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Tran MP, Ochoa Reyes D, Weitzel AJ, Saxena A, Hiller M, Cooper KL. Gene expression differences associated with intrinsic hindfoot muscle loss in the jerboa, Jaculus jaculus. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART B, MOLECULAR AND DEVELOPMENTAL EVOLUTION 2024. [PMID: 38946691 DOI: 10.1002/jez.b.23268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 05/16/2024] [Accepted: 06/17/2024] [Indexed: 07/02/2024]
Abstract
Vertebrate animals that run or jump across sparsely vegetated habitats, such as horses and jerboas, have reduced the number of distal limb bones, and many have lost most or all distal limb muscle. We previously showed that nascent muscles are present in the jerboa hindfoot at birth and that these myofibers are rapidly and completely lost soon after by a process that shares features with pathological skeletal muscle atrophy. Here, we apply an intra- and interspecies differential RNA-Seq approach, comparing jerboa and mouse muscles, to identify gene expression differences associated with the initiation and progression of jerboa hindfoot muscle loss. We show evidence for reduced hepatocyte growth factor and fibroblast growth factor signaling and an imbalance in nitric oxide signaling; all are pathways that are necessary for skeletal muscle development and regeneration. We also find evidence for phagosome formation, which hints at how myofibers may be removed by autophagy or by nonprofessional phagocytes without evidence for cell death or immune cell activation. Last, we show significant overlap between genes associated with jerboa hindfoot muscle loss and genes that are differentially expressed in a variety of human muscle pathologies and rodent models of muscle loss disorders. All together, these data provide molecular insight into the process of evolutionary and developmental muscle loss in jerboa hindfeet.
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Affiliation(s)
- Mai P Tran
- Department of Cell and Developmental Biology, University of California San Diego, La Jolla, California, USA
| | - Daniel Ochoa Reyes
- Department of Cell and Developmental Biology, University of California San Diego, La Jolla, California, USA
| | - Alexander J Weitzel
- Department of Cell and Developmental Biology, University of California San Diego, La Jolla, California, USA
| | - Aditya Saxena
- Department of Cell and Developmental Biology, University of California San Diego, La Jolla, California, USA
| | - Michael Hiller
- LOEWE Centre for Translational Biodiversity Genomics, Frankfurt, Germany
- Senckenberg Research Institute, Frankfurt, Germany
- Faculty of Biosciences, Goethe University Frankfurt, Frankfurt, Germany
| | - Kimberly L Cooper
- Department of Cell and Developmental Biology, University of California San Diego, La Jolla, California, USA
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2
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Sarasa JL, Okamoto AS, Wright MA, Pierce SE, Capellini TD. Lions & sea lions & bears, oh my: utilizing museum specimens to study the ossification sequence of carnivoran taxa. BMC ZOOL 2024; 9:10. [PMID: 38685130 PMCID: PMC11057098 DOI: 10.1186/s40850-024-00201-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 04/22/2024] [Indexed: 05/02/2024] Open
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.
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Affiliation(s)
- Jonathan L Sarasa
- University of Michigan, Ann Arbor, MI, USA
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | | | - Mark A Wright
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Stephanie E Pierce
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Terence D Capellini
- Human Evolutionary Biology, Harvard University, Cambridge, MA, USA.
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.
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Newton AH, Smith CA. Resolving the mechanisms underlying epithelial-to-mesenchymal transition of the lateral plate mesoderm. Genesis 2024; 62:e23531. [PMID: 37443419 DOI: 10.1002/dvg.23531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Revised: 06/02/2023] [Accepted: 06/28/2023] [Indexed: 07/15/2023]
Abstract
Formation of the vertebrate limb buds begins with a localized epithelial-to-mesenchymal transition (EMT) of the somatic lateral plate mesoderm (LPM). While the processes that drive proliferation and outgrowth of the limb mesenchyme are well established, the fundamental mechanisms that precede this process and initiate EMT are less understood. In this review, we outline putative drivers of EMT of the LPM, drawing from analyses across a range of vertebrates and developmental models. We detail the expression patterns of key EMT transcriptional regulators in the somatic LPM of the presumptive limb fields, and their potential role in producing a mesenchymal cell fate. These include a putative cooperative role between the EMT inducers PRRX1 and TWIST1, supported by evidence in zebrafish and chicken models but unconfirmed data from mice. As such, additional functional data are required to definitively determine the mechanisms that initiate and drive EMT of the somatic LPM, a critical transition preceding formation of the limb bud mesenchyme.
