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Napoli FR, Li X, Hurtado AA, Levine EM. Microphthalmia and disrupted retinal development due to a LacZ knock-in/knock-out allele at the Vsx2 locus. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.08.597937. [PMID: 38895315 PMCID: PMC11185793 DOI: 10.1101/2024.06.08.597937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Visual System Homeobox 2 (Vsx2) is a transcription factor expressed in the developing retina that regulates tissue identity, growth, and fate determination. Several mutations in the Vsx2 gene exist in mice, including a spontaneous nonsense mutation and two targeted missense mutations originally identified in humans. Here, we expand the genetic repertoire to include a LacZ reporter allele (Vsx2 LacZ ) designed to express beta-Galactosidase (b-GAL) and simultaneously disrupt Vsx2 function (knock-in/knock-out). The retinal expression pattern of b-GAL is concordant with VSX2, and the mutant allele is recessive. Vsx2 LacZ homozygous mice have congenital bilateral microphthalmia accompanied by defects in retinal development including ectopic expression of non-retinal genes, reduced proliferation, delayed neurogenesis, aberrant tissue morphology, and an absence of bipolar interneurons - all hallmarks of Vsx2 loss-of-function. Unexpectedly, the mutant VSX2 protein is stably expressed, and there are subtle differences in eye size and early retinal neurogenesis when compared to the null mutant, ocular retardation J. We propose that b-GAL expression from the Vsx2 LacZ allele is a reliable reporter of VSX2 expression and that the allele exhibits loss-of-function characteristics. However, the perdurance of the mutant VSX2 protein combined with subtle deviations from the null phenotype leaves open the possibility that Vsx2 LacZ allele is not a complete knock-out. The Vsx2 LacZ allele adds to the genetic toolkit for understanding Vsx2 function.
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Affiliation(s)
- Francesca R. Napoli
- Department of Ophthalmology and Visual Sciences Vanderbilt University Medical Center, Nashville TN 37232
| | - Xiaodong Li
- Department of Ophthalmology and Visual Sciences Vanderbilt University Medical Center, Nashville TN 37232
| | - Alan A. Hurtado
- Program in Chemical and Physical Biology Vanderbilt University, Nashville TN 37232
| | - Edward M. Levine
- Department of Ophthalmology and Visual Sciences Vanderbilt University Medical Center, Nashville TN 37232
- Department of Cell and Developmental Biology Vanderbilt University, Nashville TN 37232
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2
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Papaioannou VE, Behringer RR. Analysis of Mid- to Late-Gestation Phenotypes in Mice. Cold Spring Harb Protoc 2024; 2024:107973. [PMID: 37932082 DOI: 10.1101/pdb.over107973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2023]
Abstract
Mid- to late gestation is characterized by tissue differentiation, maturation, organogenesis, and growth, and many mutant genes have detrimental effects during this phase of development. The outcome may be lethal before birth or may be compatible with life but result in birth defects. Some of the common causes of death during late gestation are hematopoietic defects, cardiovascular problems, and placental insufficiency. Many morphological abnormalities, lethal or not, can be investigated with gross and histological analyses or by visualization of the developing skeleton. Molecular characterization of mutant phenotypes, guided by the expression pattern of the mutant gene, can reveal disruptions in gene expression patterns of known developmental genes. Cell proliferation and cell death assays will reveal disruptions in cellular dynamics. Various modalities of 3D imaging of intact embryos can provide volumetric information about mutant phenotypes.
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Affiliation(s)
- Virginia E Papaioannou
- Department of Genetics and Development, Columbia University Medical Center, New York, New York 10032, USA
| | - Richard R Behringer
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
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3
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Aceves M, Tucker A, Chen J, Vo K, Moses J, Amar Kumar P, Thomas H, Miranda D, Dampf G, Dietz V, Chang M, Lukose A, Jang J, Nadella S, Gillespie T, Trevino C, Buxton A, Pritchard AL, Green P, McCreedy DA, Dulin JN. Developmental stage of transplanted neural progenitor cells influences anatomical and functional outcomes after spinal cord injury in mice. Commun Biol 2023; 6:544. [PMID: 37208439 PMCID: PMC10199026 DOI: 10.1038/s42003-023-04893-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 05/02/2023] [Indexed: 05/21/2023] Open
Abstract
Neural progenitor cell (NPC) transplantation is a promising therapeutic strategy for replacing lost neurons following spinal cord injury (SCI). However, how graft cellular composition influences regeneration and synaptogenesis of host axon populations, or recovery of motor and sensory functions after SCI, is poorly understood. We transplanted developmentally-restricted spinal cord NPCs, isolated from E11.5-E13.5 mouse embryos, into sites of adult mouse SCI and analyzed graft axon outgrowth, cellular composition, host axon regeneration, and behavior. Earlier-stage grafts exhibited greater axon outgrowth, enrichment for ventral spinal cord interneurons and Group-Z spinal interneurons, and enhanced host 5-HT+ axon regeneration. Later-stage grafts were enriched for late-born dorsal horn interneuronal subtypes and Group-N spinal interneurons, supported more extensive host CGRP+ axon ingrowth, and exacerbated thermal hypersensitivity. Locomotor function was not affected by any type of NPC graft. These findings showcase the role of spinal cord graft cellular composition in determining anatomical and functional outcomes following SCI.
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Affiliation(s)
- Miriam Aceves
- Department of Biology, Texas A&M University, College Station, TX, 77843, USA
- Texas A&M Institute for Neuroscience, Texas A&M University, College Station, TX, 77843, USA
| | - Ashley Tucker
- Department of Biology, Texas A&M University, College Station, TX, 77843, USA
- Texas A&M Institute for Neuroscience, Texas A&M University, College Station, TX, 77843, USA
| | - Joseph Chen
- Department of Biology, Texas A&M University, College Station, TX, 77843, USA
| | - Katie Vo
- Department of Biology, Texas A&M University, College Station, TX, 77843, USA
| | - Joshua Moses
- Department of Biology, Texas A&M University, College Station, TX, 77843, USA
| | | | - Hannah Thomas
- Department of Biology, Texas A&M University, College Station, TX, 77843, USA
| | - Diego Miranda
- Department of Biology, Texas A&M University, College Station, TX, 77843, USA
| | - Gabrielle Dampf
- Department of Biology, Texas A&M University, College Station, TX, 77843, USA
| | - Valerie Dietz
- Department of Biology, Texas A&M University, College Station, TX, 77843, USA
| | - Matthew Chang
- Department of Biology, Texas A&M University, College Station, TX, 77843, USA
| | - Aleena Lukose
- Department of Biology, Texas A&M University, College Station, TX, 77843, USA
| | - Julius Jang
- Department of Biology, Texas A&M University, College Station, TX, 77843, USA
| | - Sneha Nadella
- Department of Biology, Texas A&M University, College Station, TX, 77843, USA
| | - Tucker Gillespie
- Department of Biology, Texas A&M University, College Station, TX, 77843, USA
| | - Christian Trevino
- Department of Biology, Texas A&M University, College Station, TX, 77843, USA
| | - Andrew Buxton
- Department of Biomedical Engineering, Texas A&M University, College Station, TX, 77843, USA
| | - Anna L Pritchard
- Department of Biomedical Engineering, Texas A&M University, College Station, TX, 77843, USA
| | | | - Dylan A McCreedy
- Department of Biology, Texas A&M University, College Station, TX, 77843, USA
- Texas A&M Institute for Neuroscience, Texas A&M University, College Station, TX, 77843, USA
- Department of Biomedical Engineering, Texas A&M University, College Station, TX, 77843, USA
| | - Jennifer N Dulin
- Department of Biology, Texas A&M University, College Station, TX, 77843, USA.
- Texas A&M Institute for Neuroscience, Texas A&M University, College Station, TX, 77843, USA.
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4
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Green RM, Lo Vercio LD, Dauter A, Barretto EC, Devine J, Vidal-García M, Marchini M, Robertson S, Zhao X, Mahika A, Shakir MB, Guo S, Boughner JC, Dean W, Lander AD, Marcucio RS, Forkert ND, Hallgrímsson B. Quantifying the relationship between cell proliferation and morphology during development of the face. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.12.540515. [PMID: 37214859 PMCID: PMC10197725 DOI: 10.1101/2023.05.12.540515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Morphogenesis requires highly coordinated, complex interactions between cellular processes: proliferation, migration, and apoptosis, along with physical tissue interactions. How these cellular and tissue dynamics drive morphogenesis remains elusive. Three dimensional (3D) microscopic imaging poses great promise, and generates elegant images. However, generating even moderate through-put quantified images is challenging for many reasons. As a result, the association between morphogenesis and cellular processes in 3D developing tissues has not been fully explored. To address this critical gap, we have developed an imaging and image analysis pipeline to enable 3D quantification of cellular dynamics along with 3D morphology for the same individual embryo. Specifically, we focus on how 3D distribution of proliferation relates to morphogenesis during mouse facial development. Our method involves imaging with light-sheet microscopy, automated segmentation of cells and tissues using machine learning-based tools, and quantification of external morphology via geometric morphometrics. Applying this framework, we show that changes in proliferation are tightly correlated to changes in morphology over the course of facial morphogenesis. These analyses illustrate the potential of this pipeline to investigate mechanistic relationships between cellular dynamics and morphogenesis during embryonic development.
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Affiliation(s)
- Rebecca M Green
- Department of Oral and Craniofacial Sciences, Center for Craniofacial and Dental Genetics, University of Pittsburgh, Pittsburgh, PA, United States
| | - Lucas D Lo Vercio
- Department of Cell Biology & Anatomy, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada
- McCaig Bone and Joint Institute, University of Calgary, Calgary, AB, Canada
| | - Andreas Dauter
- Department of Cell Biology & Anatomy, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada
- McCaig Bone and Joint Institute, University of Calgary, Calgary, AB, Canada
| | - Elizabeth C Barretto
- Department of Cell Biology & Anatomy, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada
- McCaig Bone and Joint Institute, University of Calgary, Calgary, AB, Canada
| | - Jay Devine
- Department of Cell Biology & Anatomy, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada
- McCaig Bone and Joint Institute, University of Calgary, Calgary, AB, Canada
| | - Marta Vidal-García
- Department of Cell Biology & Anatomy, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada
- McCaig Bone and Joint Institute, University of Calgary, Calgary, AB, Canada
| | | | - Samuel Robertson
- Department of Cell Biology & Anatomy, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada
| | - Xiang Zhao
- Department of Cell Biology & Anatomy, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada
| | - Anandita Mahika
- Department of Cell Biology & Anatomy, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada
- McCaig Bone and Joint Institute, University of Calgary, Calgary, AB, Canada
| | - M Bilal Shakir
- Department of Cell Biology & Anatomy, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada
- McCaig Bone and Joint Institute, University of Calgary, Calgary, AB, Canada
| | - Sienna Guo
- Department of Cell Biology & Anatomy, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada
- McCaig Bone and Joint Institute, University of Calgary, Calgary, AB, Canada
| | - Julia C Boughner
- Department of Anatomy, Physiology and Pharmacology, College of Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Wendy Dean
- Department of Cell Biology & Anatomy, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada
| | - Arthur D Lander
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, United States
| | - Ralph S Marcucio
- Department of Orthopaedic Surgery, University of California San Francisco, San Francisco, CA, United States
| | - Nils D Forkert
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada
| | - Benedikt Hallgrímsson
- Department of Cell Biology & Anatomy, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada
- McCaig Bone and Joint Institute, University of Calgary, Calgary, AB, Canada
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5
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Aristizábal O, Qiu Z, Gallego E, Aristizábal M, Mamou J, Wang Y, Ketterling JA, Turnbull DH. Longitudinal in Utero Analysis of Engrailed-1 Knockout Mouse Embryonic Phenotypes Using High-Frequency Ultrasound. ULTRASOUND IN MEDICINE & BIOLOGY 2023; 49:356-367. [PMID: 36283941 PMCID: PMC9712241 DOI: 10.1016/j.ultrasmedbio.2022.09.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 09/08/2022] [Accepted: 09/11/2022] [Indexed: 06/16/2023]
Abstract
Large-scale international efforts to generate and analyze loss-of-function mutations in each of the approximately 20,000 protein-encoding gene mutations are ongoing using the "knockout" mouse as a model organism. Because one-third of gene knockouts are expected to result in embryonic lethality, it is important to develop non-invasive in utero imaging methods to detect and monitor mutant phenotypes in mouse embryos. We describe the utility of 3-D high-frequency (40-MHz) ultrasound (HFU) for longitudinal in utero imaging of mouse embryos between embryonic days (E) 11.5 and E14.5, which represent critical stages of brain and organ development. Engrailed-1 knockout (En1-ko) mouse embryos and their normal control littermates were imaged with HFU in 3-D, enabling visualization of morphological phenotypes in the developing brains, limbs and heads of the En1-ko embryos. Recently developed deep learning approaches were used to automatically segment the embryonic brain ventricles and bodies from the 3-D HFU images, allowing quantitative volumetric analyses of the En1-ko brain phenotypes. Taken together, these results show great promise for the application of longitudinal 3-D HFU to analyze knockout mouse embryos in utero.
