mostly different QTL regions between the three designs suggests the strong impact of the dataset on the detection power, which could be due to the changes of allelic frequencies during the line selection. ConclusionsBesides efficiently detecting known and new QTL regions for feed efficiency, the combination of GWAS carried out per line or simultaneously using all individuals highlighted the identification of chromosomic regions under selection that affect various production traits.

genetics↗