RNAseq studies reveal distinct transcriptional response to vitamin A deficiency in small intestine versus colon, uncovering novel vitamin A-regulated genes

Chai, Zhi; Lyu, Yafei; Chen, Qiuyan; Wei, Cheng; Snyder, Lindsay M.; Weaver, Veronika; Sebastian, Aswathy; Albert, István; Li, Qunhua; Cantorna, Margherita T.; Ross, A. Catharine

doi:10.1016/j.jnutbio.2021.108814

Cited by 8 publications

(18 citation statements)

References 67 publications

(80 reference statements)

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“…After weaning, the mice were assigned to one of the four treatment groups (non-infected VAD, infected VAD, non-infected VAS, and infected VAS) until the end of the experiments. The VA status of the animals was confirmed by analyzing serum retinol using an ultra-performance liquid chromatography method [44].…”

Section: Animalsmentioning

confidence: 99%

“…day 5 and day 10, respectively, the time of peak infection as shown in previous studies [23,25,38]. Details on tissue collection and RNA extraction were described previously [44]. Briefly, total RNA was extracted with a Qiagen RNeasy Midi Kit, genomics DNA was removed by a TURBO DNA-free kit, and RNA quality was determined on an Agilent Bioanalyzer to ensure RNAseq libraries were constructed with RNA samples of sufficient quality (RNA integrity number, RIN > 8).…”

Section: Tissue Collection and Rna Extractionmentioning

confidence: 99%

“…Details on the methods of library preparation, sequencing, and mapping were provided before [44]. In brief, a TruSeq Stranded mRNA Library Prep kit and a HiSeq 2500 system (Illumina) were used to generate raw sequencing data.…”

Section: Rnaseq Library Preparation Sequencing and Mappingmentioning

confidence: 99%

“…For the SI study, the transcript was removed if it had less than 10 counts in more than 8 of the 12 samples or if its total count was less than 200. For the colon study, the transcript was removed if it had less than 10 counts in more than 10 of the 16 samples or if its total count was less than 220 [44]. Differential expression analyses were performed and the 2 × 2 experimental design was resolved into three effects related to infection (Figure 1b): (I) the "VAS-Inf" effect, which corresponded to the comparison between the non-infected VAS verses the infected VAS groups; (II) the "VAD-Inf" effect, which corresponded to the comparison between the non-infected VAD and the infected VAD groups; and (III) "VA effect under infection", which compared the infected VAD and the infected VAS groups.…”

Section: Differential Expressionmentioning

confidence: 99%

“…Previously, we used an RNAseq approach to characterize the effects of the VA status alone in the small intestine (SI) and the colon [44]. Our focus on VA has public health relevance because VA deficiency remains a public health issue in resource-limited areas co-incident with diarrhea prevalence.…”

Section: Introductionmentioning

confidence: 99%

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Transcriptional Profiling of the Small Intestine and the Colon Reveals Modulation of Gut Infection with Citrobacter rodentium According to the Vitamin A Status

et al. 2022

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Vitamin A (VA) deficiency and diarrheal diseases are both serious public health issues worldwide. VA deficiency is associated with impaired intestinal barrier function and increased risk of mucosal infection-related mortality. The bioactive form of VA, retinoic acid, is a well-known regulator of mucosal integrity. Using Citrobacter rodentium-infected mice as a model for diarrheal diseases in humans, previous studies showed that VA-deficient (VAD) mice failed to clear C. rodentium as compared to their VA-sufficient (VAS) counterparts. However, the distinct intestinal gene responses that are dependent on the host’s VA status still need to be discovered. The mRNAs extracted from the small intestine (SI) and the colon were sequenced and analyzed on three levels: differential gene expression, enrichment, and co-expression. C. rodentium infection interacted differentially with VA status to alter colon gene expression. Novel functional categories downregulated by this pathogen were identified, highlighted by genes related to the metabolism of VA, vitamin D, and ion transport, including improper upregulation of Cl– secretion and disrupted HCO3– metabolism. Our results suggest that derangement of micronutrient metabolism and ion transport, together with the compromised immune responses in VAD hosts, may be responsible for the higher mortality to C. rodentium under conditions of inadequate VA.

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Section: Animalsmentioning

confidence: 99%