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Affiliation(s)
- Axel H Newton
- School of BioSciences, The University of Melbourne, Melbourne, Victoria, Australia
| | - Craig A Smith
- Department of Anatomy and Physiology, Monash University, Melbourne, Victoria, Australia
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Chen Y, Tan J, Yang C, Ling Z, Xu J, Sun D, Luo F. Dynamic chromatin accessibility landscapes of osteoblast differentiation and mineralization. Biochim Biophys Acta Mol Basis Dis 2024; 1870:166938. [PMID: 37931716 DOI: 10.1016/j.bbadis.2023.166938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 10/12/2023] [Accepted: 10/29/2023] [Indexed: 11/08/2023]
Abstract
Bone acts as a self-healing organ, which undergoes continuous regeneration process that is tightly regulated by the cooperation of osteoclasts with the capability of bone resorption and osteoblasts with the capability of bone formation. Generally, bone marrow derived mesenchymal stem cells (BMSCs) differentiated to final osteoblasts have been considered as critical role in bone remodeling. In this regard, several transcription factors (TFs) whose binding sites are initially hidden deep within accessible chromatin that participate in modulating osteoblast differentiation and bone matrix mineralization. Then, it is necessary to explore further the dynamic changes about the epigenetic transcription machinery during osteoblastogenesis. Here, we performed the chromatin accessibility and transcriptomic landscape of osteoblast differentiation and mineralization by using transposase-accessible chromatin sequencing (ATAC-seq) and RNA sequencing (RNA-Seq). Our data found that global chromatin accessibility during osteoblastogenesis was extensively improved. Above this, it is shown that key target genes including Col6a3, Serpina3n, Ms4a4d, Lyz2, Phf11b and Grin3a were enriched in differential loci RNA-seq and ATAC-Seq peaks with continuous changed tendency during osteoblasts differentiation and mineralization. In addition, Analysis of Motif Enrichment (AME) was used to elucidate TFs which modulated these target genes. In this study, it was shown for the first time that these important TFs including MEF2A, PRRX1, Shox2 and HOXB13 could alter promoter accessibility of target genes during osteoblastogenesis. This helps us understand how TF binding motif accessibility influences osteoblast differentiation. In addition, it also suggests that modulating the chromatin accessibility of osteogenesis could be developed as the promising strategies to regulate bone regeneration.
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Affiliation(s)
- Yueqi Chen
- Department of Orthopedics, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, People's Republic of China; Department of Orthopedics, 76nd Group Army Hospital, Xining, People's Republic of China.
| | - Jiulin Tan
- Department of Orthopedics, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, People's Republic of China
| | - Chuan Yang
- Department of Biomedical Materials Science, Third Military Medical University (Army Medical University), Chongqing, People's Republic of China
| | - Zhiguo Ling
- Institute of Immunology, Third Military Medical University (Army Medical University), Chongqing, People's Republic of China
| | - Jianzhong Xu
- Department of Orthopedics, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, People's Republic of China
| | - Dong Sun
- Department of Orthopedics, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, People's Republic of China.
| | - Fei Luo
- Department of Orthopedics, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, People's Republic of China.
