1
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Ludwig-Husemann A, Schertl P, Shrivastava A, Geckle U, Hafner J, Schaarschmidt F, Willenbacher N, Freudenberg U, Werner C, Lee-Thedieck C. A Multifunctional Nanostructured Hydrogel as a Platform for Deciphering Niche Interactions of Hematopoietic Stem and Progenitor Cells. Adv Healthc Mater 2024; 13:e2304157. [PMID: 38870600 DOI: 10.1002/adhm.202304157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 06/10/2024] [Indexed: 06/15/2024]
Abstract
For over half a century, hematopoietic stem cells (HSCs) have been used for transplantation therapy to treat severe hematologic diseases. Successful outcomes depend on collecting sufficient donor HSCs as well as ensuring efficient engraftment. These processes are influenced by dynamic interactions of HSCs with the bone marrow niche, which can be revealed by artificial niche models. Here, a multifunctional nanostructured hydrogel is presented as a 2D platform to investigate how the interdependencies of cytokine binding and nanopatterned adhesive ligands influence the behavior of human hematopoietic stem and progenitor cells (HSPCs). The results indicate that the degree of HSPC polarization and motility, observed when cultured on gels presenting the chemokine SDF-1α and a nanoscale-defined density of a cellular (IDSP) or extracellular matrix (LDV) α4β1 integrin binding motif, are differently influenced on hydrogels functionalized with the different ligand types. Further, SDF-1α promotes cell polarization but not motility. Strikingly, the degree of differentiation correlates negatively with the nanoparticle spacing, which determines ligand density, but only for the cellular-derived IDSP motif. This mechanism potentially offers a means of predictably regulating early HSC fate decisions. Consequently, the innovative multifunctional hydrogel holds promise for deciphering dynamic HSPC-niche interactions and refining transplantation therapy protocols.
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Affiliation(s)
- Anita Ludwig-Husemann
- Institute of Cell Biology and Biophysics, Leibniz University Hannover, Herrenhäuser Str. 2, 30419, Hannover, Germany
- Institute of Functional Interfaces, Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Peter Schertl
- Institute of Cell Biology and Biophysics, Leibniz University Hannover, Herrenhäuser Str. 2, 30419, Hannover, Germany
| | - Ananya Shrivastava
- Institute of Cell Biology and Biophysics, Leibniz University Hannover, Herrenhäuser Str. 2, 30419, Hannover, Germany
| | - Udo Geckle
- Institute for Applied Materials - Energy Storage Systems, Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Johanna Hafner
- Institute for Mechanical Process Engineering and Mechanics, Applied Mechanics Group, Karlsruhe Institute of Technology (KIT), Gotthard-Franz-Str. 3, 76131, Karlsruhe, Germany
| | - Frank Schaarschmidt
- Institute of Cell Biology and Biophysics, Leibniz University Hannover, Herrenhäuser Str. 2, 30419, Hannover, Germany
| | - Norbert Willenbacher
- Institute for Mechanical Process Engineering and Mechanics, Applied Mechanics Group, Karlsruhe Institute of Technology (KIT), Gotthard-Franz-Str. 3, 76131, Karlsruhe, Germany
| | - Uwe Freudenberg
- Leibniz Institute of Polymer Research Dresden e.V, Max Bergmann Center of Biomaterials, Hohe Str. 6, 01069, Dresden, Germany
| | - Carsten Werner
- Leibniz Institute of Polymer Research Dresden e.V, Max Bergmann Center of Biomaterials, Hohe Str. 6, 01069, Dresden, Germany
- Center for Regenerative Therapies Dresden, Technical University Dresden, Fetscherstr. 105, 01307, Dresden, Germany
| | - Cornelia Lee-Thedieck
- Institute of Cell Biology and Biophysics, Leibniz University Hannover, Herrenhäuser Str. 2, 30419, Hannover, Germany
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2
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Habing KM, Alcazar CA, Duke VR, Tan YH, Willett NJ, Nakayama KH. Age-associated functional healing of musculoskeletal trauma through regenerative engineering and rehabilitation. Biomater Sci 2024. [PMID: 39172120 DOI: 10.1039/d4bm00616j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2024]
Abstract
Traumatic musculoskeletal injuries that lead to volumetric muscle loss (VML) are challenged by irreparable soft tissue damage, impaired regenerative ability, and reduced muscle function. Regenerative rehabilitation strategies involving the pairing of engineered therapeutics with exercise have guided considerable advances in the functional repair of skeletal muscle following VML. However, few studies evaluate the efficacy of regenerative rehabilitation across the lifespan. In the current study, young and aged mice are treated with an engineered muscle, consisting of nanofibrillar-aligned collagen laden with myogenic cells, in combination with voluntary running activity following a VML injury. Overall, young mice perform at higher running volumes and intensities compared to aged mice but exhibit similar volumes relative to age-matched baselines. Additionally, young mice are highly responsive to the dual treatment showing enhanced force production (p < 0.001), muscle mass (p < 0.05), and vascular density (p < 0.01) compared to age-matched controls. Aged mice display upregulation of circulating inflammatory cytokines and show no significant regenerative response to treatment, suggesting a diminished efficacy of regenerative rehabilitation in aged populations. These findings highlight the restorative potential of regenerative engineering and rehabilitation for the treatment of traumatic musculoskeletal injuries in young populations and the complimentary need for age-specific interventions and studies to serve broader patient demographics.
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Affiliation(s)
- Krista M Habing
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR, USA.
| | - Cynthia A Alcazar
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR, USA.
| | - Victoria R Duke
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR, USA.
| | - Yong How Tan
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR, USA.
| | - Nick J Willett
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR, USA.
- Knight Campus for Accelerating Scientific Impact, University of Oregon, Eugene, OR, USA
- Department of Orthopaedics, Oregon Health & Science University, Portland, OR, USA
- The Veterans Affairs Portland Health Care System, Portland, OR, USA
| | - Karina H Nakayama
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR, USA.
- Department of Orthopaedics, Oregon Health & Science University, Portland, OR, USA
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3
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Kumar U, Fang CY, Roan HY, Hsu SC, Wang CH, Chen CH. Whole-body replacement of larval myofibers generates permanent adult myofibers in zebrafish. EMBO J 2024; 43:3090-3115. [PMID: 38839992 PMCID: PMC11294464 DOI: 10.1038/s44318-024-00136-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 05/06/2024] [Accepted: 05/17/2024] [Indexed: 06/07/2024] Open
Abstract
Drastic increases in myofiber number and size are essential to support vertebrate post-embryonic growth. However, the collective cellular behaviors that enable these increases have remained elusive. Here, we created the palmuscle myofiber tagging and tracking system for in toto monitoring of the growth and fates of ~5000 fast myofibers in developing zebrafish larvae. Through live tracking of individual myofibers within the same individuals over extended periods, we found that many larval myofibers readily dissolved during development, enabling the on-site addition of new and more myofibers. Remarkably, whole-body surveillance of multicolor-barcoded myofibers further unveiled a gradual yet extensive elimination of larval myofiber populations, resulting in near-total replacement by late juvenile stages. The subsequently emerging adult myofibers are not only long-lasting, but also morphologically and functionally distinct from the larval populations. Furthermore, we determined that the elimination-replacement process is dependent on and driven by the autophagy pathway. Altogether, we propose that the whole-body replacement of larval myofibers is an inherent yet previously unnoticed process driving organismic muscle growth during vertebrate post-embryonic development.
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Affiliation(s)
- Uday Kumar
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, 11529, Taiwan
- Molecular and Biological Agricultural Sciences, Taiwan International Graduate Program, Graduate Institute of Biotechnology, National Chung-Hsing University, Taichung, Taiwan
| | - Chun-Yi Fang
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Hsiao-Yuh Roan
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Shao-Chun Hsu
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Chung-Han Wang
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Chen-Hui Chen
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, 11529, Taiwan.
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4
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Seidler AE, Donath S, Gentemann L, Buettner M, Heisterkamp A, Kalies S. Protocol for the application of single-cell damage in murine intestinal organoid models. STAR Protoc 2024; 5:103153. [PMID: 39088328 PMCID: PMC11342180 DOI: 10.1016/j.xpro.2024.103153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 05/09/2024] [Accepted: 06/05/2024] [Indexed: 08/03/2024] Open
Abstract
Spatially defined organoid damage enables the study of cellular repair processes. However, capturing dynamic events in living tissues is technically challenging. Here, we present a protocol for the application of single-cell damage in intestinal organoid models. We describe steps for isolating and cultivating murine colon organoids, lentivirus generation and transduction of organoids, single-cell ablation by a femtosecond laser, and follow-up imaging analysis. We provide examples for the image acquisition pipeline of dynamic processes in organoids using a confocal microscope. For complete details on the use and execution of this protocol, please refer to Donath et al.1,2.
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Affiliation(s)
- Anna Elisabeth Seidler
- Institute of Quantum Optics, Leibniz University Hannover, 30167 Hannover, Germany; Lower Saxony Center for Biomedical Engineering, Implant Research and Development (NIFE), 30625 Hannover, Germany.
| | - Sören Donath
- Institute of Quantum Optics, Leibniz University Hannover, 30167 Hannover, Germany; Lower Saxony Center for Biomedical Engineering, Implant Research and Development (NIFE), 30625 Hannover, Germany
| | - Lara Gentemann
- Institute of Quantum Optics, Leibniz University Hannover, 30167 Hannover, Germany; Lower Saxony Center for Biomedical Engineering, Implant Research and Development (NIFE), 30625 Hannover, Germany; REBIRTH Research Center for Translational Regenerative Medicine, 30625 Hannover, Germany
| | - Manuela Buettner
- REBIRTH Research Center for Translational Regenerative Medicine, 30625 Hannover, Germany; Institute for Laboratory Animal Science, Hannover Medical School, 30625 Hannover, Germany
| | - Alexander Heisterkamp
- Institute of Quantum Optics, Leibniz University Hannover, 30167 Hannover, Germany; Lower Saxony Center for Biomedical Engineering, Implant Research and Development (NIFE), 30625 Hannover, Germany
| | - Stefan Kalies
- Institute of Quantum Optics, Leibniz University Hannover, 30167 Hannover, Germany; Lower Saxony Center for Biomedical Engineering, Implant Research and Development (NIFE), 30625 Hannover, Germany; REBIRTH Research Center for Translational Regenerative Medicine, 30625 Hannover, Germany.
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5
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Gybeľ T, Čada Š, Klementová D, Schwalm MP, Berger BT, Šebesta M, Knapp S, Bryja V. Splice variants of CK1α and CK1α-like: Comparative analysis of subcellular localization, kinase activity, and function in the Wnt signaling pathway. J Biol Chem 2024; 300:107407. [PMID: 38796065 PMCID: PMC11255964 DOI: 10.1016/j.jbc.2024.107407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 04/19/2024] [Accepted: 05/07/2024] [Indexed: 05/28/2024] Open
Abstract
Members of the casein kinase 1 (CK1) family are important regulators of multiple signaling pathways. CK1α is a well-known negative regulator of the Wnt/β-catenin pathway, which promotes the degradation of β-catenin via its phosphorylation of Ser45. In contrast, the closest paralog of CK1α, CK1α-like, is a poorly characterized kinase of unknown function. In this study, we show that the deletion of CK1α, but not CK1α-like, resulted in a strong activation of the Wnt/β-catenin pathway. Wnt-3a treatment further enhanced the activation, which suggests there are at least two modes, a CK1α-dependent and Wnt-dependent, of β-catenin regulation. Rescue experiments showed that only two out of ten naturally occurring splice CK1α/α-like variants were able to rescue the augmented Wnt/β-catenin signaling caused by CK1α deficiency in cells. Importantly, the ability to phosphorylate β-catenin on Ser45 in the in vitro kinase assay was required but not sufficient for such rescue. Our compound CK1α and GSK3α/β KO models suggest that the additional nonredundant function of CK1α in the Wnt pathway beyond Ser45-β-catenin phosphorylation includes Axin phosphorylation. Finally, we established NanoBRET assays for the three most common CK1α splice variants as well as CK1α-like. Target engagement data revealed comparable potency of known CK1α inhibitors for all CK1α variants but not for CK1α-like. In summary, our work brings important novel insights into the biology of CK1α, including evidence for the lack of redundancy with other CK1 kinases in the negative regulation of the Wnt/β-catenin pathway at the level of β-catenin and Axin.
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Affiliation(s)
- Tomáš Gybeľ
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Štěpán Čada
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Darja Klementová
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic; CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Martin P Schwalm
- Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany; Structural Genomics Consortium, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany; German Cancer Consortium (DKTK)/German Cancer Research Center (DKFZ), DKTK Site Frankfurt-Mainz, Heidelberg, Germany
| | - Benedict-Tilman Berger
- Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany; Structural Genomics Consortium, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany
| | - Marek Šebesta
- CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Stefan Knapp
- Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany; Structural Genomics Consortium, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany; German Cancer Consortium (DKTK)/German Cancer Research Center (DKFZ), DKTK Site Frankfurt-Mainz, Heidelberg, Germany
| | - Vítězslav Bryja
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic; Department of Cytokinetics, Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic.
