PXD046961-1

PXD046961 is an original dataset announced via ProteomeXchange.

Title	Effects of ALS-associated tRNA-derived stress-induced RNA on the transcriptomic and proteomic profile of primary neurons in vitro
Description	LtRNA-derived stress-induced RNAs (tiRNAs) are a new class of small non-coding RNA that have emerged as important regulators of cellular stress responses. tiRNAs are derived from specific tRNA cleavage by the stress-induced ribonuclease angiogenin (ANG). Loss-of-function mutations in the ANG gene are linked to amyotrophic lateral sclerosis (ALS), and elevated levels of specific tiRNAs were recently identified in ALS patient serum samples. However, the biological role of tiRNA production in neuronal stress responses and neurodegeneration remains largely unknown. Here, we sought to evaluate the genome-wide regulation of neuronal stress responses by tiRNAs. First, we demonstrated that a specific tiRNA, 5’tiRNA Gly-GCC , is upregulated in primary neurons exposed to disease-relevant stresses and in the spinal cord of a TDP-43 mouse model of ALS. We then performed whole-transcript RNA sequencing and label-free mass spectrometry on primary neurons transfected with a synthetic mimic of endogenous 5’tiRNA Gly-GCC to identify its effects on global gene and protein expression. Quantitative proteomics identified more than 200 differentially expressed proteins in the 5’tiRNA Gly-GCC mimic-transfected neurons compared to control, however RNA sequencing did not identify any differentially expressed genes in response to tiRNA transfection. Functional enrichment analysis of the proteomic data revealed downregulation of proteins involved in translation initiation, RNA and protein metabolism and also enrichment of pathways associated with several neurodegenerative diseases, including ALS. Together, these findings suggest that 5’tiRNA Gly-GCC is an ALS-associated tiRNA that functions
HostingRepository	PRIDE
AnnounceDate	2024-12-28
AnnouncementXML	Submission_2024-12-28_13:47:46.677.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Kieran Wynne
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	timsTOF Pro

Revision	Datetime	Status	ChangeLog Entry
0	2023-11-14 14:53:32	ID requested
⏵ 1	2024-12-28 13:47:47	announced

Jirstr, ö, m E, Matveeva A, Baindoor S, Donovan P, Ma Q, Morrissey EP, Arijs I, Boeckx B, Lambrechts D, Garcia-Munoz A, Dillon ET, Wynne K, Ying Z, Matallanas D, Hogg MC, Prehn JHM, on the transcriptomic and proteomic profile of primary neurons in vitro. Exp Neurol, 385():115128(2025) [pubmed]

10.1016/j.expneurol.2024.115128;

submitter keyword: Transcriptome, Proteome,ALS, RNA, Neurons.

Prof Jochen H. M. Prehn
contact affiliation	Prof Jochen H. M. Prehn Department of Physiology and Medical Physics Royal College of Surgeons in Ireland 123 St Stephen’s Green Dublin 2, Ireland
contact email	prehn@rcsi.ie
lab head
Kieran Wynne
contact affiliation	University College Dublin
contact email	kieran.wynne1@ucd.ie
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD046961
     1. Label: PRIDE project
     2. Name: Effects of ALS-associated tRNA-derived stress-induced RNA on the transcriptomic and proteomic profile of primary neurons in vitro