Dataset Information

Proteoform Detection in 17000 Single Nuclei from Differentiating Skin Keratinocytes

ABSTRACT: We analyzed over 17000 single nuclei derived from the differentiating human epidermal keratinocytes using single-nucleus Proteoform imaging Mass Spectrometry (snPiMS). This study enabled highly sensitive detection of intact proteoforms of core histones and variants along with other nuclear proteins from the single nucleus. Integration of snPiMS data enabled distinct proteoform-defined clusters, with a continuum from proliferative progenitors through active cell-cycle phases to the terminal differentiation. This study establishes snPiMS as a powerful platform for cell-type and state characterization at the intact proteoform level, complementing single-nucleus transcriptomic frameworks and advancing the frontier of single-cell proteomics (SCP).

INSTRUMENT(S): Q Exactive Plus

ORGANISM(S): Homo Sapiens (ncbitaxon:9606)

SUBMITTER: Neil L Kelleher

PROVIDER: MSV000100310 | MassIVE | Mon Dec 22 14:23:00 GMT 2025

REPOSITORIES: MassIVE

ACCESS DATA

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Project description:Targets of Retinoic Acid (RA) and 3,4-didehydroretinoic acid (ddRA) were identified in primary human epidermal keratinocytes grown in the presence of atRA or ddRA for 4 and 24 hours. Retinoids (natural forms and synthetic derivatives of vitamin A) are used as therapeutic agents for numerous skin diseases such as keratinization disorders (e.g. ichthyoses) and psoriasis. Two endogenous ligands for retinoic acid receptors exist, retinoic acid (atRA) and 3,4-didehydroretinoic acid (ddRA). In primary human epidermal keratinocytes many transcriptional targets for atRA are known, whereas the targets for ddRA are unknown. In an attempt to determine the targets, we compared the effect of atRA and ddRA on transcriptional profiles in undifferentiated and differentiating human primary keratinocytes. First, as expected, many genes were induced or suppressed in response to keratinocyte differentiation. Furthermore, the two retinoids affected substantially more genes in differentiated keratinocytes (more than 350) than in proliferating keratinocytes (20). In differentiating keratinocytes markers of cornification were suppressed suggesting a de-differentiating effect by the two retinoids. When comparing the expression profile of atRA to that of ddRA, no differently regulated genes were found. The array analysis also found that a minor number of miRNAs and a large number of non-coding transcripts were changed during differentiation and in response to the two retinoids. Furthermore, the expression of all, except one, genes known to cause autosomal recessive congenital ichthyosis (ARCI) were found to be induced by differentiation. These results comprehensively document that atRA and ddRA exert similar transcriptional changes in keratinocytes and also add new insights into the molecular mechanism influenced by retinoids in the epidermis. Furthermore, it suggests which ARCI patients could benefit from therapy with retinoids. Proliferating and differentiated keratinocytes were harvested after 4 and 24 hours after treatment with atRA, ddRA and vehicle for RNA extraction and hybridization on Affymetrix microarrays. Triplicate samples were generated for each time point and each treatment.

Dataset Information

Proteoform Detection in 17000 Single Nuclei from Differentiating Skin Keratinocytes

Dataset's files

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets