72 results on '"Capellini TD"'
Search Results
2. Genome-wide association of phenotypes based on clustering patterns of hand osteoarthritis identify WNT9A as novel osteoarthritis gene
- Author
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Boer, Cindy, Yau, MS, Rice, SJ, Almeida, R, Cheung, K, Styrkarsdottir, U, Southam, L, Broer, Linda, Wilkinson, JM, Uitterlinden, André, Zeggini, E, Felson, D, Loughlin, J, Young, M, Capellini, TD, Meulenbelt, I, van Meurs, Joyce, Boer, Cindy, Yau, MS, Rice, SJ, Almeida, R, Cheung, K, Styrkarsdottir, U, Southam, L, Broer, Linda, Wilkinson, JM, Uitterlinden, André, Zeggini, E, Felson, D, Loughlin, J, Young, M, Capellini, TD, Meulenbelt, I, and van Meurs, Joyce
- Abstract
Background Despite recent advances in the understanding of the genetic architecture of osteoarthritis (OA), only two genetic loci have been identified for OA of the hand, in part explained by the complexity of the different hand joints and heterogeneity of OA pathology. Methods We used data from the Rotterdam Study (RSI, RSII and RSIII) to create three hand OA phenotypes based on clustering patterns of radiographic OA severity to increase power in our modest discovery genome-wide association studies in the RS (n=8700), and sought replication in an independent cohort, the Framingham Heart Study (n=1203). We used multiple approaches that leverage different levels of information and functional data to further investigate the underlying biological mechanisms and candidate genes for replicated loci. We also attempted to replicate known OA loci at other joint sites, including the hips and knees. Results We found two novel genome-wide significant loci for OA in the thumb joints. We identified WNT9A as a possible novel causal gene involved in OA pathogenesis. Furthermore, several previously identified genetic loci for OA seem to confer risk for OA across multiple joints: TGFa, RUNX2, COL27A1, ASTN2, IL11 and GDF5 loci. Conclusions We identified a robust novel genetic locus for hand OA on chromosome 1, of which WNT9A is the most likely causal gene. In addition, multiple genetic loci were identified to be associated with OA across multiple joints. Our study confirms the potential for novel insight into the genetic architecture of OA by using biologically meaningful stratified phenotypes.
- Published
- 2021
3. Tendon-to-bone attachment cells are bi-fated < and > are regulated by shared enhancers < and > KLF transcription factors
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Kult, S, Olender, T, Osterwalder, M, Krief, S, Blecher-Gonen, R, Ben-Moshe, S, Farack, L, Keren-Shaul, H, Leshkowitz, D, Salame, TM, Capellini, TD, Itzkovitz, S, Amit, I, Visel, A, and Zelzer, E
- Subjects
Genetics & Heredity ,Clinical Sciences ,Genetics - Published
- 2020
4. A robust method for RNA extraction and purification from a single adult mouse tendon
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Grinstein, M, primary, Dingwall, HL, additional, Shah, RR, additional, Capellini, TD, additional, and Galloway, JL, additional
- Published
- 2018
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5. Functional genomics of human skeletal development and the patterning of height heritability.
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Richard D, Muthuirulan P, Young M, Yengo L, Vedantam S, Marouli E, Bartell E, Hirschhorn J, and Capellini TD
- Abstract
Underlying variation in height are regulatory changes to chondrocytes, cartilage cells comprising long-bone growth plates. Currently, we lack knowledge on epigenetic regulation and gene expression of chondrocytes sampled across the human skeleton, and therefore we cannot understand basic regulatory mechanisms controlling height biology. We first rectify this issue by generating extensive epigenetic and transcriptomic maps from chondrocytes sampled from different growth plates across developing human skeletons, discovering novel regulatory networks shaping human bone/joint development. Next, using these maps in tandem with height genome-wide association study (GWAS) signals, we disentangle the regulatory impacts that skeletal element-specific versus global-acting variants have on skeletal growth, revealing the prime importance of regulatory pleiotropy in controlling height variation. Finally, as height is highly heritable, and thus often the test case for complex-trait genetics, we leverage these datasets within a testable omnigenic model framework to discover novel chondrocyte developmental modules and peripheral-acting factors shaping height biology and skeletal growth., Competing Interests: Declaration of interests E.B. is a recent employee of Empirico Inc, a position that was obtained after his contributions were made to the paper. J.H. has equity in Camp4 Therapeutics., (Copyright © 2024 The Author(s). Published by Elsevier Inc. All rights reserved.)
- Published
- 2024
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6. Complex regulatory interactions at GDF5 shape joint morphology and osteoarthritis disease risk.
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Coveney CR, Maridas D, Chen H, Muthuirulan P, Liu Z, Jagoda E, Yarlagadda S, Movahhedi M, Proffen B, Rosen V, Kiapour AM, and Capellini TD
- Abstract
Our ability to pinpoint causal variants using GWAS is dependent on understanding the dynamic epigenomic and epistatic context of each associated locus. Being the best studied skeletal locus, GDF5 associates with many diseases and has a complex cis-regulatory architecture. We interrogate GDF5 regulatory interactions and model disease variants in vitro and in vivo . For all regulatory regions we see that local epigenetic activation/repression impacts patterns of joint-specific expression and disease risk. By modeling the most cited risk variant in mice we found that it had no impact on expression, joint morphology, or disease. Yet, we identified significant epistatic expression interactions between this risk variant and others lying within regulatory regions subject to repression or activation. These findings are important lessons on how regulatory interactions and local epistasis work in the etiology of disease risk, and that assessment of individual variants of high GWAS significance need not alone be considered causal., Competing Interests: Competing Interests The following individuals have competing interests: Dr. Hao Chen (Genentech); Dr. Ata Kiapour (MIACH orthopedics), Dr. Pushpanathan Muthuirulan (23&Me); Dr. Zun Liu (Sanofi); Dr. Vicki Rosen (Incyte Pharmaceuticals; Lightning Pharmaceuticals). All other authors do not have competing interests.
- Published
- 2024
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7. A latent Axin2 + /Scx + progenitor pool is the central organizer of tendon healing.
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Grinstein M, Tsai SL, Montoro D, Freedman BR, Dingwall HL, Villaseñor S, Zou K, Sade-Feldman M, Tanaka MJ, Mooney DJ, Capellini TD, Rajagopal J, and Galloway JL
- Abstract
A tendon's ordered extracellular matrix (ECM) is essential for transmitting force but is also highly prone to injury. How tendon cells embedded within and surrounding this dense ECM orchestrate healing is not well understood. Here, we identify a specialized quiescent Scx
+ /Axin2+ population in mouse and human tendons that initiates healing and is a major functional contributor to repair. Axin2+ cells express stem cell markers, expand in vitro, and have multilineage differentiation potential. Following tendon injury, Axin2+ -descendants infiltrate the injury site, proliferate, and differentiate into tenocytes. Transplantation assays of Axin2-labeled cells into injured tendons reveal their dual capacity to significantly proliferate and differentiate yet retain their Axin2+ identity. Specific loss of Wnt secretion in Axin2+ or Scx+ cells disrupts their ability to respond to injury, severely compromising healing. Our work highlights an unusual paradigm, wherein specialized Axin2+ /Scx+ cells rely on self-regulation to maintain their identity as key organizers of tissue healing., (© 2024. The Author(s).)- Published
- 2024
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8. Parallel Evolution at the Regulatory Base-Pair Level Contributes to Mammalian Interspecific Differences in Polygenic Traits.
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Okamoto AS and Capellini TD
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- Animals, Humans, Mice, Primates genetics, Regulatory Sequences, Nucleic Acid, Biological Evolution, Species Specificity, Polymorphism, Single Nucleotide, Multifactorial Inheritance, Evolution, Molecular, Mammals genetics
- Abstract
Parallel evolution occurs when distinct lineages with similar ancestral states converge on a new phenotype. Parallel evolution has been well documented at the organ, gene pathway, and amino acid sequence level but in theory, it can also occur at individual nucleotides within noncoding regions. To examine the role of parallel evolution in shaping the biology of mammalian complex traits, we used data on single-nucleotide polymorphisms (SNPs) influencing human intraspecific variation to predict trait values in other species for 11 complex traits. We found that the alleles at SNP positions associated with human intraspecific height and red blood cell (RBC) count variation are associated with interspecific variation in the corresponding traits across mammals. These associations hold for deeper branches of mammalian evolution as well as between strains of collaborative cross mice. While variation in RBC count between primates uses both ancient and more recently evolved genomic regions, we found that only primate-specific elements were correlated with primate body size. We show that the SNP positions driving these signals are flanked by conserved sequences, maintain synteny with target genes, and overlap transcription factor binding sites. This work highlights the potential of conserved but tunable regulatory elements to be reused in parallel to facilitate evolutionary adaptation in mammals., (© The Author(s) 2024. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution.)
- Published
- 2024
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9. Survival analysis on subchondral bone length for total knee replacement.
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Surendran T, Park LK, Lauber MV, Cha B, Jhun RS, Capellini TD, Kumar D, Felson DT, and Kolachalama VB
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- Humans, Female, Male, Aged, Middle Aged, Survival Analysis, Knee Joint diagnostic imaging, Knee Joint surgery, Knee Joint pathology, Arthroplasty, Replacement, Knee, Osteoarthritis, Knee diagnostic imaging, Osteoarthritis, Knee surgery, Magnetic Resonance Imaging methods, Disease Progression
- Abstract
Objective: Use subchondral bone length (SBL), a new MRI-derived measure that reflects the extent of cartilage loss and bone flattening, to predict the risk of progression to total knee replacement (TKR)., Methods: We employed baseline MRI data from the Osteoarthritis Initiative (OAI), focusing on 760 men and 1214 women with bone marrow lesions (BMLs) and joint space narrowing (JSN) scores, to predict the progression to TKR. To minimize bias from analyzing both knees of a participant, only the knee with a higher Kellgren-Lawrence (KL) grade was considered, given its greater potential need for TKR. We utilized the Kaplan-Meier survival curves and Cox proportional hazards models, incorporating raw and normalized values of SBL, JSN, and BML as predictors. The study included subgroup analyses for different demographics and clinical characteristics, using models for raw and normalized SBL (merged, femoral, tibial), BML (merged, femoral, tibial), and JSN (medial and lateral compartments). Model performance was evaluated using the time-dependent area under the curve (AUC), Brier score, and Concordance index to gauge accuracy, calibration, and discriminatory power. Knee joint and region-level analyses were conducted to determine the effectiveness of SBL, JSN, and BML in predicting TKR risk., Results: The SBL model, incorporating data from both the femur and tibia, demonstrated a predictive capacity for TKR that closely matched the performance of the BML score and the JSN grade. The Concordance index of the SBL model was 0.764, closely mirroring the BML's 0.759 and slightly below JSN's 0.788. The Brier score for the SBL model stood at 0.069, showing comparability with BML's 0.073 and a minor difference from JSN's 0.067. Regarding the AUC, the SBL model achieved 0.803, nearly identical to BML's 0.802 and slightly lower than JSN's 0.827., Conclusion: SBL's capacity to predict the risk of progression to TKR highlights its potential as an effective imaging biomarker for knee osteoarthritis., (© 2024. The Author(s), under exclusive licence to International Skeletal Society (ISS).)