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6
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Bour RK, Garner GT, Peirce SM, Christ GJ. Optimized Biomanufacturing for Treatment of Volumetric Muscle Loss Enables Physiomimetic Recovery. Tissue Eng Part A 2024. [PMID: 38832858 DOI: 10.1089/ten.tea.2023.0315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2024] Open
Abstract
Volumetric muscle loss (VML) injuries are defined by loss of sufficient skeletal muscle to produce persistent deficits in muscle form and function, with devastating lifelong consequences to both soldiers and civilians. There are currently no satisfactory treatments for VML injuries. The work described herein details the implementation of a fully enclosed bioreactor environment (FEBE) system that efficiently interfaces with our existing automated bioprinting and advanced biomanufacturing methods for cell deposition on sheet-based scaffolds for our previously described tissue-engineered muscle repair (TEMR) technology platform. Briefly, the TEMR technology consists of a porcine bladder acellular matrix seeded with skeletal muscle progenitor cells and preconditioned via 10% uniaxial cyclic stretch in a bioreactor. Overall, TEMR implantation in an established rat tibialis anterior (TA) VML injury model can result in 60 to ∼90% functional recovery. However, our original study documented >50% failure rate. That is, more than half of the implanted TEMR constructs produced no functional improvement beyond no treatment/repair. The high failure rate was attributed to the untoward mechanical disruption of TEMR during surgical implantation. In a follow-up study, adjustments were made to the geometry of both the VML injury and the TEMR construct, and the "nonresponder" group was reduced from over half the TEMR-treated animals to just 33%. Nonetheless, additional improvement is needed for clinical applicability. The main objectives of the current study were twofold: (1) explore the use of advanced biomanufacturing methods (i.e., FEBE bioreactor) to further improve TEMR reliability (i.e., increase functional response rate), (2) determine if previously established bioprinting methods, when coupled to the customized FEBE system would further improve the rate, magnitude or amplitude of functional outcomes following TEMR implantation in the same rat TA VML injury model. The current study demonstrates the unequivocal benefits of a customized bioreactor system that reduces manipulation of TEMR during cell seeding and maturation via bioprinting while simultaneously maximizing TEMR stability throughout the biofabrication process. This new biomanufacturing strategy not only accelerated the rate of functional recovery, but also eliminated all TEMR failures. In addition, implementation of bioprinting resulted in more physiomimetic skeletal muscle characteristics of repaired muscle tissue.
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Affiliation(s)
- Rachel K Bour
- Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia, USA
| | - Gavin T Garner
- Department of Mechanical Engineering, University of Virginia, Charlottesville, Virginia, USA
| | - Shayn M Peirce
- Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia, USA
- Department of Plastic Surgery, University of Virginia, Charlottesville, Virginia, USA
| | - George J Christ
- Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia, USA
- Department of Orthopaedic Surgery, University of Virginia, Charlottesville, Virginia, USA
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7
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Transitions in development - an interview with Ariel Waisman. Development 2024; 151:dev203129. [PMID: 38885080 DOI: 10.1242/dev.203129] [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: 06/20/2024]
Abstract
Ariel Waisman is a CONICET Junior Researcher in the Laboratory of Applied Research in Neurosciences at FLENI in Buenos Aires, Argentina. Ariel's group studies gene regulatory networks in human pluripotent stem cells to address mechanisms of development and cardiac differentiation, among other topics. We spoke to Ariel over Teams to learn more about his career path, the research interests in his group, and the challenges faced by researchers in Argentina and the Global South.
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8
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Flores-Opazo M, Kopinke D, Helmbacher F, Fernández-Verdejo R, Tuñón-Suárez M, Lynch GS, Contreras O. Fibro-adipogenic progenitors in physiological adipogenesis and intermuscular adipose tissue remodeling. Mol Aspects Med 2024; 97:101277. [PMID: 38788527 DOI: 10.1016/j.mam.2024.101277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 04/27/2024] [Accepted: 05/13/2024] [Indexed: 05/26/2024]
Abstract
Excessive accumulation of intermuscular adipose tissue (IMAT) is a common pathological feature in various metabolic and health conditions and can cause muscle atrophy, reduced function, inflammation, insulin resistance, cardiovascular issues, and unhealthy aging. Although IMAT results from fat accumulation in muscle, the mechanisms underlying its onset, development, cellular components, and functions remain unclear. IMAT levels are influenced by several factors, such as changes in the tissue environment, muscle type and origin, extent and duration of trauma, and persistent activation of fibro-adipogenic progenitors (FAPs). FAPs are a diverse and transcriptionally heterogeneous population of stromal cells essential for tissue maintenance, neuromuscular stability, and tissue regeneration. However, in cases of chronic inflammation and pathological conditions, FAPs expand and differentiate into adipocytes, resulting in the development of abnormal and ectopic IMAT. This review discusses the role of FAPs in adipogenesis and how they remodel IMAT. It highlights evidence supporting FAPs and FAP-derived adipocytes as constituents of IMAT, emphasizing their significance in adipose tissue maintenance and development, as well as their involvement in metabolic disorders, chronic pathologies and diseases. We also investigated the intricate molecular pathways and cell interactions governing FAP behavior, adipogenesis, and IMAT accumulation in chronic diseases and muscle deconditioning. Finally, we hypothesize that impaired cellular metabolic flexibility in dysfunctional muscles impacts FAPs, leading to IMAT. A deeper understanding of the biology of IMAT accumulation and the mechanisms regulating FAP behavior and fate are essential for the development of new therapeutic strategies for several debilitating conditions.
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Affiliation(s)
| | - Daniel Kopinke
- Department of Pharmacology and Therapeutics, University of Florida, Gainesville, 32610, FL, USA; Myology Institute, University of Florida College of Medicine, Gainesville, FL, USA.
| | | | - Rodrigo Fernández-Verdejo
- Pennington Biomedical Research Center, Louisiana State University, Baton Rouge, LA, USA; Laboratorio de Fisiología Del Ejercicio y Metabolismo (LABFEM), Escuela de Kinesiología, Facultad de Medicina, Universidad Finis Terrae, Chile.
| | - Mauro Tuñón-Suárez
- Laboratorio de Fisiología Del Ejercicio y Metabolismo (LABFEM), Escuela de Kinesiología, Facultad de Medicina, Universidad Finis Terrae, Chile.
| | - Gordon S Lynch
- Centre for Muscle Research, Department of Anatomy and Physiology, The University of Melbourne, Melbourne, Victoria, Parkville 3010, Australia.
| | - Osvaldo Contreras
- Developmental and Regenerative Biology Division, Victor Chang Cardiac Research Institute, Darlinghurst, NSW, 2010, Australia; School of Clinical Medicine, UNSW Sydney, Kensington, NSW 2052, Australia.
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9
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Matchett KP, Wilson-Kanamori JR, Portman JR, Kapourani CA, Fercoq F, May S, Zajdel E, Beltran M, Sutherland EF, Mackey JBG, Brice M, Wilson GC, Wallace SJ, Kitto L, Younger NT, Dobie R, Mole DJ, Oniscu GC, Wigmore SJ, Ramachandran P, Vallejos CA, Carragher NO, Saeidinejad MM, Quaglia A, Jalan R, Simpson KJ, Kendall TJ, Rule JA, Lee WM, Hoare M, Weston CJ, Marioni JC, Teichmann SA, Bird TG, Carlin LM, Henderson NC. Multimodal decoding of human liver regeneration. Nature 2024; 630:158-165. [PMID: 38693268 PMCID: PMC11153152 DOI: 10.1038/s41586-024-07376-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 04/02/2024] [Indexed: 05/03/2024]
Abstract
The liver has a unique ability to regenerate1,2; however, in the setting of acute liver failure (ALF), this regenerative capacity is often overwhelmed, leaving emergency liver transplantation as the only curative option3-5. Here, to advance understanding of human liver regeneration, we use paired single-nucleus RNA sequencing combined with spatial profiling of healthy and ALF explant human livers to generate a single-cell, pan-lineage atlas of human liver regeneration. We uncover a novel ANXA2+ migratory hepatocyte subpopulation, which emerges during human liver regeneration, and a corollary subpopulation in a mouse model of acetaminophen (APAP)-induced liver regeneration. Interrogation of necrotic wound closure and hepatocyte proliferation across multiple timepoints following APAP-induced liver injury in mice demonstrates that wound closure precedes hepatocyte proliferation. Four-dimensional intravital imaging of APAP-induced mouse liver injury identifies motile hepatocytes at the edge of the necrotic area, enabling collective migration of the hepatocyte sheet to effect wound closure. Depletion of hepatocyte ANXA2 reduces hepatocyte growth factor-induced human and mouse hepatocyte migration in vitro, and abrogates necrotic wound closure following APAP-induced mouse liver injury. Together, our work dissects unanticipated aspects of liver regeneration, demonstrating an uncoupling of wound closure and hepatocyte proliferation and uncovering a novel migratory hepatocyte subpopulation that mediates wound closure following liver injury. Therapies designed to promote rapid reconstitution of normal hepatic microarchitecture and reparation of the gut-liver barrier may advance new areas of therapeutic discovery in regenerative medicine.
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Affiliation(s)
- K P Matchett
- Centre for Inflammation Research, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, UK
| | - J R Wilson-Kanamori
- Centre for Inflammation Research, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, UK
| | - J R Portman
- Centre for Inflammation Research, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, UK
| | - C A Kapourani
- Centre for Inflammation Research, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, UK
- MRC Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- School of Informatics, University of Edinburgh, Edinburgh, UK
| | - F Fercoq
- Cancer Research UK Beatson Institute, Glasgow, UK
| | - S May
- Cancer Research UK Beatson Institute, Glasgow, UK
| | - E Zajdel
- Centre for Inflammation Research, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, UK
| | - M Beltran
- Centre for Inflammation Research, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, UK
| | - E F Sutherland
- Centre for Inflammation Research, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, UK
| | - J B G Mackey
- Cancer Research UK Beatson Institute, Glasgow, UK
| | - M Brice
- Centre for Inflammation Research, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, UK
| | - G C Wilson
- Centre for Inflammation Research, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, UK
| | - S J Wallace
- Centre for Inflammation Research, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, UK
| | - L Kitto
- Centre for Inflammation Research, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, UK
| | - N T Younger
- Centre for Inflammation Research, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, UK
| | - R Dobie
- Centre for Inflammation Research, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, UK
| | - D J Mole
- Centre for Inflammation Research, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, UK
- University Department of Clinical Surgery, University of Edinburgh, Edinburgh, UK
| | - G C Oniscu
- Edinburgh Transplant Centre, Royal Infirmary of Edinburgh, Edinburgh, UK
- Division of Transplant Surgery, CLINTEC, Karolinska Institutet, Stockholm, Sweden
| | - S J Wigmore
- Centre for Inflammation Research, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, UK
- University Department of Clinical Surgery, University of Edinburgh, Edinburgh, UK
| | - P Ramachandran
- Centre for Inflammation Research, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, UK
| | - C A Vallejos
- MRC Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- The Alan Turing Institute, London, UK
| | - N O Carragher
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - M M Saeidinejad
- Institute for Liver and Digestive Health, University College London, London, UK
| | - A Quaglia
- Department of Cellular Pathology, Royal Free London NHS Foundation Trust, London, UK
- UCL Cancer Institute, University College London, London, UK
| | - R Jalan
- Institute for Liver and Digestive Health, University College London, London, UK
- European Foundation for the Study of Chronic Liver Failure, Barcelona, Spain
| | - K J Simpson
- Department of Hepatology, University of Edinburgh and Scottish Liver Transplant Unit, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - T J Kendall
- Centre for Inflammation Research, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, UK
| | - J A Rule
- Department of Internal Medicine, University of Texas, Southwestern Medical Center, Dallas, TX, USA
| | - W M Lee
- Department of Internal Medicine, University of Texas, Southwestern Medical Center, Dallas, TX, USA
| | - M Hoare
- Early Cancer Institute, University of Cambridge, Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - C J Weston
- NIHR Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust and University of Birmingham, Birmingham, UK
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK
| | - J C Marioni
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
- Wellcome Genome Campus, Wellcome Sanger Institute, Cambridge, UK
| | - S A Teichmann
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
- Wellcome Genome Campus, Wellcome Sanger Institute, Cambridge, UK
- Department of Physics, Cavendish Laboratory, Cambridge, UK
| | - T G Bird
- Centre for Inflammation Research, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, UK
- Cancer Research UK Beatson Institute, Glasgow, UK
| | - L M Carlin
- Cancer Research UK Beatson Institute, Glasgow, UK
- School of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - N C Henderson
- Centre for Inflammation Research, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, UK.
