Evidence map›Paper›PMID 36798299›Full record

ArticlebioRxiv : the preprint server for biology2023

Retrospective identification of intrinsic factors that mark pluripotency potential in rare somatic cells.

Naveen Jain, Yogesh Goyal, Margaret C Dunagin, Christopher J Cote, Ian A Mellis, Benjamin Emert, Connie L Jiang, Ian P Dardani, Sam Reffsin, Arjun Raj

Open access · greenAbstract readPreprint
In one paragraph

Article in bioRxiv : the preprint server for biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed, 7 citations in OpenAlex.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

10 authors at 2 institutions in 1 country.

Naveen JainGenetics and Epigenetics Program, Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
Yogesh GoyalDepartment of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
Margaret C DunaginDepartment of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, PA, USA.
Christopher J CoteDepartment of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, PA, USA.
Ian A MellisGenomics and Computational Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
Benjamin EmertGenomics and Computational Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
Connie L JiangGenetics and Epigenetics Program, Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
Ian P DardaniDepartment of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, PA, USA.
Sam ReffsinDepartment of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, PA, USA.
Arjun RajDepartment of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, PA, USA.
University of Pennsylvania · USNorthwestern University · US

Funding

MEDICAL SCIENTIST TRAINING PROGRAMT32GM007170 · NIGMS · UNIVERSITY OF PENNSYLVANIA · PI BRASS, LAWRENCE F · 1985 to 2022
$54.0M
Training Program in Computational GenomicsT32HG000046 · NHGRI · UNIVERSITY OF PENNSYLVANIA · PI JUNHYONG KIM, Mingyao Li · 1999 to 2026
$9.5M
HEMATOPOIESIS TRAINING GRANTT32DK007780 · NIDDK · UNIVERSITY OF PENNSYLVANIA · PI TONG, WEI · 1999 to 2023
$6.7M
Engineering and Imaging 3D genome structure-function dynamics across time scalesU01DK127405 · NIDDK · UNIVERSITY OF PENNSYLVANIA · PI BLOBEL, GERD A, PHILLIPS-CREMINS, JENNIFER ELIZABETH · 2020 to 2024
$5.7M
Decoding the bridges and barriers to cellular reprogramming and lineage identityR01GM137425 · NIGMS · UNIVERSITY OF PENNSYLVANIA · PI JAIN, RAJAN, RAJ, ARJUN · 2019 to 2023
$5.6M
An integrated approach to melanoma metastasis and therapy resistance: effects of age-related changes in the ECM and the biomechanics of the skinR01CA232256 · NCI · WISTAR INSTITUTE · PI CUKIERMAN, EDNA, RAJ, ARJUN · 2019 to 2023
$3.0M
Understanding and Overcoming Resistance to BRAF/MEK Kinase Inhibitors in MelanomaR01CA238237 · NCI · UNIVERSITY OF PENNSYLVANIA · PI HERLYN, MEENHARD F, RAJ, ARJUN · 2020 to 2024
$2.9M
Lineage Analysis of Cellular States Predicting Reprogramming into iPSCsF30HD103378 · NICHD · UNIVERSITY OF PENNSYLVANIA · PI JAIN, NAVEEN · 2020 to 2022
$118k
Single-molecule resolution of RNA editing of mRNAs: visualizing GRIA2 editing in situ in ALSF30NS100595 · NINDS · UNIVERSITY OF PENNSYLVANIA · PI MELLIS, IAN ALEXANDER · 2017 to 2019
$108k
Connecting molecular phenotype with cell fate using single-cell barcoding and RNA FISHF30CA236129 · NCI · UNIVERSITY OF PENNSYLVANIA · PI EMERT, BENJAMIN · 2019 to 2020
$59k
Revealing the molecular underpinnings of transcriptional heterogeneityF30HG010822 · NHGRI · UNIVERSITY OF PENNSYLVANIA · PI JIANG, CONNIE LAN · 2020 to 2020
$33k
NCI NIH HHS F30 CA236129NCI NIH HHS R01 CA232256NCI NIH HHS R01 CA238237NHGRI NIH HHS F30 HG010822NHGRI NIH HHS T32 HG000046NICHD NIH HHS F30 HD103378NIDDK NIH HHS T32 DK007780NIDDK NIH HHS U01 DK127405NIGMS NIH HHS R01 GM137425NIGMS NIH HHS T32 GM007170NINDS NIH HHS F30 NS100595
6 · The paper itself

Abstract

Pluripotency can be induced in somatic cells by the expression of the four "Yamanaka" factors OCT4, KLF4, SOX2, and MYC. However, even in homogeneous conditions, usually only a rare subset of cells admit reprogramming, and the molecular characteristics of this subset remain unknown. Here, we apply retrospective clone tracing to identify and characterize the individual human fibroblast cells that are primed for reprogramming. These fibroblasts showed markers of increased cell cycle speed and decreased fibroblast activation. Knockdown of a fibroblast activation factor identified by our analysis led to increased reprogramming efficiency, identifying it as a barrier to reprogramming. Changing the frequency of reprogramming by inhibiting the activity of LSD1 led to an enlarging of the pool of cells that were primed for reprogramming. Our results show that even homogeneous cell populations can exhibit heritable molecular variability that can dictate whether individual rare cells will reprogram or not.

Identifiers

PMID36798299
PMCPMC9934612
OpenAlexW4320037637

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-ND
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.