- Published
- 2024
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10. Leveraging single cell multiomic analyses to identify factors that drive human chondrocyte cell fate.
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Venkatasubramanian D, Senevirathne G, Capellini TD, and Craft AM
- Abstract
Cartilage plays a crucial role in skeletal development and function, and abnormal development contributes to genetic and age-related skeletal disease. To better understand how human cartilage develops in vivo , we jointly profiled the transcriptome and open chromatin regions in individual nuclei recovered from distal femurs at 2 fetal timepoints. We used these multiomic data to identify transcription factors expressed in distinct chondrocyte subtypes, link accessible regulatory elements with gene expression, and predict transcription factor-based regulatory networks that are important for growth plate or epiphyseal chondrocyte differentiation. We developed a human pluripotent stem cell platform for interrogating the function of predicted transcription factors during chondrocyte differentiation and used it to test NFATC2 . We expect new regulatory networks we uncovered using multiomic data to be important for promoting cartilage health and treating disease, and our platform to be a useful tool for studying cartilage development in vitro ., Statement of Significance: The identity and integrity of the articular cartilage lining our joints are crucial to pain-free activities of daily living. Here we identified a gene regulatory landscape of human chondrogenesis at single cell resolution, which is expected to open new avenues of research aimed at mitigating cartilage diseases that affect hundreds of millions of individuals world-wide.
- Published
- 2024
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11. Lions & sea lions & bears, oh my: utilizing museum specimens to study the ossification sequence of carnivoran taxa.
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Sarasa JL, Okamoto AS, Wright MA, Pierce SE, and Capellini TD
- Abstract
Background: Mammalian skeletons are largely formed before birth. Heterochronic changes in skeletal formation can be investigated by comparing the order of ossification for different elements of the skeleton. Due to the challenge of collecting prenatal specimens in viviparous taxa, opportunistically collected museum specimens provide the best material for studying prenatal skeletal development across many mammalian species. Previous studies have investigated ossification sequence in a range of mammalian species, but little is known about the pattern of bone formation in Carnivora. Carnivorans have diverse ecologies, diets, and biomechanical specializations and are well-suited for investigating questions in evolutionary biology. Currently, developmental data on carnivorans is largely limited to domesticated species. To expand available data on carnivoran skeletal development, we used micro-computed tomography (micro-CT) to non-invasively evaluate the degree of ossification in all prenatal carnivoran specimens housed in the Harvard Museum of Comparative Zoology. By coding the presence or absence of bones in each specimen, we constructed ossification sequences for each species. Parsimov-based genetic inference (PGi) was then used to identify heterochronic shifts between carnivoran lineages and reconstruct the ancestral ossification sequence of Carnivora., Results: We used micro-CT to study prenatal ossification sequence in six carnivora species: Eumetopias jubatus (Steller sea lion, n = 6), Herpestes javanicus (small Indian mongoose, n = 1), Panthera leo (lion, n = 1), Urocyon cinereoargenteus (gray fox, n = 1), Ursus arctos arctos (Eurasian brown bear, n = 1), and Viverricula indica (small Indian civet, n = 5). Due to the relatively later stage of collection for the available specimens, few heterochronic shifts were identified. Ossification sequences of feliform species showed complete agreement with the domestic cat. In caniforms, the bear and fox ossification sequences largely matched the dog, but numerous heterochronic shifts were identified in the sea lion., Conclusions: We use museum specimens to generate cranial and postcranial micro-CT data on six species split between the two major carnivoran clades: Caniformia and Feliformia. Our data suggest that the ossification sequence of domestic dogs and cats are likely good models for terrestrial caniforms and feliforms, respectively, but not pinnipeds., (© 2024. The Author(s).)
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- 2024
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12. A spatio-temporally constrained gene regulatory network directed by PBX1/2 acquires limb patterning specificity via HAND2.
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Losa M, Barozzi I, Osterwalder M, Hermosilla-Aguayo V, Morabito A, Chacón BH, Zarrineh P, Girdziusaite A, Benazet JD, Zhu J, Mackem S, Capellini TD, Dickel D, Bobola N, Zuniga A, Visel A, Zeller R, and Selleri L
- Subjects
- Animals, Mice, Homeodomain Proteins metabolism, Pre-B-Cell Leukemia Transcription Factor 1 genetics, Gene Regulatory Networks, Transcription Factors genetics, Transcription Factors metabolism
- Abstract
A lingering question in developmental biology has centered on how transcription factors with widespread distribution in vertebrate embryos can perform tissue-specific functions. Here, using the murine hindlimb as a model, we investigate the elusive mechanisms whereby PBX TALE homeoproteins, viewed primarily as HOX cofactors, attain context-specific developmental roles despite ubiquitous presence in the embryo. We first demonstrate that mesenchymal-specific loss of PBX1/2 or the transcriptional regulator HAND2 generates similar limb phenotypes. By combining tissue-specific and temporally controlled mutagenesis with multi-omics approaches, we reconstruct a gene regulatory network (GRN) at organismal-level resolution that is collaboratively directed by PBX1/2 and HAND2 interactions in subsets of posterior hindlimb mesenchymal cells. Genome-wide profiling of PBX1 binding across multiple embryonic tissues further reveals that HAND2 interacts with subsets of PBX-bound regions to regulate limb-specific GRNs. Our research elucidates fundamental principles by which promiscuous transcription factors cooperate with cofactors that display domain-restricted localization to instruct tissue-specific developmental programs., (© 2023. The Author(s).)
- Published
- 2023
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13. Molecular mechanism of synovial joint site specification and induction in developing vertebrate limbs.
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Yadav US, Biswas T, Singh PN, Gupta P, Chakraborty S, Delgado I, Zafar H, Capellini TD, Torres M, and Bandyopadhyay A
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- Animals, Myeloid Ecotropic Viral Integration Site 1 Protein genetics, Myeloid Ecotropic Viral Integration Site 1 Protein metabolism, Vertebrates genetics, Vertebrates metabolism, Extremities, Gene Expression Regulation, Developmental, Transcription Factors genetics, Transcription Factors metabolism, Joints metabolism
- Abstract
The vertebrate appendage comprises three primary segments, the stylopod, zeugopod and autopod, each separated by joints. The molecular mechanisms governing the specification of joint sites, which define segment lengths and thereby limb architecture, remain largely unknown. Existing literature suggests that reciprocal gradients of retinoic acid (RA) and fibroblast growth factor (FGF) signaling define the expression domains of the putative segment markers Meis1, Hoxa11 and Hoxa13. Barx1 is expressed in the presumptive joint sites. Our data demonstrate that RA-FGF signaling gradients define the expression domain of Barx1 in the first presumptive joint site. When misexpressed, Barx1 induces ectopic interzone-like structures, and its loss of function partially blocks interzone development. Simultaneous perturbations of RA-FGF signaling gradients result in predictable shifts of Barx1 expression domains along the proximo-distal axis and, consequently, in the formation of repositioned joints. Our data suggest that during early limb bud development in chick, Meis1 and Hoxa11 expression domains are overlapping, whereas the Barx1 expression domain resides within the Hoxa11 expression domain. However, once the interzone is formed, the expression domains are refined and the Barx1 expression domain becomes congruent with the border of these two putative segment markers., Competing Interests: Competing interests The authors declare no competing or financial interests., (© 2023. Published by The Company of Biologists Ltd.)
- Published
- 2023
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14. Human and African ape myosin heavy chain content and the evolution of hominin skeletal muscle.
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Queeno SR, Reiser PJ, Orr CM, Capellini TD, Sterner KN, and O'Neill MC
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- Humans, Animals, Pan troglodytes, Muscle, Skeletal, Muscle Fibers, Skeletal, Protein Isoforms, Mammals, Myosin Heavy Chains genetics, Hominidae
- Abstract
Humans are unique among terrestrial mammals in our manner of walking and running, reflecting 7 to 8 Ma of musculoskeletal evolution since diverging with the genus Pan. One component of this is a shift in our skeletal muscle biology towards a predominance of myosin heavy chain (MyHC) I isoforms (i.e. slow fibers) across our pelvis and lower limbs, which distinguishes us from chimpanzees. Here, new MyHC data from 35 pelvis and hind limb muscles of a Western gorilla (Gorilla gorilla) are presented. These data are combined with a similar chimpanzee dataset to assess the MyHC I content of humans in comparison to African apes (chimpanzees and gorillas) and other terrestrial mammals. The responsiveness of human skeletal muscle to behavioral interventions is also compared to the human-African ape differential. Humans are distinct from African apes and among a small group of terrestrial mammals whose pelvis and lower limb muscle is slow fiber dominant, on average. Behavioral interventions, including immobilization, bed rest, spaceflight and exercise, can induce modest decreases and increases in human MyHC I content (i.e. -9.3% to 2.3%, n = 2033 subjects), but these shifts are much smaller than the mean human-African ape differential (i.e. 31%). Taken together, these results indicate muscle fiber content is likely an evolvable trait under selection in the hominin lineage. As such, we highlight potential targets of selection in the genome (e.g. regions that regulate MyHC content) that may play an important role in hominin skeletal muscle evolution., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023. Published by Elsevier Inc.)
- Published
- 2023
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15. The Notch-mediated circuitry in the evolution and generation of new cell lineages: the tooth model.
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Mitsiadis TA, Pagella P, Capellini TD, and Smith MM
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- Pregnancy, Female, Mice, Animals, Cell Lineage genetics, Serrate-Jagged Proteins metabolism, Cell Differentiation physiology, Carrier Proteins, Mammals metabolism, Membrane Proteins metabolism, Receptors, Notch genetics, Receptors, Notch metabolism
- Abstract
The Notch pathway is an ancient, evolutionary conserved intercellular signaling mechanism that is involved in cell fate specification and proper embryonic development. The Jagged2 gene, which encodes a ligand for the Notch family of receptors, is expressed from the earliest stages of odontogenesis in epithelial cells that will later generate the enamel-producing ameloblasts. Homozygous Jagged2 mutant mice exhibit abnormal tooth morphology and impaired enamel deposition. Enamel composition and structure in mammals are tightly linked to the enamel organ that represents an evolutionary unit formed by distinct dental epithelial cell types. The physical cooperativity between Notch ligands and receptors suggests that Jagged2 deletion could alter the expression profile of Notch receptors, thus modifying the whole Notch signaling cascade in cells within the enamel organ. Indeed, both Notch1 and Notch2 expression are severely disturbed in the enamel organ of Jagged2 mutant teeth. It appears that the deregulation of the Notch signaling cascade reverts the evolutionary path generating dental structures more reminiscent of the enameloid of fishes rather than of mammalian enamel. Loss of interactions between Notch and Jagged proteins may initiate the suppression of complementary dental epithelial cell fates acquired during evolution. We propose that the increased number of Notch homologues in metazoa enabled incipient sister cell types to form and maintain distinctive cell fates within organs and tissues along evolution., (© 2023. The Author(s).)