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK.
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10
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Norris AM, Fierman KE, Campbell J, Pitale R, Shahraj M, Kopinke D. Studying intramuscular fat deposition and muscle regeneration: insights from a comparative analysis of mouse strains, injury models, and sex differences. Skelet Muscle 2024; 14:12. [PMID: 38812056 PMCID: PMC11134715 DOI: 10.1186/s13395-024-00344-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Accepted: 05/13/2024] [Indexed: 05/31/2024] Open
Abstract
Intramuscular fat (IMAT) infiltration, pathological adipose tissue that accumulates between muscle fibers, is a shared hallmark in a diverse set of diseases including muscular dystrophies and diabetes, spinal cord and rotator cuff injuries, as well as sarcopenia. While the mouse has been an invaluable preclinical model to study skeletal muscle diseases, they are also resistant to IMAT formation. To better understand this pathological feature, an adequate pre-clinical model that recapitulates human disease is necessary. To address this gap, we conducted a comprehensive in-depth comparison between three widely used mouse strains: C57BL/6J, 129S1/SvlmJ and CD1. We evaluated the impact of strain, sex and injury type on IMAT formation, myofiber regeneration and fibrosis. We confirm and extend previous findings that a Glycerol (GLY) injury causes significantly more IMAT and fibrosis compared to Cardiotoxin (CTX). Additionally, females form more IMAT than males after a GLY injury, independent of strain. Of all strains, C57BL/6J mice, both females and males, are the most resistant to IMAT formation. In regard to injury-induced fibrosis, we found that the 129S strain formed the least amount of scar tissue. Surprisingly, C57BL/6J of both sexes demonstrated complete myofiber regeneration, while both CD1 and 129S1/SvlmJ strains still displayed smaller myofibers 21 days post injury. In addition, our data indicate that myofiber regeneration is negatively correlated with IMAT and fibrosis. Combined, our results demonstrate that careful consideration and exploration are needed to determine which injury type, mouse model/strain and sex to utilize as preclinical model especially for modeling IMAT formation.
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Affiliation(s)
- Alessandra M Norris
- Department of Pharmacology and Therapeutics, Myology Institute, University of Florida, Gainesville, FL, USA
| | - Kiara E Fierman
- Department of Pharmacology and Therapeutics, Myology Institute, University of Florida, Gainesville, FL, USA
| | - Jillian Campbell
- Department of Pharmacology and Therapeutics, Myology Institute, University of Florida, Gainesville, FL, USA
| | - Rhea Pitale
- Department of Pharmacology and Therapeutics, Myology Institute, University of Florida, Gainesville, FL, USA
| | - Muhammad Shahraj
- Department of Pharmacology and Therapeutics, Myology Institute, University of Florida, Gainesville, FL, USA
| | - Daniel Kopinke
- Department of Pharmacology and Therapeutics, Myology Institute, University of Florida, Gainesville, FL, USA.
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11
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Kristensen MA, Rich KK, Mogensen TC, Damsgaard Jensen AM, Fex Svenningsen Å, Zhang M. Focal Traumatic Brain Injury Impairs the Integrity of the Basement Membrane of Hindlimb Muscle Fibers Revealed by Extracellular Matrix Immunoreactivity. Life (Basel) 2024; 14:543. [PMID: 38792565 PMCID: PMC11121831 DOI: 10.3390/life14050543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 03/27/2024] [Accepted: 04/22/2024] [Indexed: 05/26/2024] Open
Abstract
Traumatic brain injury (TBI) stands as a prominent global cause of disability, with motor deficits being a common consequence. Despite its widespread impact, the precise pathological mechanisms underlying motor deficits after TBI remain elusive. In this study, hindlimb postural asymmetry (HL-PA) development in rats subjected to focal TBI was investigated to explore the potential roles of collagen IV and laminin within the extracellular matrix (ECM) of selected hindlimb muscles in the emergence of motor deficits following TBI. A focal TBI was induced by ablating the left sensorimotor cortex in rats and motor deficits were assessed by measuring HL-PA. The expression of laminin and collagen IV in eight selected muscles on each side of the hindlimbs from both TBI- and sham-operated rats were studied using immunohistochemistry and semi-quantitatively analyzed. The results indicated that the TBI rats exhibited HL-PA, characterized by flexion of the contralateral (right) hindlimb. In the sham-operated rats, the immunoreactive components of laminin and collagen IV were evenly and smoothly distributed along the border of the muscle fibers in all the investigated muscles. In contrast, in the TBI rats, the pattern was broken into aggregated, granule-like, immunoreactive components. Such a labeling pattern was detected in all the investigated muscles both from the contra- and ipsilateral sides of the TBI rats. However, in TBI rats, most of the muscles from the contralateral hindlimb showed a significantly increased expression of these two proteins in comparison with those from the ipsilateral hindlimb. In comparison to sham-operated rats, there was a significant increase in laminin and collagen IV expression in various contralateral hindlimb muscles in the TBI rats. These findings suggest potential implications of laminin and collagen IV in the development of motor deficits following a focal TBI.
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Affiliation(s)
- Mette Albæk Kristensen
- Department of Molecular Medicine, University of Southern Denmark, DK-5230 Odense, Denmark; (M.A.K.); (K.K.R.); (T.C.M.); (Å.F.S.)
| | - Karen Kalhøj Rich
- Department of Molecular Medicine, University of Southern Denmark, DK-5230 Odense, Denmark; (M.A.K.); (K.K.R.); (T.C.M.); (Å.F.S.)
| | - Tobias Christian Mogensen
- Department of Molecular Medicine, University of Southern Denmark, DK-5230 Odense, Denmark; (M.A.K.); (K.K.R.); (T.C.M.); (Å.F.S.)
| | | | - Åsa Fex Svenningsen
- Department of Molecular Medicine, University of Southern Denmark, DK-5230 Odense, Denmark; (M.A.K.); (K.K.R.); (T.C.M.); (Å.F.S.)
- Brain Research—Inter Disciplinary Guided Excellence (BRIDGE), University of Southern Denmark, DK-5230 Odense, Denmark
| | - Mengliang Zhang
- Department of Molecular Medicine, University of Southern Denmark, DK-5230 Odense, Denmark; (M.A.K.); (K.K.R.); (T.C.M.); (Å.F.S.)
- Brain Research—Inter Disciplinary Guided Excellence (BRIDGE), University of Southern Denmark, DK-5230 Odense, Denmark
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12
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Vlad D, Zaidem M, Perico C, Sedelnikova O, Bhattacharya S, Langdale JA. The WIP6 transcription factor TOO MANY LATERALS specifies vein type in C 4 and C 3 grass leaves. Curr Biol 2024; 34:1670-1686.e10. [PMID: 38531358 DOI: 10.1016/j.cub.2024.03.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 02/04/2024] [Accepted: 03/07/2024] [Indexed: 03/28/2024]
Abstract
Grass leaves are invariantly strap shaped with an elongated distal blade and a proximal sheath that wraps around the stem. Underpinning this shape is a scaffold of leaf veins, most of which extend in parallel along the proximo-distal leaf axis. Differences between species are apparent both in the vein types that develop and in the distance between veins across the medio-lateral leaf axis. A prominent engineering goal is to increase vein density in leaves of C3 photosynthesizing species to facilitate the introduction of the more efficient C4 pathway. Here, we discover that the WIP6 transcription factor TOO MANY LATERALS (TML) specifies vein rank in both maize (C4) and rice (C3). Loss-of-function tml mutations cause large lateral veins to develop in positions normally occupied by smaller intermediate veins, and TML transcript localization in wild-type leaves is consistent with a role in suppressing lateral vein development in procambial cells that form intermediate veins. Attempts to manipulate TML function in rice were unsuccessful because transgene expression was silenced, suggesting that precise TML expression is essential for shoot viability. This finding may reflect the need to prevent the inappropriate activation of downstream targets or, given that transcriptome analysis revealed altered cytokinin and auxin signaling profiles in maize tml mutants, the need to prevent local or general hormonal imbalances. Importantly, rice tml mutants display an increased occupancy of veins in the leaf, providing a step toward an anatomical chassis for C4 engineering. Collectively, a conserved mechanism of vein rank specification in grass leaves has been revealed.
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Affiliation(s)
- Daniela Vlad
- Department of Biology, University of Oxford, South Parks Rd, Oxford OX1 3RB, UK
| | - Maricris Zaidem
- Department of Biology, University of Oxford, South Parks Rd, Oxford OX1 3RB, UK
| | - Chiara Perico
- Department of Biology, University of Oxford, South Parks Rd, Oxford OX1 3RB, UK
| | - Olga Sedelnikova
- Department of Biology, University of Oxford, South Parks Rd, Oxford OX1 3RB, UK
| | - Samik Bhattacharya
- Resolve BioSciences GmbH, Alfred-Nobel-Straße 10, 40789 Monheim am Rhein, Germany
| | - Jane A Langdale
- Department of Biology, University of Oxford, South Parks Rd, Oxford OX1 3RB, UK.
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13
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Benucci S, Ruiz A, Franchini M, Ruggiero L, Zoppi D, Sitsapesan R, Lindsay C, Pelczar P, Pietrangelo L, Protasi F, Treves S, Zorzato F. A novel, patient-derived RyR1 mutation impairs muscle function and calcium homeostasis in mice. J Gen Physiol 2024; 156:e202313486. [PMID: 38445312 PMCID: PMC10911087 DOI: 10.1085/jgp.202313486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 12/20/2023] [Accepted: 02/09/2024] [Indexed: 03/07/2024] Open
Abstract
RYR1 is the most commonly mutated gene associated with congenital myopathies, a group of early-onset neuromuscular conditions of variable severity. The functional effects of a number of dominant RYR1 mutations have been established; however, for recessive mutations, these effects may depend on multiple factors, such as the formation of a hypomorphic allele, or on whether they are homozygous or compound heterozygous. Here, we functionally characterize a new transgenic mouse model knocked-in for mutations identified in a severely affected child born preterm and presenting limited limb movement. The child carried the homozygous c.14928C>G RYR1 mutation, resulting in the p.F4976L substitution. In vivo and ex vivo assays revealed that homozygous mice fatigued sooner and their muscles generated significantly less force compared with their WT or heterozygous littermates. Electron microscopy, biochemical, and physiological analyses showed that muscles from RyR1 p.F4976L homozygous mice have the following properties: (1) contain fewer calcium release units and show areas of myofibrillar degeneration, (2) contain less RyR1 protein, (3) fibers show smaller electrically evoked calcium transients, and (4) their SR has smaller calcium stores. In addition, single-channel recordings indicate that RyR1 p.F4976L exhibits higher Po in the presence of 100 μM [Ca2+]. Our mouse model partly recapitulates the clinical picture of the homozygous human patient and provides significant insight into the functional impact of this mutation. These results will help understand the pathology of patients with similar RYR1 mutations.
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Affiliation(s)
- Sofia Benucci
- Departments of Biomedicine and Neurology, Basel University Hospital, Basel, Switzerland
| | - Alexis Ruiz
- Departments of Biomedicine and Neurology, Basel University Hospital, Basel, Switzerland
| | - Martina Franchini
- Departments of Biomedicine and Neurology, Basel University Hospital, Basel, Switzerland
| | - Lucia Ruggiero
- Dipartimento di Neuroscienze, Scienze Riproduttive ed Odontostomatologiche, Università degli Studi di Napoli Federico II, Napoli, Italy
| | - Dario Zoppi
- Dipartimento di Neuroscienze, Scienze Riproduttive ed Odontostomatologiche, Università degli Studi di Napoli Federico II, Napoli, Italy
| | | | - Chris Lindsay
- Department of Pharmacology, University of Oxford, Oxford, UK
| | - Pawel Pelczar
- Center for Transgenic Models, University of Basel, Basel, Switzerland
| | - Laura Pietrangelo
- DMSI, Department of Medicine and Aging Sciences and CAST, Center for Advanced Studies and Technology, University G. d’Annunzio of Chieti-Pescara, Chieti, Italy
| | - Feliciano Protasi
- DMSI, Department of Medicine and Aging Sciences and CAST, Center for Advanced Studies and Technology, University G. d’Annunzio of Chieti-Pescara, Chieti, Italy
| | - Susan Treves
- Departments of Biomedicine and Neurology, Basel University Hospital, Basel, Switzerland
- Department of Life Science and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Francesco Zorzato
- Departments of Biomedicine and Neurology, Basel University Hospital, Basel, Switzerland
- Department of Life Science and Biotechnology, University of Ferrara, Ferrara, Italy
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14
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Lair B, Lac M, Frassin L, Brunet M, Buléon M, Feuillet G, Maslo C, Marquès M, Monbrun L, Bourlier V, Montastier E, Viguerie N, Tavernier G, Laurens C, Moro C. Common mouse models of chronic kidney disease are not associated with cachexia. Commun Biol 2024; 7:346. [PMID: 38509307 PMCID: PMC10954638 DOI: 10.1038/s42003-024-06021-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 03/07/2024] [Indexed: 03/22/2024] Open
Abstract
The 5/6 nephrectomy and adenine-induced nephropathy mouse models have been extensively used to study Chronic Kidney Disease (CKD)-related cachexia. One common caveat of these CKD models is the cross-sectional nature of comparisons made versus controls. We here performed a comprehensive longitudinal assessment of body composition and energy metabolism in both models. The most striking finding is that weight loss is largely driven by reduced food intake which promotes rapid loss of lean and fat mass. However, in both models, mice catch up weight and lean mass a few days after the surgery or when they are switched back to standard chow diet. Muscle force and mass are fully recovered and no sign of cachexia is observed. Our data demonstrate that the time-course of kidney failure and weight loss are unrelated in these common CKD models. These data highlight the need to reconsider the relative contribution of direct and indirect mechanisms to muscle wasting observed in CKD.