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Affiliation(s)
- Orlando Aristizábal
- Skirball Institute of Biomolecular Medicine and Department of Radiology, New York University Grossman School of Medicine, New York, New York, USA
| | - Ziming Qiu
- Department of Electrical and Computer Engineering, New York University Tandon School of Engineering, New York, New York, USA
| | - Estefania Gallego
- Skirball Institute of Biomolecular Medicine and Department of Radiology, New York University Grossman School of Medicine, New York, New York, USA
| | - Matias Aristizábal
- Skirball Institute of Biomolecular Medicine and Department of Radiology, New York University Grossman School of Medicine, New York, New York, USA
| | - Jonathan Mamou
- Department of Radiology, Weill Cornell Medicine, New York, New York, USA
| | - Yao Wang
- Department of Electrical and Computer Engineering, New York University Tandon School of Engineering, New York, New York, USA
| | | | - Daniel H Turnbull
- Skirball Institute of Biomolecular Medicine and Department of Radiology, New York University Grossman School of Medicine, New York, New York, USA.
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6
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Madgwick S, Luli S, Sellier H, Butterworth JA, Leslie J, Moore AJ, Corbin EK, Yemm AI, Chiremba RT, Tiniakos D, Oakley F, Perkins ND, Hunter JE. Claspin haploinsufficiency leads to defects in fertility, hyperplasia and an increased oncogenic potential. Biochem J 2022; 479:2115-2130. [PMID: 36240068 PMCID: PMC9704638 DOI: 10.1042/bcj20220101] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 09/21/2022] [Accepted: 09/23/2022] [Indexed: 12/13/2022]
Abstract
Claspin is an adaptor protein required for ATR-dependent phosphorylation of CHK1 during S-phase following DNA replication stress. Claspin expression is highly variable in cancer, with low levels frequently correlating with poor patient survival. To learn more about the biological consequences of reduced Claspin expression and its effects on tumorigenesis, we investigated mice with a heterozygous knockout of the Clspn gene. Claspin haploinsufficiency resulted in reduced female fertility and a maternally inherited defect in oocyte meiosis I cell cycle progression. Furthermore, aged Clspn+/- mice developed spontaneous lymphoid hyperplasia and increased susceptibility to non-alcoholic fatty liver disease. Importantly, we demonstrate a tumour suppressor role for Claspin. Reduced Claspin levels result in increased liver damage and tumourigenesis in the DEN model of hepatocellular carcinoma. These data reveal that Clspn haploinsufficiency has widespread unanticipated biological effects and establishes the importance of Claspin as a regulatory node controlling tumorigenesis and multiple disease aetiologies.
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Affiliation(s)
- Suzanne Madgwick
- Newcastle University Biosciences Institute, Wolfson Childhood Cancer Research Centre, Level 6, Herschel Building, Newcastle University, Brewery Lane, Newcastle upon Tyne NE1 7RU, U.K
| | - Saimir Luli
- Preclinical In Vivo Imaging Facility, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne NE2 4HH, U.K
| | - Helene Sellier
- Newcastle University Biosciences Institute, Wolfson Childhood Cancer Research Centre, Level 6, Herschel Building, Newcastle University, Brewery Lane, Newcastle upon Tyne NE1 7RU, U.K
| | - Jacqueline A. Butterworth
- Newcastle University Biosciences Institute, Wolfson Childhood Cancer Research Centre, Level 6, Herschel Building, Newcastle University, Brewery Lane, Newcastle upon Tyne NE1 7RU, U.K
| | - Jack Leslie
- Newcastle Fibrosis Research Group, Newcastle University Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne NE2 4HH, U.K
| | - Adam J. Moore
- Newcastle University Biosciences Institute, Wolfson Childhood Cancer Research Centre, Level 6, Herschel Building, Newcastle University, Brewery Lane, Newcastle upon Tyne NE1 7RU, U.K
| | - Emma K. Corbin
- Newcastle University Biosciences Institute, Wolfson Childhood Cancer Research Centre, Level 6, Herschel Building, Newcastle University, Brewery Lane, Newcastle upon Tyne NE1 7RU, U.K
| | - Adrian I. Yemm
- Newcastle University Biosciences Institute, Wolfson Childhood Cancer Research Centre, Level 6, Herschel Building, Newcastle University, Brewery Lane, Newcastle upon Tyne NE1 7RU, U.K
| | - Robson T. Chiremba
- Newcastle University Biosciences Institute, Wolfson Childhood Cancer Research Centre, Level 6, Herschel Building, Newcastle University, Brewery Lane, Newcastle upon Tyne NE1 7RU, U.K
| | - Dina Tiniakos
- Newcastle Fibrosis Research Group, Newcastle University Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne NE2 4HH, U.K
| | - Fiona Oakley
- Newcastle Fibrosis Research Group, Newcastle University Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne NE2 4HH, U.K
| | - Neil D. Perkins
- Newcastle University Biosciences Institute, Wolfson Childhood Cancer Research Centre, Level 6, Herschel Building, Newcastle University, Brewery Lane, Newcastle upon Tyne NE1 7RU, U.K
| | - Jill E. Hunter
- Newcastle University Biosciences Institute, Wolfson Childhood Cancer Research Centre, Level 6, Herschel Building, Newcastle University, Brewery Lane, Newcastle upon Tyne NE1 7RU, U.K
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7
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Profiling development of abdominal organs in the pig. Sci Rep 2022; 12:16245. [PMID: 36171243 PMCID: PMC9519580 DOI: 10.1038/s41598-022-19960-5] [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: 01/26/2022] [Accepted: 09/07/2022] [Indexed: 11/25/2022] Open
Abstract
The pig is an ideal model system for studying human development and disease due to its similarities to human anatomy, physiology, size, and genome. Further, advances in CRISPR gene editing have made genetically engineered pigs viable models for the study of human pathologies and congenital anomalies. However, a detailed atlas illustrating pig development is necessary for identifying and modeling developmental defects. Here we describe normal development of the pig abdominal system and show examples of congenital defects that can arise in CRISPR gene edited SAP130 mutant pigs. Normal pigs at different gestational ages from day 20 (D20) to term were examined and the configuration of the abdominal organs was studied using 3D histological reconstructions with episcopic confocal microscopy, magnetic resonance imaging (MRI) and necropsy. This revealed prominent mesonephros, a transient embryonic organ present only during embryogenesis, at D20, while the developing metanephros that will form the permanent kidney are noted at D26. By D64 the mesonephroi are absent and only the metanephroi remain. The formation of the liver and pancreas was observed by D20 and complete by D30 and D35 respectively. The spleen and adrenal glands are first identified at D26 and completed by D42. The developing bowel and the gonads are identified at D20. The bowel appears completely rotated by D42, and testes in the male were descended at D64. This atlas and the methods used are excellent tools for identifying developmental pathologies of the abdominal organs in the pig at different stages of development.
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8
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Dalmasso G, Musy M, Niksic M, Robert-Moreno A, Badía-Careaga C, Sanz-Ezquerro JJ, Sharpe J. 4D reconstruction of murine developmental trajectories using spherical harmonics. Dev Cell 2022; 57:2140-2150.e5. [PMID: 36055247 PMCID: PMC9481268 DOI: 10.1016/j.devcel.2022.08.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 05/02/2022] [Accepted: 08/11/2022] [Indexed: 11/30/2022]
Abstract
Normal organogenesis cannot be recapitulated in vitro for mammalian organs, unlike in species including Drosophila and zebrafish. Available 3D data in the form of ex vivo images only provide discrete snapshots of the development of an organ morphology. Here, we propose a computer-based approach to recreate its continuous evolution in time and space from a set of 3D volumetric images. Our method is based on the remapping of shape data into the space of the coefficients of a spherical harmonics expansion where a smooth interpolation over time is simpler. We tested our approach on mouse limb buds and embryonic hearts. A key advantage of this method is that the resulting 4D trajectory can take advantage of all the available data while also being able to interpolate well through time intervals for which there are little or no data. This allows for a quantitative, data-driven 4D description of mouse limb morphogenesis. Computer-based method recreating a 3D plus time evolution of a set of volumetric images Technique based on the interpolation of the coefficients of spherical harmonics Data-driven quantitative 4D description of limb and heart morphogenesis Quantitatively reliable baseline description of organ development
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Affiliation(s)
- Giovanni Dalmasso
- European Molecular Biology Laboratory (EMBL-Barcelona), 08003 Barcelona, Spain.
| | - Marco Musy
- European Molecular Biology Laboratory (EMBL-Barcelona), 08003 Barcelona, Spain
| | - Martina Niksic
- Centre for Genomic Regulation (CRG), 08003 Barcelona, Spain
| | | | | | - Juan Jose Sanz-Ezquerro
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), 28029 Madrid, Spain; Centro Nacional de Biotecnologia (CSIC Madrid), 28049 Madrid, Spain
| | - James Sharpe
- European Molecular Biology Laboratory (EMBL-Barcelona), 08003 Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain.
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9
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Santella A, Kolotuev I, Kizilyaprak C, Bao Z. Cross-modality synthesis of EM time series and live fluorescence imaging. eLife 2022; 11:77918. [PMID: 35666127 PMCID: PMC9213002 DOI: 10.7554/elife.77918] [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: 02/15/2022] [Accepted: 06/05/2022] [Indexed: 11/13/2022] Open
Abstract
Analyses across imaging modalities allow the integration of complementary spatiotemporal information about brain development, structure, and function. However, systematic atlasing across modalities is limited by challenges to effective image alignment. We combine highly spatially resolved electron microscopy (EM) and highly temporally resolved time-lapse fluorescence microscopy (FM) to examine the emergence of a complex nervous system in Caenorhabditis elegans embryogenesis. We generate an EM time series at four classic developmental stages and create a landmark-based co-optimization algorithm for cross-modality image alignment, which handles developmental heterochrony among datasets to achieve accurate single-cell level alignment. Synthesis based on the EM series and time-lapse FM series carrying different cell-specific markers reveals critical dynamic behaviors across scales of identifiable individual cells in the emergence of the primary neuropil, the nerve ring, as well as a major sensory organ, the amphid. Our study paves the way for systematic cross-modality data synthesis in C. elegans and demonstrates a powerful approach that may be applied broadly.
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Affiliation(s)
- Anthony Santella
- Molecular Cytology Core, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Irina Kolotuev
- Electron Microscopy Facility, University of Lausanne, Lausanne, Switzerland
| | | | - Zhirong Bao
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, United States
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10
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MusMorph, a database of standardized mouse morphology data for morphometric meta-analyses. Sci Data 2022; 9:230. [PMID: 35614082 PMCID: PMC9133120 DOI: 10.1038/s41597-022-01338-x] [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: 11/15/2021] [Accepted: 04/13/2022] [Indexed: 11/08/2022] Open
Abstract
Complex morphological traits are the product of many genes with transient or lasting developmental effects that interact in anatomical context. Mouse models are a key resource for disentangling such effects, because they offer myriad tools for manipulating the genome in a controlled environment. Unfortunately, phenotypic data are often obtained using laboratory-specific protocols, resulting in self-contained datasets that are difficult to relate to one another for larger scale analyses. To enable meta-analyses of morphological variation, particularly in the craniofacial complex and brain, we created MusMorph, a database of standardized mouse morphology data spanning numerous genotypes and developmental stages, including E10.5, E11.5, E14.5, E15.5, E18.5, and adulthood. To standardize data collection, we implemented an atlas-based phenotyping pipeline that combines techniques from image registration, deep learning, and morphometrics. Alongside stage-specific atlases, we provide aligned micro-computed tomography images, dense anatomical landmarks, and segmentations (if available) for each specimen (N = 10,056). Our workflow is open-source to encourage transparency and reproducible data collection. The MusMorph data and scripts are available on FaceBase ( www.facebase.org , https://doi.org/10.25550/3-HXMC ) and GitHub ( https://github.com/jaydevine/MusMorph ).
