PXD028799

PXD028799 is an original dataset announced via ProteomeXchange.

Title	Revisiting the Hayflick Limit: Insights from an Integrated Analysis of Changing Transcripts, Proteins, Metabolites and Chromatin.
Description	Replicative senescence (RS) as a model has become the central focus of research into cellular aging in vitro. Despite decades of study, this process through which cells cease dividing is not fully understood in culture, and even much less so in vivo during development and with aging. Here, we revisit Hayflick’s original observation of RS in WI-38 human fetal lung fibroblasts equipped with a battery of high dimensional modern techniques and analytical methods to deeply profile the process of RS across each aspect of the central dogma and beyond. We applied and integrated RNA-seq, proteomics, metabolomics, and ATAC-seq to a high resolution RS time course. We found that the transcriptional changes that underlie RS manifest early, gradually increase, and correspond to a concomitant global increase in accessibility in nucleolar and lamin associated domains. During RS WI-38 fibroblast gene expression patterns acquire a striking resemblance to those of myofibroblasts in a process similar to the epithelial to mesenchymal transition (EMT). This observation is supported at the transcriptional, proteomic, and metabolomic levels of cellular biology. In addition, we provide evidence suggesting that this conversion is regulated by the transcription factors YAP1/TEAD1 and the signaling molecule TGF-β2.
HostingRepository	PRIDE
AnnounceDate	2022-05-27
AnnouncementXML	Submission_2022-05-27_05:23:35.983.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Fiona McAllister
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2021-09-28 03:09:56	ID requested
⏵ 1	2022-05-27 05:23:36	announced

Chan M, Yuan H, Soifer I, Maile TM, Wang RY, Ireland A, O'Brien JJ, Goudeau J, Chan LJG, Vijay T, Freund A, Kenyon C, Bennett BD, McAllister FE, Kelley DR, Roy M, Cohen RL, Levinson AD, Botstein D, Hendrickson DG, Novel insights from a multiomics dissection of the Hayflick limit. Elife, 11():(2022) [pubmed]

submitter keyword: Hayflick Limit, Proteomics

Fiona Elizabeth McAllister
contact affiliation	Calico Life Sciences, CA, USA
contact email	fiona@calicolabs.com
lab head
Fiona McAllister
contact affiliation	Calico Life Sciences LLC
contact email	fiona@calicolabs.com
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD028799
     1. Label: PRIDE project
     2. Name: Revisiting the Hayflick Limit: Insights from an Integrated Analysis of Changing Transcripts, Proteins, Metabolites and Chromatin.