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- 2023
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16. Epigenetics as a mediator of genetic risk in osteoarthritis: role during development, homeostasis, aging, and disease progression.
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Richard D, Capellini TD, and Diekman BO
- Subjects
- Adult, Humans, Genome-Wide Association Study, Epigenesis, Genetic genetics, Aging genetics, Homeostasis genetics, Risk Factors, Disease Progression, Genetic Predisposition to Disease genetics, Osteoarthritis genetics
- Abstract
The identification of genomic loci that are associated with osteoarthritis (OA) has provided a starting point for understanding how genetic variation activates catabolic processes in the joint. However, genetic variants can only alter gene expression and cellular function when the epigenetic environment is permissive to these effects. In this review, we provide examples of how epigenetic shifts at distinct life stages can alter the risk for OA, which we posit is critical for the proper interpretation of genome-wide association studies (GWAS). During development, intensive work on the growth and differentiation factor 5 ( GDF5 ) locus has revealed the importance of tissue-specific enhancer activity in controlling both joint development and the subsequent risk for OA. During homeostasis in adults, underlying genetic risk factors may help establish beneficial or catabolic "set points" that dictate tissue function, with a strong cumulative effect on OA risk. During aging, methylation changes and the reorganization of chromatin can "unmask" the effects of genetic variants. The destructive function of variants that alter aging would only mediate effects after reproductive competence and thus avoid any evolutionary selection pressure, as consistent with larger frameworks of biological aging and its relationship to disease. A similar "unmasking" may occur during OA progression, which is supported by the finding of distinct expression quantitative trait loci (eQTLs) in chondrocytes depending on the degree of tissue degradation. Finally, we propose that massively parallel reporter assays (MPRAs) will be a valuable tool to test the function of putative OA GWAS variants in chondrocytes from different life stages.
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- 2023
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17. The functional and evolutionary impacts of human-specific deletions in conserved elements.
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Xue JR, Mackay-Smith A, Mouri K, Garcia MF, Dong MX, Akers JF, Noble M, Li X, Lindblad-Toh K, Karlsson EK, Noonan JP, Capellini TD, Brennand KJ, Tewhey R, Sabeti PC, and Reilly SK
- Subjects
- Humans, Conserved Sequence genetics, Genome, Genomics, RNA-Binding Proteins genetics, Evolution, Molecular, Sequence Deletion, Brain growth & development, Gene Expression Regulation, Developmental
- Abstract
Conserved genomic sequences disrupted in humans may underlie uniquely human phenotypic traits. We identified and characterized 10,032 human-specific conserved deletions (hCONDELs). These short (average 2.56 base pairs) deletions are enriched for human brain functions across genetic, epigenomic, and transcriptomic datasets. Using massively parallel reporter assays in six cell types, we discovered 800 hCONDELs conferring significant differences in regulatory activity, half of which enhance rather than disrupt regulatory function. We highlight several hCONDELs with putative human-specific effects on brain development, including HDAC5 , CPEB4 , and PPP2CA . Reverting an hCONDEL to the ancestral sequence alters the expression of LOXL2 and developmental genes involved in myelination and synaptic function. Our data provide a rich resource to investigate the evolutionary mechanisms driving new traits in humans and other species.
- Published
- 2023
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18. Lineage-specific differences and regulatory networks governing human chondrocyte development.
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Richard D, Pregizer S, Venkatasubramanian D, Raftery RM, Muthuirulan P, Liu Z, Capellini TD, and Craft AM
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- Humans, Animals, Mice, Cell Differentiation genetics, Growth Plate, Transcription Factors genetics, Transcription Factors metabolism, Chondrogenesis genetics, Chondrocytes metabolism, Cartilage
- Abstract
To address large gaps in our understanding of the molecular regulation of articular and growth plate cartilage development in humans, we used our directed differentiation approach to generate these distinct cartilage tissues from human embryonic stem cells. The resulting transcriptomic profiles of hESC-derived articular and growth plate chondrocytes were similar to fetal epiphyseal and growth plate chondrocytes, with respect to genes both known and previously unknown to cartilage biology. With the goal to characterize the regulatory landscapes accompanying these respective transcriptomes, we mapped chromatin accessibility in hESC-derived chondrocyte lineages, and mouse embryonic chondrocytes, using ATAC-sequencing. Integration of the expression dataset with the differentially accessible genomic regions revealed lineage-specific gene regulatory networks. We validated functional interactions of two transcription factors (TFs) (RUNX2 in growth plate chondrocytes and RELA in articular chondrocytes) with their predicted genomic targets. The maps we provide thus represent a framework for probing regulatory interactions governing chondrocyte differentiation. This work constitutes a substantial step towards comprehensive and comparative molecular characterizations of distinct chondrogenic lineages and sheds new light on human cartilage development and biology., Competing Interests: DR, SP, DV, RR, PM, ZL, TC, AC No competing interests declared, (© 2023, Richard, Pregizer et al.)
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- 2023
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19. Regulatory dissection of the severe COVID-19 risk locus introgressed by Neanderthals.
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Jagoda E, Marnetto D, Senevirathne G, Gonzalez V, Baid K, Montinaro F, Richard D, Falzarano D, LeBlanc EV, Colpitts CC, Banerjee A, Pagani L, and Capellini TD
- Subjects
- Humans, Animals, SARS-CoV-2 genetics, Genetics, Population, COVID-19 genetics, Neanderthals genetics, Virus Diseases
- Abstract
Individuals infected with the SARS-CoV-2 virus present with a wide variety of symptoms ranging from asymptomatic to severe and even lethal outcomes. Past research has revealed a genetic haplotype on chromosome 3 that entered the human population via introgression from Neanderthals as the strongest genetic risk factor for the severe response to COVID-19. However, the specific variants along this introgressed haplotype that contribute to this risk and the biological mechanisms that are involved remain unclear. Here, we assess the variants present on the risk haplotype for their likelihood of driving the genetic predisposition to severe COVID-19 outcomes. We do this by first exploring their impact on the regulation of genes involved in COVID-19 infection using a variety of population genetics and functional genomics tools. We then perform a locus-specific massively parallel reporter assay to individually assess the regulatory potential of each allele on the haplotype in a multipotent immune-related cell line. We ultimately reduce the set of over 600 linked genetic variants to identify four introgressed alleles that are strong functional candidates for driving the association between this locus and severe COVID-19. Using reporter assays in the presence/absence of SARS-CoV-2 , we find evidence that these variants respond to viral infection. These variants likely drive the locus' impact on severity by modulating the regulation of two critical chemokine receptor genes: CCR1 and CCR5 . These alleles are ideal targets for future functional investigations into the interaction between host genomics and COVID-19 outcomes., Competing Interests: EJ, DM, GS, VG, KB, FM, DR, DF, EL, CC, AB, LP, TC No competing interests declared, (© 2023, Jagoda, Marnetto et al.)
- Published
- 2023
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20. The developmental impacts of natural selection on human pelvic morphology.
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Young M, Richard D, Grabowski M, Auerbach BM, de Bakker BS, Hagoort J, Muthuirulan P, Kharkar V, Kurki HK, Betti L, Birkenstock L, Lewton KL, and Capellini TD
- Subjects
- Animals, Biological Evolution, Female, Humans, Parturition, Pregnancy, Selection, Genetic, Hominidae anatomy & histology, Pelvis anatomy & histology
- Abstract
Evolutionary responses to selection for bipedalism and childbirth have shaped the human pelvis, a structure that differs substantially from that in apes. Morphology related to these factors is present by birth, yet the developmental-genetic mechanisms governing pelvic shape remain largely unknown. Here, we pinpoint and characterize a key gestational window when human-specific pelvic morphology becomes recognizable, as the ilium and the entire pelvis acquire traits essential for human walking and birth. We next use functional genomics to molecularly characterize chondrocytes from different pelvic subelements during this window to reveal their developmental-genetic architectures. We then find notable evidence of ancient selection and genetic constraint on regulatory sequences involved in ilium expansion and growth, findings complemented by our phenotypic analyses showing that variation in iliac traits is reduced in humans compared to African apes. Our datasets provide important resources for musculoskeletal biology and begin to elucidate developmental mechanisms that shape human-specific morphology.
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- 2022
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21. Intronic regulation of SARS-CoV-2 receptor (ACE2) expression mediated by immune signaling and oxidative stress pathways.
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Richard D, Muthuirulan P, Aguiar J, Doxey AC, Banerjee A, Mossman K, Hirota J, and Capellini TD
- Abstract
The angiotensin-converting enzyme 2 (ACE2) protein is a key catalytic regulator of the renin-angiotensin system (RAS), involved in fluid homeostasis and blood pressure modulation. ACE2 also serves as a cell-surface receptor for some coronaviruses such as SARS-CoV and SARS-CoV-2 . Improved characterization of ACE2 regulation may help us understand the effects of pre-existing conditions on COVID-19 incidence, as well as pathogenic dysregulation following viral infection. Here, we perform bioinformatic analyses to hypothesize on ACE2 gene regulation in two different physiological contexts, identifying putative regulatory elements of ACE2 expression. We perform functional validation of our computational predictions via targeted CRISPR-Cas9 deletions of these elements in vitro , finding them responsive to immune signaling and oxidative-stress pathways. This contributes to our understanding of ACE2 gene regulation at baseline and immune challenge. Our work supports pursuit of these putative mechanisms in our understanding of infection/disease caused by current, and future, SARS-related viruses such as SARS-CoV-2 ., Competing Interests: The authors declare no competing interests., (© 2022 The Author(s).)
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- 2022
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22. Author Correction: Joint disease-specificity at the regulatory base-pair level.
- Author
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Muthuirulan P, Zhao D, Young M, Richard D, Liu Z, Emami A, Portilla G, Hosseinzadeh S, Cao J, Maridas D, Sedlak M, Menghini D, Cheng L, Li L, Ding X, Ding Y, Rosen V, Kiapour AM, and Capellini TD
- Published
- 2022
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23. Interspecies transcriptomics identify genes that underlie disproportionate foot growth in jerboas.