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11
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Krzyspiak J, Khodakhah K, Hébert JM. Potential Variables for Improved Reproducibility of Neuronal Cell Grafts at Stroke Sites. Cells 2022; 11:1656. [PMID: 35626693 PMCID: PMC9139220 DOI: 10.3390/cells11101656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 05/14/2022] [Accepted: 05/16/2022] [Indexed: 01/27/2023] Open
Abstract
Interest is growing in using cell replacements to repair the damage caused by an ischemic stroke. Yet, the usefulness of cell transplants can be limited by the variability observed in their successful engraftment. For example, we recently showed that, although the inclusion of donor-derived vascular cells was necessary for the formation of large grafts (up to 15 mm3) at stroke sites in mice, the size of the grafts overall remained highly variable. Such variability can be due to differences in the cells used for transplantation or the host environment. Here, as possible factors affecting engraftment, we test host sex, host age, the extent of ischemic damage, time of transplant after ischemia, minor differences in donor cell maturity, and cell viability at the time of transplantation. We find that graft size at stroke sites correlates with the size of ischemic damage, host sex (females having graft sizes that correlate with damage), donor cell maturity, and host age, but not with the time of transplant after stroke. A general linear model revealed that graft size is best predicted by stroke severity combined with donor cell maturity. These findings can serve as a guide to improving the reproducibility of cell-based repair therapies.
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Affiliation(s)
- Joanna Krzyspiak
- Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA; (J.K.); (K.K.)
- Stem Cell Institute, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA
| | - Kamran Khodakhah
- Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA; (J.K.); (K.K.)
| | - Jean M. Hébert
- Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA; (J.K.); (K.K.)
- Stem Cell Institute, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA
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12
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Zhao C, Cai Z. Three-dimensional quantitative mass spectrometry imaging in complex system: From subcellular to whole organism. MASS SPECTROMETRY REVIEWS 2022; 41:469-487. [PMID: 33300181 DOI: 10.1002/mas.21674] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Revised: 10/13/2020] [Accepted: 10/22/2020] [Indexed: 06/12/2023]
Abstract
Mass spectrometry imaging (MSI) has been applied for label-free three-dimensional (3D) imaging from position array across the whole organism, which provides high-dimensional quantitative data of inorganic or organic compounds that may play an important role in the regulation of cellular signaling, including metals, metabolites, lipids, drugs, peptides, and proteins. While MSI is suitable for investigation of the spatial distribution of molecules, it has a limitation with visualization and quantification of multiple molecules. 3D-MSI, however, can be applied toward exploring metabolic pathway as well as the interactions of lipid-protein, protein-protein, and metal-protein in complex systems from subcellular to the whole organism through an untargeted methodology. In this review, we highlight the methods and applications of MS-based 3D imaging to address the complexity of molecular interaction from nano- to micrometer lateral resolution, with particular focus on: (a) common and hybrid 3D-MSI techniques; (b) quantitative MSI methodology, including the methods using a stable isotope labeling internal standard (SILIS) and SILIS-free approaches with tissue extinction coefficient or virtual calibration; (c) reconstruction of the 3D organ; (d) application of 3D-MSI for biomarker screening and environmental toxicological research. 3D-MSI quantitative analysis provides accurate spatial information and quantitative variation of biomolecules, which may be valuable for the exploration of the molecular mechanism of the disease progresses and toxicological assessment of environmental pollutants in the whole organism. Additionally, we also discuss the challenges and perspectives on the future of 3D quantitative MSI.
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Affiliation(s)
- Chao Zhao
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Hong Kong SAR, China
- Institute of Biomedical and Health Engineering, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Zongwei Cai
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Hong Kong SAR, China
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13
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Yi W, Mueller T, Rücklin M, Richardson MK. Developmental neuroanatomy of the rosy bitterling Rhodeus ocellatus (Teleostei: Cypriniformes)-A microCT study. J Comp Neurol 2022; 530:2132-2153. [PMID: 35470436 PMCID: PMC9245027 DOI: 10.1002/cne.25324] [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: 03/08/2021] [Revised: 02/09/2022] [Accepted: 03/17/2022] [Indexed: 11/11/2022]
Abstract
Bitterlings are carp-like teleost fish (Cypriniformes: Acheilanathidae) known for their specialized brood parasitic lifestyle. Bitterling embryos, in fact, develop inside the gill chamber of their freshwater mussel hosts. However, little is known about how their parasitic lifestyle affects brain development in comparison to nonparasitic species. Here, we document the development of the brain of the rosy bitterling, Rhodeus ocellatus, at four embryonic stages of 165, 185, 210, 235 hours postfertilization (hpf) using micro-computed tomography (microCT). Focusing on developmental regionalization and brain ventricular organization, we relate the development of the brain divisions to those described for zebrafish using the prosomeric model as a reference paradigm. Segmentation and three-dimensional visualization of the ventricular system allowed us to identify changes in the longitudinal brain axis as a result of cephalic flexure during development. The results show that during early embryonic and larval development, histological differentiation, tissue boundaries, periventricular proliferation zones, and ventricular spaces are all detectable by microCT. The results of this study visualized with differential CT profiles are broadly consistent with comparable histological studies, and with the genoarchitecture of teleosts like the zebrafish. Compared to the zebrafish, our study identifies distinct developmental heterochronies in the rosy bitterling, such as a precocious development of the inferior lobe.
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Affiliation(s)
- Wenjing Yi
- Institute of Biology, University of Leiden, Sylvius Laboratory, Leiden, the Netherlands.,Vertebrate Evolution, Development and Ecology, Naturalis Biodiversity Center, Leiden, the Netherlands
| | - Thomas Mueller
- Vertebrate Evolution, Development and Ecology, Naturalis Biodiversity Center, Leiden, the Netherlands.,Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | - Martin Rücklin
- Institute of Biology, University of Leiden, Sylvius Laboratory, Leiden, the Netherlands.,Vertebrate Evolution, Development and Ecology, Naturalis Biodiversity Center, Leiden, the Netherlands
| | - Michael K Richardson
- Institute of Biology, University of Leiden, Sylvius Laboratory, Leiden, the Netherlands.,Vertebrate Evolution, Development and Ecology, Naturalis Biodiversity Center, Leiden, the Netherlands
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14
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Savriama Y, Tautz D. Testing the accuracy of 3D automatic landmarking via genome-wide association studies. G3 (BETHESDA, MD.) 2022; 12:jkab443. [PMID: 35100368 PMCID: PMC9210295 DOI: 10.1093/g3journal/jkab443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 12/16/2021] [Indexed: 11/13/2022]
Abstract
Various advances in 3D automatic phenotyping and landmark-based geometric morphometric methods have been made. While it is generally accepted that automatic landmarking compromises the capture of the biological variation, no studies have directly tested the actual impact of such landmarking approaches in analyses requiring a large number of specimens and for which the precision of phenotyping is crucial to extract an actual biological signal adequately. Here, we use a recently developed 3D atlas-based automatic landmarking method to test its accuracy in detecting QTLs associated with craniofacial development of the house mouse skull and lower jaws for a large number of specimens (circa 700) that were previously phenotyped via a semiautomatic landmarking method complemented with manual adjustment. We compare both landmarking methods with univariate and multivariate mapping of the skull and the lower jaws. We find that most significant SNPs and QTLs are not recovered based on the data derived from the automatic landmarking method. Our results thus confirm the notion that information is lost in the automated landmarking procedure although somewhat dependent on the analyzed structure. The automatic method seems to capture certain types of structures slightly better, such as lower jaws whose shape is almost entirely summarized by its outline and could be assimilated as a 2D flat object. By contrast, the more apparent 3D features exhibited by a structure such as the skull are not adequately captured by the automatic method. We conclude that using 3D atlas-based automatic landmarking methods requires careful consideration of the experimental question.
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Affiliation(s)
- Yoland Savriama
- Department Evolutionary Genetics, Max-Planck Institute for Evolutionary Biology, 24306 Plön, Germany
| | - Diethard Tautz
- Department Evolutionary Genetics, Max-Planck Institute for Evolutionary Biology, 24306 Plön, Germany
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15
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Ogoke O, Guiggey D, Mon T, Shamul C, Ross S, Rao S, Parashurama N. Spatiotemporal imaging and analysis of mouse and human liver bud morphogenesis. Dev Dyn 2021; 251:662-686. [PMID: 34665487 DOI: 10.1002/dvdy.429] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 09/07/2021] [Accepted: 09/28/2021] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND The process of liver organogenesis has served as a paradigm for organ formation. However, there remains a lack of understanding regarding early mouse and human liver bud morphogenesis and early liver volumetric growth. Elucidating dynamic changes in liver volumes is critical for understanding organ development, implementing toxicological studies, and for modeling hPSC-derived liver organoid growth. New visualization, analysis, and experimental techniques are desperately needed. RESULTS Here, we combine observational data with digital resources, new 3D imaging approaches, retrospective analysis of liver volume data, mathematical modeling, and experiments with hPSC-derived liver organoids. Mouse and human liver organogenesis, characterized by exponential growth, demonstrate distinct spatial features and growth curves over time, which we mathematically modeled using Gompertz models. Visualization of liver-epithelial and septum transversum mesenchyme (STM) interactions suggests extended interactions, which together with new spatial features may be responsible for extensive exponential growth. These STM interactions are modeled with a novel in vitro human pluripotent stem cell (hPSC)-derived hepatic organoid system that exhibits cell migration. CONCLUSIONS Our methods enhance our understanding of liver organogenesis, with new 3D visualization, analysis, mathematical modeling, and in vitro models with hPSCs. Our approach highlights mouse and human differences and provides potential hypothesis for further investigation in vitro and in vivo.
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Affiliation(s)
- Ogechi Ogoke
- Department of Chemical and Biological Engineering, University at Buffalo (State University of New York), Buffalo, New York, USA
| | - Daniel Guiggey
- Department of Chemical and Biological Engineering, University at Buffalo (State University of New York), Buffalo, New York, USA
| | - Tala Mon
- Department of Chemical and Biological Engineering, University at Buffalo (State University of New York), Buffalo, New York, USA
| | - Claire Shamul
- Department of Chemical and Biological Engineering, University at Buffalo (State University of New York), Buffalo, New York, USA
| | - Shatoni Ross
- Department of Chemical and Biological Engineering, University at Buffalo (State University of New York), Buffalo, New York, USA
| | - Saroja Rao
- Department of Biological Sciences, College of Arts and Sciences, University at Buffalo (State University of New York), Buffalo, New York, USA
| | - Natesh Parashurama
- Department of Chemical and Biological Engineering, University at Buffalo (State University of New York), Buffalo, New York, USA.,Clinical and Translation Research Center (CTRC), University at Buffalo (State University of New York), Buffalo, New York, USA.,Department of Biomedical Engineering, University at Buffalo (State University of New York), Buffalo, New York, USA.,Center for Cell, Gene, and Tissue Engineering (CGTE), University at Buffalo (State University of New York), Buffalo, New York, USA
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16
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Qiu Z, Xu T, Langerman J, Das W, Wang C, Nair N, Aristizabal O, Mamou J, Turnbull DH, Ketterling JA, Wang Y. A Deep Learning Approach for Segmentation, Classification, and Visualization of 3-D High-Frequency Ultrasound Images of Mouse Embryos. IEEE TRANSACTIONS ON ULTRASONICS, FERROELECTRICS, AND FREQUENCY CONTROL 2021; 68:2460-2471. [PMID: 33755564 PMCID: PMC8274381 DOI: 10.1109/tuffc.2021.3068156] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Segmentation and mutant classification of high-frequency ultrasound (HFU) mouse embryo brain ventricle (BV) and body images can provide valuable information for developmental biologists. However, manual segmentation and identification of BV and body requires substantial time and expertise. This article proposes an accurate, efficient and explainable deep learning pipeline for automatic segmentation and classification of the BV and body. For segmentation, a two-stage framework is implemented. The first stage produces a low-resolution segmentation map, which is then used to crop a region of interest (ROI) around the target object and serve as the probability map of the autocontext input for the second-stage fine-resolution refinement network. The segmentation then becomes tractable on high-resolution 3-D images without time-consuming sliding windows. The proposed segmentation method significantly reduces inference time (102.36-0.09 s/volume ≈ 1000× faster) while maintaining high accuracy comparable to previous sliding-window approaches. Based on the BV and body segmentation map, a volumetric convolutional neural network (CNN) is trained to perform a mutant classification task. Through backpropagating the gradients of the predictions to the input BV and body segmentation map, the trained classifier is found to largely focus on the region where the Engrailed-1 (En1) mutation phenotype is known to manifest itself. This suggests that gradient backpropagation of deep learning classifiers may provide a powerful tool for automatically detecting unknown phenotypes associated with a known genetic mutation.
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17
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Knudsen TB, Spielmann M, Megason SG, Faustman EM. Single-cell profiling for advancing birth defects research and prevention. Birth Defects Res 2021; 113:546-559. [PMID: 33496083 PMCID: PMC8562675 DOI: 10.1002/bdr2.1870] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 12/10/2020] [Accepted: 01/05/2021] [Indexed: 12/12/2022]
Abstract
Cellular analysis of developmental processes and toxicities has traditionally entailed bulk methods (e.g., transcriptomics) that lack single cell resolution or tissue localization methods (e.g., immunostaining) that allow only a few genes to be monitored in each experiment. Recent technological advances have enabled interrogation of genomic function at the single-cell level, providing new opportunities to unravel developmental pathways and processes with unprecedented resolution. Here, we review emerging technologies of single-cell RNA-sequencing (scRNA-seq) to globally characterize the gene expression sets of different cell types and how different cell types emerge from earlier cell states in development. Cell atlases of experimental embryology and human embryogenesis at single-cell resolution will provide an encyclopedia of genes that define key stages from gastrulation to organogenesis. This technology, combined with computational models to discover key organizational principles, was recognized by Science magazine as the "Breakthrough of the year" for 2018 due to transformative potential on the way we study how human cells mature over a lifetime, how tissues regenerate, and how cells change in diseases (e.g., patient-derived organoids to screen disease-specific targets and design precision therapy). Profiling transcriptomes at the single-cell level can fulfill the need for greater detail in the molecular progression of all cell lineages, from pluripotency to adulthood and how cell-cell signaling pathways control progression at every step. Translational opportunities emerge for elucidating pathogenesis of genetic birth defects with cellular precision and improvements for predictive toxicology of chemical teratogenesis.
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Affiliation(s)
- Thomas B Knudsen
- Center for Computational Toxicology and Exposure, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina, USA
| | - Malte Spielmann
- Human Molecular Genomics, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Institute of Human Genetics, University of Lübeck, Lübeck, Germany
| | - Sean G Megason
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Elaine M Faustman
- Department of Environmental & Occupational Health Sciences, University of Washington, School of Public Health, Seattle, Washington, USA
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18
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Horner NR, Venkataraman S, Armit C, Casero R, Brown JM, Wong MD, van Eede MC, Henkelman RM, Johnson S, Teboul L, Wells S, Brown SD, Westerberg H, Mallon AM. LAMA: automated image analysis for the developmental phenotyping of mouse embryos. Development 2021; 148:dev192955. [PMID: 33574040 PMCID: PMC8015254 DOI: 10.1242/dev.192955] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 12/21/2020] [Indexed: 11/20/2022]
Abstract
Advanced 3D imaging modalities, such as micro-computed tomography (micro-CT), have been incorporated into the high-throughput embryo pipeline of the International Mouse Phenotyping Consortium (IMPC). This project generates large volumes of raw data that cannot be immediately exploited without significant resources of personnel and expertise. Thus, rapid automated annotation is crucial to ensure that 3D imaging data can be integrated with other multi-dimensional phenotyping data. We present an automated computational mouse embryo phenotyping pipeline that harnesses the large amount of wild-type control data available in the IMPC embryo pipeline in order to address issues of low mutant sample number as well as incomplete penetrance and variable expressivity. We also investigate the effect of developmental substage on automated phenotyping results. Designed primarily for developmental biologists, our software performs image pre-processing, registration, statistical analysis and segmentation of embryo images. We also present a novel anatomical E14.5 embryo atlas average and, using it with LAMA, show that we can uncover known and novel dysmorphology from two IMPC knockout lines.
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Affiliation(s)
- Neil R Horner
- Medical Research Council Harwell Institute, Harwell OX11 0RD, UK
| | - Shanmugasundaram Venkataraman
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine (IGMM), University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Chris Armit
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine (IGMM), University of Edinburgh, Edinburgh EH4 2XU, UK
- BGI Hong Kong, 26/F, Kings Wing Plaza 2, 1 On Kwan Street, Shek Mun, New Territories, Hong Kong
| | - Ramón Casero
- Medical Research Council Harwell Institute, Harwell OX11 0RD, UK
| | - James M Brown
- School of Computer Science, University of Lincoln, Lincoln LN6 7TS
| | - Michael D Wong
- Mouse Imaging Centre, Hospital for Sick Children, Toronto, Ontario M5T 3H7, Canada
| | - Matthijs C van Eede
- Mouse Imaging Centre, Hospital for Sick Children, Toronto, Ontario M5T 3H7, Canada
| | - R Mark Henkelman
- Mouse Imaging Centre, Hospital for Sick Children, Toronto, Ontario M5T 3H7, Canada
| | - Sara Johnson
- Medical Research Council Harwell Institute, Harwell OX11 0RD, UK
| | - Lydia Teboul
- Medical Research Council Harwell Institute, Harwell OX11 0RD, UK
| | - Sara Wells
- Medical Research Council Harwell Institute, Harwell OX11 0RD, UK
| | - Steve D Brown
- Medical Research Council Harwell Institute, Harwell OX11 0RD, UK
| | | | - Ann-Marie Mallon
- Medical Research Council Harwell Institute, Harwell OX11 0RD, UK
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19
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Munro DAD, Bradford BM, Mariani SA, Hampton DW, Vink CS, Chandran S, Hume DA, Pridans C, Priller J. CNS macrophages differentially rely on an intronic Csf1r enhancer for their development. Development 2020; 147:147/23/dev194449. [PMID: 33323375 PMCID: PMC7758622 DOI: 10.1242/dev.194449] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 10/26/2020] [Indexed: 12/29/2022]
Abstract
The central nervous system hosts parenchymal macrophages, known as microglia, and non-parenchymal macrophages, collectively termed border-associated macrophages (BAMs). Microglia, but not BAMs, were reported to be absent in mice lacking a conserved Csf1r enhancer: the fms-intronic regulatory element (FIRE). However, it is unknown whether FIRE deficiency also impacts BAM arrival and/or maintenance. Here, we show that macrophages in the ventricular system of the brain, including Kolmer's epiplexus macrophages, are absent in Csf1rΔFIRE/ΔFIRE mice. Stromal choroid plexus BAMs are also considerably reduced. During normal development, we demonstrate that intracerebroventricular macrophages arrive from embryonic day 10.5, and can traverse ventricular walls in embryonic slice cultures. In Csf1rΔFIRE/ΔFIRE embryos, the arrival of both primitive microglia and intracerebroventricular macrophages was eliminated, whereas the arrival of cephalic mesenchyme and stromal choroid plexus BAMs was only partially restricted. Our results provide new insights into the development and regulation of different CNS macrophage populations. Summary: Deletion of the fms-intronic regulatory element of Csf1r in mouse disrupts the engraftment and maintenance of central nervous system macrophages in a compartment-specific manner.
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Affiliation(s)
- David A D Munro
- UK Dementia Research Institute at The University of Edinburgh, Chancellor's Building, Edinburgh EH16 4SB, UK
| | - Barry M Bradford
- The Roslin Institute & Royal (Dick) School of Veterinary Sciences, The University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
| | - Samanta A Mariani
- Centre for Inflammation Research, Queen's Medical Research Institute, The University of Edinburgh, Edinburgh EH16 4TJ, UK
| | - David W Hampton
- Euan MacDonald Centre for MND Research, The University of Edinburgh, Edinburgh EH16 4SB, UK.,Centre for Clinical Brain Sciences, The University of Edinburgh, Edinburgh EH16 4SB, UK
| | - Chris S Vink
- Centre for Inflammation Research, Queen's Medical Research Institute, The University of Edinburgh, Edinburgh EH16 4TJ, UK
| | - Siddharthan Chandran
- UK Dementia Research Institute at The University of Edinburgh, Chancellor's Building, Edinburgh EH16 4SB, UK.,Euan MacDonald Centre for MND Research, The University of Edinburgh, Edinburgh EH16 4SB, UK.,Centre for Clinical Brain Sciences, The University of Edinburgh, Edinburgh EH16 4SB, UK.,Anne Rowling Regenerative Neurology Clinic, The University of Edinburgh, Edinburgh EH16 4SB, UK
| | - David A Hume
- Mater Research Institute, University of Queensland, Translational Research Institute, Woolloongabba Q4102, Australia
| | - Clare Pridans
- The University of Edinburgh Centre for Inflammation Research, The Queen's Medical Research Institute, Edinburgh BioQuarter, 47 Little France Crescent, Edinburgh EH16 4TJ, UK.,Simons Initiative for the Developing Brain, Centre for Discovery Brain Sciences, The University of Edinburgh, Hugh Robson Building, George Square, Edinburgh EH8 9XD, UK
| | - Josef Priller
- UK Dementia Research Institute at The University of Edinburgh, Chancellor's Building, Edinburgh EH16 4SB, UK .,Centre for Clinical Brain Sciences, The University of Edinburgh, Edinburgh EH16 4SB, UK.,Department of Neuropsychiatry and Laboratory of Molecular Psychiatry, Charité - Universitätsmedizin Berlin, 10117 Berlin, Germany
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20
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Markel M, Ginzel M, Peukert N, Schneider H, Haak R, Mayer S, Suttkus A, Lacher M, Kluth D, Gosemann J. High resolution three-dimensional imaging and measurement of lung, heart, liver, and diaphragmatic development in the fetal rat based on micro-computed tomography (micro-CT). J Anat 2020; 238:1042-1054. [PMID: 33289078 PMCID: PMC7930770 DOI: 10.1111/joa.13355] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 10/21/2020] [Accepted: 10/21/2020] [Indexed: 11/30/2022] Open
Abstract
Understanding of normal fetal organ development is crucial for the evaluation of the pathogenesis of congenital anomalies. Various techniques have been used to generate imaging of fetal rat organogenesis, such as histological dissection with 3-dimensional reconstruction and scanning electron microscopy. However, these techniques did not imply quantitative measurements of developing organs (volumes, surface areas of organs). Furthermore, a partial or total destruction of the embryos prior to analysis was inevitable. Recently, micro-computed tomography (micro-CT) has been established as a novel tool to investigate embryonic development in non-dissected embryos of rodents. In this study, we used the micro-CT technique to generate 4D datasets of rat embryos aged between embryonic day 15-22 and newborns. Lungs, hearts, diaphragms, and livers were digitally segmented in order to measure organ volumes and analyze organ development as well as generate high-resolution 3D images. These data provide objective values compiling a 4D atlas of pulmonary, cardiac, diaphragmatic, and hepatic development in the fetal rat.
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Affiliation(s)
- Moritz Markel
- Department of Pediatric SurgeryUniversity of LeipzigLeipzigGermany
| | - Marco Ginzel
- Department of Pediatric SurgeryUniversity of LeipzigLeipzigGermany
- Department of NeonatologyUniversity of TübingenTübingenGermany
| | - Nicole Peukert
- Department of Pediatric SurgeryUniversity of LeipzigLeipzigGermany
| | - Hartmut Schneider
- Department of Cariology, Endodontology and PeriodontologyUniversity of LeipzigLeipzigGermany
| | - Rainer Haak
- Department of Cariology, Endodontology and PeriodontologyUniversity of LeipzigLeipzigGermany
| | - Steffi Mayer
- Department of Pediatric SurgeryUniversity of LeipzigLeipzigGermany
| | - Anne Suttkus
- Department of Pediatric SurgeryUniversity of LeipzigLeipzigGermany
| | - Martin Lacher
- Department of Pediatric SurgeryUniversity of LeipzigLeipzigGermany
| | - Dietrich Kluth
- Department of Pediatric SurgeryUniversity of LeipzigLeipzigGermany
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21
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Hamdy N, Eide S, Sun HS, Feng ZP. Animal models for neonatal brain injury induced by hypoxic ischemic conditions in rodents. Exp Neurol 2020; 334:113457. [PMID: 32889009 DOI: 10.1016/j.expneurol.2020.113457] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 08/28/2020] [Accepted: 08/30/2020] [Indexed: 02/06/2023]
Abstract
Neonatal hypoxia-ischemia and resulting encephalopathies are of significant concern. Intrapartum asphyxia is a leading cause of neonatal death globally. Among surviving infants, there remains a high incidence of hypoxic-ischemic encephalopathy due to neonatal hypoxic-ischemic brain injury, manifesting as mild conditions including attention deficit hyperactivity disorder, and debilitating disorders such as cerebral palsy. Various animal models of neonatal hypoxic brain injury have been implemented to explore cellular and molecular mechanisms, assess the potential of novel therapeutic strategies, and characterize the functional and behavioural correlates of injury. Each of the animal models has individual advantages and limitations. The present review looks at several widely-used and alternative rodent models of neonatal hypoxia and hypoxia-ischemia; it highlights their strengths and limitations, and their potential for continued and improved use.
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Affiliation(s)
- Nancy Hamdy
- Department of Physiology, Faculty of Medicine, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Sarah Eide
- Department of Physiology, Faculty of Medicine, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Hong-Shuo Sun
- Department of Physiology, Faculty of Medicine, University of Toronto, Toronto, Ontario M5S 1A8, Canada; Department of Surgery, Faculty of Medicine, University of Toronto, Toronto, Ontario M5S 1A8, Canada.
| | - Zhong-Ping Feng
- Department of Physiology, Faculty of Medicine, University of Toronto, Toronto, Ontario M5S 1A8, Canada.
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22
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Wang S, Larina IV, Larin KV. Label-free optical imaging in developmental biology [Invited]. BIOMEDICAL OPTICS EXPRESS 2020; 11:2017-2040. [PMID: 32341864 PMCID: PMC7173889 DOI: 10.1364/boe.381359] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 01/30/2020] [Accepted: 02/25/2020] [Indexed: 05/03/2023]
Abstract
Application of optical imaging in developmental biology marks an exciting frontier in biomedical optics. Optical resolution and imaging depth allow for investigation of growing embryos at subcellular, cellular, and whole organism levels, while the complexity and variety of embryonic processes set multiple challenges stimulating the development of various live dynamic embryonic imaging approaches. Among other optical methods, label-free optical techniques attract an increasing interest as they allow investigation of developmental mechanisms without application of exogenous markers or fluorescent reporters. There has been a boost in development of label-free optical imaging techniques for studying embryonic development in animal models over the last decade, which revealed new information about early development and created new areas for investigation. Here, we review the recent progress in label-free optical embryonic imaging, discuss specific applications, and comment on future developments at the interface of photonics, engineering, and developmental biology.
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Affiliation(s)
- Shang Wang
- Department of Biomedical Engineering, Stevens Institute of Technology, 1 Castle Point Terrace, Hoboken, NJ 07030, USA
| | - Irina V. Larina
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Kirill V. Larin
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
- Department of Biomedical Engineering, University of Houston, 3605 Cullen Boulevard, Houston, TX 77204, USA
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23
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Huang Y, Li M, Huang D, Qiu Q, Lin W, Liu J, Yang W, Yao Y, Yan G, Qu N, Tuchin VV, Fan S, Liu G, Zhao Q, Chen X. Depth-Resolved Enhanced Spectral-Domain OCT Imaging of Live Mammalian Embryos Using Gold Nanoparticles as Contrast Agent. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2019; 15:e1902346. [PMID: 31304667 DOI: 10.1002/smll.201902346] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 06/21/2019] [Indexed: 05/12/2023]
Abstract
High-resolution and real-time visualization of the morphological changes during embryonic development are critical for studying congenital anomalies. Optical coherence tomography (OCT) has been used to investigate the process of embryogenesis. However, the structural visibility of the embryo is decreased with the depth due to signal roll-off and high light scattering. To overcome these obstacles, in this study, combined is a spectral-domain OCT (SD-OCT) with gold nanorods (GNRs) for 2D/3D imaging of live mouse embryos. Inductively coupled plasma mass spectrometry is used to confirm that GNRs can be effectively delivered to the embryos during ex vivo culture. OCT signal, image contrast, and penetration depth are all enhanced on the embryos with GNRs. These results show that after GNR treatment, more accurate spatial localization and better contrasting of the borders among organs can be observed on E9.5 and E10.5 mouse embryos. Furthermore, the strong optical absorbance of GNRs results in much clearer 3D images of the embryos, which can be used for calculating the heart areas and volumes of E9.5 and E10.5 embryos. These findings provide a promising strategy for monitoring organ development and detecting congenital structural abnormalities in mice.
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Affiliation(s)
- Yali Huang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Organ Transplantation Institute, Center for Molecular Imaging and Translational Medicine, School of Medicine, School of Public Health, Xiamen University, Xiamen, 361102, China
| | - Minghui Li
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Organ Transplantation Institute, Center for Molecular Imaging and Translational Medicine, School of Medicine, School of Public Health, Xiamen University, Xiamen, 361102, China
| | - Doudou Huang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Organ Transplantation Institute, Center for Molecular Imaging and Translational Medicine, School of Medicine, School of Public Health, Xiamen University, Xiamen, 361102, China
| | - Qi Qiu
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Organ Transplantation Institute, Center for Molecular Imaging and Translational Medicine, School of Medicine, School of Public Health, Xiamen University, Xiamen, 361102, China
| | - Wenzhen Lin
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Organ Transplantation Institute, Center for Molecular Imaging and Translational Medicine, School of Medicine, School of Public Health, Xiamen University, Xiamen, 361102, China
| | - Jiyan Liu
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Organ Transplantation Institute, Center for Molecular Imaging and Translational Medicine, School of Medicine, School of Public Health, Xiamen University, Xiamen, 361102, China
| | - Wensheng Yang
- Department of Pathology, Affiliated Chenggong Hospital, Xiamen University, Xiamen, 361000, China
| | - Youliang Yao
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Organ Transplantation Institute, Center for Molecular Imaging and Translational Medicine, School of Medicine, School of Public Health, Xiamen University, Xiamen, 361102, China
| | - Guoliang Yan
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Organ Transplantation Institute, Center for Molecular Imaging and Translational Medicine, School of Medicine, School of Public Health, Xiamen University, Xiamen, 361102, China
| | - Ning Qu
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Organ Transplantation Institute, Center for Molecular Imaging and Translational Medicine, School of Medicine, School of Public Health, Xiamen University, Xiamen, 361102, China
| | - Valery V Tuchin
- Research-Educational Institute of Optics and Biophotonics, Saratov State University, Saratov, 410012, Russia
- Laboratory of Laser Diagnostics of Technical and Living Systems, Institute of Precision Mechanics and Control of the Russian Academy of Science, Saratov, 410028, Russia
- Laboratory of Molecular Imaging, Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, 119071, Russia
- Interdisciplinary Laboratory of Biophotonics, Tomsk State University, Tomsk, 634050, Russia
| | - Shanhui Fan
- College of Life Information Science and Instrument Engineering, Hangzhou Dianzi University, Hangzhou, 310018, China
| | - Gang Liu
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Organ Transplantation Institute, Center for Molecular Imaging and Translational Medicine, School of Medicine, School of Public Health, Xiamen University, Xiamen, 361102, China
| | - Qingliang Zhao
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Organ Transplantation Institute, Center for Molecular Imaging and Translational Medicine, School of Medicine, School of Public Health, Xiamen University, Xiamen, 361102, China
| | - Xiaoyuan Chen
- Laboratory of Molecular Imaging and Nanomedicine, National Institute of Biomedical Imaging and Bioengineering (NIBIB), National Institutes of Health (NIH), Bethesda, MD, 20892, USA
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24
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Ban S, Cho NH, Min E, Bae JK, Ahn Y, Shin S, Park SA, Lee Y, Jung W. Label-free optical projection tomography for quantitative three-dimensional anatomy of mouse embryo. JOURNAL OF BIOPHOTONICS 2019; 12:e201800481. [PMID: 30729697 DOI: 10.1002/jbio.201800481] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Revised: 02/04/2019] [Accepted: 02/05/2019] [Indexed: 05/19/2023]
Abstract
Recent progress in three-dimensional optical imaging techniques allows visualization of many comprehensive biological specimens. Optical clearing methods provide volumetric and quantitative information by overcoming the limited depth of light due to scattering. However, current imaging technologies mostly rely on the synthetic or genetic fluorescent labels, thus limits its application to whole-body visualization of generic mouse models. Here, we report a label-free optical projection tomography (LF-OPT) technique for quantitative whole mouse embryo imaging. LF-OPT is based on the attenuation contrast of light rather than fluorescence, and it utilizes projection imaging technique similar to computed tomography for visualizing the volumetric structure. We demonstrate this with a collection of mouse embryo morphologies in different stages using LF-OPT. Additionally, we extract quantitative organ information applicable toward high-throughput phenotype screening. Our results indicate that LF-OPT can provide multi-scale morphological information in various tissues including bone, which can be difficult in conventional optical imaging technique.
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Affiliation(s)
- Sungbea Ban
- Samsung Electro-Mechanics, Global Technology Center (GTC), Suwon, Republic of Korea
| | - Nam Hyun Cho
- Department of Otorhinolaryngology, Harvard Medical School, Boston, Massachusetts
- Massachusetts Eye and Ear Infirmary, Boston, Massachusetts
| | - Eunjung Min
- Rowland Institute at Harvard, Cambridge, Massachusetts
| | - Jung Kweon Bae
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
| | - Yujin Ahn
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
| | - Sungwon Shin
- Department of Mechanical Engineering, Sogang University, Seoul, Republic of Korea
| | - Soo-Ah Park
- In Vivo Research Center, UNIST Central Research Facilities, Ulsan, Republic of Korea
| | - Yoonsung Lee
- Center for Genomic Integrity Institute for Basic Science, UNIST, Ulsan, Republic of Korea
| | - Woonggyu Jung
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
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25
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Hsu CW, Kalaga S, Akoma U, Rasmussen TL, Christiansen AE, Dickinson ME. High Resolution Imaging of Mouse Embryos and Neonates with X-Ray Micro-Computed Tomography. ACTA ACUST UNITED AC 2019; 9:e63. [PMID: 31195428 DOI: 10.1002/cpmo.63] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Iodine-contrast micro-computed tomography (microCT) 3D imaging provides a non-destructive and high-throughput platform for studying mouse embryo and neonate development. Here we provide protocols on preparing mouse embryos and neonates between embryonic day 8.5 (E8.5) to postnatal day 4 (P4) for iodine-contrast microCT imaging. With the implementation of the STABILITY method to create a polymer-tissue hybrid structure, we have demonstrated that not only is soft tissue shrinkage minimized but also the minimum required time for soft tissue staining with iodine is decreased, especially for E18.5 to P4 samples. In addition, we also provide a protocol on using commercially available X-CLARITYTM hydrogel solution to create the similar polymer-tissue hybrid structure on delicate early post-implantation stage (E8.5 to E14.5) embryos. With its simple sample staining and mounting processes, this protocol is easy to adopt and implement for most of the commercially available, stand-alone microCT systems in order to study mouse development between early post-implantation to early postnatal stages. © 2019 by John Wiley & Sons, Inc.