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Affiliation(s)
- Benjamin Lair
- Team MetaDiab, Institute of Metabolic and Cardiovascular Diseases, INSERM/Paul Sabatier University UMR1297, Toulouse, France
| | - Marlène Lac
- Team MetaDiab, Institute of Metabolic and Cardiovascular Diseases, INSERM/Paul Sabatier University UMR1297, Toulouse, France
| | - Lucas Frassin
- Team MetaDiab, Institute of Metabolic and Cardiovascular Diseases, INSERM/Paul Sabatier University UMR1297, Toulouse, France
| | - Manon Brunet
- Team Renal Fibrosis and Chronic Kidney Diseases, Institute of Metabolic and Cardiovascular Diseases, INSERM/Paul Sabatier University UMR1297, Toulouse, France
| | - Marie Buléon
- Team Renal Fibrosis and Chronic Kidney Diseases, Institute of Metabolic and Cardiovascular Diseases, INSERM/Paul Sabatier University UMR1297, Toulouse, France
| | - Guylène Feuillet
- Team Renal Fibrosis and Chronic Kidney Diseases, Institute of Metabolic and Cardiovascular Diseases, INSERM/Paul Sabatier University UMR1297, Toulouse, France
| | - Claire Maslo
- Team MetaDiab, Institute of Metabolic and Cardiovascular Diseases, INSERM/Paul Sabatier University UMR1297, Toulouse, France
| | - Marie Marquès
- Team MetaDiab, Institute of Metabolic and Cardiovascular Diseases, INSERM/Paul Sabatier University UMR1297, Toulouse, France
| | - Laurent Monbrun
- Team MetaDiab, Institute of Metabolic and Cardiovascular Diseases, INSERM/Paul Sabatier University UMR1297, Toulouse, France
| | - Virginie Bourlier
- Team MetaDiab, Institute of Metabolic and Cardiovascular Diseases, INSERM/Paul Sabatier University UMR1297, Toulouse, France
| | - Emilie Montastier
- Team MetaDiab, Institute of Metabolic and Cardiovascular Diseases, INSERM/Paul Sabatier University UMR1297, Toulouse, France
| | - Nathalie Viguerie
- Team MetaDiab, Institute of Metabolic and Cardiovascular Diseases, INSERM/Paul Sabatier University UMR1297, Toulouse, France
| | - Geneviève Tavernier
- Team MetaDiab, Institute of Metabolic and Cardiovascular Diseases, INSERM/Paul Sabatier University UMR1297, Toulouse, France
| | - Claire Laurens
- Team MetaDiab, Institute of Metabolic and Cardiovascular Diseases, INSERM/Paul Sabatier University UMR1297, Toulouse, France
| | - Cedric Moro
- Team MetaDiab, Institute of Metabolic and Cardiovascular Diseases, INSERM/Paul Sabatier University UMR1297, Toulouse, France.
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15
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Alsup AM, Fowlds K, Cho M, Luber JM. BetaBuddy: An automated end-to-end computer vision pipeline for analysis of calcium fluorescence dynamics in β-cells. PLoS One 2024; 19:e0299549. [PMID: 38489336 PMCID: PMC10942061 DOI: 10.1371/journal.pone.0299549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 02/12/2024] [Indexed: 03/17/2024] Open
Abstract
Insulin secretion from pancreatic β-cells is integral in maintaining the delicate equilibrium of blood glucose levels. Calcium is known to be a key regulator and triggers the release of insulin. This sub-cellular process can be monitored and tracked through live-cell imaging and subsequent cell segmentation, registration, tracking, and analysis of the calcium level in each cell. Current methods of analysis typically require the manual outlining of β-cells, involve multiple software packages, and necessitate multiple researchers-all of which tend to introduce biases. Utilizing deep learning algorithms, we have therefore created a pipeline to automatically segment and track thousands of cells, which greatly reduces the time required to gather and analyze a large number of sub-cellular images and improve accuracy. Tracking cells over a time-series image stack also allows researchers to isolate specific calcium spiking patterns and spatially identify those of interest, creating an efficient and user-friendly analysis tool. Using our automated pipeline, a previous dataset used to evaluate changes in calcium spiking activity in β-cells post-electric field stimulation was reanalyzed. Changes in spiking activity were found to be underestimated previously with manual segmentation. Moreover, the machine learning pipeline provides a powerful and rapid computational approach to examine, for example, how calcium signaling is regulated by intracellular interactions.
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Affiliation(s)
- Anne M. Alsup
- Department of Bioengineering, University of Texas at Arlington, Arlington, TX, United States of America
| | - Kelli Fowlds
- Department of Bioengineering, University of Texas at Arlington, Arlington, TX, United States of America
| | - Michael Cho
- Department of Bioengineering, University of Texas at Arlington, Arlington, TX, United States of America
| | - Jacob M. Luber
- Department of Bioengineering, University of Texas at Arlington, Arlington, TX, United States of America
- Department of Computer Science and Engineering, University of Texas at Arlington, Arlington, TX, United States of America
- Multi-Interprofessional Center for Health Informatics, University of Texas at Arlington, Arlington, TX, United States of America
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16
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Lin HP, Petersen JD, Gilsrud AJ, Madruga A, D’Silva TM, Huang X, Shammas MK, Randolph NP, Li Y, Jones DR, Pacold ME, Narendra DP. DELE1 promotes translation-associated homeostasis, growth, and survival in mitochondrial myopathy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.29.582673. [PMID: 38529505 PMCID: PMC10962736 DOI: 10.1101/2024.02.29.582673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/27/2024]
Abstract
Mitochondrial dysfunction causes devastating disorders, including mitochondrial myopathy. Here, we identified that diverse mitochondrial myopathy models elicit a protective mitochondrial integrated stress response (mt-ISR), mediated by OMA1-DELE1 signaling. The response was similar following disruptions in mtDNA maintenance, from knockout of Tfam, and mitochondrial protein unfolding, from disease-causing mutations in CHCHD10 (G58R and S59L). The preponderance of the response was directed at upregulating pathways for aminoacyl-tRNA biosynthesis, the intermediates for protein synthesis, and was similar in heart and skeletal muscle but more limited in brown adipose challenged with cold stress. Strikingly, models with early DELE1 mt-ISR activation failed to grow and survive to adulthood in the absence of Dele1, accounting for some but not all of OMA1's protection. Notably, the DELE1 mt-ISR did not slow net protein synthesis in stressed striated muscle, but instead prevented loss of translation-associated proteostasis in muscle fibers. Together our findings identify that the DELE1 mt-ISR mediates a stereotyped response to diverse forms of mitochondrial stress and is particularly critical for maintaining growth and survival in early-onset mitochondrial myopathy.
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Affiliation(s)
- Hsin-Pin Lin
- Inherited Movement Disorders Unit, Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jennifer D. Petersen
- Inherited Movement Disorders Unit, Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Alexandra J. Gilsrud
- Inherited Movement Disorders Unit, Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Angelo Madruga
- Inherited Movement Disorders Unit, Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Theresa M. D’Silva
- Inherited Movement Disorders Unit, Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Xiaoping Huang
- Inherited Movement Disorders Unit, Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mario K. Shammas
- Inherited Movement Disorders Unit, Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Nicholas P. Randolph
- Inherited Movement Disorders Unit, Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yan Li
- Proteomics Core Facility, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Drew R. Jones
- Department of Radiation Oncology, NYU Langone Health, New York, United States
| | - Michael E. Pacold
- Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, United States
- Perlmutter Cancer Center, NYU Langone Health, New York, United States
| | - Derek P. Narendra
- Inherited Movement Disorders Unit, Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
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17
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Lork AA, Rabasco S, Ernst C, du Toit A, Rizzoli SO, Phan NTN. Subcellular protein turnover in human neural progenitor cells revealed by correlative electron microscopy and nanoscale secondary ion mass spectrometry imaging. Chem Sci 2024; 15:3311-3322. [PMID: 38425528 PMCID: PMC10901485 DOI: 10.1039/d3sc05629e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 01/13/2024] [Indexed: 03/02/2024] Open
Abstract
Protein turnover is a critical process for accurate cellular function, in which damaged proteins in the cells are gradually replaced with newly synthesized ones. Many previous studies on cellular protein turnover have used stable isotopic labelling by amino acids in cell culture (SILAC), followed by proteomic bulk analysis. However, this approach does not take into account the heterogeneity observed at the single-cell and subcellular levels. To address this, we investigated the protein turnover of neural progenitor cells at the subcellular resolution, using correlative TEM and NanoSIMS imaging, relying on a pulse-chase analysis of isotopically-labelled protein precusors. Cellular protein turnover was found significantly heterogenous across individual organelles, which indicates a possible relation between protein turnover and subcellular activity. In addition, different isotopically-labelled amino acids provided different turnover patterns, in spite of all being protein precursors, suggesting that they undergo distinct protein synthesis and metabolic pathways at the subcellular level.
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Affiliation(s)
- Alicia A Lork
- Department of Chemistry and Molecular Biology University of Gothenburg SE-412 96 Gothenburg Sweden
| | - Stefania Rabasco
- Department of Chemistry and Molecular Biology University of Gothenburg SE-412 96 Gothenburg Sweden
| | - Carl Ernst
- Human Genetics, McGill University H4H1R3 Montreal Canada
| | - André du Toit
- Department of Chemistry and Molecular Biology University of Gothenburg SE-412 96 Gothenburg Sweden
| | - Silvio O Rizzoli
- Department of Neuro- and Sensory Physiology, University Medical Center Göttingen, Center for Biostructural Imaging of Neurodegeneration Göttingen Germany
| | - Nhu T N Phan
- Department of Chemistry and Molecular Biology University of Gothenburg SE-412 96 Gothenburg Sweden
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18
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Brun A, Mougeot G, Denis P, Collin ML, Pouchin P, Montaurier C, Walrand S, Capel F, Gueugneau M. A new bio imagery user-friendly tool for automatic morphometry measurement on muscle cell cultures and histological sections. Sci Rep 2024; 14:3108. [PMID: 38326394 PMCID: PMC11269594 DOI: 10.1038/s41598-024-53658-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Accepted: 02/03/2024] [Indexed: 02/09/2024] Open
Abstract
TRUEFAD (TRUE Fiber Atrophy Distinction) is a bioimagery user-friendly tool developed to allow consistent and automatic measurement of myotube diameter in vitro, muscle fiber size and type using rodents and human muscle biopsies. This TRUEFAD package was set up to standardize and dynamize muscle research via easy-to-obtain images run on an open-source plugin for FIJI. We showed here both the robustness and the performance of our pipelines to correctly segment muscle cells and fibers. We evaluated our pipeline on real experiment image sets and showed consistent reliability across images and conditions. TRUEFAD development makes possible systematical and rapid screening of substances impacting muscle morphology for helping scientists focus on their hypothesis rather than image analysis.
