Mapping molecular landmarks of human skeletal ontogeny and pluripotent stem cell-derived articular chondrocytes

Ferguson, Gabriel B.; Handel, Ben Van; Bay, Maxwell; Fiziev, Petko; Org, Tõnis; Lee, Siyoung; Shkhyan, Ruzanna; Banks, Nicholas W.; Scheinberg, Mila; Wu, Ling; Saitta, B.; Elphingstone, Joseph; Larson, A. Noelle; Riester, Scott M.; Pyle, April D.; Bernthal, Nicholas M.; Mikkola, Hanna; Ernst, Jason; Wijnen, André J. van; Bonaguidi, Michael A.; Evseenko, Denis

doi:10.1038/s41467-018-05573-y

Cited by 58 publications

(91 citation statements)

References 65 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…NLGN1 encodes neuroligin 1, which is a postsynaptic adhesion molecule involved in the regulation of glutamatergic transmission. More recently it was shown that NLGN1 is expressed during chondrogenesis and marks cellular identity of articular chondrocytes 27…”

Section: Discussionmentioning

confidence: 99%

RNA sequencing data integration reveals an miRNA interactome of osteoarthritis cartilage

et al. 2018

View full text Add to dashboard Cite

ObjectiveTo uncover the microRNA (miRNA) interactome of the osteoarthritis (OA) pathophysiological process in the cartilage.MethodsWe performed RNA sequencing in 130 samples (n=35 and n=30 pairs for messenger RNA (mRNA) and miRNA, respectively) on macroscopically preserved and lesioned OA cartilage from the same patient and performed differential expression (DE) analysis of miRNA and mRNAs. To build an OA-specific miRNA interactome, a prioritisation scheme was applied based on inverse Pearson’s correlations and inverse DE of miRNAs and mRNAs. Subsequently, these were filtered by those present in predicted (TargetScan/microT-CDS) and/or experimentally validated (miRTarBase/TarBase) public databases. Pathway enrichment analysis was applied to elucidate OA-related pathways likely mediated by miRNA regulatory mechanisms.ResultsWe found 142 miRNAs and 2387 mRNAs to be differentially expressed between lesioned and preserved OA articular cartilage. After applying prioritisation towards likely miRNA-mRNA targets, a regulatory network of 62 miRNAs targeting 238 mRNAs was created. Subsequent pathway enrichment analysis of these mRNAs (or genes) elucidated that genes within the ‘nervous system development’ are likely mediated by miRNA regulatory mechanisms (familywise error=8.4×10−5). Herein NTF3 encodes neurotrophin-3, which controls survival and differentiation of neurons and which is closely related to the nerve growth factor.ConclusionsBy an integrated approach of miRNA and mRNA sequencing data of OA cartilage, an OA miRNA interactome and related pathways were elucidated. Our functional data demonstrated interacting levels at which miRNA affects expression of genes in the cartilage and exemplified the complexity of functionally validating a network of genes that may be targeted by multiple miRNAs.

show abstract

Section: Discussionmentioning

confidence: 99%

RNA sequencing data integration reveals an miRNA interactome of osteoarthritis cartilage

et al. 2018

View full text Add to dashboard Cite

show abstract

“…However, functional studies are required to elucidate the molecular mechanism whereby these variants increase OA risk. Integrating genetic variants with genome-wide datasets of cartilage AI 52 , chromatin states 57 and open chromatin regions 77 will inform functional analyses of these loci. RNA sequencing studies have characterised new chondrocyte subtypes 60 and systematically identified all miRNAs 53 , lncRNAs 54 and circRNAs 73 present in OA cartilage.…”

Section: Discussionmentioning

confidence: 99%

“…A wealth of novel human skeletal transcriptomic analyses were published the last year, including RNAseq based datasets of OA cartilage 52e55 , timecourse analysis of in vitro chondrogenesis 56,57 and profiling of human foetal chondrocytes, myoblasts, osteoblasts, ligamentocytes and tenocytes 57 . Such RNAseq datasets generate a huge treasure trove of gene expression information, although the published studies typically focus only on a small subset of the data, with the remaining data either relegated to supplemental files or not provided.…”

Section: Transcriptomicsmentioning

confidence: 99%

“…Techniques used for the latter analyses, namely chromatin immunoprecipitation sequencing (ChIPseq) and DHS mapping, have previously required unfeasibly large number of freshly isolated cells (typically 1 Â 10 6 to 2 Â 10 7 cells), preventing such studies in cartilage. However, this has changed within the last year with publication of the first reports of histone ChIPseq and mapping of open chromatin regions in human chondrocytes 57,77 .…”