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Affiliation(s)
- Chih-Wei Hsu
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, Texas.,Optical Imaging and Vital Microscopy Core, Baylor College of Medicine, Houston, Texas
| | - Sowmya Kalaga
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, Texas.,Optical Imaging and Vital Microscopy Core, Baylor College of Medicine, Houston, Texas
| | - Uchechukwu Akoma
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, Texas
| | - Tara L Rasmussen
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, Texas
| | - Audrey E Christiansen
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, Texas
| | - Mary E Dickinson
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, Texas.,Optical Imaging and Vital Microscopy Core, Baylor College of Medicine, Houston, Texas.,Cardiovascular Research Institute, Baylor College of Medicine, Houston, Texas
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26
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Percival CJ, Devine J, Darwin BC, Liu W, van Eede M, Henkelman RM, Hallgrimsson B. The effect of automated landmark identification on morphometric analyses. J Anat 2019; 234:917-935. [PMID: 30901082 DOI: 10.1111/joa.12973] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/07/2019] [Indexed: 01/20/2023] Open
Abstract
Morphometric analysis of anatomical landmarks allows researchers to identify specific morphological differences between natural populations or experimental groups, but manually identifying landmarks is time-consuming. We compare manually and automatically generated adult mouse skull landmarks and subsequent morphometric analyses to elucidate how switching from manual to automated landmarking will impact morphometric analysis results for large mouse (Mus musculus) samples (n = 1205) that represent a wide range of 'normal' phenotypic variation (62 genotypes). Other studies have suggested that the use of automated landmarking methods is feasible, but this study is the first to compare the utility of current automated approaches to manual landmarking for a large dataset that allows the quantification of intra- and inter-strain variation. With this unique sample, we investigated how switching to a non-linear image registration-based automated landmarking method impacts estimated differences in genotype mean shape and shape variance-covariance structure. In addition, we tested whether an initial registration of specimen images to genotype-specific averages improves automatic landmark identification accuracy. Our results indicated that automated landmark placement was significantly different than manual landmark placement but that estimated skull shape covariation was correlated across methods. The addition of a preliminary genotype-specific registration step as part of a two-level procedure did not substantially improve on the accuracy of one-level automatic landmark placement. The landmarks with the lowest automatic landmark accuracy are found in locations with poor image registration alignment. The most serious outliers within morphometric analysis of automated landmarks displayed instances of stochastic image registration error that are likely representative of errors common when applying image registration methods to micro-computed tomography datasets that were initially collected with manual landmarking in mind. Additional efforts during specimen preparation and image acquisition can help reduce the number of registration errors and improve registration results. A reduction in skull shape variance estimates were noted for automated landmarking methods compared with manual landmarking. This partially reflects an underestimation of more extreme genotype shapes and loss of biological signal, but largely represents the fact that automated methods do not suffer from intra-observer landmarking error. For appropriate samples and research questions, our image registration-based automated landmarking method can eliminate the time required for manual landmarking and have a similar power to identify shape differences between inbred mouse genotypes.
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Affiliation(s)
| | - Jay Devine
- Department of Cell Biology and Anatomy, University of Calgary, Calgary, AB, Canada
| | - Benjamin C Darwin
- Mouse Imaging Centre, The Hospital for Sick Children, Toronto, ON, Canada
| | - Wei Liu
- Department of Cell Biology and Anatomy, University of Calgary, Calgary, AB, Canada
| | - Matthijs van Eede
- Mouse Imaging Centre, The Hospital for Sick Children, Toronto, ON, Canada
| | - R Mark Henkelman
- Mouse Imaging Centre, The Hospital for Sick Children, Toronto, ON, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Benedikt Hallgrimsson
- Department of Cell Biology and Anatomy, University of Calgary, Calgary, AB, Canada.,Alberta Children's Hospital Research Institute for Child and Maternal Health, University of Calgary, Calgary, AB, Canada.,The McCaig Institute for Bone and Joint Health, University of Calgary, Calgary, AB, Canada
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27
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Dominguez Gonzalez B, Billion K, Rous S, Pavie B, Lange C, Goodchild R. Excess LINC complexes impair brain morphogenesis in a mouse model of recessive TOR1A disease. Hum Mol Genet 2019; 27:2154-2170. [PMID: 29868845 DOI: 10.1093/hmg/ddy125] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 04/06/2018] [Indexed: 01/08/2023] Open
Abstract
Heterozygosity for the TOR1A-Δgag mutation causes semi-penetrant childhood-onset dystonia (OMIM #128100). More recently, homozygous TOR1A mutations were shown to cause severe neurological dysfunction in infants. However, there is little known about the recessive cases, including whether existing reports define the full spectrum of recessive TOR1A disease. Here we describe abnormal brain morphogenesis in ∼30% of Tor1a-/- mouse embryos while, in contrast, this is not found in Tor1aΔgag/Δgag mice. The abnormal Tor1a-/- brains contain excess neural tissue, as well as proliferative zone cytoarchitectural defects related to radial glial cell polarity and cytoskeletal organization. In cultured cells torsinA effects the linker of nucleoskeleton and cytoskeleton (LINC) complex that couples the nucleus and cytoskeleton. Here we identify that torsinA loss elevates LINC complex levels in the proliferative zone, and that genetic reduction of LINC complexes prevents abnormal brain morphogenesis in Tor1a-/- embryos. These data show that Tor1a affects radial glial cells via a LINC complex mediated mechanism. They also predict human TOR1A disease will include incompletely penetrant defects in embryonic brain morphogenesis in cases where mutations ablate TOR1A function.
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Affiliation(s)
- Beatriz Dominguez Gonzalez
- VIB & KU Leuven Centre for Brain & Disease Research, Campus Gasthuisberg, 3000 Leuven, Belgium.,Department of Neurosciences, Campus Gasthuisberg, KU Leuven, 3000 Leuven, Belgium
| | - Karolien Billion
- VIB & KU Leuven Centre for Brain & Disease Research, Campus Gasthuisberg, 3000 Leuven, Belgium.,Department of Neurosciences, Campus Gasthuisberg, KU Leuven, 3000 Leuven, Belgium
| | - Stef Rous
- VIB & KU Leuven Centre for Brain & Disease Research, Campus Gasthuisberg, 3000 Leuven, Belgium.,Department of Neurosciences, Campus Gasthuisberg, KU Leuven, 3000 Leuven, Belgium
| | - Benjamin Pavie
- VIB & KU Leuven Centre for Brain & Disease Research, Campus Gasthuisberg, 3000 Leuven, Belgium.,VIB Bio Imaging Core, Campus Gasthuisberg, 3000 Leuven, Belgium
| | - Christian Lange
- DFG-Research Center and Cluster of Excellence for Regenerative Therapies (CRTD), Technische Universität Dresden, Fetscherstr. 105, D-01307, Dresden, Germany
| | - Rose Goodchild
- VIB & KU Leuven Centre for Brain & Disease Research, Campus Gasthuisberg, 3000 Leuven, Belgium.,Department of Neurosciences, Campus Gasthuisberg, KU Leuven, 3000 Leuven, Belgium
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28
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Brown SDM, Holmes CC, Mallon AM, Meehan TF, Smedley D, Wells S. High-throughput mouse phenomics for characterizing mammalian gene function. Nat Rev Genet 2018; 19:357-370. [PMID: 29626206 PMCID: PMC6582361 DOI: 10.1038/s41576-018-0005-2] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
We are entering a new era of mouse phenomics, driven by large-scale and economical generation of mouse mutants coupled with increasingly sophisticated and comprehensive phenotyping. These studies are generating large, multidimensional gene-phenotype data sets, which are shedding new light on the mammalian genome landscape and revealing many hitherto unknown features of mammalian gene function. Moreover, these phenome resources provide a wealth of disease models and can be integrated with human genomics data as a powerful approach for the interpretation of human genetic variation and its relationship to disease. In the future, the development of novel phenotyping platforms allied to improved computational approaches, including machine learning, for the analysis of phenotype data will continue to enhance our ability to develop a comprehensive and powerful model of mammalian gene-phenotype space.
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Affiliation(s)
| | - Chris C Holmes
- Nuffield Department of Medicine and Department of Statistics, University of Oxford, Oxford, UK.
| | | | - Terrence F Meehan
- European Molecular Biology Laboratory - European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
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29
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Boughner JC, van Eede MC, Spring S, Yu LX, Rostampour N, Henkelman RM. P63 expression plays a role in developmental rate, embryo size, and local morphogenesis. Dev Dyn 2018; 247:779-787. [DOI: 10.1002/dvdy.24622] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 01/23/2018] [Accepted: 01/30/2018] [Indexed: 12/16/2022] Open
Affiliation(s)
- Julia C. Boughner
- Department of Anatomy & Cell Biology, College of Medicine; University of Saskatchewan; Saskatoon Saskatchewan Canada
| | | | - Shoshana Spring
- Mouse Imaging Centre; Hospital for Sick Children; Toronto Ontario Canada
| | - Lisa X. Yu
- Mouse Imaging Centre; Hospital for Sick Children; Toronto Ontario Canada
| | - Nasim Rostampour
- Department of Anatomy & Cell Biology, College of Medicine; University of Saskatchewan; Saskatoon Saskatchewan Canada
| | - R. Mark Henkelman
- Mouse Imaging Centre; Hospital for Sick Children; Toronto Ontario Canada
- Department of Medical Biophysics; University of Toronto; Toronto Ontario Canada
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30
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Three-dimensional microCT imaging of murine embryonic development from immediate post-implantation to organogenesis: application for phenotyping analysis of early embryonic lethality in mutant animals. Mamm Genome 2017; 29:245-259. [PMID: 29170794 PMCID: PMC5887010 DOI: 10.1007/s00335-017-9723-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 10/09/2017] [Indexed: 10/28/2022]
Abstract
In this work, we applied three-dimensional microCT imaging to study murine embryogenesis in the range from immediate post-implantation period (embryonic day 5.5) to mid-gestation (embryonic day 12.5) with the resolution up to 1.4 µm/voxel. Also, we introduce an imaging procedure for non-invasive volumetric estimation of an entire litter of embryos within the maternal uterine structures. This method allows for an accurate, detailed and systematic morphometric analysis of both embryonic and extra-embryonic components during embryogenesis. Three-dimensional imaging of unperturbed embryos was performed to visualize the egg cylinder, primitive streak, gastrulation and early organogenesis stages of murine development in the C57Bl6/N mouse reference strain. Further, we applied our microCT imaging protocol to determine the earliest point when embryonic development is arrested in a mouse line with knockout for tRNA splicing endonuclease subunit Tsen54 gene. Our analysis determined that the embryonic development in Tsen54 null embryos does not proceed beyond implantation. We demonstrated that application of microCT imaging to entire litter of non-perturbed embryos greatly facilitate studies to unravel gene function during early embryogenesis and to determine the precise point at which embryonic development is arrested in mutant animals. The described method is inexpensive, does not require lengthy embryos dissection and can be applicable for detailed analysis of mutant mice at laboratory scale as well as for high-throughput projects.
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31
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Geyer SH, Reissig LF, Hüsemann M, Höfle C, Wilson R, Prin F, Szumska D, Galli A, Adams DJ, White J, Mohun TJ, Weninger WJ. Morphology, topology and dimensions of the heart and arteries of genetically normal and mutant mouse embryos at stages S21-S23. J Anat 2017; 231:600-614. [PMID: 28776665 PMCID: PMC5603791 DOI: 10.1111/joa.12663] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/31/2017] [Indexed: 12/23/2022] Open
Abstract
Accurate identification of abnormalities in the mouse embryo depends not only on comparisons with appropriate, developmental stage‐matched controls, but also on an appreciation of the range of anatomical variation that can be expected during normal development. Here we present a morphological, topological and metric analysis of the heart and arteries of mouse embryos harvested on embryonic day (E)14.5, based on digital volume data of whole embryos analysed by high‐resolution episcopic microscopy (HREM). By comparing data from 206 genetically normal embryos, we have analysed the range and frequency of normal anatomical variations in the heart and major arteries across Theiler stages S21–S23. Using this, we have identified abnormalities in these structures among 298 embryos from mutant mouse lines carrying embryonic lethal gene mutations produced for the Deciphering the Mechanisms of Developmental Disorders (DMDD) programme. We present examples of both commonly occurring abnormal phenotypes and novel pathologies that most likely alter haemodynamics in these genetically altered mouse embryos. Our findings offer a reference baseline for identifying accurately abnormalities of the heart and arteries in embryos that have largely completed organogenesis.
