Evidence map›Paper›PMID 30376879›Full record

ArticleStem cell research & therapy2018

Identifying deer antler uhrf1 proliferation and s100a10 mineralization genes using comparative RNA-seq.

Dai Fei Elmer Ker, Dan Wang, Rashmi Sharma, Bin Zhang, Ben Passarelli, Norma Neff, Chunyi Li, William Maloney, Stephen Quake, Yunzhi Peter Yang

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Stem cell research & therapy, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.

0numbers the graph read from it
0cells of the map it votes in
11citing papers in PubMed
1.5field-weighted citation impact, top 17% of its field
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

11 citing papers in PubMed, 32 citations in OpenAlex.

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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

10 authors at 4 institutions in 2 countries.

Dai Fei Elmer KerDepartment of Orthopaedic Surgery, Stanford University, 300 Pasteur Drive, Stanford, CA, 94305, USA.
Dan WangDepartment of Orthopaedic Surgery, Stanford University, 300 Pasteur Drive, Stanford, CA, 94305, USA.
Rashmi SharmaDepartment of Bioengineering, Stanford University, Shriram Center 443 Via Ortega, Stanford, CA, 94305, USA.
Bin ZhangDepartment of Orthopaedic Surgery, Stanford University, 300 Pasteur Drive, Stanford, CA, 94305, USA.
Ben PassarelliScientific Computing Core, Calico Life Sciences LLC, 1170 Veterans Blvd., South San Francisco, CA, 94080, USA.
Norma NeffDepartment of Bioengineering, Stanford University, Shriram Center 443 Via Ortega, Stanford, CA, 94305, USA.
Chunyi LiState Key Lab for Molecular Biology of Special Economic Animals, 4899 Juye Street, Changchun, 130112, Jilin, China.
William MaloneyDepartment of Orthopaedic Surgery, Stanford University, 300 Pasteur Drive, Stanford, CA, 94305, USA.
Stephen QuakeDepartment of Bioengineering, Stanford University, Shriram Center 443 Via Ortega, Stanford, CA, 94305, USA.
Yunzhi Peter YangDepartment of Orthopaedic Surgery, Stanford University, 300 Pasteur Drive, Stanford, CA, 94305, USA. ypyang@stanford.edu.
Stanford University · USEnzo Life Sciences (United States) · USFranciscan University of Steubenville · USInstitute of Special Animal and Plant Sciences · CN

Funding

Microengineered Osteons for Bone Tissue EngineeringR01AR057837 · NIAMS · UNIVERSITY OF TEXAS HLTH SCI CTR HOUSTON · PI YANG, YUNZHI · 2010 to 2018
$5.1M
Engineering Vascularized Bone Tissues By Microfabrication And ScaffoldingR01DE021468 · NIDCR · UNIVERSITY OF TEXAS HLTH SCI CTR HOUSTON · PI YANG, YUNZHI · 2011 to 2014
$1.8M
BD Canto II RUO CytometerS10RR027431 · NCRR · STANFORD UNIVERSITY · PI NOLAN, GARRY P · 2010 to 2010
$236k
NCRR NIH HHS S10 RR027431NIAMS NIH HHS R01 AR057837NIDCR NIH HHS R01 DE021468NIH HHS R01AR057837NIH HHS R01DE021468
6 · The paper itself

Abstract

backgroundDeer antlers are bony structures that re-grow at very high rates, making them an attractive model for studying rapid bone regeneration.

methodsTo identify the genes that are involved in this fast pace of bone growth, an in vitro RNA-seq model that paralleled the sharp differences in bone growth between deer antlers and humans was established. Subsequently, RNA-seq (> 60 million reads per library) was used to compare transcriptomic profiles. Uniquely expressed deer antler proliferation as well as mineralization genes were identified via a combination of differential gene expression and subtraction analysis. Thereafter, the physiological relevance as well as contributions of these identified genes were determined by immunofluorescence, gene overexpression, and gene knockdown studies.

resultsCell characterization studies showed that in vitro-cultured deer antler-derived reserve mesenchyme (RM) cells exhibited high osteogenic capabilities and cell surface markers similar to in vivo counterparts. Under identical culture conditions, deer antler RM cells proliferated faster (8.6-11.7-fold increase in cell numbers) and exhibited increased osteogenic differentiation (17.4-fold increase in calcium mineralization) compared to human mesenchymal stem cells (hMSCs), paralleling in vivo conditions. Comparative RNA-seq identified 40 and 91 previously unknown and uniquely expressed fallow deer (FD) proliferation and mineralization genes, respectively, including uhrf1 and s100a10. Immunofluorescence studies showed that uhrf1 and s100a10 were expressed in regenerating deer antlers while gene overexpression and gene knockdown studies demonstrated the proliferation contributions of uhrf1 and mineralization capabilities of s100a10.

conclusionUsing a simple, in vitro comparative RNA-seq approach, novel genes pertinent to fast bony antler regeneration were identified and their proliferative/osteogenic function was verified via gene overexpression, knockdown, and immunostaining. This combinatorial approach may be applicable to discover unique gene contributions between any two organisms for a given phenomenon-of-interest.

Indexed as

AnimalsAntlersCalcification, PhysiologicCCAAT-Enhancer-Binding ProteinsCell DifferentiationCell ProliferationCells, CulturedDeerHumansMesenchymal Stem CellsModels, BiologicalOsteogenesisReproducibility of ResultsS100 ProteinsSequence Analysis, RNACCAAT-Enhancer-Binding ProteinsS100 ProteinsBone regenerationComparative RNA-seqDeer antlers100a10uhrf1

Identifiers

PMID30376879
PMCPMC6208050
OpenAlexW2898763544

What OpenQuestion holds

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LicenceCC BY
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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.