Section: Genome-wide Mapping Of Open Chromatin and Histone Modificationsmentioning

confidence: 99%

See 1 more Smart Citation

Osteoarthritis year in review 2019: genetics, genomics and epigenetics

Reynard

Barter

2020

Osteoarthritis and Cartilage

View full text Add to dashboard Cite

s u m m a r yAlthough osteoarthritis (OA) aetiology is complex, genetic, genomic and epigenetic studies published within the last decade have advanced our understanding of the molecular processes underlying this common musculoskeletal disease. The purpose of this narrative review is to highlight the key research articles within the OA genetics, genomics and epigenetics fields that were published between April 2018 and April 2019. The review focuses on the identification of new OA genetic risk loci, genomics techniques that have been used for the first time in human cartilage and new publicly available databases, and datasets that will aid OA functional studies.Fifty-six new OA susceptibility loci were identified by two large scale genome wide association study meta-analyses, increasing the number of genome-wide significant risk loci to 90. OA risk variants are enriched near genes involved in skeletal development and morphology, and show genetic overlap with height, hip shape, bone area and developmental dysplasia of the hip. Several functional studies of OA loci were published, including a genome-wide analysis of genetic variation on cartilage gene expression. A specialised data portal for exploring cross-species skeletal transcriptomic datasets has been developed, and the first use of cartilage single cell RNAseq analysis reported. This year also saw the systematic identification of all microRNAs, long non-coding RNAs and circular RNAs expressed in human OA cartilage. Putative transcriptional regulatory regions have been mapped in human chondrocytes genome-wide, providing a dataset that will facilitate the prioritisation and characterisation of OA genetic and epigenetic loci.

show abstract

“…However, in mammals only RSPO2 , and not RSPO3 , seems to be implicated in AER function [42–44]. Similarly, species-specific modifications in the gene regulatory networks driving skeletal cell type maturation have been reported [45, 46]. Together with recent scRNA-seq studies in other vertebrate model organisms [30, 47, 48], our dataset now opens new avenues for a comprehensive assessment of molecular similarities and divergences in patterning-relevant cell populations of the developing limb, across all major tetrapod clades.…”

Section: Discussionmentioning

confidence: 99%

A Single-cell Transcriptomic Atlas of the Developing Chicken Limb

Feregrino

Sacher

Parnas

et al. 2019

Preprint

View full text Add to dashboard Cite

17Background. Through precise implementation of distinct cell type specification programs, 18 differentially regulated in both space and time, complex patterns emerge during 19 organogenesis. Thanks to its easy experimental accessibility, the developing chicken limb has 20 long served as a paradigm to study vertebrate pattern formation. Through decades' worth of 21 research, we now have a firm grasp on the molecular mechanisms driving limb formation at 22 the tissue-level. However, to elucidate the dynamic interplay between transcriptional cell type 23 specification programs and pattern formation at its relevant cellular scale, we lack 24 appropriately resolved molecular data at the genome-wide level. Here, making use of droplet-25 based single-cell RNA-sequencing, we catalogue the developmental emergence of distinct 26 tissue types and their transcriptome dynamics in the distal chicken limb, the so-called 27 autopod, at cellular resolution. 28Results. Using single-cell RNA-sequencing technology, we sequenced a total of 17,628 cells 29 coming from three key developmental stages of chicken autopod patterning. Overall, we 30 identified 23 cell populations with distinct transcriptional profiles. Amongst them were small, 31 albeit essential populations like the apical ectodermal ridge, demonstrating the ability to 32 detect even rare cell types. Moreover, we uncovered the existence of molecularly distinct sub-33 populations within previously defined compartments of the developing limb, some of which 34 have important signaling functions during autopod pattern formation. Finally, we inferred 35 gene co-expression modules that coincide with distinct tissue types across developmental 36 time, and used them to track patterning-relevant cell populations of the forming digits.37Conclusions. We provide a comprehensive functional genomics resource to study the 38 molecular effectors of chicken limb patterning at cellular resolution. Our single-cell 39 transcriptomic atlas captures all major cell populations of the developing autopod, and 40 highlights the transcriptional complexity in many of its components. Finally, integrating our 41 data-set with other single-cell transcriptomics resources will enable researchers to assess 42 molecular similarities in orthologous cell types across the major tetrapod clades, and provide 43 an extensive candidate gene list to functionally test cell-type-specific drivers of limb 44 morphological diversification. 45 46 Background 50 Embryonic pattern formation relies on the tight coordination of numerous developmental 51 processes, across multiple scales of complexity. From seemingly homogenous progenitor 52 populations, different cell types get specified and arranged in intricate patterns, to give rise to 53 functional tissues and organs. As progenitors mostly share a common genome, this 54 phenotypic specialization relies on the precise execution of distinct gene regulatory networks, 55 to enable cell type specification and ensuing pattern formation [1-3]. Slight deviations in 56 these p...

show abstract

Mapping molecular landmarks of human skeletal ontogeny and pluripotent stem cell-derived articular chondrocytes

Cited by 58 publications

References 65 publications

RNA sequencing data integration reveals an miRNA interactome of osteoarthritis cartilage

RNA sequencing data integration reveals an miRNA interactome of osteoarthritis cartilage

Osteoarthritis year in review 2019: genetics, genomics and epigenetics

A Single-cell Transcriptomic Atlas of the Developing Chicken Limb

Contact Info

Product

Resources

About