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Kun E, Javan EM, Smith O, Gulamali F, de la Fuente J, Flynn BI, Vajrala K, Trutner Z, Jayakumar P, Tucker-Drob EM, Sohail M, Singh T, Narasimhan VM. The genetic architecture and evolution of the human skeletal form. Science 2023; 381:eadf8009. [PMID: 37471560 PMCID: PMC11075689 DOI: 10.1126/science.adf8009] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 06/20/2023] [Indexed: 07/22/2023]
Abstract
The human skeletal form underlies bipedalism, but the genetic basis of skeletal proportions (SPs) is not well characterized. We applied deep-learning models to 31,221 x-rays from the UK Biobank to extract a comprehensive set of SPs, which were associated with 145 independent loci genome-wide. Structural equation modeling suggested that limb proportions exhibited strong genetic sharing but were independent of width and torso proportions. Polygenic score analysis identified specific associations between osteoarthritis and hip and knee SPs. In contrast to other traits, SP loci were enriched in human accelerated regions and in regulatory elements of genes that are differentially expressed between humans and great apes. Combined, our work identifies specific genetic variants that affect the skeletal form and ties a major evolutionary facet of human anatomical change to pathogenesis.
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Affiliation(s)
- Eucharist Kun
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA
| | - Emily M. Javan
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA
| | - Olivia Smith
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA
| | - Faris Gulamali
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Javier de la Fuente
- Department of Psychology, The University of Texas at Austin, Austin, TX, USA
| | - Brianna I. Flynn
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA
| | - Kushal Vajrala
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA
| | - Zoe Trutner
- Department of Surgery and Perioperative Care, The University of Texas at Austin, Austin, TX, USA
| | - Prakash Jayakumar
- Department of Surgery and Perioperative Care, The University of Texas at Austin, Austin, TX, USA
| | | | - Mashaal Sohail
- Centro de Ciencias Genómicas (CCG), Universidad Nacional Autónoma de México (UNAM), 62209 Cuernavaca, Mexico
| | - Tarjinder Singh
- Department of Psychiatry, Columbia University Irving Medical Center, New York, NY, USA
- The New York Genome Center, New York, NY, USA
- Mortimer B. Zuckerman Mind Brain Behavior Institute at Columbia University, New York, NY, USA
| | - Vagheesh M. Narasimhan
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA
- Department of Statistics and Data Science, The University of Texas at Austin, Austin, TX, USA
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Kun E, Javan EM, Smith O, Gulamali F, de la Fuente J, Flynn BI, Vajrala K, Trutner Z, Jayakumar P, Tucker-Drob EM, Sohail M, Singh T, Narasimhan VM. The genetic architecture of the human skeletal form. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.03.521284. [PMID: 36712136 PMCID: PMC9881884 DOI: 10.1101/2023.01.03.521284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The human skeletal form underlies our ability to walk on two legs, but unlike standing height, the genetic basis of limb lengths and skeletal proportions is less well understood. Here we applied a deep learning model to 31,221 whole body dual-energy X-ray absorptiometry (DXA) images from the UK Biobank (UKB) to extract 23 different image-derived phenotypes (IDPs) that include all long bone lengths as well as hip and shoulder width, which we analyzed while controlling for height. All skeletal proportions are highly heritable (∼40-50%), and genome-wide association studies (GWAS) of these traits identified 179 independent loci, of which 102 loci were not associated with height. These loci are enriched in genes regulating skeletal development as well as associated with rare human skeletal diseases and abnormal mouse skeletal phenotypes. Genetic correlation and genomic structural equation modeling indicated that limb proportions exhibited strong genetic sharing but were genetically independent of width and torso proportions. Phenotypic and polygenic risk score analyses identified specific associations between osteoarthritis (OA) of the hip and knee, the leading causes of adult disability in the United States, and skeletal proportions of the corresponding regions. We also found genomic evidence of evolutionary change in arm-to-leg and hip-width proportions in humans consistent with striking anatomical changes in these skeletal proportions in the hominin fossil record. In contrast to cardiovascular, auto-immune, metabolic, and other categories of traits, loci associated with these skeletal proportions are significantly enriched in human accelerated regions (HARs), and regulatory elements of genes differentially expressed through development between humans and the great apes. Taken together, our work validates the use of deep learning models on DXA images to identify novel and specific genetic variants affecting the human skeletal form and ties a major evolutionary facet of human anatomical change to pathogenesis.