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Affiliation(s)
- Aurélien Brun
- UMR1019 Unité de Nutrition Humaine (UNH), INRAE, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Guillaume Mougeot
- iGReD CNRS, INSERM Université Clermont Auvergne, Clermont-Ferrand, France
| | - Philippe Denis
- UMR1019 Unité de Nutrition Humaine (UNH), INRAE, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Marie Laure Collin
- UMR1019 Unité de Nutrition Humaine (UNH), INRAE, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Pierre Pouchin
- iGReD CNRS, INSERM Université Clermont Auvergne, Clermont-Ferrand, France
| | - Christophe Montaurier
- UMR1019 Unité de Nutrition Humaine (UNH), INRAE, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Stéphane Walrand
- UMR1019 Unité de Nutrition Humaine (UNH), INRAE, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Frédéric Capel
- UMR1019 Unité de Nutrition Humaine (UNH), INRAE, Université Clermont Auvergne, Clermont-Ferrand, France.
| | - Marine Gueugneau
- UMR1019 Unité de Nutrition Humaine (UNH), INRAE, Université Clermont Auvergne, Clermont-Ferrand, France
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19
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Gu S, Wen C, Xiao Z, Huang Q, Jiang Z, Liu H, Gao J, Li J, Sun C, Yang N. MyoV: a deep learning-based tool for the automated quantification of muscle fibers. Brief Bioinform 2024; 25:bbad528. [PMID: 38271484 PMCID: PMC10810329 DOI: 10.1093/bib/bbad528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 12/06/2023] [Accepted: 12/15/2023] [Indexed: 01/27/2024] Open
Abstract
Accurate approaches for quantifying muscle fibers are essential in biomedical research and meat production. In this study, we address the limitations of existing approaches for hematoxylin and eosin-stained muscle fibers by manually and semiautomatically labeling over 660 000 muscle fibers to create a large dataset. Subsequently, an automated image segmentation and quantification tool named MyoV is designed using mask regions with convolutional neural networks and a residual network and feature pyramid network as the backbone network. This design enables the tool to allow muscle fiber processing with different sizes and ages. MyoV, which achieves impressive detection rates of 0.93-0.96 and precision levels of 0.91-0.97, exhibits a superior performance in quantification, surpassing both manual methods and commonly employed algorithms and software, particularly for whole slide images (WSIs). Moreover, MyoV is proven as a powerful and suitable tool for various species with different muscle development, including mice, which are a crucial model for muscle disease diagnosis, and agricultural animals, which are a significant meat source for humans. Finally, we integrate this tool into visualization software with functions, such as segmentation, area determination and automatic labeling, allowing seamless processing for over 400 000 muscle fibers within a WSI, eliminating the model adjustment and providing researchers with an easy-to-use visual interface to browse functional options and realize muscle fiber quantification from WSIs.
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Affiliation(s)
- Shuang Gu
- State Key Laboratory of Animal Biotech Breeding and Frontier Science Center for Molecular Design Breeding, China Agricultural University, Beijing 100193, China
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing 100193, China
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Chaoliang Wen
- State Key Laboratory of Animal Biotech Breeding and Frontier Science Center for Molecular Design Breeding, China Agricultural University, Beijing 100193, China
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing 100193, China
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
- Sanya Institute of China Agricultural University, Hainan 572025, China
| | - Zhen Xiao
- School of Computer and Information, Hefei University of Technology, Anhui 230009, China
| | - Qiang Huang
- State Key Laboratory of Animal Biotech Breeding and Frontier Science Center for Molecular Design Breeding, China Agricultural University, Beijing 100193, China
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing 100193, China
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Zheyi Jiang
- State Key Laboratory of Animal Biotech Breeding and Frontier Science Center for Molecular Design Breeding, China Agricultural University, Beijing 100193, China
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing 100193, China
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Honghong Liu
- State Key Laboratory of Animal Biotech Breeding and Frontier Science Center for Molecular Design Breeding, China Agricultural University, Beijing 100193, China
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing 100193, China
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Jia Gao
- State Key Laboratory of Animal Biotech Breeding and Frontier Science Center for Molecular Design Breeding, China Agricultural University, Beijing 100193, China
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing 100193, China
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Junying Li
- State Key Laboratory of Animal Biotech Breeding and Frontier Science Center for Molecular Design Breeding, China Agricultural University, Beijing 100193, China
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing 100193, China
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
- Sanya Institute of China Agricultural University, Hainan 572025, China
| | - Congjiao Sun
- State Key Laboratory of Animal Biotech Breeding and Frontier Science Center for Molecular Design Breeding, China Agricultural University, Beijing 100193, China
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing 100193, China
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
- Sanya Institute of China Agricultural University, Hainan 572025, China
| | - Ning Yang
- State Key Laboratory of Animal Biotech Breeding and Frontier Science Center for Molecular Design Breeding, China Agricultural University, Beijing 100193, China
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing 100193, China
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
- Sanya Institute of China Agricultural University, Hainan 572025, China
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20
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Van Doorselaer L, Verboven P, Nicolai B. Automatic 3D cell segmentation of fruit parenchyma tissue from X-ray micro CT images using deep learning. PLANT METHODS 2024; 20:12. [PMID: 38243306 PMCID: PMC10799452 DOI: 10.1186/s13007-024-01137-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 01/08/2024] [Indexed: 01/21/2024]
Abstract
BACKGROUND High quality 3D information of the microscopic plant tissue morphology-the spatial organization of cells and intercellular spaces in tissues-helps in understanding physiological processes in a wide variety of plants and tissues. X-ray micro-CT is a valuable tool that is becoming increasingly available in plant research to obtain 3D microstructural information of the intercellular pore space and individual pore sizes and shapes of tissues. However, individual cell morphology is difficult to retrieve from micro-CT as cells cannot be segmented properly due to negligible density differences at cell-to-cell interfaces. To address this, deep learning-based models were trained and tested to segment individual cells using X-ray micro-CT images of parenchyma tissue samples from apple and pear fruit with different cell and porosity characteristics. RESULTS The best segmentation model achieved an Aggregated Jaccard Index (AJI) of 0.86 and 0.73 for apple and pear tissue, respectively, which is an improvement over the current benchmark method that achieved AJIs of 0.73 and 0.67. Furthermore, the neural network was able to detect other plant tissue structures such as vascular bundles and stone cell clusters (brachysclereids), of which the latter were shown to strongly influence the spatial organization of pear cells. Based on the AJIs, apple tissue was found to be easier to segment, as the porosity and specific surface area of the pore space are higher and lower, respectively, compared to pear tissue. Moreover, samples with lower pore network connectivity, proved very difficult to segment. CONCLUSIONS The proposed method can be used to automatically quantify 3D cell morphology of plant tissue from micro-CT instead of opting for laborious manual annotations or less accurate segmentation approaches. In case fruit tissue porosity or pore network connectivity is too low or the specific surface area of the pore space too high, native X-ray micro-CT is unable to provide proper marker points of cell outlines, and one should rely on more elaborate contrast-enhancing scan protocols.
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Affiliation(s)
- Leen Van Doorselaer
- Mechatronics, Biostatistics and Sensors (MeBioS), Biosystems Department, KU Leuven, Leuven, Belgium
| | - Pieter Verboven
- Mechatronics, Biostatistics and Sensors (MeBioS), Biosystems Department, KU Leuven, Leuven, Belgium.
| | - Bart Nicolai
- Mechatronics, Biostatistics and Sensors (MeBioS), Biosystems Department, KU Leuven, Leuven, Belgium
- Flanders Centre of Postharvest Biology, Leuven, Belgium
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21
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Castor-Macias JA, Larouche JA, Wallace EC, Spence BD, Eames A, Duran P, Yang BA, Fraczek PM, Davis CA, Brooks SV, Maddipati KR, Markworth JF, Aguilar CA. Maresin 1 repletion improves muscle regeneration after volumetric muscle loss. eLife 2023; 12:e86437. [PMID: 38131691 PMCID: PMC10807862 DOI: 10.7554/elife.86437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 12/21/2023] [Indexed: 12/23/2023] Open
Abstract
The acute traumatic or surgical loss of skeletal muscle, known as volumetric muscle loss (VML), is a devastating type of injury that results in exacerbated and persistent inflammation followed by fibrosis. The mechanisms that mediate the magnitude and duration of the inflammatory response and ensuing fibrosis after VML remain understudied, and as such, the development of regenerative therapies has been limited. To address this need, we profiled how lipid mediators, which are potent regulators of the immune response after injury, varied with VML injuries that heal or result in fibrosis. We observed that non-healing VML injuries displayed increased pro-inflammatory eicosanoids and a lack of pro-resolving lipid mediators. Treatment of VML with a pro-resolving lipid mediator synthesized from docosahexaenoic acid, called Maresin 1, ameliorated fibrosis through reduction of neutrophils and macrophages and enhanced recovery of muscle strength. These results expand our knowledge of the dysregulated immune response that develops after VML and identify a novel immuno-regenerative therapeutic modality in Maresin 1.
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Affiliation(s)
- Jesus A Castor-Macias
- Department of Biomedical Engineering, University of MichiganAnn ArborUnited States
- Biointerfaces Institute, University of MichiganAnn ArborUnited States
| | - Jacqueline A Larouche
- Department of Biomedical Engineering, University of MichiganAnn ArborUnited States
- Biointerfaces Institute, University of MichiganAnn ArborUnited States
| | - Emily C Wallace
- Department of Biomedical Engineering, University of MichiganAnn ArborUnited States
| | - Bonnie D Spence
- Department of Biomedical Engineering, University of MichiganAnn ArborUnited States
| | - Alec Eames
- Department of Biomedical Engineering, University of MichiganAnn ArborUnited States
| | - Pamela Duran
- Department of Biomedical Engineering, University of MichiganAnn ArborUnited States
- Biointerfaces Institute, University of MichiganAnn ArborUnited States
| | - Benjamin A Yang
- Department of Biomedical Engineering, University of MichiganAnn ArborUnited States
- Biointerfaces Institute, University of MichiganAnn ArborUnited States
| | - Paula M Fraczek
- Department of Biomedical Engineering, University of MichiganAnn ArborUnited States
- Biointerfaces Institute, University of MichiganAnn ArborUnited States
| | - Carol A Davis
- Department of Molecular & Integrative Physiology, University of MichiganAnn ArborUnited States
| | - Susan V Brooks
- Department of Biomedical Engineering, University of MichiganAnn ArborUnited States
- Department of Molecular & Integrative Physiology, University of MichiganAnn ArborUnited States
| | - Krishna Rao Maddipati
- Department of Pathology, Lipidomics Core Facility, Wayne State UniversityDetroitUnited States
| | - James F Markworth
- Department of Animal Sciences, Purdue UniversityWest Lafayette, IndianaUnited States
| | - Carlos A Aguilar
- Department of Biomedical Engineering, University of MichiganAnn ArborUnited States
- Biointerfaces Institute, University of MichiganAnn ArborUnited States
- Program in Cellular and Molecular Biology, University of MichiganAnn ArborUnited States
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22
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Tsarouhas V, Liu D, Tsikala G, Engström Y, Strigini M, Samakovlis C. A surfactant lipid layer of endosomal membranes facilitates airway gas filling in Drosophila. Curr Biol 2023; 33:5132-5146.e5. [PMID: 37992718 DOI: 10.1016/j.cub.2023.10.058] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 09/14/2023] [Accepted: 10/26/2023] [Indexed: 11/24/2023]
Abstract
The mechanisms underlying the construction of an air-liquid interface in respiratory organs remain elusive. Here, we use live imaging and genetic analysis to describe the morphogenetic events generating an extracellular lipid lining of the Drosophila airways required for their gas filing and animal survival. We show that sequential Rab39/Syx1A/Syt1-mediated secretion of lysosomal acid sphingomyelinase (Drosophila ASM [dASM]) and Rab11/35/Syx1A/Rop-dependent exosomal secretion provides distinct components for lipid film assembly. Tracheal inactivation of Rab11 or Rab35 or loss of Rop results in intracellular accumulation of exosomal, multi-vesicular body (MVB)-derived vesicles. On the other hand, loss of dASM or Rab39 causes luminal bubble-like accumulations of exosomal membranes and liquid retention in the airways. Inactivation of the exosomal secretion in dASM mutants counteracts this phenotype, arguing that the exosomal secretion provides the lipid vesicles and that secreted lysosomal dASM organizes them into a continuous film. Our results reveal the coordinated functions of extracellular vesicle and lysosomal secretions in generating a lipid layer crucial for airway gas filling and survival.
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Affiliation(s)
- Vasilios Tsarouhas
- Stockholm University, Department of Molecular Biosciences, The Wenner-Gren Institute, 10691 Stockholm, Sweden; Science for Life Laboratory, SciLifeLab, 171 65 Stockholm, Sweden.
| | - Dan Liu
- Stockholm University, Department of Molecular Biosciences, The Wenner-Gren Institute, 10691 Stockholm, Sweden
| | - Georgia Tsikala
- Stockholm University, Department of Molecular Biosciences, The Wenner-Gren Institute, 10691 Stockholm, Sweden; IMBB, 70013 Heraklion, Crete, Greece
| | - Ylva Engström
- Stockholm University, Department of Molecular Biosciences, The Wenner-Gren Institute, 10691 Stockholm, Sweden
| | | | - Christos Samakovlis
- Stockholm University, Department of Molecular Biosciences, The Wenner-Gren Institute, 10691 Stockholm, Sweden; Science for Life Laboratory, SciLifeLab, 171 65 Stockholm, Sweden; ECCPS, Justus Liebig University of Giessen, 35390 Giessen, Germany.