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Saxena A, Sharma V, Muthuirulan P, Neufeld SJ, Tran MP, Gutierrez HL, Chen KD, Erberich JM, Birmingham A, Capellini TD, Cobb J, Hiller M, and Cooper KL
- Subjects
- Animals, Extremities, Foot, Mice, Transcription Factors metabolism, Rodentia, Transcriptome
- Abstract
Despite the great diversity of vertebrate limb proportion and our deep understanding of the genetic mechanisms that drive skeletal elongation, little is known about how individual bones reach different lengths in any species. Here, we directly compare the transcriptomes of homologous growth cartilages of the mouse (Mus musculus) and bipedal jerboa (Jaculus jaculus), the latter of which has "mouse-like" arms but extremely long metatarsals of the feet. Intersecting gene-expression differences in metatarsals and forearms of the two species revealed that about 10% of orthologous genes are associated with the disproportionately rapid elongation of neonatal jerboa feet. These include genes and enriched pathways not previously associated with endochondral elongation as well as those that might diversify skeletal proportion in addition to their known requirements for bone growth throughout the skeleton. We also identified transcription regulators that might act as "nodes" for sweeping differences in genome expression between species. Among these, Shox2, which is necessary for proximal limb elongation, has gained expression in jerboa metatarsals where it has not been detected in other vertebrates. We show that Shox2 is sufficient to increase mouse distal limb length, and a nearby putative cis-regulatory region is preferentially accessible in jerboa metatarsals. In addition to mechanisms that might directly promote growth, we found evidence that jerboa foot elongation may occur in part by de-repressing latent growth potential. The genes and pathways that we identified here provide a framework to understand the modular genetic control of skeletal growth and the remarkable malleability of vertebrate limb proportion., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2021 Elsevier Inc. All rights reserved.)
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- 2022
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24. Detection of Neanderthal Adaptively Introgressed Genetic Variants That Modulate Reporter Gene Expression in Human Immune Cells.
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Jagoda E, Xue JR, Reilly SK, Dannemann M, Racimo F, Huerta-Sanchez E, Sankararaman S, Kelso J, Pagani L, Sabeti PC, and Capellini TD
- Subjects
- Animals, Gene Expression, Humans, Inflammation, Genetic Variation, Genome, Human, Immunity, Innate genetics, Neanderthals genetics
- Abstract
Although some variation introgressed from Neanderthals has undergone selective sweeps, little is known about its functional significance. We used a Massively Parallel Reporter Assay (MPRA) to assay 5,353 high-frequency introgressed variants for their ability to modulate the gene expression within 170 bp of endogenous sequence. We identified 2,548 variants in active putative cis-regulatory elements (CREs) and 292 expression-modulating variants (emVars). These emVars are predicted to alter the binding motifs of important immune transcription factors, are enriched for associations with neutrophil and white blood cell count, and are associated with the expression of genes that function in innate immune pathways including inflammatory response and antiviral defense. We combined the MPRA data with other data sets to identify strong candidates to be driver variants of positive selection including an emVar that may contribute to protection against severe COVID-19 response. We endogenously deleted two CREs containing expression-modulation variants linked to immune function, rs11624425 and rs80317430, identifying their primary genic targets as ELMSAN1, and PAN2 and STAT2, respectively, three genes differentially expressed during influenza infection. Overall, we present the first database of experimentally identified expression-modulating Neanderthal-introgressed alleles contributing to potential immune response in modern humans., (© The Author(s) 2021. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.)
- Published
- 2022
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25. Subchondral Bone Length in Knee Osteoarthritis: A Deep Learning-Derived Imaging Measure and Its Association With Radiographic and Clinical Outcomes.
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Chang GH, Park LK, Le NA, Jhun RS, Surendran T, Lai J, Seo H, Promchotichai N, Yoon G, Scalera J, Capellini TD, Felson DT, and Kolachalama VB
- Subjects
- Aged, Disease Progression, Female, Humans, Magnetic Resonance Imaging, Male, Middle Aged, Severity of Illness Index, Cartilage, Articular diagnostic imaging, Deep Learning, Knee Joint diagnostic imaging, Osteoarthritis, Knee diagnostic imaging
- Abstract
Objective: To develop a bone shape measure that reflects the extent of cartilage loss and bone flattening in knee osteoarthritis (OA) and test it against estimates of disease severity., Methods: A fast region-based convolutional neural network was trained to crop the knee joints in sagittal dual-echo steady-state magnetic resonance imaging sequences obtained from the Osteoarthritis Initiative (OAI). Publicly available annotations of the cartilage and menisci were used as references to annotate the tibia and the femur in 61 knees. Another deep neural network (U-Net) was developed to learn these annotations. Model predictions were compared to radiologist-driven annotations on an independent test set (27 knees). The U-Net was applied to automatically extract the knee joint structures on the larger OAI data set (n = 9,434 knees). We defined subchondral bone length (SBL), a novel shape measure characterizing the extent of overlying cartilage and bone flattening, and examined its relationship with radiographic joint space narrowing (JSN), concurrent pain and disability (according to the Western Ontario and McMaster Universities Osteoarthritis Index), as well as subsequent partial or total knee replacement. Odds ratios (ORs) and 95% confidence intervals (95% CIs) for each outcome were estimated using relative changes in SBL from the OAI data set stratified into quartiles., Results: The mean SBL values for knees with JSN were consistently different from knees without JSN. Greater changes of SBL from baseline were associated with greater pain and disability. For knees with medial or lateral JSN, the ORs for future knee replacement between the lowest and highest quartiles corresponding to SBL changes were 5.68 (95% CI 3.90-8.27) and 7.19 (95% CI 3.71-13.95), respectively., Conclusion: SBL quantified OA status based on JSN severity and shows promise as an imaging marker in predicting clinical and structural OA outcomes., (© 2021, American College of Rheumatology.)
- Published
- 2021
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26. Joint disease-specificity at the regulatory base-pair level.
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Muthuirulan P, Zhao D, Young M, Richard D, Liu Z, Emami A, Portilla G, Hosseinzadeh S, Cao J, Maridas D, Sedlak M, Menghini D, Cheng L, Li L, Ding X, Ding Y, Rosen V, Kiapour AM, and Capellini TD
- Subjects
- Animals, Chondrocytes, Disease Models, Animal, Gene Expression Regulation, Genetic Predisposition to Disease, Genome-Wide Association Study, Growth Differentiation Factor 5 genetics, Growth Differentiation Factor 5 metabolism, Humans, Mice, Phenotype, Regulatory Sequences, Nucleic Acid, Exons, Hip Dislocation genetics, Hip Dislocation metabolism, Osteoarthritis, Knee genetics, Osteoarthritis, Knee metabolism
- Abstract
Given the pleiotropic nature of coding sequences and that many loci exhibit multiple disease associations, it is within non-coding sequence that disease-specificity likely exists. Here, we focus on joint disorders, finding among replicated loci, that GDF5 exhibits over twenty distinct associations, and we identify causal variants for two of its strongest associations, hip dysplasia and knee osteoarthritis. By mapping regulatory regions in joint chondrocytes, we pinpoint two variants (rs4911178; rs6060369), on the same risk haplotype, which reside in anatomical site-specific enhancers. We show that both variants have clinical relevance, impacting disease by altering morphology. By modeling each variant in humanized mice, we observe joint-specific response, correlating with GDF5 expression. Thus, we uncouple separate regulatory variants on a common risk haplotype that cause joint-specific disease. By broadening our perspective, we finally find that patterns of modularity at GDF5 are also found at over three-quarters of loci with multiple GWAS disease associations.
- Published
- 2021
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27. Shifting epigenetic contexts influence regulatory variation and disease risk.
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Richard D and Capellini TD
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- Aging genetics, Base Sequence, Chromatin metabolism, Genetic Loci, Genome, Human, Genome-Wide Association Study, Humans, Quantitative Trait, Heritable, Risk Factors, Epigenesis, Genetic, Genetic Predisposition to Disease, Genetic Variation
- Abstract
Epigenetic shifts are a hallmark of aging that impact transcriptional networks at regulatory level. These shifts may modify the effects of genetic regulatory variants during aging and contribute to disease pathomechanism. However, these shifts occur on the backdrop of epigenetic changes experienced throughout an individual's development into adulthood; thus, the phenotypic, and ultimately fitness, effects of regulatory variants subject to developmental- versus aging-related epigenetic shifts may differ considerably. Natural selection therefore may act differently on variants depending on their changing epigenetic context, which we propose as a novel lens through which to consider regulatory sequence evolution and phenotypic effects. Here, we define genomic regions subjected to altered chromatin accessibility as tissues transition from their fetal to adult forms, and subsequently from early to late adulthood. Based on these epigenomic datasets, we examine patterns of evolutionary constraint and potential functional impacts of sequence variation (e.g., genetic disease risk associations). We find that while the signals observed with developmental epigenetic changes are consistent with stronger fitness consequences (i.e., negative selection pressures), they tend to have weaker effects on genetic risk associations for aging-related diseases. Conversely, we see stronger effects of variants with increased local accessibility in adult tissues, strongest in young adult when compared to old. We propose a model for how epigenetic status of a region may influence the effects of evolutionary relevant sequence variation, and suggest that such a perspective on gene regulatory networks may elucidate our understanding of aging biology.
- Published
- 2021
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28. Experimental and natural evidence of SARS-CoV-2-infection-induced activation of type I interferon responses.
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Banerjee A, El-Sayes N, Budylowski P, Jacob RA, Richard D, Maan H, Aguiar JA, Demian WL, Baid K, D'Agostino MR, Ang JC, Murdza T, Tremblay BJ, Afkhami S, Karimzadeh M, Irving AT, Yip L, Ostrowski M, Hirota JA, Kozak R, Capellini TD, Miller MS, Wang B, Mubareka S, McGeer AJ, McArthur AG, Doxey AC, and Mossman K
- Abstract
Type I interferons (IFNs) are our first line of defense against virus infection. Recent studies have suggested the ability of SARS-CoV-2 proteins to inhibit IFN responses. Emerging data also suggest that timing and extent of IFN production is associated with manifestation of COVID-19 severity. In spite of progress in understanding how SARS-CoV-2 activates antiviral responses, mechanistic studies into wild-type SARS-CoV-2-mediated induction and inhibition of human type I IFN responses are scarce. Here we demonstrate that SARS-CoV-2 infection induces a type I IFN response in vitro and in moderate cases of COVID-19. In vitro stimulation of type I IFN expression and signaling in human airway epithelial cells is associated with activation of canonical transcriptions factors, and SARS-CoV-2 is unable to inhibit exogenous induction of these responses. Furthermore, we show that physiological levels of IFNα detected in patients with moderate COVID-19 is sufficient to suppress SARS-CoV-2 replication in human airway cells., Competing Interests: The authors declare no competing interests., (© 2021 The Author(s).)
