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Batten's Disease proteomics using iTRAQ LC-MS/MS

ABSTRACT: Proteomic analysis using iTRAQ technique to identify global changes in Batten's disease samples using iPSCs derived from keratinocytes and differentiated to iNPCs Three separate mass spectrometry runs were carried out and results were combined using seaMASS and Bayesian analysis

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Cell Culture, Neural Progenitor Cell

DISEASE(S): Neuronal Ceroid Lipofuscinosis 7

SUBMITTER: Aseel Sharaireh

LAB HEAD: Tristan R McKay

PROVIDER: PXD033069 | Pride | 2025-11-10

REPOSITORIES: Pride

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Dataset's files

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			Action	DRS
	20190830_AS_iTRAQ_8_plex_3.group	Other
	20190904_AS_iTRAQ_8_plex_2.group	Other
	20190906_AS_8_PLEX_1B_01.group	Other
	Battens-BD.M_v_BD.P.csv	Csv
	Battens-C.M_v_BD.M.csv	Csv

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Publications

CLN7 protein functions at the interface between endolysosomes and stress granules to promote cell survival.

Sharaireh Aseel A Guevara-Ferrer Marta M Ludlaim Anna M AM Humphries Jonathan D JD Phillips Alexander M AM Dowsey Andrew W AW Zhang Zehan Z Counsell John R JR Unwin Richard D RD Mole Sara E SE Rahim Ahad A AA McKay Tristan R TR

Cell death & disease 20251031 1

Inherited biallelic mutations in the CLN7 gene result in the variant late infantile onset neuronal ceroid lipofuscinosis, a subtype of Batten disease (BD), a severe and fatal childhood neurodegenerative disease. Intriguingly, CLN7 genetic variants have also been associated with retinopathies, amyotrophic lateral sclerosis, and frontotemporal dementia. CLN7 encodes a transmembrane protein localizing to endolysosomal membranes with outward-facing chloride channel activity. Loss of CLN7 function re ...[more]

PMID: 41173878

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Localised protein expression changes in different regions of human Alzheimer’s brain correlate with disease severity - Motor cortex

Project description:Human brain tissue was obtained from the New Zealand Brain Bank from donors with Alzheimer's disease (AD) or age-matched controls (n=9/group). Mean post mortem delays were ~12h. Six distinct brain regions were dissected, Hippocampus, Cingulate Gyrus, Entorhinal Cortex (severely affected), Motor and Sensory Cortex (less affected) and Cerebellum (spared). Protein was extracted from each sample and, each region was analysed independently. For each region, samples were divided into 3 sets of 3 cases and 3 controls and assigned to an iTRAQ 8 plex, alongside two aliquots of a pooled QC sample. Samples were digested, iTRAQ labelled and analysed. For each region, between 3000 and 4200 proteins were compared between AD and control, identifying a series of known and novel protein expression changes associated with the progression of AD.

2019-02-15 | PXD008807 | Pride

APEX protemics of the inhibitory receptors CLTA-4, LAG-3 and TIM-3

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2023-10-26 | PXD044064 | Pride

Investigation of isoAsp accumulation to antioxidative enzymes during thermal stress and their repair by PROTEIN L-ISOASPARTYL METHYLTRANSFERASE (PIMT).

Project description:The formation of isoAsp residues from Asp and Asn residues in proteins and peptides is accelerated under stressful environments and has detrimental effects on protein structure and function. PROTEIN L-ISOASPARTYL METHYLTRANSFERASE (PIMT) is a protein repairing enzyme which revert such deleterious isoAsp residues to normal aspartyl residues as a protein repair process. In present work, we aim to study the isoaspartyl formation of antioxidative enzymes, superoxide dismutase (SOD) and catalase (CAT) under stressful environments and their repair by PIMT in Arabidopsis. The role of PIMT in repairing these enzymes for the plant survival under heat and oxidative stress were investigated through molecular, biochemical approaches in Arabidopsis. We demonstrated that isoAsp accumulation in proteins increase upon heat and oxidative stress, and PIMT activity is essential to restrict such isoAsp accumulation. We demonstrated that PIMT play an important role under heat and oxidative stress by restricting stress-induced deleterious isoAsp accumulation in proteins. Analyses of PIMT overexpression and RNAi lines suggest that PIMT maintains ROS homeostasis by protecting the functionality of antioxidative enzymes from isoAsp mediated damage under stressful environments. To confirm further whether Asn residues of antioxidative enzymes indeed susceptible to isoAsp formation, we used bacterially expressed and purified recombinant proteins for MS analyses. Purified proteins were subjected to thermal insult and then MS/MS analyses were carried out to identify isoAsp modification. Our MS analyses suggest that these antioxidative enzymes are indeed susceptible to isoAsp formation under thermal stress.

2019-12-18 | PXD016240 | Pride

SUZ12 immunoprecipitation followed by protein indentification via mass spectrometry (SUZ12 IP-MS) in mESCs of SUZ12 WT, delta exon 4, KO, and KO rescues with SUZ12-L and SUZ12-S

Project description:Suz12 exon 4 encodes 23 amino acids (aa 129–152 in SUZ12-L) that partially overlap with the WD-binding domain 1 (WDB1, 110–145). We reasoned that exon 4 skipping might alter the structure of SUZ12 and, possibly, PRC2 composition. To explore this possibility, we generated ESCs that lack the Suz12 exon 4 via CRISPR-Cas9–induced deletion. In addition, to rule out any biases due to the expression levels and/or SUZ12 epitope masking, we generated Suz12 knockout (KO) ESCs (herein, KO) in which Suz12 expression was subsequently rescued by re-introducing either the Suz12-L or Suz12-S mouse isoform fused to a triple-Flag tag under the regulation of a CAG promoter (KO+L/S; Figures S2H–S2K). We performed SUZ12 immunoprecipitation coupled with mass spectrometry (IP-MS) in the WT and ∆ex4 clones to compare their interactomes and with a flag antibody in the KO and rescue cell lines. As expected, no peptides corresponding to exon 4 were retrieved in ∆ex4 samples, while the rest of the sequence displayed similar coverage. Comparison of interactors in the two conditions revealed that SUZ12 binding to AEBP2 and JARID2 was strongly reduced in ∆ex4 cells with respect to WT cells, whereas SUZ12 binding to most core components or to PRC2.1-specific factors was unchanged or only slightly increased . These observations were confirmed by SUZ12 IP followed by Western blot (WB). Flag IP-MS in rescue cells confirmed that, while the long isoform was able to correctly form comparable amounts of both PRC2.1 and PRC2.2 subtypes, interaction of the SUZ12-S with PRC2.2-specific factors was drastically reduced.

2024-03-18 | PXD046660 | Pride

Comparative endometrial proteomics among fertile women, intrauterine device carriers, and recurrent implantation failure patients using iTRAQ methodology

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2019-11-06 | PXD011094 | Pride

Chinese giant salamander liver LC-MS/MS

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Modulation of murine bone marrow derived dendritic cells by IL-4

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SWATH-MS data showing differential protein expression due to the ModS methyltransferase of Streptococcus suis

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