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23
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Du G, Zhang P, Guo J, Pang X, Kan G, Zeng B, Chen X, Liang J, Zhan Y. MF-Net: Automated Muscle Fiber Segmentation From Immunofluorescence Images Using a Local-Global Feature Fusion Network. J Digit Imaging 2023; 36:2411-2426. [PMID: 37714969 PMCID: PMC10584774 DOI: 10.1007/s10278-023-00890-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 07/20/2023] [Accepted: 07/24/2023] [Indexed: 09/17/2023] Open
Abstract
Histological assessment of skeletal muscle slices is very important for the accurate evaluation of weightless muscle atrophy. The accurate identification and segmentation of muscle fiber boundary is an important prerequisite for the evaluation of skeletal muscle fiber atrophy. However, there are many challenges to segment muscle fiber from immunofluorescence images, including the presence of low contrast in fiber boundaries in immunofluorescence images and the influence of background noise. Due to the limitations of traditional convolutional neural network-based segmentation methods in capturing global information, they cannot achieve ideal segmentation results. In this paper, we propose a muscle fiber segmentation network (MF-Net) method for effective segmentation of macaque muscle fibers in immunofluorescence images. The network adopts a dual encoder branch composed of convolutional neural networks and transformer to effectively capture local and global feature information in the immunofluorescence image, highlight foreground features, and suppress irrelevant background noise. In addition, a low-level feature decoder module is proposed to capture more global context information by combining different image scales to supplement the missing detail pixels. In this study, a comprehensive experiment was carried out on the immunofluorescence datasets of six macaques' weightlessness models and compared with the state-of-the-art deep learning model. It is proved from five segmentation indices that the proposed automatic segmentation method can be accurately and effectively applied to muscle fiber segmentation in shank immunofluorescence images.
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Affiliation(s)
| | - Peng Zhang
- China Astronaut Research and Training Center, Beijing, 100094, People's Republic of China
| | - Jianzhong Guo
- Institute of Applied Acoustics, School of Physics and Information Technology, Shaanxi Normal University, Xi'an, 710062, China
| | - Xiangsheng Pang
- China Astronaut Research and Training Center, Beijing, 100094, People's Republic of China
| | - Guanghan Kan
- China Astronaut Research and Training Center, Beijing, 100094, People's Republic of China
| | - Bin Zeng
- China Astronaut Research and Training Center, Beijing, 100094, People's Republic of China
| | - Xiaoping Chen
- China Astronaut Research and Training Center, Beijing, 100094, People's Republic of China.
| | - Jimin Liang
- School of Electronic Engineering, Xidian University, Xi'an, Shaanxi, 710071, China.
| | - Yonghua Zhan
- School of Life Science and Technology, Xidian University & Engineering Research Center of Molecular and Neuro Imaging, Ministry of Education, Xi'an, Shaanxi, 710126, China.
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24
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Charrasse S, Poquillon T, Saint-Omer C, Pastore M, Bordignon B, Frye RE, Reynes C, Racine V, Aouacheria A. Quantitative assessment of mitochondrial morphology relevant for studies on cellular health and environmental toxicity. Comput Struct Biotechnol J 2023; 21:5609-5619. [PMID: 38047232 PMCID: PMC10690410 DOI: 10.1016/j.csbj.2023.11.015] [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] [Indexed: 12/05/2023] Open
Abstract
Mitochondria are essential organelles that play crucial roles in cellular energy metabolism, calcium signaling and apoptosis. Their importance in tissue homeostasis and stress responses, combined to their ability to transition between various structural and functional states, make them excellent organelles for monitoring cellular health. Quantitative assessment of mitochondrial morphology can therefore provide valuable insights into environmentally-induced cell damage. High-content screening (HCS) provides a powerful tool for analyzing organelles and cellular substructures. We developed a fully automated and miniaturized HCS wet-plus-dry pipeline (MITOMATICS) exploiting mitochondrial morphology as a marker for monitoring cellular health or damage. MITOMATICS uses an in-house, proprietary software (MitoRadar) to enable fast, exhaustive and cost-effective analysis of mitochondrial morphology and its inherent diversity in live cells. We applied our pipeline and big data analytics software to assess the mitotoxicity of selected chemicals, using the mitochondrial uncoupler CCCP as an internal control. Six different pesticides (inhibiting complexes I, II and III of the mitochondrial respiratory chain) were tested as individual compounds and five other pesticides present locally in Occitanie (Southern France) were assessed in combination to determine acute mitotoxicity. Our results show that the assayed pesticides exhibit specific signatures when used as single compounds or chemical mixtures and that they function synergistically to impact mitochondrial architecture. Study of environment-induced mitochondrial damage has the potential to open new fields in mechanistic toxicology, currently underexplored by regulatory toxicology and exposome research. Such exploration could inform health policy guidelines and foster pharmacological intervention, water, air and soil pollution control and food safety.
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Affiliation(s)
- Sophie Charrasse
- Institut des Sciences de l′Evolution de Montpellier (ISEM, UMR 5554, CNRS/UM/IRD/EPHE), Université de Montpellier, Montpellier, France
| | - Titouan Poquillon
- Institut des Sciences de l′Evolution de Montpellier (ISEM, UMR 5554, CNRS/UM/IRD/EPHE), Université de Montpellier, Montpellier, France
- QuantaCell SAS, Hôpital Saint Eloi, IRMB, 80 avenue Augustin Fliche, 34090 Montpellier, France
| | - Charlotte Saint-Omer
- Institut des Sciences de l′Evolution de Montpellier (ISEM, UMR 5554, CNRS/UM/IRD/EPHE), Université de Montpellier, Montpellier, France
| | - Manuela Pastore
- STATABIO BioCampus, Univ. Montpellier, CNRS, INSERM, Montpellier, France
| | - Benoit Bordignon
- Montpellier Ressources Imagerie, BioCampus, University of Montpellier, CNRS, INSERM, Montpellier, France
| | | | - Christelle Reynes
- STATABIO BioCampus, Univ. Montpellier, CNRS, INSERM, Montpellier, France
- IGF, Univ. Montpellier, CNRS, INSERM, Montpellier, France
| | - Victor Racine
- QuantaCell SAS, Hôpital Saint Eloi, IRMB, 80 avenue Augustin Fliche, 34090 Montpellier, France
| | - Abdel Aouacheria
- Institut des Sciences de l′Evolution de Montpellier (ISEM, UMR 5554, CNRS/UM/IRD/EPHE), Université de Montpellier, Montpellier, France
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25
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Luscombe VB, Baena-López LA, Bataille CJR, Russell AJ, Greaves DR. Kinetic insights into agonist-dependent signalling bias at the pro-inflammatory G-protein coupled receptor GPR84. Eur J Pharmacol 2023; 956:175960. [PMID: 37543157 PMCID: PMC10804997 DOI: 10.1016/j.ejphar.2023.175960] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 08/01/2023] [Accepted: 08/02/2023] [Indexed: 08/07/2023]
Abstract
GPR84 is an orphan G-protein coupled receptor (GPCR) linked to inflammation. Strategies targeting GPR84 to prevent excessive inflammation in disease are hampered by a lack of understanding of its precise functional role. We have developed heterologous cell lines with low GPR84 expression levels that phenocopy the response of primary cells in a label-free cell electrical impedance (CEI) sensing system that measures cell morphology and adhesion. We then investigated the signalling profile and membrane localisation of GPR84 upon treatment with 6-OAU and DL-175, two agonists known to differentially influence immune cell function. When compared to 6-OAU, DL-175 was found to exhibit a delayed impedance response, a delayed and suppressed activation of Akt, which together correlated with an impaired ability to internalise GPR84 from the plasma membrane. The signalling differences were transient and occurred only at early time points in the low expressing cell lines, highlighting the importance of receptor number and kinetic readouts when evaluating signalling bias. Our findings open new ways to understand GPR84 signalling and evaluate the effect of newly developed agonists.
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Affiliation(s)
- Vincent B Luscombe
- Sir William Dunn School of Pathology, South Parks Rd, University of Oxford, Oxford, Oxfordshire, OX1 3RE, United Kingdom
| | - Luis Alberto Baena-López
- Sir William Dunn School of Pathology, South Parks Rd, University of Oxford, Oxford, Oxfordshire, OX1 3RE, United Kingdom
| | - Carole J R Bataille
- Department of Chemistry, Mansfield Rd, University of Oxford, Oxford, Oxfordshire, OX1 3TA, United Kingdom
| | - Angela J Russell
- Department of Chemistry, Mansfield Rd, University of Oxford, Oxford, Oxfordshire, OX1 3TA, United Kingdom; Department of Pharmacology, Mansfield Rd, University of Oxford, Oxford, Oxfordshire, OX1 3TA, United Kingdom
| | - David R Greaves
- Sir William Dunn School of Pathology, South Parks Rd, University of Oxford, Oxford, Oxfordshire, OX1 3RE, United Kingdom.
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26
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Becker M, Joseph SS, Garcia-Carrizo F, Tom RZ, Opaleva D, Serr I, Tschöp MH, Schulz TJ, Hofmann SM, Daniel C. Regulatory T cells require IL6 receptor alpha signaling to control skeletal muscle function and regeneration. Cell Metab 2023; 35:1736-1751.e7. [PMID: 37734370 PMCID: PMC10563138 DOI: 10.1016/j.cmet.2023.08.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 02/27/2023] [Accepted: 08/31/2023] [Indexed: 09/23/2023]
Abstract
Muscle-residing regulatory T cells (Tregs) control local tissue integrity and function. However, the molecular interface connecting Treg-based regulation with muscle function and regeneration remains largely unexplored. Here, we show that exercise fosters a stable induction of highly functional muscle-residing Tregs with increased expression of amphiregulin (Areg), EGFR, and ST2. Mechanistically, we find that mice lacking IL6Rα on T cells (TKO) harbor significant reductions in muscle Treg functionality and satellite and fibro-adipogenic progenitor cells, which are required for muscle regeneration. Using exercise and sarcopenia models, IL6Rα TKO mice demonstrate deficits in Tregs, their functional maturation, and a more pronounced decline in muscle mass. Muscle injury models indicate that IL6Rα TKO mice have significant disabilities in muscle regeneration. Treg gain of function restores impaired muscle repair in IL6Rα TKO mice. Of note, pharmacological IL6R blockade in WT mice phenocopies deficits in muscle function identified in IL6Rα TKO mice, thereby highlighting the clinical implications of the findings.
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Affiliation(s)
- Maike Becker
- Research Unit Type 1 Diabetes Immunology, Helmholtz Diabetes Center at Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Munich-Neuherberg, Germany; German Center for Diabetes Research (DZD), 85764 Munich-Neuherberg, Germany
| | - Sini S Joseph
- German Center for Diabetes Research (DZD), 85764 Munich-Neuherberg, Germany; Institute for Diabetes and Obesity, Helmholtz Diabetes Center at Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Munich-Neuherberg, Germany; Division of Metabolic Diseases, Department of Medicine, Technische Universität München, 80333 Munich, Germany
| | - Francisco Garcia-Carrizo
- German Center for Diabetes Research (DZD), 85764 Munich-Neuherberg, Germany; Department of Adipocyte Development and Nutrition, German Institute of Human Nutrition Potsdam-Rehbrücke, 14558 Nuthetal, Germany
| | - Robby Z Tom
- German Center for Diabetes Research (DZD), 85764 Munich-Neuherberg, Germany; Institute for Diabetes and Regeneration, Helmholtz Diabetes Center at Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Munich-Neuherberg, Germany; Department of Medicine IV, University Hospital, LMU Munich, 80336 Munich, Germany
| | - Daria Opaleva
- Research Unit Type 1 Diabetes Immunology, Helmholtz Diabetes Center at Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Munich-Neuherberg, Germany; German Center for Diabetes Research (DZD), 85764 Munich-Neuherberg, Germany
| | - Isabelle Serr
- Research Unit Type 1 Diabetes Immunology, Helmholtz Diabetes Center at Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Munich-Neuherberg, Germany; German Center for Diabetes Research (DZD), 85764 Munich-Neuherberg, Germany
| | - Matthias H Tschöp
- German Center for Diabetes Research (DZD), 85764 Munich-Neuherberg, Germany; Institute for Diabetes and Obesity, Helmholtz Diabetes Center at Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Munich-Neuherberg, Germany; Division of Metabolic Diseases, Department of Medicine, Technische Universität München, 80333 Munich, Germany
| | - Tim J Schulz
- German Center for Diabetes Research (DZD), 85764 Munich-Neuherberg, Germany; Department of Adipocyte Development and Nutrition, German Institute of Human Nutrition Potsdam-Rehbrücke, 14558 Nuthetal, Germany; University of Potsdam, Institute of Nutritional Science, Potsdam-Rehbrücke, 14558 Nuthetal, Germany
| | - Susanna M Hofmann
- German Center for Diabetes Research (DZD), 85764 Munich-Neuherberg, Germany; Institute for Diabetes and Regeneration, Helmholtz Diabetes Center at Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Munich-Neuherberg, Germany; Department of Medicine IV, University Hospital, LMU Munich, 80336 Munich, Germany
| | - Carolin Daniel
- Research Unit Type 1 Diabetes Immunology, Helmholtz Diabetes Center at Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Munich-Neuherberg, Germany; German Center for Diabetes Research (DZD), 85764 Munich-Neuherberg, Germany; Division of Clinical Pharmacology, Department of Medicine IV, Ludwig-Maximilians-Universität München, 80337 Munich, Germany.