- Published
- 2021
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29. Single Cell Omics for Musculoskeletal Research.
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Rai MF, Wu CL, Capellini TD, Guilak F, Dicks AR, Muthuirulan P, Grandi F, Bhutani N, and Westendorf JJ
- Subjects
- Chromatin Immunoprecipitation Sequencing, Flow Cytometry, Homeostasis physiology, Humans, RNA-Seq, Musculoskeletal Development physiology, Musculoskeletal Diseases physiopathology, Musculoskeletal System cytology, Single-Cell Analysis methods
- Abstract
Purpose of Review: The ability to analyze the molecular events occurring within individual cells as opposed to populations of cells is revolutionizing our understanding of musculoskeletal tissue development and disease. Single cell studies have the great potential of identifying cellular subpopulations that work in a synchronized fashion to regenerate and repair damaged tissues during normal homeostasis. In addition, such studies can elucidate how these processes break down in disease as well as identify cellular subpopulations that drive the disease. This review highlights three emerging technologies: single cell RNA sequencing (scRNA-seq), Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq), and Cytometry by Time-Of-Flight (CyTOF) mass cytometry., Recent Findings: Technological and bioinformatic tools to analyze the transcriptome, epigenome, and proteome at the individual cell level have advanced rapidly making data collection relatively easy; however, understanding how to access and interpret the data remains a challenge for many scientists. It is, therefore, of paramount significance to educate the musculoskeletal community on how single cell technologies can be used to answer research questions and advance translation. This article summarizes talks given during a workshop on "Single Cell Omics" at the 2020 annual meeting of the Orthopedic Research Society. Studies that applied scRNA-seq, ATAC-seq, and CyTOF mass cytometry to cartilage development and osteoarthritis are reviewed. This body of work shows how these cutting-edge tools can advance our understanding of the cellular heterogeneity and trajectories of lineage specification during development and disease.
- Published
- 2021
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30. Genome-wide association of phenotypes based on clustering patterns of hand osteoarthritis identify WNT9A as novel osteoarthritis gene.
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Boer CG, Yau MS, Rice SJ, Coutinho de Almeida R, Cheung K, Styrkarsdottir U, Southam L, Broer L, Wilkinson JM, Uitterlinden AG, Zeggini E, Felson D, Loughlin J, Young M, Capellini TD, Meulenbelt I, and van Meurs JB
- Subjects
- Cluster Analysis, Fibrillar Collagens genetics, Genome-Wide Association Study, Humans, Phenotype, Hand Joints diagnostic imaging, Osteoarthritis complications, Osteoarthritis diagnostic imaging, Osteoarthritis genetics, Wnt Proteins genetics
- Abstract
Background: Despite recent advances in the understanding of the genetic architecture of osteoarthritis (OA), only two genetic loci have been identified for OA of the hand, in part explained by the complexity of the different hand joints and heterogeneity of OA pathology., Methods: We used data from the Rotterdam Study (RSI, RSII and RSIII) to create three hand OA phenotypes based on clustering patterns of radiographic OA severity to increase power in our modest discovery genome-wide association studies in the RS (n=8700), and sought replication in an independent cohort, the Framingham Heart Study (n=1203). We used multiple approaches that leverage different levels of information and functional data to further investigate the underlying biological mechanisms and candidate genes for replicated loci. We also attempted to replicate known OA loci at other joint sites, including the hips and knees., Results: We found two novel genome-wide significant loci for OA in the thumb joints. We identified WNT9A as a possible novel causal gene involved in OA pathogenesis. Furthermore, several previously identified genetic loci for OA seem to confer risk for OA across multiple joints: TGFa , RUNX2 , COL27A1 , ASTN2 , IL11 and GDF5 loci., Conclusions: We identified a robust novel genetic locus for hand OA on chromosome 1, of which WNT9A is the most likely causal gene. In addition, multiple genetic loci were identified to be associated with OA across multiple joints. Our study confirms the potential for novel insight into the genetic architecture of OA by using biologically meaningful stratified phenotypes., Competing Interests: Competing interests: None declared., (© Author(s) (or their employer(s)) 2021. Re-use permitted under CC BY-NC. No commercial re-use. See rights and permissions. Published by BMJ.)
- Published
- 2021
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31. Bi-fated tendon-to-bone attachment cells are regulated by shared enhancers and KLF transcription factors.
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Kult S, Olender T, Osterwalder M, Markman S, Leshkowitz D, Krief S, Blecher-Gonen R, Ben-Moshe S, Farack L, Keren-Shaul H, Salame TM, Capellini TD, Itzkovitz S, Amit I, Visel A, and Zelzer E
- Subjects
- Animals, Bone and Bones, Female, Kruppel-Like Factor 4 genetics, Kruppel-Like Factor 4 metabolism, Kruppel-Like Transcription Factors metabolism, Mice, Regulatory Sequences, Nucleic Acid, Tendons, Chondrocytes metabolism, Kruppel-Like Transcription Factors genetics, Tenocytes metabolism, Transcriptome
- Abstract
The mechanical challenge of attaching elastic tendons to stiff bones is solved by the formation of a unique transitional tissue. Here, we show that murine tendon-to-bone attachment cells are bi-fated, activating a mixture of chondrocyte and tenocyte transcriptomes, under regulation of shared regulatory elements and Krüppel-like factors (KLFs) transcription factors. High-throughput bulk and single-cell RNA sequencing of humeral attachment cells revealed expression of hundreds of chondrogenic and tenogenic genes, which was validated by in situ hybridization and single-molecule ISH. ATAC sequencing showed that attachment cells share accessible intergenic chromatin areas with either tenocytes or chondrocytes. Epigenomic analysis revealed enhancer signatures for most of these regions. Transgenic mouse enhancer reporter assays verified the shared activity of some of these enhancers. Finally, integrative chromatin and motif analyses and transcriptomic data implicated KLFs as regulators of attachment cells. Indeed, blocking expression of both Klf2 and Klf4 in developing limb mesenchyme impaired their differentiation., Competing Interests: SK, TO, MO, SM, DL, SK, RB, SB, LF, HK, TS, TC, SI, IA, AV, EZ No competing interests declared, (© 2021, Kult et al.)
- Published
- 2021
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32. Identification of IGF2BP1-related lncRNA-miRNA-mRNA network in goat skeletal muscle satellite cells.
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Xu X, Leng J, Zhang X, Capellini TD, Chen Y, Yang L, Chen Z, Zheng S, Zhang X, Zhan S, Wang L, Zhong T, Guo J, Niu L, Wang Y, Dai D, Zhang H, Li L, and Cao J
- Subjects
- Animals, Gene Regulatory Networks, Goats genetics, Phosphatidylinositol 3-Kinases, RNA, Messenger genetics, MicroRNAs genetics, RNA, Long Noncoding, Satellite Cells, Skeletal Muscle
- Abstract
Insulin-like growth factor 2 mRNA-binding protein 1 (IGF2BP1) plays essential roles in the proliferation of skeletal muscle satellite cells (MuSCs). Increasing evidence has shown that IGF2BP1 regulates the expression of noncoding RNAs and mRNAs. However, the related molecular network remains to be fully understood. Therefore, we performed RNA sequencing and analyzed the microRNAs (miRNAs), long noncoding RNAs (lncRNAs), and mRNAs differentially expressed in goat MuSCs treated with IGF2BP1 overexpressing and empty vectors. A total of 36 miRNAs, 59 lncRNAs, and 44 mRNAs were differentially expressed caused by IGF2BP1. Expectedly, they were enriched in muscle development-related Rap1, PI3K-AKT, and FoxO signaling pathways. Finally, we constructed a lncRNA-miRNA-mRNA interaction network containing 30 lncRNAs, 15 miRNAs, and 34 mRNAs, in which several miRNAs, including miR-133a-3p, miR-204-5p, miR-125a-3p, miR-145-3p, and miR-423-5p, relate with cell growth and participate in muscle development. Overall, we constructed an IGF2BP1-related network, which provides new insight into the myogenic proliferation of goat., (© 2021 Japanese Society of Animal Science.)
- Published
- 2021
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33. Correction to: Assessment of knee pain from MR imaging using a convolutional Siamese network.
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Chang GH, Felson DT, Qiu S, Guermazi A, Capellini TD, and Kolachalama VB
- Abstract
The original version of this article, published on 13 February 2020, unfortunately contained a mistake.
- Published
- 2020
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34. Biological clocks and incremental growth line formation in dentine.
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Papakyrikos AM, Arora M, Austin C, Boughner JC, Capellini TD, Dingwall HL, Greba Q, Howland JG, Kato A, Wang XP, and Smith TM
- Subjects
- ARNTL Transcription Factors genetics, Animals, Mice, Mice, Knockout, Rats, Rats, Wistar, Biological Clocks genetics, Circadian Rhythm genetics, Dentin growth & development
- Abstract
Dentine- and enamel-forming cells secrete matrix in consistent rhythmic phases, resulting in the formation of successive microscopic growth lines inside tooth crowns and roots. Experimental studies of various mammals have proven that these lines are laid down in subdaily, daily (circadian), and multidaily rhythms, but it is less clear how these rhythms are initiated and maintained. In 2001, researchers reported that lesioning the so-called master biological clock, the suprachiasmatic nucleus (SCN), halted daily line formation in rat dentine, whereas subdaily lines persisted. More recently, a key clock gene (Bmal1) expressed in the SCN in a circadian manner was also found to be active in dentine- and enamel- secretory cells. To probe these potential neurological and local mechanisms for the production of rhythmic lines in teeth, we reexamined the role of the SCN in growth line formation in Wistar rats and investigated the presence of daily lines in Bmal1 knockout mice (Bmal1
-/- ). In contrast to the results of the 2001 study, we found that both daily and subdaily growth lines persisted in rat dentine after complete or partial SCN lesion in the majority of individuals. In mice, after transfer into constant darkness, daily rhythms continued to manifest as incremental lines in the dentine of each Bmal1 genotype (wild-type, Bmal+/- , and Bmal1-/- ). These results affirm that the manifestation of biological rhythms in teeth is a robust phenomenon, imply a more autonomous role of local biological clocks in tooth growth than previously suggested, and underscore the need further to elucidate tissue-specific circadian biology and its role in incremental line formation. Investigations of this nature will strengthen an invaluable system for determining growth rates and calendar ages from mammalian hard tissues, as well as documenting the early lives of fossil hominins and other primates., (© 2020 Anatomical Society.)- Published
- 2020
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35. Assessment of knee pain from MR imaging using a convolutional Siamese network.