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Affiliation(s)
- Eucharist Kun
- Department of Integrative Biology, The University of Texas at Austin
| | - Emily M Javan
- Department of Integrative Biology, The University of Texas at Austin
| | - Olivia Smith
- Department of Integrative Biology, The University of Texas at Austin
| | | | | | - Brianna I Flynn
- Department of Integrative Biology, The University of Texas at Austin
| | - Kushal Vajrala
- Department of Integrative Biology, The University of Texas at Austin
| | - Zoe Trutner
- Department of Surgery and Perioperative Care, The University of Texas at Austin
| | - Prakash Jayakumar
- Department of Surgery and Perioperative Care, The University of Texas at Austin
| | | | - Mashaal Sohail
- Centro de Ciencias Genómicas (CCG), Universidad Nacional Autónoma de México (UNAM)
| | - Tarjinder Singh
- The Department of Psychiatry at Columbia University Irving Medical Center
- The New York Genome Center
- Mortimer B. Zuckerman Mind Brain Behavior Institute at Columbia University
| | - Vagheesh M Narasimhan
- Department of Integrative Biology, The University of Texas at Austin
- Department of Statistics and Data Science, The University of Texas at Austin
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Dubois‐Mignon T, Monget P. Gene essentiality and variability: What is the link? A within‐ and between‐species perspective. Bioessays 2022; 44:e2200132. [DOI: 10.1002/bies.202200132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 08/17/2022] [Accepted: 08/30/2022] [Indexed: 11/07/2022]
Affiliation(s)
- Tania Dubois‐Mignon
- Institut de Biologie de l’École Normale Supérieure Université PSL 46 rue d'Ulm Paris 75005 France
| | - Philippe Monget
- Physiologie de la Reproduction et des Comportements, Centre Val de Loire – UMR INRAE, CNRS, IFCE Université de Tours Nouzilly France
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Are Copy Number Variations within the FecB Gene Significantly Associated with Morphometric Traits in Goats? Animals (Basel) 2022; 12:ani12121547. [PMID: 35739883 PMCID: PMC9219420 DOI: 10.3390/ani12121547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 06/04/2022] [Accepted: 06/09/2022] [Indexed: 12/02/2022] Open
Abstract
The Booroola fecundity (FecB) gene is a major fertility-related gene first identified in Booroola sheep. Numerous studies have investigated whether the FecB gene is a major fecundity gene in goats or whether there are other genes that play a critical role in goat fertility. Nevertheless, little attention has been paid to the role of the FecB gene in the body morphometric traits of goats, despite the positive relationship discerned between litter size and growth. We identified five copy number variations (CNVs) within the FecB gene in 641 goats, including 318 Shaanbei white cashmere (SBWC) goats, 203 Guizhou Heima (GZHM) goats, and 120 Nubian goats, which exhibited different distributions among these populations. Our results revealed that these five CNVs were significantly associated with goat morphometric traits (p < 0.05). The normal type of CNV3 was the dominant type and displayed superior phenotypes in both litter size and morphometric traits, making it an effective marker for goat breeding. Consequently, LD blocks in the region of 10 Mb upstream and downstream from FecB and potential transcription factors (TFs) that could bind with the CNVs were analyzed via bioinformatics. Although no significant LD block was detected, our results illustrated that these CNVs could bind to growth-related TFs and indirectly affect the growth development of the goats. We identified potential markers to promote litter size and growth, and we offer a theoretical foundation for further breeding work.
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Okamura DM, Nguyen ED, Beier DR, Majesky MW. Wound healing and regeneration in spiny mice (Acomys cahirinus). Curr Top Dev Biol 2022; 148:139-164. [DOI: 10.1016/bs.ctdb.2022.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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