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27
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Tejedera-Villafranca A, Montolio M, Ramón-Azcón J, Fernández-Costa JM. Mimicking sarcolemmal damage in vitro: a contractile 3D model of skeletal muscle for drug testing in Duchenne muscular dystrophy. Biofabrication 2023; 15:045024. [PMID: 37725998 DOI: 10.1088/1758-5090/acfb3d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 09/19/2023] [Indexed: 09/21/2023]
Abstract
Duchenne muscular dystrophy (DMD) is the most prevalent neuromuscular disease diagnosed in childhood. It is a progressive and wasting disease, characterized by a degeneration of skeletal and cardiac muscles caused by the lack of dystrophin protein. The absence of this crucial structural protein leads to sarcolemmal fragility, resulting in muscle fiber damage during contraction. Despite ongoing efforts, there is no cure available for DMD patients. One of the primary challenges is the limited efficacy of current preclinical tools, which fail in modeling the biological complexity of the disease. Human-based three-dimensional (3D) cell culture methods appear as a novel approach to accelerate preclinical research by enhancing the reproduction of pathophysiological processes in skeletal muscle. In this work, we developed a patient-derived functional 3D skeletal muscle model of DMD that reproduces the sarcolemmal damage found in the native DMD muscle. These bioengineered skeletal muscle tissues exhibit contractile functionality, as they responded to electrical pulse stimulation. Sustained contractile regimes induced the loss of myotube integrity, mirroring the pathological myotube breakdown inherent in DMD due to sarcolemmal instability. Moreover, damaged DMD tissues showed disease functional phenotypes, such as tetanic fatigue. We also evaluated the therapeutic effect of utrophin upregulator drug candidates on the functionality of the skeletal muscle tissues, thus providing deeper insight into the real impact of these treatments. Overall, our findings underscore the potential of bioengineered 3D skeletal muscle technology to advance DMD research and facilitate the development of novel therapies for DMD and related neuromuscular disorders.
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Affiliation(s)
- Ainoa Tejedera-Villafranca
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST), C/Baldiri Reixac 10-12, E08028 Barcelona, Spain
| | - Marisol Montolio
- Duchenne Parent Project España, E28032 Madrid, Spain
- Department of Cell Biology, Physiology and Immunology, Faculty of Biology, University of Barcelona, E08027 Barcelona, Spain
| | - Javier Ramón-Azcón
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST), C/Baldiri Reixac 10-12, E08028 Barcelona, Spain
- Institució Catalana de Reserca i Estudis Avançats (ICREA), Passeig de Lluís Companys, 23, E08010 Barcelona, Spain
| | - Juan M Fernández-Costa
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST), C/Baldiri Reixac 10-12, E08028 Barcelona, Spain
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Lundquist A, Lázár E, Han NS, Emanuelsson EB, Reitzner SM, Chapman MA, Shirokova V, Alkass K, Druid H, Petri S, Sundberg CJ, Bergmann O. FiNuTyper: Design and validation of an automated deep learning-based platform for simultaneous fiber and nucleus type analysis in human skeletal muscle. Acta Physiol (Oxf) 2023; 239:e13982. [PMID: 37097015 DOI: 10.1111/apha.13982] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 03/30/2023] [Accepted: 04/21/2023] [Indexed: 04/26/2023]
Abstract
AIM While manual quantification is still considered the gold standard for skeletal muscle histological analysis, it is time-consuming and prone to investigator bias. To address this challenge, we assembled an automated image analysis pipeline, FiNuTyper (Fiber and Nucleus Typer). METHODS We integrated recently developed deep learning-based image segmentation methods, optimized for unbiased evaluation of fresh and postmortem human skeletal muscle, and utilized SERCA1 and SERCA2 as type-specific myonucleus and myofiber markers after validating them against the traditional use of MyHC isoforms. RESULTS Parameters including cross-sectional area, myonuclei per fiber, myonuclear domain, central myonuclei per fiber, and grouped myofiber ratio were determined in a fiber-type-specific manner, revealing that a large degree of sex- and muscle-related heterogeneity could be detected using the pipeline. Our platform was also tested on pathological muscle tissue (ALS and IBM) and adapted for the detection of other resident cell types (leucocytes, satellite cells, capillary endothelium). CONCLUSION In summary, we present an automated image analysis tool for the simultaneous quantification of myofiber and myonuclear types, to characterize the composition and structure of healthy and diseased human skeletal muscle.
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Affiliation(s)
- August Lundquist
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Enikő Lázár
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Nan S Han
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Eric B Emanuelsson
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Stefan M Reitzner
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
- Department for Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Mark A Chapman
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
- Department of Integrated Engineering, University of San Diego, San Diego, USA
| | - Vera Shirokova
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Kanar Alkass
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Henrik Druid
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Susanne Petri
- Department of Neurology, Hanover Medical School, Hanover, Germany
| | - Carl J Sundberg
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
- Department of Learning, Informatics, Management, and Ethics, Karolinska Institutet, Stockholm, Sweden
| | - Olaf Bergmann
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
- Center for Regenerative Therapies Dresden, Technische Universität Dresden, Dresden, Germany
- Pharmacology and Toxicology, University Medical Center Göttingen (UMG), Göttingen, Germany
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Pizza FX, Buckley KH. Regenerating Myofibers after an Acute Muscle Injury: What Do We Really Know about Them? Int J Mol Sci 2023; 24:12545. [PMID: 37628725 PMCID: PMC10454182 DOI: 10.3390/ijms241612545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 08/02/2023] [Accepted: 08/04/2023] [Indexed: 08/27/2023] Open
Abstract
Injury to skeletal muscle through trauma, physical activity, or disease initiates a process called muscle regeneration. When injured myofibers undergo necrosis, muscle regeneration gives rise to myofibers that have myonuclei in a central position, which contrasts the normal, peripheral position of myonuclei. Myofibers with central myonuclei are called regenerating myofibers and are the hallmark feature of muscle regeneration. An important and underappreciated aspect of muscle regeneration is the maturation of regenerating myofibers into a normal sized myofiber with peripheral myonuclei. Strikingly, very little is known about processes that govern regenerating myofiber maturation after muscle injury. As knowledge of myofiber formation and maturation during embryonic, fetal, and postnatal development has served as a foundation for understanding muscle regeneration, this narrative review discusses similarities and differences in myofiber maturation during muscle development and regeneration. Specifically, we compare and contrast myonuclear positioning, myonuclear accretion, myofiber hypertrophy, and myofiber morphology during muscle development and regeneration. We also discuss regenerating myofibers in the context of different types of myofiber necrosis (complete and segmental) after muscle trauma and injurious contractions. The overall goal of the review is to provide a framework for identifying cellular and molecular processes of myofiber maturation that are unique to muscle regeneration.
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Affiliation(s)
- Francis X. Pizza
- Department of Exercise and Rehabilitation Sciences, University of Toledo, Toledo, OH 43606, USA
| | - Kole H. Buckley
- Division of Gastroenterology and Hepatology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA;
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Mauro S, Bolognesi MM, Villa N, Capitoli G, Furia L, Mascadri F, Zucchini N, Totis M, Faretta M, Galimberti S, Bovo G, Cattoretti G. A DNA damage response-like phenotype defines a third of colon cancers at onset. FASEB J 2023; 37:e23020. [PMID: 37342943 DOI: 10.1096/fj.202300132r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 04/12/2023] [Accepted: 05/23/2023] [Indexed: 06/23/2023]
Abstract
Colon adenocarcinoma (COAD) has a limited range of diversified, personalized therapeutic opportunities, besides DNA hypermutating cases; thus, both new targets or broadening existing strategies for personalized intervention are of interest. Routinely processed material from 246 untreated COADs with clinical follow-up was probed for evidence of DNA damage response (DDR), that is, the gathering of DDR-associated molecules at discrete nuclear spots, by multiplex immunofluorescence and immunohistochemical staining for DDR complex proteins (γH2AX, pCHK2, and pNBS1). We also tested the cases for type I interferon response, T-lymphocyte infiltration (TILs), and mutation mismatch repair defects (MMRd), known to be associated with defects of DNA repair. FISH analysis for chromosome 20q copy number variations was obtained. A total of 33.7% of COAD display a coordinated DDR on quiescent, non-senescent, non-apoptotic glands, irrespective of TP53 status, chromosome 20q abnormalities, and type I IFN response. Clinicopathological parameters did not differentiate DDR+ cases from the other cases. TILs were equally present in DDR and non-DDR cases. DDR+ MMRd cases were preferentially retaining wild-type MLH1. The outcome after 5FU-based chemotherapy was not different in the two groups. DDR+ COAD represents a subgroup not aligned with known diagnostic, prognostic, or therapeutic categories, with potential new targeted treatment opportunities, exploiting the DNA damage repair pathways.
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Affiliation(s)
- Stefania Mauro
- Pathology, Vimercate Hospital, ASST-Brianza, Vimercate, Italy
| | - Maddalena M Bolognesi
- Pathology, Department of Medicine and Surgery, Universitá di Milano-Bicocca, Monza, Italy
| | - Nicoletta Villa
- Genetics, Fondazione IRCCS San Gerardo dei Tintori Monza, Monza, Italy
| | - Giulia Capitoli
- Bicocca Bioinformatics Biostatistics and Bioimaging B4 Center, School of Medicine and Surgery, Universitá di Milano-Bicocca, Monza, Italy
| | - Laura Furia
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Milan, Italy
| | - Francesco Mascadri
- Pathology, Department of Medicine and Surgery, Universitá di Milano-Bicocca, Monza, Italy
| | - Nicola Zucchini
- Pathology, Fondazione IRCCS San Gerardo dei Tintori Monza, Monza, Italy
| | - Mauro Totis
- GI Surgery, Fondazione IRCCS San Gerardo dei Tintori Monza, Monza, Italy
| | - Mario Faretta
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Milan, Italy
| | - Stefania Galimberti
- Bicocca Bioinformatics Biostatistics and Bioimaging B4 Center, School of Medicine and Surgery, Universitá di Milano-Bicocca, Monza, Italy
| | - Giorgio Bovo
- Pathology, Vimercate Hospital, ASST-Brianza, Vimercate, Italy
| | - Giorgio Cattoretti
- Pathology, Department of Medicine and Surgery, Universitá di Milano-Bicocca, Monza, Italy
- Pathology, Fondazione IRCCS San Gerardo dei Tintori Monza, Monza, Italy
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Norris AM, Appu AB, Johnson CD, Zhou LY, McKellar DW, Renault MA, Hammers D, Cosgrove BD, Kopinke D. Hedgehog signaling via its ligand DHH acts as cell fate determinant during skeletal muscle regeneration. Nat Commun 2023; 14:3766. [PMID: 37355632 PMCID: PMC10290686 DOI: 10.1038/s41467-023-39506-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 06/16/2023] [Indexed: 06/26/2023] Open
Abstract
Successful muscle regeneration relies on the interplay of multiple cell populations. However, the signals required for this coordinated intercellular crosstalk remain largely unknown. Here, we describe how the Hedgehog (Hh) signaling pathway controls the fate of fibro/adipogenic progenitors (FAPs), the cellular origin of intramuscular fat (IMAT) and fibrotic scar tissue. Using conditional mutagenesis and pharmacological Hh modulators in vivo and in vitro, we identify DHH as the key ligand that acts as a potent adipogenic brake by preventing the adipogenic differentiation of FAPs. Hh signaling also impacts muscle regeneration, albeit indirectly through induction of myogenic factors in FAPs. Our results also indicate that ectopic and sustained Hh activation forces FAPs to adopt a fibrogenic fate resulting in widespread fibrosis. In this work, we reveal crucial post-developmental functions of Hh signaling in balancing tissue regeneration and fatty fibrosis. Moreover, they provide the exciting possibility that mis-regulation of the Hh pathway with age and disease could be a major driver of pathological IMAT formation.