- Author
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Chang GH, Felson DT, Qiu S, Guermazi A, Capellini TD, and Kolachalama VB
- Subjects
- Aged, Area Under Curve, Female, Humans, Knee diagnostic imaging, Male, Middle Aged, Neural Networks, Computer, Radiography, Severity of Illness Index, Arthralgia diagnostic imaging, Deep Learning, Knee Joint diagnostic imaging, Magnetic Resonance Imaging, Osteoarthritis, Knee diagnostic imaging, Synovitis diagnostic imaging
- Abstract
Objectives: It remains difficult to characterize the source of pain in knee joints either using radiographs or magnetic resonance imaging (MRI). We sought to determine if advanced machine learning methods such as deep neural networks could distinguish knees with pain from those without it and identify the structural features that are associated with knee pain., Methods: We constructed a convolutional Siamese network to associate MRI scans obtained on subjects from the Osteoarthritis Initiative (OAI) with frequent unilateral knee pain comparing the knee with frequent pain to the contralateral knee without pain. The Siamese network architecture enabled pairwise learning of information from two-dimensional (2D) sagittal intermediate-weighted turbo spin echo slices obtained from similar locations on both knees. Class activation mapping (CAM) was utilized to create saliency maps, which highlighted the regions most associated with knee pain. The MRI scans and the CAMs of each subject were reviewed by an expert radiologist to identify the presence of abnormalities within the model-predicted regions of high association., Results: Using 10-fold cross-validation, our model achieved an area under curve (AUC) value of 0.808. When individuals whose knee WOMAC pain scores were not discordant were excluded, model performance increased to 0.853. The radiologist review revealed that about 86% of the cases that were predicted correctly had effusion-synovitis within the regions that were most associated with pain., Conclusions: This study demonstrates a proof of principle that deep learning can be applied to assess knee pain from MRI scans., Key Points: • Our article is the first to leverage a deep learning framework to associate MR images of the knee with knee pain. • We developed a convolutional Siamese network that had the ability to fuse information from multiple two-dimensional (2D) MRI slices from the knee with pain and the contralateral knee of the same individual without pain to predict unilateral knee pain. • Our model achieved an area under curve (AUC) value of 0.808. When individuals who had WOMAC pain scores that were not discordant for knees (pain discordance < 3) were excluded, model performance increased to 0.853.
- Published
- 2020
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36. Evolutionary Selection and Constraint on Human Knee Chondrocyte Regulation Impacts Osteoarthritis Risk.
- Author
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Richard D, Liu Z, Cao J, Kiapour AM, Willen J, Yarlagadda S, Jagoda E, Kolachalama VB, Sieker JT, Chang GH, Muthuirulan P, Young M, Masson A, Konrad J, Hosseinzadeh S, Maridas DE, Rosen V, Krawetz R, Roach N, and Capellini TD
- Subjects
- Animals, Biological Evolution, Chondrocytes metabolism, Evolution, Molecular, Genetic Predisposition to Disease genetics, Growth Differentiation Factor 5 genetics, Growth Differentiation Factor 5 metabolism, HEK293 Cells, Humans, Knee physiology, Mice, NIH 3T3 Cells, Regulatory Sequences, Nucleic Acid genetics, Risk Factors, Chondrocytes physiology, Knee Joint physiology, Osteoarthritis genetics
- Abstract
During human evolution, the knee adapted to the biomechanical demands of bipedalism by altering chondrocyte developmental programs. This adaptive process was likely not without deleterious consequences to health. Today, osteoarthritis occurs in 250 million people, with risk variants enriched in non-coding sequences near chondrocyte genes, loci that likely became optimized during knee evolution. We explore this relationship by epigenetically profiling joint chondrocytes, revealing ancient selection and recent constraint and drift on knee regulatory elements, which also overlap osteoarthritis variants that contribute to disease heritability by tending to modify constrained functional sequence. We propose a model whereby genetic violations to regulatory constraint, tolerated during knee development, lead to adult pathology. In support, we discover a causal enhancer variant (rs6060369) present in billions of people at a risk locus (GDF5-UQCC1), showing how it impacts mouse knee-shape and osteoarthritis. Overall, our methods link an evolutionarily novel aspect of human anatomy to its pathogenesis., Competing Interests: Declaration of Interests The authors declare no competing interests., (Copyright © 2020 Elsevier Inc. All rights reserved.)
- Published
- 2020
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37. Variation in mouse pelvic morphology maps to locations enriched in Sox9 Class II and Pitx1 regulatory features.
- Author
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Roseman CC, Capellini TD, Jagoda E, Williams SA, Grabowski M, O'Connor C, Polk JD, and Cheverud JM
- Subjects
- Animals, Biological Evolution, Gene Expression Regulation, Developmental, Genomics, Genotype, Mice, Paired Box Transcription Factors genetics, Polymorphism, Single Nucleotide, Quantitative Trait Loci, SOX9 Transcription Factor genetics, Paired Box Transcription Factors metabolism, Pelvis growth & development, SOX9 Transcription Factor metabolism
- Abstract
Variation in pelvic morphology has a complex genetic basis and its patterning and specification is governed by conserved developmental pathways. Whether the mechanisms underlying the differentiation and specification of the pelvis also produce the morphological covariation on which natural selection may act, is still an open question in evolutionary developmental biology. We use high-resolution quantitative trait locus (QTL) mapping in the F
34 generation of an advanced intercross experiment (LG,SM-G34 ) to characterize the genetic architecture of the mouse pelvis. We test the prediction that genomic features linked to developmental patterning and differentiation of the hind limb and pelvis and the regulation of chondrogenesis are overrepresented in QTL. We find 31 single QTL trait associations at the genome- or chromosome-wise significance level coalescing to 27 pleiotropic loci. We recover further QTL at a more relaxed significance threshold replicating locations found in a previous experiment in an earlier generation of the same population. QTL were more likely than chance to harbor Pitx1 and Sox9 Class II chromatin immunoprecipitation-seq features active during development of skeletal features. There was weak or no support for the enrichment of seven more categories of developmental features drawn from the literature. Our results suggest that genotypic variation is channeled through a subset of developmental processes involved in the generation of phenotypic variation in the pelvis. This finding indicates that the evolvability of complex traits may be subject to biases not evident from patterns of covariance among morphological features or developmental patterning when either is considered in isolation., (© 2020 Wiley Periodicals, Inc.)- Published
- 2020
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38. Regulation of Gdf5 expression in joint remodelling, repair and osteoarthritis.
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Kania K, Colella F, Riemen AHK, Wang H, Howard KA, Aigner T, Dell'Accio F, Capellini TD, Roelofs AJ, and De Bari C
- Subjects
- Animals, Cartilage, Articular injuries, Cartilage, Articular metabolism, Female, Genetic Predisposition to Disease, Growth Differentiation Factor 5 genetics, Humans, Knee Joint metabolism, Male, Menisci, Tibial, Mice, Osteoarthritis genetics, Osteoarthritis metabolism, Cartilage, Articular pathology, Chondrogenesis, Gene Expression Regulation, Growth Differentiation Factor 5 metabolism, Knee Joint pathology, Osteoarthritis pathology
- Abstract
Growth and Differentiation Factor 5 (GDF5) is a key risk locus for osteoarthritis (OA). However, little is known regarding regulation of Gdf5 expression following joint tissue damage. Here, we employed Gdf5-LacZ reporter mouse lines to assess the spatiotemporal activity of Gdf5 regulatory sequences in experimental OA following destabilisation of the medial meniscus (DMM) and after acute cartilage injury and repair. Gdf5 expression was upregulated in articular cartilage post-DMM, and was increased in human OA cartilage as determined by immunohistochemistry and microarray analysis. Gdf5 expression was also upregulated during cartilage repair in mice and was switched on in injured synovium in prospective areas of cartilage formation, where it inversely correlated with expression of the transcriptional co-factor Yes-associated protein (Yap). Indeed, overexpression of Yap suppressed Gdf5 expression in chondroprogenitors in vitro. Gdf5 expression in both mouse injury models required regulatory sequence downstream of Gdf5 coding exons. Our findings suggest that Gdf5 upregulation in articular cartilage and synovium is a generic response to knee injury that is dependent on downstream regulatory sequence and in progenitors is associated with chondrogenic specification. We propose a role for Gdf5 in tissue remodelling and repair after injury, which may partly underpin its association with OA risk.
- Published
- 2020
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39. Mendelian Randomization Analysis Reveals a Causal Influence of Circulating Sclerostin Levels on Bone Mineral Density and Fractures.
- Author
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Zheng J, Maerz W, Gergei I, Kleber M, Drechsler C, Wanner C, Brandenburg V, Reppe S, Gautvik KM, Medina-Gomez C, Shevroja E, Gilly A, Park YC, Dedoussis G, Zeggini E, Lorentzon M, Henning P, Lerner UH, Nilsson KH, Movérare-Skrtic S, Baird D, Elsworth B, Falk L, Groom A, Capellini TD, Grundberg E, Nethander M, Ohlsson C, Davey Smith G, and Tobias JH
- Subjects
- Aged, Animals, Bone and Bones pathology, Child, DNA Methylation, Gene Expression Regulation, Genome-Wide Association Study, Humans, Meta-Analysis as Topic, Mice, Middle Aged, Models, Biological, Phenotype, Quantitative Trait Loci genetics, RNA, Messenger genetics, RNA, Messenger metabolism, Adaptor Proteins, Signal Transducing blood, Bone Density genetics, Fractures, Bone blood, Fractures, Bone genetics, Mendelian Randomization Analysis
- Abstract
In bone, sclerostin is mainly osteocyte-derived and plays an important local role in adaptive responses to mechanical loading. Whether circulating levels of sclerostin also play a functional role is currently unclear, which we aimed to examine by two-sample Mendelian randomization (MR). A genetic instrument for circulating sclerostin, derived from a genomewide association study (GWAS) meta-analysis of serum sclerostin in 10,584 European-descent individuals, was examined in relation to femoral neck bone mineral density (BMD; n = 32,744) in GEFOS and estimated bone mineral density (eBMD) by heel ultrasound (n = 426,824) and fracture risk (n = 426,795) in UK Biobank. Our GWAS identified two novel serum sclerostin loci, B4GALNT3 (standard deviation [SD]) change in sclerostin per A allele (β = 0.20, p = 4.6 × 10
-49 ) and GALNT1 (β = 0.11 per G allele, p = 4.4 × 10-11 ). B4GALNT3 is an N-acetyl-galactosaminyltransferase, adding a terminal LacdiNAc disaccharide to target glycocoproteins, found to be predominantly expressed in kidney, whereas GALNT1 is an enzyme causing mucin-type O-linked glycosylation. Using these two single-nucleotide polymorphisms (SNPs) as genetic instruments, MR revealed an inverse causal relationship between serum sclerostin and femoral neck BMD (β = -0.12, 95% confidence interval [CI] -0.20 to -0.05) and eBMD (β = -0.12, 95% CI -0.14 to -0.10), and a positive relationship with fracture risk (β = 0.11, 95% CI 0.01 to 0.21). Colocalization analysis demonstrated common genetic signals within the B4GALNT3 locus for higher sclerostin, lower eBMD, and greater B4GALNT3 expression in arterial tissue (probability >99%). Our findings suggest that higher sclerostin levels are causally related to lower BMD and greater fracture risk. Hence, strategies for reducing circulating sclerostin, for example by targeting glycosylation enzymes as suggested by our GWAS results, may prove valuable in treating osteoporosis. © 2019 The Authors. Journal of Bone and Mineral Research published by Wiley Periodicals, Inc., (© 2019 The Authors. Journal of Bone and Mineral Research published by Wiley Periodicals, Inc.)- Published
- 2019
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40. Complex Phenotypes: Mechanisms Underlying Variation in Human Stature.