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Affiliation(s)
- Stefan H Geyer
- Division of Anatomy & MIC, Medical University of Vienna, Vienna, Austria
| | - Lukas F Reissig
- Division of Anatomy & MIC, Medical University of Vienna, Vienna, Austria
| | - Markus Hüsemann
- Division of Anatomy & MIC, Medical University of Vienna, Vienna, Austria
| | - Cordula Höfle
- Division of Anatomy & MIC, Medical University of Vienna, Vienna, Austria
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32
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Inspiration from heart development: Biomimetic development of functional human cardiac organoids. Biomaterials 2017; 142:112-123. [PMID: 28732246 DOI: 10.1016/j.biomaterials.2017.07.021] [Citation(s) in RCA: 94] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 07/10/2017] [Accepted: 07/11/2017] [Indexed: 01/02/2023]
Abstract
Recent progress in human organoids has provided 3D tissue systems to model human development, diseases, as well as develop cell delivery systems for regenerative therapies. While direct differentiation of human embryoid bodies holds great promise for cardiac organoid production, intramyocardial cell organization during heart development provides biological foundation to fabricate human cardiac organoids with defined cell types. Inspired by the intramyocardial organization events in coronary vasculogenesis, where a diverse, yet defined, mixture of cardiac cell types self-organizes into functional myocardium in the absence of blood flow, we have developed a defined method to produce scaffold-free human cardiac organoids that structurally and functionally resembled the lumenized vascular network in the developing myocardium, supported hiPSC-CM development and possessed fundamental cardiac tissue-level functions. In particular, this development-driven strategy offers a robust, tunable system to examine the contributions of individual cell types, matrix materials and additional factors for developmental insight, biomimetic matrix composition to advance biomaterial design, tissue/organ-level drug screening, and cell therapy for heart repair.
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33
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Wilson R, Geyer SH, Reissig L, Rose J, Szumska D, Hardman E, Prin F, McGuire C, Ramirez-Solis R, White J, Galli A, Tudor C, Tuck E, Mazzeo CI, Smith JC, Robertson E, Adams DJ, Mohun T, Weninger WJ. Highly variable penetrance of abnormal phenotypes in embryonic lethal knockout mice. Wellcome Open Res 2017. [PMID: 27996060 DOI: 10.12688/wellcomeopenres.9899.1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Background: Identifying genes that are essential for mouse embryonic development and survival through term is a powerful and unbiased way to discover possible genetic determinants of human developmental disorders. Characterising the changes in mouse embryos that result from ablation of lethal genes is a necessary first step towards uncovering their role in normal embryonic development and establishing any correlates amongst human congenital abnormalities. Methods: Here we present results gathered to date in the Deciphering the Mechanisms of Developmental Disorders (DMDD) programme, cataloguing the morphological defects identified from comprehensive imaging of 220 homozygous mutant and 114 wild type embryos from 42 lethal and subviable lines, analysed at E14.5. Results: Virtually all mutant embryos show multiple abnormal phenotypes and amongst the 42 lines these affect most organ systems. Within each mutant line, the phenotypes of individual embryos form distinct but overlapping sets. Subcutaneous edema, malformations of the heart or great vessels, abnormalities in forebrain morphology and the musculature of the eyes are all prevalent phenotypes, as is loss or abnormal size of the hypoglossal nerve.Conclusions: Overall, the most striking finding is that no matter how profound the malformation, each phenotype shows highly variable penetrance within a mutant line. These findings have challenging implications for efforts to identify human disease correlates.
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Affiliation(s)
| | - Stefan H Geyer
- Division of Anatomy, Center for Anatomy & Cell Biology, Medical University of Vienna, Wien, Austria
| | - Lukas Reissig
- Division of Anatomy, Center for Anatomy & Cell Biology, Medical University of Vienna, Wien, Austria
| | - Julia Rose
- Division of Anatomy, Center for Anatomy & Cell Biology, Medical University of Vienna, Wien, Austria
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Wolfgang J Weninger
- Division of Anatomy, Center for Anatomy & Cell Biology, Medical University of Vienna, Wien, Austria
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34
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Wilson R, Geyer SH, Reissig L, Rose J, Szumska D, Hardman E, Prin F, McGuire C, Ramirez-Solis R, White J, Galli A, Tudor C, Tuck E, Mazzeo CI, Smith JC, Robertson E, Adams DJ, Mohun T, Weninger WJ. Highly variable penetrance of abnormal phenotypes in embryonic lethal knockout mice. Wellcome Open Res 2017; 1:1. [PMID: 27996060 PMCID: PMC5159622 DOI: 10.12688/wellcomeopenres.9899.2] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/14/2017] [Indexed: 11/20/2022] Open
Abstract
Background: Identifying genes that are essential for mouse embryonic development and survival through term is a powerful and unbiased way to discover possible genetic determinants of human developmental disorders. Characterising the changes in mouse embryos that result from ablation of lethal genes is a necessary first step towards uncovering their role in normal embryonic development and establishing any correlates amongst human congenital abnormalities. Methods: Here we present results gathered to date in the Deciphering the Mechanisms of Developmental Disorders (DMDD) programme, cataloguing the morphological defects identified from comprehensive imaging of 220 homozygous mutant and 114 wild type embryos from 42 lethal and subviable lines, analysed at E14.5. Results: Virtually all mutant embryos show multiple abnormal phenotypes and amongst the 42 lines these affect most organ systems. Within each mutant line, the phenotypes of individual embryos form distinct but overlapping sets. Subcutaneous edema, malformations of the heart or great vessels, abnormalities in forebrain morphology and the musculature of the eyes are all prevalent phenotypes, as is loss or abnormal size of the hypoglossal nerve. Conclusions: Overall, the most striking finding is that no matter how profound the malformation, each phenotype shows highly variable penetrance within a mutant line. These findings have challenging implications for efforts to identify human disease correlates.
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Affiliation(s)
| | - Stefan H Geyer
- Division of Anatomy, Center for Anatomy & Cell Biology, Medical University of Vienna, Wien, Austria
| | - Lukas Reissig
- Division of Anatomy, Center for Anatomy & Cell Biology, Medical University of Vienna, Wien, Austria
| | - Julia Rose
- Division of Anatomy, Center for Anatomy & Cell Biology, Medical University of Vienna, Wien, Austria
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Wolfgang J Weninger
- Division of Anatomy, Center for Anatomy & Cell Biology, Medical University of Vienna, Wien, Austria
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35
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Geyer SH, Reissig L, Rose J, Wilson R, Prin F, Szumska D, Ramirez-Solis R, Tudor C, White J, Mohun TJ, Weninger WJ. A staging system for correct phenotype interpretation of mouse embryos harvested on embryonic day 14 (E14.5). J Anat 2017; 230:710-719. [PMID: 28185240 PMCID: PMC5382591 DOI: 10.1111/joa.12590] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/02/2016] [Indexed: 01/09/2023] Open
Abstract
We present a simple and quick system for accurately scoring the developmental progress of mouse embryos harvested on embryonic day 14 (E14.5). Based solely on the external appearance of the maturing forelimb, we provide a convenient way to distinguish six developmental sub‐stages. Using a variety of objective morphometric data obtained from the commonly used C57BL/6N mouse strain, we show that these stages correlate precisely with the growth of the entire embryo and its organs. Applying the new staging system to phenotype analyses of E14.5 embryos of 58 embryonic lethal null mutant lines from the DMDD research programme (https://dmdd.org.uk) and its pilot, we show that homozygous mutant embryos are frequently delayed in development. To demonstrate the importance of our staging system for correct phenotype interpretation, we describe stage‐specific changes of the palate, heart and gut, and provide examples in which correct diagnosis of malformations relies on correct staging.
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Affiliation(s)
- Stefan H Geyer
- Centre for Anatomy and Cell Biology & MIC, Medical University of Vienna, Vienna, Austria
| | - Lukas Reissig
- Centre for Anatomy and Cell Biology & MIC, Medical University of Vienna, Vienna, Austria
| | - Julia Rose
- Centre for Anatomy and Cell Biology & MIC, Medical University of Vienna, Vienna, Austria
| | - Robert Wilson
- The Francis Crick Institute Mill Hill Laboratory, London, UK
| | - Fabrice Prin
- The Francis Crick Institute Mill Hill Laboratory, London, UK
| | | | | | | | - Jacqui White
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | - Timothy J Mohun
- The Francis Crick Institute Mill Hill Laboratory, London, UK
| | - Wolfgang J Weninger
- Centre for Anatomy and Cell Biology & MIC, Medical University of Vienna, Vienna, Austria
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Hsu CW, Wong L, Rasmussen TL, Kalaga S, McElwee ML, Keith LC, Bohat R, Seavitt JR, Beaudet AL, Dickinson ME. Three-dimensional microCT imaging of mouse development from early post-implantation to early postnatal stages. Dev Biol 2016; 419:229-236. [PMID: 27671873 PMCID: PMC5405732 DOI: 10.1016/j.ydbio.2016.09.011] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Revised: 09/09/2016] [Accepted: 09/10/2016] [Indexed: 12/25/2022]
Abstract
In this work, we report the use of iodine-contrast microCT to perform high-throughput 3D morphological analysis of mouse embryos and neonates between embryonic day 8.5 to postnatal day 3, with high spatial resolution up to 3µm/voxel. We show that mouse embryos at early stages can be imaged either within extra embryonic tissues such as the yolk sac or the decidua without physically disturbing the embryos. This method enables a full, undisturbed analysis of embryo turning, allantois development, vitelline vessels remodeling, yolk sac and early placenta development, which provides increased insights into early embryonic lethality in mutant lines. Moreover, these methods are inexpensive, simple to learn and do not require substantial processing time, making them ideal for high throughput analysis of mouse mutants with embryonic and early postnatal lethality.
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Affiliation(s)
- Chih-Wei Hsu
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA; Optical Imaging and Vital Microscopy Core, Baylor College of Medicine, Houston, TX 77030, USA
| | - Leeyean Wong
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Tara L Rasmussen
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sowmya Kalaga
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA; Optical Imaging and Vital Microscopy Core, Baylor College of Medicine, Houston, TX 77030, USA
| | - Melissa L McElwee
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Lance C Keith
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ritu Bohat
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - John R Seavitt
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Arthur L Beaudet
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Mary E Dickinson
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA; Optical Imaging and Vital Microscopy Core, Baylor College of Medicine, Houston, TX 77030, USA; Cardiovascular Research Institute, Baylor College of Medicine, Houston, TX 77030, USA.
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37
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Dickinson ME, Flenniken AM, Ji X, Teboul L, Wong MD, White JK, Meehan TF, Weninger WJ, Westerberg H, Adissu H, Baker CN, Bower L, Brown JM, Caddle LB, Chiani F, Clary D, Cleak J, Daly MJ, Denegre JM, Doe B, Dolan ME, Edie SM, Fuchs H, Gailus-Durner V, Galli A, Gambadoro A, Gallegos J, Guo S, Horner NR, Hsu CW, Johnson SJ, Kalaga S, Keith LC, Lanoue L, Lawson TN, Lek M, Mark M, Marschall S, Mason J, McElwee ML, Newbigging S, Nutter LM, Peterson KA, Ramirez-Solis R, Rowland DJ, Ryder E, Samocha KE, Seavitt JR, Selloum M, Szoke-Kovacs Z, Tamura M, Trainor AG, Tudose I, Wakana S, Warren J, Wendling O, West DB, Wong L, Yoshiki A, MacArthur DG, Tocchini-Valentini GP, Gao X, Flicek P, Bradley A, Skarnes WC, Justice MJ, Parkinson HE, Moore M, Wells S, Braun RE, Svenson KL, de Angelis MH, Herault Y, Mohun T, Mallon AM, Henkelman RM, Brown SD, Adams DJ, Lloyd KK, McKerlie C, Beaudet AL, Bucan M, Murray SA. High-throughput discovery of novel developmental phenotypes. Nature 2016; 537:508-514. [PMID: 27626380 PMCID: PMC5295821 DOI: 10.1038/nature19356] [Citation(s) in RCA: 792] [Impact Index Per Article: 99.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 08/10/2016] [Indexed: 12/29/2022]
Abstract
Approximately one-third of all mammalian genes are essential for life. Phenotypes resulting from knockouts of these genes in mice have provided tremendous insight into gene function and congenital disorders. As part of the International Mouse Phenotyping Consortium effort to generate and phenotypically characterize 5,000 knockout mouse lines, here we identify 410 lethal genes during the production of the first 1,751 unique gene knockouts. Using a standardized phenotyping platform that incorporates high-resolution 3D imaging, we identify phenotypes at multiple time points for previously uncharacterized genes and additional phenotypes for genes with previously reported mutant phenotypes. Unexpectedly, our analysis reveals that incomplete penetrance and variable expressivity are common even on a defined genetic background. In addition, we show that human disease genes are enriched for essential genes, thus providing a dataset that facilitates the prioritization and validation of mutations identified in clinical sequencing efforts.
