{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Hui-Chen Hsieh"],"organism":["Caenorhabditis elegans"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15698"],"description":["Effector-triggered immunity (ETI) safeguards intestinal epithelial cells (IECs) by surveilling bacterial virulence effectors and effector-induced cellular stress, such as plasma membrane damage induced by pore-forming toxins (PFTs). However, the knowledge about ETI regulators in maintaining IEC homeostasis in vivo remained elusive. Plasma membrane integrity (PMI) and microvilli morphology are essential for barrier function and nutrient absorption of IECs; thus, PFT effectors compromise these structures are detrimental to animal survival. Here, we identify a conserved ETI program in IECs of C. elegans and humans. The intestinal ETI regulator methyl-HLH-30/TFEB upregulates a novel intrinsic cellular defense (INCED) orchestrator Y54G11A.4/TTC38. This pathway coordinates restorations of PMI, microvilli architecture, and nutrient uptake by promoting phase condensation of the microtubule organizer PTRN-1/CAMSAP through an HSP70/HSP90 chaperone system. Our findings reveal an ETI program integrating host defense with holistic epithelial repair and delineating a novel and conserved ETI-induced INCED program for mucosal homeostasis across metazoans."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Nucleic Acid Extraction - Total RNA was extracted using TRIzol (Invitrogen, 15596026) and cleaned-up with RNeasy Mini Kit (Qiagen, 74104)","Sample Collection - Synchronized L4-to-young adult stage C. elegans were fed with E. coli OP50 harboring either pQE9 or pQE9-Cry5B for 3 hours at 25°C following RNA extraction.","Library Construction - RNA libraries for RNA-seq wre prepared using TruSeq Stranded mRNA Library Prep Kit (Illumina, San Diego, CA, USA) following manufacturer's protocols","Sequencing - RNA libraries for RNA-seq wre prepared using TruSeq Stranded mRNA Library Prep Kit (Illumina, San Diego, CA, USA) following manufacturer's protocols"],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - \\\"Low-quality reads and contaminating adapter sequences were cleaned using fastp 0.22.0 --detect_adapter_for_pe -l 25 \\         --cut_right --cut_window_size 1 \\\" \\\"The paired-end reads were aligned to the reference genome c_elegans.PRJNA13758.WS294.genomic.fa using STAR 2.7.10b                                                                                                           --readFilesCommand zcat \\          --outSAMtype BAM Unsorted \\          --quantTranscriptomeBan Singleend \\          --outFilterType BySJout \\          --alignSJoverhangMin 8 \\          --outFilterMultimapNmax 20 \\          --alignSJDBoverhangMin 1 \\          --outFilterMismatchNmax 999 \\          --outFilterMismatchNoverReadLmax 0.04 \\          --alignIntronMin 20 \\          --alignIntronMax 1000000 \\          --alignMatesGapMax 1000000 \\          --quantMode TranscriptomeSAM \\          --outSAMattributes NH HI AS NM MD\\\" the matrix of gene counts were generated using Salmon 1.10.3 with --gcBias --seqBias"],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["N/C","Illumina NovaSeq 6000"],"study_type":["RNA-seq of coding RNA"],"species":["Caenorhabditis elegans"],"pubmed_authors":["Hui-Chen Hsieh"],"additional_accession":[]},"is_claimable":false,"name":"Conserved immune regulator HLH-30/TFEB couples pore-forming toxin damage sensing to intestine homeostasis via TTC38 signal orchestrator","description":"Effector-triggered immunity (ETI) safeguards intestinal epithelial cells (IECs) by surveilling bacterial virulence effectors and effector-induced cellular stress, such as plasma membrane damage induced by pore-forming toxins (PFTs). However, the knowledge about ETI regulators in maintaining IEC homeostasis in vivo remained elusive. Plasma membrane integrity (PMI) and microvilli morphology are essential for barrier function and nutrient absorption of IECs; thus, PFT effectors compromise these structures are detrimental to animal survival. Here, we identify a conserved ETI program in IECs of C. elegans and humans. The intestinal ETI regulator methyl-HLH-30/TFEB upregulates a novel intrinsic cellular defense (INCED) orchestrator Y54G11A.4/TTC38. This pathway coordinates restorations of PMI, microvilli architecture, and nutrient uptake by promoting phase condensation of the microtubule organizer PTRN-1/CAMSAP through an HSP70/HSP90 chaperone system. Our findings reveal an ETI program integrating host defense with holistic epithelial repair and delineating a novel and conserved ETI-induced INCED program for mucosal homeostasis across metazoans.","dates":{"release":"2025-11-11T00:00:00Z","modification":"2026-05-28T11:43:16.015Z","creation":"2025-10-10T13:29:00.944Z"},"accession":"E-MTAB-15698","cross_references":{"ENA":["ERP181360"],"EFO":["EFO_0002944","EFO_0004170","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184"]}}