- Author
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Muthuirulan P and Capellini TD
- Subjects
- Anthropometry, Genome-Wide Association Study, Humans, Phenotype, Biological Evolution, Body Height genetics, Body Height physiology
- Abstract
Purpose of Review: The goal of the review is to provide a comprehensive overview of the current understanding of the mechanisms underlying variation in human stature., Recent Findings: Human height is an anthropometric trait that varies considerably within human populations as well as across the globe. Historically, much research focus was placed on understanding the biology of growth plate chondrocytes and how modifications to core chondrocyte proliferation and differentiation pathways potentially shaped height attainment in normal as well as pathological contexts. Recently, much progress has been made to improve our understanding regarding the mechanisms underlying the normal and pathological range of height variation within as well as between human populations, and today, it is understood to reflect complex interactions among a myriad of genetic, environmental, and evolutionary factors. Indeed, recent improvements in genetics (e.g., GWAS) and breakthroughs in functional genomics (e.g., whole exome sequencing, DNA methylation analysis, ATAC-sequencing, and CRISPR) have shed light on previously unknown pathways/mechanisms governing pathological and common height variation. Additionally, the use of an evolutionary perspective has also revealed important mechanisms that have shaped height variation across the planet. This review provides an overview of the current knowledge of the biological mechanisms underlying height variation by highlighting new research findings on skeletal growth control with an emphasis on previously unknown pathways/mechanisms influencing pathological and common height variation. In this context, this review also discusses how evolutionary forces likely shaped the genomic architecture of height across the globe.
- Published
- 2019
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41. A distinct transition from cell growth to physiological homeostasis in the tendon.
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Grinstein M, Dingwall HL, O'Connor LD, Zou K, Capellini TD, and Galloway JL
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- Achilles Tendon physiology, Animals, Extracellular Matrix genetics, Extracellular Matrix physiology, Mice, Stem Cells metabolism, Achilles Tendon growth & development, Cell Cycle genetics, Cell Proliferation physiology, Homeostasis genetics
- Abstract
Changes in cell proliferation define transitions from tissue growth to physiological homeostasis. In tendons, a highly organized extracellular matrix undergoes significant postnatal expansion to drive growth, but once formed, it appears to undergo little turnover. However, tendon cell activity during growth and homeostatic maintenance is less well defined. Using complementary methods of genetic H2B-GFP pulse-chase labeling and BrdU incorporation in mice, we show significant postnatal tendon cell proliferation, correlating with longitudinal Achilles tendon growth. Around day 21, there is a transition in cell turnover with a significant decline in proliferation. After this time, we find low amounts of homeostatic tendon cell proliferation from 3 to 20 months. These results demonstrate that tendons harbor significant postnatal mitotic activity, and limited, but detectable activity in adult and aged stages. It also points towards the possibility that the adult tendon harbors resident tendon progenitor populations, which would have important therapeutic implications., Competing Interests: MG, HD, LO, KZ, TC, JG No competing interests declared, (© 2019, Grinstein et al.)
- Published
- 2019
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42. Exercise-induced loading increases ilium cortical area in a selectively bred mouse model.
- Author
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Lewton KL, Ritzman T, Copes LE, Garland T Jr, and Capellini TD
- Subjects
- Animals, Female, Male, Mice, Mice, Inbred ICR, Cortical Bone anatomy & histology, Cortical Bone physiology, Ilium anatomy & histology, Ilium physiology, Physical Conditioning, Animal physiology, Running physiology
- Abstract
Objectives: Little is known about how ilium cortical bone responds to loading. Using a mouse model, this study presents data testing the hypothesis that iliac cross-sectional properties are altered in response to increased activity., Materials and Methods: The sample derives from lines of High Runner (HR) mice bred for increased wheel-running activity. Four treatment groups of female mice were tested: non-selected control lines housed without (N = 19) and with wheels (N = 20), and HR mice housed without (N = 17) and with wheels (N = 18) for 13 weeks beginning at weaning. Each pelvis was μCT-scanned, cross-sectional properties (cortical area-Ct.Ar, total area-Tt.Ar, polar moment of area, and polar section modulus) were determined from the ilium midshaft, and robusticity indices (ratio of the square root of Ct.Ar or Tt.Ar to caudal ilium length) were calculated. Mixed models were implemented with linetype, wheel access, and presence of the mini-muscle phenotype as fixed effects, replicate line nested within linetype as a random effect, and body mass as a covariate., Results: Results demonstrate that the mouse ilium morphologically resembles a long bone in cross section. Body mass and the mini-muscle phenotype were significant predictors of iliac cross-sectional properties. Wheel access only had a statistically significant effect on Ct.Ar and its robusticity index, with greater values in mice with wheel access., Discussion: These results suggest that voluntary exercise increases cortical area, but does not otherwise strengthen the ilium in these mice, corroborating previous studies on the effect of increased wheel-running activity on femoral and humeral cross-sectional properties in these mice., (© 2019 Wiley Periodicals, Inc.)
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- 2019
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43. Identification of Novel Loci Associated With Hip Shape: A Meta-Analysis of Genomewide Association Studies.
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Baird DA, Evans DS, Kamanu FK, Gregory JS, Saunders FR, Giuraniuc CV, Barr RJ, Aspden RM, Jenkins D, Kiel DP, Orwoll ES, Cummings SR, Lane NE, Mullin BH, Williams FM, Richards JB, Wilson SG, Spector TD, Faber BG, Lawlor DA, Grundberg E, Ohlsson C, Pettersson-Kymmer U, Capellini TD, Richard D, Beck TJ, Evans DM, Paternoster L, Karasik D, and Tobias JH
- Subjects
- Animals, Bone Density genetics, Genome-Wide Association Study, Hip Fractures pathology, Humans, Longitudinal Studies, Mice, Osteoporotic Fractures pathology, Femur Head, Genetic Loci, Hip Fractures genetics, Linkage Disequilibrium, Osteoporotic Fractures genetics, Polymorphism, Single Nucleotide
- Abstract
We aimed to report the first genomewide association study (GWAS) meta-analysis of dual-energy X-ray absorptiometry (DXA)-derived hip shape, which is thought to be related to the risk of both hip osteoarthritis and hip fracture. Ten hip shape modes (HSMs) were derived by statistical shape modeling using SHAPE software, from hip DXA scans in the Avon Longitudinal Study of Parents and Children (ALSPAC; adult females), TwinsUK (mixed sex), Framingham Osteoporosis Study (FOS; mixed), Osteoporotic Fractures in Men study (MrOS), and Study of Osteoporotic Fractures (SOF; females) (total N = 15,934). Associations were adjusted for age, sex, and ancestry. Five genomewide significant (p < 5 × 10
-9 , adjusted for 10 independent outcomes) single-nucleotide polymorphisms (SNPs) were associated with HSM1, and three SNPs with HSM2. One SNP, in high linkage disequilibrium with rs2158915 associated with HSM1, was associated with HSM5 at genomewide significance. In a look-up of previous GWASs, three of the identified SNPs were associated with hip osteoarthritis, one with hip fracture, and five with height. Seven SNPs were within 200 kb of genes involved in endochondral bone formation, namely SOX9, PTHrP, RUNX1, NKX3-2, FGFR4, DICER1, and HHIP. The SNP adjacent to DICER1 also showed osteoblast cis-regulatory activity of GSC, in which mutations have previously been reported to cause hip dysplasia. For three of the lead SNPs, SNPs in high LD (r2 > 0.5) were identified, which intersected with open chromatin sites as detected by ATAC-seq performed on embryonic mouse proximal femora. In conclusion, we identified eight SNPs independently associated with hip shape, most of which were associated with height and/or mapped close to endochondral bone formation genes, consistent with a contribution of processes involved in limb growth to hip shape and pathological sequelae. These findings raise the possibility that genetic studies of hip shape might help in understanding potential pathways involved in hip osteoarthritis and hip fracture. © 2018 The Authors. Journal of Bone and Mineral Research Published by Wiley Periodicals, Inc., (© 2018 The Authors. Journal of Bone and Mineral Research Published by Wiley Periodicals, Inc.)- Published
- 2019
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44. Genetics of scapula and pelvis development: An evolutionary perspective.
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Young M, Selleri L, and Capellini TD
- Subjects
- Animals, Evolution, Molecular, Fishes classification, Fishes embryology, Homeodomain Proteins genetics, Homeodomain Proteins metabolism, Pelvic Bones embryology, Scapula embryology, T-Box Domain Proteins genetics, T-Box Domain Proteins metabolism, Vertebrates classification, Vertebrates embryology, Fishes genetics, Gene Expression Regulation, Developmental, Pelvic Bones metabolism, Scapula metabolism, Vertebrates genetics
- Abstract
In tetrapods, the scapular and pelvic girdles perform the important function of anchoring the limbs to the trunk of the body and facilitating the movement of each appendage. This shared function, however, is one of relatively few similarities between the scapula and pelvis, which have significantly different morphologies, evolutionary histories, embryonic origins, and underlying genetic pathways. The scapula evolved in jawless fish prior to the pelvis, and its embryonic development is unique among bones in that it is derived from multiple progenitor cell populations, including the dermomyotome, somatopleure, and neural crest. Conversely, the pelvis evolved several million years later in jawed fish, and it develops from an embryonic somatopleuric cell population. The genetic networks controlling the formation of the pelvis and scapula also share similarities and differences, with a number of genes shaping only one or the other, while other gene products such as PBX transcription factors act as hierarchical developmental regulators of both girdle structures. Here, we provide a detailed review of the cellular processes and genetic networks underlying pelvis and scapula formation in tetrapods, while also highlighting unanswered questions about girdle evolution and development., (© 2019 Elsevier Inc. All rights reserved.)
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- 2019
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45. A novel enhancer near the Pitx1 gene influences development and evolution of pelvic appendages in vertebrates.