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Affiliation(s)
- Mary E. Dickinson
- Department of Molecular Physiology and Biophysics, Houston, Texas, USA
| | - Ann M. Flenniken
- The Centre for Phenogenomics, Toronto, Ontario, Canada
- Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Xiao Ji
- Genomics and Computational Biology Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia PA 19104
| | - Lydia Teboul
- Medical Research Council Harwell (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire, UK
| | - Michael D. Wong
- The Centre for Phenogenomics, Toronto, Ontario, Canada
- Mouse Imaging Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Jacqueline K. White
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Terrence F. Meehan
- European Molecular Biology Laboratory- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Wolfgang J. Weninger
- Centre for Anatomy and Cell Biology, Medical University of Vienna, Vienna, Austria
| | - Henrik Westerberg
- Medical Research Council Harwell (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire, UK
| | - Hibret Adissu
- The Centre for Phenogenomics, Toronto, Ontario, Canada
- The Hospital for Sick Children, Toronto, Ontario, Canada
| | | | - Lynette Bower
- Mouse Biology Program, University of California, Davis
| | - James M. Brown
- Medical Research Council Harwell (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire, UK
| | | | - Francesco Chiani
- Monterotondo Mouse Clinic, Italian National Research Council (CNR), Institute of Cell Biology and Neurobiology, Monterotondo Scalo, Itally
| | - Dave Clary
- Mouse Biology Program, University of California, Davis
| | - James Cleak
- Medical Research Council Harwell (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire, UK
| | - Mark J. Daly
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston MA, USA
- Program in Medical and Population Genetics, Broad Institute MIT and Harvard, Cambridge, MA, USA
| | | | - Brendan Doe
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | | | | | - Helmut Fuchs
- Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Experimental Genetics and German Mouse Clinic, Neuherberg, Germany
| | - Valerie Gailus-Durner
- Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Experimental Genetics and German Mouse Clinic, Neuherberg, Germany
| | - Antonella Galli
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Alessia Gambadoro
- Monterotondo Mouse Clinic, Italian National Research Council (CNR), Institute of Cell Biology and Neurobiology, Monterotondo Scalo, Itally
| | - Juan Gallegos
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - Shiying Guo
- SKL of Pharmaceutical Biotechnology and Model Animal Research Center, Collaborative Innovation Center for Genetics and Development, Nanjing Biomedical Research Institute, Nanjing University, China
| | - Neil R. Horner
- Medical Research Council Harwell (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire, UK
| | - Chih-wei Hsu
- Department of Molecular Physiology and Biophysics, Houston, Texas, USA
| | - Sara J. Johnson
- Medical Research Council Harwell (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire, UK
| | - Sowmya Kalaga
- Department of Molecular Physiology and Biophysics, Houston, Texas, USA
| | - Lance C. Keith
- Department of Molecular Physiology and Biophysics, Houston, Texas, USA
| | - Louise Lanoue
- Mouse Biology Program, University of California, Davis
| | - Thomas N. Lawson
- Medical Research Council Harwell (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire, UK
| | - Monkol Lek
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston MA, USA
- Program in Medical and Population Genetics, Broad Institute MIT and Harvard, Cambridge, MA, USA
| | - Manuel Mark
- Infrastructure Nationale PHENOMIN, Institut Clinique de la Souris (ICS), et Institut de Génétique Biologie Moléculaire et Cellulaire (IGBMC) CNRS, INSERM, University of Strasbourg, Illkirch-Graffenstaden, France
| | - Susan Marschall
- Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Experimental Genetics and German Mouse Clinic, Neuherberg, Germany
| | - Jeremy Mason
- European Molecular Biology Laboratory- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | | | - Susan Newbigging
- The Centre for Phenogenomics, Toronto, Ontario, Canada
- The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Lauryl M.J. Nutter
- The Centre for Phenogenomics, Toronto, Ontario, Canada
- The Hospital for Sick Children, Toronto, Ontario, Canada
| | | | - Ramiro Ramirez-Solis
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | | | - Edward Ryder
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Kaitlin E. Samocha
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston MA, USA
- Program in Medical and Population Genetics, Broad Institute MIT and Harvard, Cambridge, MA, USA
| | - John R. Seavitt
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - Mohammed Selloum
- Infrastructure Nationale PHENOMIN, Institut Clinique de la Souris (ICS), et Institut de Génétique Biologie Moléculaire et Cellulaire (IGBMC) CNRS, INSERM, University of Strasbourg, Illkirch-Graffenstaden, France
| | - Zsombor Szoke-Kovacs
- Medical Research Council Harwell (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire, UK
| | | | | | - Ilinca Tudose
- European Molecular Biology Laboratory- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | | | - Jonathan Warren
- European Molecular Biology Laboratory- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Olivia Wendling
- Infrastructure Nationale PHENOMIN, Institut Clinique de la Souris (ICS), et Institut de Génétique Biologie Moléculaire et Cellulaire (IGBMC) CNRS, INSERM, University of Strasbourg, Illkirch-Graffenstaden, France
| | - David B. West
- Children’s Hospital Oakland Research Institute, Oakland, CA 94609
| | - Leeyean Wong
- Department of Molecular Physiology and Biophysics, Houston, Texas, USA
| | | | | | - Daniel G. MacArthur
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston MA, USA
- Program in Medical and Population Genetics, Broad Institute MIT and Harvard, Cambridge, MA, USA
| | - Glauco P. Tocchini-Valentini
- Monterotondo Mouse Clinic, Italian National Research Council (CNR), Institute of Cell Biology and Neurobiology, Monterotondo Scalo, Itally
| | - Xiang Gao
- SKL of Pharmaceutical Biotechnology and Model Animal Research Center, Collaborative Innovation Center for Genetics and Development, Nanjing Biomedical Research Institute, Nanjing University, China
| | - Paul Flicek
- European Molecular Biology Laboratory- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Allan Bradley
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - William C. Skarnes
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Monica J. Justice
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
- The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Helen E. Parkinson
- European Molecular Biology Laboratory- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | | | - Sara Wells
- Medical Research Council Harwell (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire, UK
| | | | | | - Martin Hrabe de Angelis
- Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Experimental Genetics and German Mouse Clinic, Neuherberg, Germany
- Chair of Experimental Genetics, School of Life Science Weihenstephan, Technische Universität München, Freising
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Yann Herault
- Infrastructure Nationale PHENOMIN, Institut Clinique de la Souris (ICS), et Institut de Génétique Biologie Moléculaire et Cellulaire (IGBMC) CNRS, INSERM, University of Strasbourg, Illkirch-Graffenstaden, France
| | - Tim Mohun
- The Francis Crick Institute Mill Hill Laboratory, The Ridgeway, Mill Hill, London, UK
| | - Ann-Marie Mallon
- Medical Research Council Harwell (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire, UK
| | - R. Mark Henkelman
- The Centre for Phenogenomics, Toronto, Ontario, Canada
- Mouse Imaging Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Steve D.M. Brown
- Medical Research Council Harwell (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire, UK
| | - David J. Adams
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | | | - Colin McKerlie
- The Centre for Phenogenomics, Toronto, Ontario, Canada
- The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Arthur L. Beaudet
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - Maja Bucan
- Departments of Genetics and Psychiatry, Perlman School of Medicine, University of Pennsylvania, Philadelphia PA 19104
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Men J, Huang Y, Solanki J, Zeng X, Alex A, Jerwick J, Zhang Z, Tanzi RE, Li A, Zhou C. Optical Coherence Tomography for Brain Imaging and Developmental Biology. IEEE JOURNAL OF SELECTED TOPICS IN QUANTUM ELECTRONICS : A PUBLICATION OF THE IEEE LASERS AND ELECTRO-OPTICS SOCIETY 2016; 22:6803213. [PMID: 27721647 PMCID: PMC5049888 DOI: 10.1109/jstqe.2015.2513667] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Optical coherence tomography (OCT) is a promising research tool for brain imaging and developmental biology. Serving as a three-dimensional optical biopsy technique, OCT provides volumetric reconstruction of brain tissues and embryonic structures with micrometer resolution and video rate imaging speed. Functional OCT enables label-free monitoring of hemodynamic and metabolic changes in the brain in vitro and in vivo in animal models. Due to its non-invasiveness nature, OCT enables longitudinal imaging of developing specimens in vivo without potential damage from surgical operation, tissue fixation and processing, and staining with exogenous contrast agents. In this paper, various OCT applications in brain imaging and developmental biology are reviewed, with a particular focus on imaging heart development. In addition, we report findings on the effects of a circadian gene (Clock) and high-fat-diet on heart development in Drosophila melanogaster. These findings contribute to our understanding of the fundamental mechanisms connecting circadian genes and obesity to heart development and cardiac diseases.
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Affiliation(s)
- Jing Men
- Department of Electrical and Computer Engineering, Center for Photonics and Nanoelectronics, and Bioengineering Program, Lehigh University, Bethlehem, PA, USA, 18015
| | - Yongyang Huang
- Department of Electrical and Computer Engineering, Center for Photonics and Nanoelectronics, and Bioengineering Program, Lehigh University, Bethlehem, PA, USA, 18015
| | - Jitendra Solanki
- Department of Electrical and Computer Engineering, Center for Photonics and Nanoelectronics, and Bioengineering Program, Lehigh University, Bethlehem, PA, USA, 18015
| | - Xianxu Zeng
- Department of Electrical and Computer Engineering, Center for Photonics and Nanoelectronics, and Bioengineering Program, Lehigh University, Bethlehem, PA, USA, 18015
- Third Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, P.R. China, 450000
| | - Aneesh Alex
- Department of Electrical and Computer Engineering, Center for Photonics and Nanoelectronics, and Bioengineering Program, Lehigh University, Bethlehem, PA, USA, 18015
| | - Jason Jerwick
- Department of Electrical and Computer Engineering, Center for Photonics and Nanoelectronics, and Bioengineering Program, Lehigh University, Bethlehem, PA, USA, 18015
| | - Zhan Zhang
- Third Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, P.R. China, 450000
| | - Rudolph E. Tanzi
- Genetics and Aging Research Unit, Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA, 02129
| | - Airong Li
- Genetics and Aging Research Unit, Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA, 02129
| | - Chao Zhou
- Department of Electrical and Computer Engineering, Center for Photonics and Nanoelectronics, and Bioengineering Program, Lehigh University, Bethlehem, PA, USA, 18015
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Clarkson MD. Representation of anatomy in online atlases and databases: a survey and collection of patterns for interface design. BMC DEVELOPMENTAL BIOLOGY 2016; 16:18. [PMID: 27206491 PMCID: PMC4875762 DOI: 10.1186/s12861-016-0116-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 05/09/2016] [Indexed: 12/17/2022]
Abstract
BACKGROUND A large number of online atlases and databases have been developed to mange the rapidly growing amount of data describing embryogenesis. As these community resources continue to evolve, it is important to understand how representations of anatomy can facilitate the sharing and integration of data. In addition, attention to the design of the interfaces is critical to make online resources useful and usable. RESULTS I first present a survey of online atlases and gene expression resources for model organisms, with a focus on methods of semantic and spatial representation of anatomy. A total of 14 anatomical atlases and 21 gene expression resources are included. This survey demonstrates how choices in semantic representation, in the form of ontologies, can enhance interface search functions and provide links between relevant information. This survey also reviews methods for spatially representing anatomy in online resources. I then provide a collection of patterns for interface design based on the atlases and databases surveyed. These patterns include methods for displaying graphics, integrating semantic and spatial representations, organizing information, and querying databases to find genes expressed in anatomical structures. CONCLUSIONS This collection of patterns for interface design will assist biologists and software developers in planning the interfaces of new atlases and databases or enhancing existing ones. They also show the benefits of standardizing semantic and spatial representations of anatomy by demonstrating how interfaces can use standardization to provide enhanced functionality.
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Affiliation(s)
- Melissa D Clarkson
- Department of Biological Structure, School of Medicine, University of Washington, Seattle, WA, USA.
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