- Author
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Thompson AC, Capellini TD, Guenther CA, Chan YF, Infante CR, Menke DB, and Kingsley DM
- Subjects
- Animals, Base Sequence, Chromosomes, Artificial, Bacterial metabolism, Conserved Sequence, Fishes embryology, Gene Expression Regulation, Developmental, Genetic Loci, Genome, Hindlimb growth & development, Lizards embryology, Mice, Paired Box Transcription Factors metabolism, Sequence Deletion, Biological Evolution, Enhancer Elements, Genetic, Paired Box Transcription Factors genetics, Pelvis growth & development, Vertebrates genetics, Vertebrates growth & development
- Abstract
Vertebrate pelvic reduction is a classic example of repeated evolution. Recurrent loss of pelvic appendages in sticklebacks has previously been linked to natural mutations in a pelvic enhancer that maps upstream of Pitx1 . The sequence of this upstream PelA enhancer is not conserved to mammals, so we have surveyed a large region surrounding the mouse Pitx1 gene for other possible hind limb control sequences. Here we identify a new pelvic enhancer, PelB , that maps downstream rather than upstream of Pitx1. PelB drives expression in the posterior portion of the developing hind limb, and deleting the sequence from mice alters the size of several hind limb structures. PelB sequences are broadly conserved from fish to mammals. A wild stickleback population lacking the pelvis has an insertion/deletion mutation that disrupts the structure and function of PelB , suggesting that changes in this ancient enhancer contribute to evolutionary modification of pelvic appendages in nature., Competing Interests: AT, TC, CG, YC, CI, DM, DK No competing interests declared, (© 2018, Thompson et al.)
- Published
- 2018
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46. The role of Gdf5 regulatory regions in development of hip morphology.
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Kiapour AM, Cao J, Young M, and Capellini TD
- Subjects
- Animals, Gene Deletion, Male, Mice, Inbred BALB C, Mutation, Regulatory Sequences, Nucleic Acid, Gene Expression Regulation, Developmental, Growth Differentiation Factor 5 genetics, Hip anatomy & histology, Hip growth & development
- Abstract
Given GDF5 involvement in hip development, and osteoarthritis (OA) and developmental hip dysplasia (DDH) risk, here we sought to assess the role(s) of GDF5 and its regulatory sequence on the development of hip morphology linked to injury risk. The brachypodism (bp) mouse, which harbors a Gdf5 inactivating mutation, was used to survey how Gdf5 loss of function impacts the development of hip morphology. Two transgenic Gdf5 reporter BAC lines were used to assess the spatiotemporal expression of Gdf5 regulatory sequences. Each BAC line was also used to assess the functional roles of upstream and downstream sequence on hip morphology. bp/bp mice had shorter femora with smaller femoral heads and necks as well as larger alpha angles, smaller anterior offsets, and smaller acetabula, compared to bp/+ mice (p<0.04). Regulatory sequences downstream of Gdf5 drove strong prenatal (E17) expression and low postnatal (6 months) expression across regions of femoral head and acetabulum. Conversely, upstream regulatory sequences drove very low expression at E17 and no detectable expression at 6 months. Importantly, downstream, but not upstream Gdf5 regulatory sequences fully restored all the key morphologic features disrupted in bp/bp mice. Hip morphology is profoundly affected by Gdf5 absence, and downstream regulatory sequences mediate its effects by controlling Gdf5 expression during development. This downstream region contains numerous enhancers harboring risk variants related to hip OA, DDH, and dislocation. We posit that subtle alterations to morphology driven by changes in downstream regulatory sequence underlie this locus' role in hip injury risk., Competing Interests: The authors have declared that no competing interests exist.
- Published
- 2018
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47. A robust method for RNA extraction and purification from a single adult mouse tendon.
- Author
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Grinstein M, Dingwall HL, Shah RR, Capellini TD, and Galloway JL
- Abstract
Background: Mechanistic understanding of tendon molecular and cellular biology is crucial toward furthering our abilities to design new therapies for tendon and ligament injuries and disease. Recent transcriptomic and epigenomic studies in the field have harnessed the power of mouse genetics to reveal new insights into tendon biology. However, many mouse studies pool tendon tissues or use amplification methods to perform RNA analysis, which can significantly increase the experimental costs and limit the ability to detect changes in expression of low copy transcripts., Methods: Single Achilles tendons were harvested from uninjured, contralateral injured, and wild type mice between three and five months of age, and RNA was extracted. RNA Integrity Number (RIN) and concentration were determined, and RT-qPCR gene expression analysis was performed., Results: After testing several RNA extraction approaches on single adult mouse Achilles tendons, we developed a protocol that was successful at obtaining high RIN and sufficient concentrations suitable for RNA analysis. We found that the RNA quality was sensitive to the time between tendon harvest and homogenization, and the RNA quality and concentration was dependent on the duration of homogenization. Using this method, we demonstrate that analysis of Scx gene expression in single mouse tendons reduces the biological variation caused by pooling tendons from multiple mice. We also show successful use of this approach to analyze Sox9 and Col1a2 gene expression changes in injured compared with uninjured control tendons., Discussion: Our work presents a robust, cost-effective, and straightforward method to extract high quality RNA from a single adult mouse Achilles tendon at sufficient amounts for RT-qPCR as well as RNA-seq. We show this can reduce variation and decrease the overall costs associated with experiments. This approach can also be applied to other skeletal tissues, as well as precious human samples., Competing Interests: The authors declare that they have no competing interests.
- Published
- 2018
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48. Impact of broad regulatory regions on Gdf5 expression and function in knee development and susceptibility to osteoarthritis.
- Author
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Pregizer SK, Kiapour AM, Young M, Chen H, Schoor M, Liu Z, Cao J, Rosen V, and Capellini TD
- Subjects
- Animals, Genetic Predisposition to Disease, Growth Differentiation Factor 5 metabolism, Knee Joint metabolism, Knee Joint pathology, Mice, Mice, Inbred BALB C, Mice, Transgenic, Mutation, Regulatory Sequences, Nucleic Acid genetics, Spatio-Temporal Analysis, X-Ray Microtomography, Growth Differentiation Factor 5 genetics, Knee Joint embryology, Osteoarthritis, Knee genetics
- Abstract
Objectives: Given the role of growth and differentiation factor 5 ( GDF5 ) in knee development and osteoarthritis risk, we sought to characterise knee defects resulting from Gdf5 loss of function and how its regulatory regions control knee formation and morphology., Methods: The brachypodism ( bp ) mouse line, which harbours an inactivating mutation in Gdf5 , was used to survey how Gdf5 loss of function impacts knee morphology, while two transgenic Gdf5 reporter bacterial artificial chromosome mouse lines were used to assess the spatiotemporal activity and function of Gdf5 regulatory sequences in the context of clinically relevant knee anatomical features., Results: Knees from homozygous bp mice ( bp/bp ) exhibit underdeveloped femoral condyles and tibial plateaus, no cruciate ligaments, and poorly developed menisci. Secondary ossification is also delayed in the distal femur and proximal tibia. bp/bp mice have significantly narrower femoral condyles, femoral notches and tibial plateaus, and curvier medial femoral condyles, shallower trochlea, steeper lateral tibial slopes and smaller tibial spines. Regulatory sequences upstream from Gdf5 were weakly active in the prenatal knee, while downstream regulatory sequences were active throughout life. Importantly, downstream but not upstream Gdf5 regulatory sequences fully restored all the key morphological features disrupted in the bp/bp mice., Conclusions: Knee morphology is profoundly affected by Gdf5 absence, and downstream regulatory sequences mediate its effects by controlling Gdf5 expression in knee tissues. This downstream region contains numerous enhancers harbouring human variants that span the osteoarthritis association interval. We posit that subtle alterations to morphology driven by changes in downstream regulatory sequence underlie this locus' role in osteoarthritis risk., Competing Interests: Competing interests: None declared., (© Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2018. All rights reserved. No commercial use is permitted unless otherwise expressly granted.)
- Published
- 2018
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49. Disentangling Immediate Adaptive Introgression from Selection on Standing Introgressed Variation in Humans.
- Author
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Jagoda E, Lawson DJ, Wall JD, Lambert D, Muller C, Westaway M, Leavesley M, Capellini TD, Mirazón Lahr M, Gerbault P, Thomas MG, Migliano AB, Willerslev E, Metspalu M, and Pagani L
- Abstract
Recent studies have reported evidence suggesting that portions of contemporary human genomes introgressed from archaic hominin populations went to high frequencies due to positive selection. However, no study to date has specifically addressed the postintrogression population dynamics of these putative cases of adaptive introgression. Here, for the first time, we specifically define cases of immediate adaptive introgression (iAI) in which archaic haplotypes rose to high frequencies in humans as a result of a selective sweep that occurred shortly after the introgression event. We define these cases as distinct from instances of selection on standing introgressed variation (SI), in which an introgressed haplotype initially segregated neutrally and subsequently underwent positive selection. Using a geographically diverse data set, we report novel cases of selection on introgressed variation in living humans and shortlist among these cases those whose selective sweeps are more consistent with having been the product of iAI rather than SI. Many of these novel inferred iAI haplotypes have potential biological relevance, including three that contain immune-related genes in West Siberians, South Asians, and West Eurasians. Overall, our results suggest that iAI may not represent the full picture of positive selection on archaically introgressed haplotypes in humans and that more work needs to be done to analyze the role of SI in the archaic introgression landscape of living humans., (© The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.)
- Published
- 2018
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50. Epigenetic profiling of growth plate chondrocytes sheds insight into regulatory genetic variation influencing height.
- Author
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Guo M, Liu Z, Willen J, Shaw CP, Richard D, Jagoda E, Doxey AC, Hirschhorn J, and Capellini TD
- Subjects
- Animals, Chromatin metabolism, Genetic Loci, Humans, Mice, Body Height, Chondrocytes physiology, Epigenesis, Genetic, Genetic Variation, Growth Plate cytology
- Abstract
GWAS have identified hundreds of height-associated loci. However, determining causal mechanisms is challenging, especially since height-relevant tissues (e.g. growth plates) are difficult to study. To uncover mechanisms by which height GWAS variants function, we performed epigenetic profiling of murine femoral growth plates. The profiled open chromatin regions recapitulate known chondrocyte and skeletal biology, are enriched at height GWAS loci, particularly near differentially expressed growth plate genes, and enriched for binding motifs of transcription factors with roles in chondrocyte biology. At specific loci, our analyses identified compelling mechanisms for GWAS variants. For example, at CHSY1 , we identified a candidate causal variant (rs9920291) overlapping an open chromatin region. Reporter assays demonstrated that rs9920291 shows allelic regulatory activity, and CRISPR/Cas9 targeting of human chondrocytes demonstrates that the region regulates CHSY1 expression. Thus, integrating biologically relevant epigenetic information (here, from growth plates) with genetic association results can identify biological mechanisms important for human growth.
- Published
- 2017
- Full Text
- View/download PDF
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