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Affiliation(s)
- Alessandra M Norris
- Department of Pharmacology and Therapeutics, Myology Institute, University of Florida, Gainesville, FL, USA
| | - Ambili Bai Appu
- Department of Pharmacology and Therapeutics, Myology Institute, University of Florida, Gainesville, FL, USA
| | - Connor D Johnson
- Department of Pharmacology and Therapeutics, Myology Institute, University of Florida, Gainesville, FL, USA
| | - Lylybell Y Zhou
- Department of Pharmacology and Therapeutics, Myology Institute, University of Florida, Gainesville, FL, USA
| | - David W McKellar
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Marie-Ange Renault
- Biology of Cardiovascular Diseases, INSERM, University of Bordeaux, Pessac, France
| | - David Hammers
- Department of Pharmacology and Therapeutics, Myology Institute, University of Florida, Gainesville, FL, USA
| | - Benjamin D Cosgrove
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Daniel Kopinke
- Department of Pharmacology and Therapeutics, Myology Institute, University of Florida, Gainesville, FL, USA.
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Lamin V, Mani AM, Singh MV, Dokun AO. Endothelial Progenitor Cells and Macrophage Subsets Recruitment in Postischemic Mouse Hind Limbs. J Vasc Res 2023; 60:148-159. [PMID: 37336198 DOI: 10.1159/000530732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 03/14/2023] [Indexed: 06/21/2023] Open
Abstract
INTRODUCTION Peripheral arterial disease (PAD) occurs from atherosclerotic obstruction of arteries in the lower extremities. Restoration of perfusion requires angiogenesis and arteriogenesis through migration and differentiation of endothelial progenitor cells (EPCs) and macrophages at the site of injury. The time of recruitment has not been fully investigated. In this study, we investigated the infiltration of these cells in murine hind limb ischemia (HLI) model of PAD. METHODS EPCs and M1-like and M2-like macrophages from ischemic skeletal muscles were quantified by flow cytometry at day-0, 1, 3, 7, and 14 post-HLI. RESULTS The abundance of EPCs increased from day 1 and was highest on day 7 until day 14. M1-like population similarly increased and was highest on day 14 during the experiment. M2-like population was significantly greater than M1-like at baseline but surpassed the highest value of M1-like by day 7 during the experiment. Muscle regeneration and capillary density also increased and were highest at days 3 and 7, respectively, during the experiment. All mice achieved near full perfusion recovery by day 14. CONCLUSION Thus, we observed a gradual increase in the percentage of EPC's and this was temporally paralleled with initial increase in M1-like followed by sustained increased in M2-like macrophages and perfusion recovered post-HLI.
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Affiliation(s)
- Victor Lamin
- Division of Endocrinology and Metabolism, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Arul M Mani
- Division of Endocrinology and Metabolism, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Madhu V Singh
- Division of Endocrinology and Metabolism, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Ayotunde O Dokun
- Division of Endocrinology and Metabolism, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
- Fraternal Order of Eagles Diabetes Research Center, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
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Memon TA, Sun L, Almestica-Roberts M, Deering-Rice CE, Moos PJ, Reilly CA. Inhibition of TRPA1, Endoplasmic Reticulum Stress, Human Airway Epithelial Cell Damage, and Ectopic MUC5AC Expression by Vasaka ( Adhatoda vasica; Malabar Nut) Tea. Pharmaceuticals (Basel) 2023; 16:890. [PMID: 37375837 DOI: 10.3390/ph16060890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 06/13/2023] [Accepted: 06/14/2023] [Indexed: 06/29/2023] Open
Abstract
This study tested whether a medicinal plant, Vasaka, typically consumed as a tea to treat respiratory malaise, could protect airway epithelial cells (AECs) from wood smoke particle-induced damage and prevent pathological mucus production. Wood/biomass smoke is a pneumotoxic air pollutant. Mucus normally protects the airways, but excessive production can obstruct airflow and cause respiratory distress. Vasaka tea pre- and co-treatment dose-dependently inhibited mucin 5AC (MUC5AC) mRNA induction by AECs treated with wood smoke particles. This correlated with transient receptor potential ankyrin-1 (TRPA1) inhibition, an attenuation of endoplasmic reticulum (ER) stress, and AEC damage/death. Induction of mRNA for anterior gradient 2, an ER chaperone/disulfide isomerase required for MUC5AC production, and TRP vanilloid-3, a gene that suppresses ER stress and wood smoke particle-induced cell death, was also attenuated. Variable inhibition of TRPA1, ER stress, and MUC5AC mRNA induction was observed using selected chemicals identified in Vasaka tea including vasicine, vasicinone, apigenin, vitexin, isovitexin, isoorientin, 9-oxoODE, and 9,10-EpOME. Apigenin and 9,10-EpOME were the most cytoprotective and mucosuppressive. Cytochrome P450 1A1 (CYP1A1) mRNA was also induced by Vasaka tea and wood smoke particles. Inhibition of CYP1A1 enhanced ER stress and MUC5AC mRNA expression, suggesting a possible role in producing protective oxylipins in stressed cells. The results provide mechanistic insights and support for the purported benefits of Vasaka tea in treating lung inflammatory conditions, raising the possibility of further development as a preventative and/or restorative therapy.
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Affiliation(s)
- Tosifa A Memon
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Utah Health, Salt Lake City, UT 84112, USA
| | - Lili Sun
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Utah Health, Salt Lake City, UT 84112, USA
| | - Marysol Almestica-Roberts
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Utah Health, Salt Lake City, UT 84112, USA
| | - Cassandra E Deering-Rice
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Utah Health, Salt Lake City, UT 84112, USA
- Center for Human Toxicology, College of Pharmacy, University of Utah Health, Salt Lake City, UT 84112, USA
| | - Philip J Moos
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Utah Health, Salt Lake City, UT 84112, USA
| | - Christopher A Reilly
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Utah Health, Salt Lake City, UT 84112, USA
- Center for Human Toxicology, College of Pharmacy, University of Utah Health, Salt Lake City, UT 84112, USA
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Takei Y, Yang Y, White J, Yun J, Prasad M, Ombelets LJ, Schindler S, Cai L. High-resolution spatial multi-omics reveals cell-type specific nuclear compartments. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.07.539762. [PMID: 37214923 PMCID: PMC10197539 DOI: 10.1101/2023.05.07.539762] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The mammalian nucleus is compartmentalized by diverse subnuclear structures. These subnuclear structures, marked by nuclear bodies and histone modifications, are often cell-type specific and affect gene regulation and 3D genome organization1-3. Understanding nuclear organization requires identifying the molecular constituents of subnuclear structures and mapping their associations with specific genomic loci in individual cells, within complex tissues. Here, we introduce two-layer DNA seqFISH+, which allows simultaneous mapping of 100,049 genomic loci, together with nascent transcriptome for 17,856 genes and a diverse set of immunofluorescently labeled subnuclear structures all in single cells in cell lines and adult mouse cerebellum. Using these multi-omics datasets, we showed that repressive chromatin compartments are more variable by cell type than active compartments. We also discovered a single exception to this rule: an RNA polymerase II (RNAPII)-enriched compartment was associated with long, cell-type specific genes (> 200kb), in a manner distinct from nuclear speckles. Further, our analysis revealed that cell-type specific facultative and constitutive heterochromatin compartments marked by H3K27me3 and H4K20me3 are enriched at specific genes and gene clusters, respectively, and shape radial chromosomal positioning and inter-chromosomal interactions in neurons and glial cells. Together, our results provide a single-cell high-resolution multi-omics view of subnuclear compartments, associated genomic loci, and their impacts on gene regulation, directly within complex tissues.
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Affiliation(s)
- Yodai Takei
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Yujing Yang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Jonathan White
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Jina Yun
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Meera Prasad
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | | | | | - Long Cai
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
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Oltmer J, Rosenblum EW, Williams EM, Roy J, Llamas-Rodriguez J, Perosa V, Champion SN, Frosch MP, Augustinack JC. Stereology neuron counts correlate with deep learning estimates in the human hippocampal subregions. Sci Rep 2023; 13:5884. [PMID: 37041300 PMCID: PMC10090178 DOI: 10.1038/s41598-023-32903-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 04/04/2023] [Indexed: 04/13/2023] Open
Abstract
Hippocampal subregions differ in specialization and vulnerability to cell death. Neuron death and hippocampal atrophy have been a marker for the progression of Alzheimer's disease. Relatively few studies have examined neuronal loss in the human brain using stereology. We characterize an automated high-throughput deep learning pipeline to segment hippocampal pyramidal neurons, generate pyramidal neuron estimates within the human hippocampal subfields, and relate our results to stereology neuron counts. Based on seven cases and 168 partitions, we vet deep learning parameters to segment hippocampal pyramidal neurons from the background using the open-source CellPose algorithm, and show the automated removal of false-positive segmentations. There was no difference in Dice scores between neurons segmented by the deep learning pipeline and manual segmentations (Independent Samples t-Test: t(28) = 0.33, p = 0.742). Deep-learning neuron estimates strongly correlate with manual stereological counts per subregion (Spearman's correlation (n = 9): r(7) = 0.97, p < 0.001), and for each partition individually (Spearman's correlation (n = 168): r(166) = 0.90, p <0 .001). The high-throughput deep-learning pipeline provides validation to existing standards. This deep learning approach may benefit future studies in tracking baseline and resilient healthy aging to the earliest disease progression.
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Affiliation(s)
- Jan Oltmer
- Department of Radiology, Athinoula A. Martinos Center, Massachusetts General Hospital, Charlestown, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Emma W Rosenblum
- Department of Radiology, Athinoula A. Martinos Center, Massachusetts General Hospital, Charlestown, MA, USA
| | - Emily M Williams
- Department of Radiology, Athinoula A. Martinos Center, Massachusetts General Hospital, Charlestown, MA, USA
| | - Jessica Roy
- Department of Radiology, Athinoula A. Martinos Center, Massachusetts General Hospital, Charlestown, MA, USA
| | - Josué Llamas-Rodriguez
- Department of Radiology, Athinoula A. Martinos Center, Massachusetts General Hospital, Charlestown, MA, USA
| | - Valentina Perosa
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, J. Philip Kistler Stroke Research Center, Cambridge Str. 175, Suite 300, Boston, MA, 02114, USA
- Department of Neurology, Otto-Von-Guericke University, Magdeburg, Germany
| | - Samantha N Champion
- Department of Neuropathology, Massachusetts General Hospital, Boston, MA, USA
| | - Matthew P Frosch
- Department of Neuropathology, Massachusetts General Hospital, Boston, MA, USA
| | - Jean C Augustinack
- Department of Radiology, Athinoula A. Martinos Center, Massachusetts General Hospital, Charlestown, MA, USA.
- Harvard Medical School, Boston, MA, USA.
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Alsup AM, Fowlds K, Cho M, Luber JM. BetaBuddy: An end-to-end computer vision pipeline for the automated analysis of insulin secreting β-cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.06.535890. [PMID: 37066375 PMCID: PMC10104060 DOI: 10.1101/2023.04.06.535890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Insulin secretion from pancreatic β-cells is integral in maintaining the delicate equilibrium of blood glucose levels. Calcium is known to be a key regulator and triggers the release of insulin. This sub-cellular process can be monitored and tracked through live-cell imaging and subsequent cell segmentation, registration, tracking, and analysis of the calcium level in each cell. Current methods of analysis typically require the manual outlining of β-cells, involve multiple software packages, and necessitate multiple researchers - all of which tend to introduce biases. Utilizing deep learning algorithms, we have therefore created a pipeline to automatically segment and track thousands of cells, which greatly reduces the time required to gather and analyze a large number of sub-cellular images and improve accuracy. Tracking cells over a time-series image stack also allows researchers to isolate specific calcium spiking patterns and spatially identify those of interest, creating an efficient and user-friendly analysis tool. Using our automated pipeline, a previous dataset used to evaluate changes in calcium spiking activity in β-cells post-electric field stimulation was reanalyzed. Changes in spiking activity were found to be underestimated previously with manual segmentation. Moreover, the machine learning pipeline provides a powerful and rapid computational approach to examine, for example, how calcium signaling is regulated by intracellular interactions in a cluster of β-cells.
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Affiliation(s)
- Anne M. Alsup
- Department of Bioengineering, University of Texas at Arlington, Arlington, TX, United States of America
| | - Kelli Fowlds
- Department of Bioengineering, University of Texas at Arlington, Arlington, TX, United States of America
| | - Michael Cho
- Department of Bioengineering, University of Texas at Arlington, Arlington, TX, United States of America
| | - Jacob M. Luber
- Department of Bioengineering, University of Texas at Arlington, Arlington, TX, United States of America
- Department of Computer Science and Engineering, University of Texas at Arlington, Arlington, TX, United States of America
- Multi-Interprofessional Center for Health Informatics, University of Texas at Arlington, Arlington, TX, United States of America
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Lesage M, Thomas M, Pécot T, Ly TK, Hinfray N, Beaudouin R, Neumann M, Lovell-Badge R, Bugeon J, Thermes V. An end-to-end pipeline based on open source deep learning tools for reliable analysis of complex 3D images of ovaries. Development 2023; 150:dev201185. [PMID: 36971372 DOI: 10.1242/dev.201185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 03/13/2023] [Indexed: 03/29/2023]
Abstract
Computational analysis of bio-images by deep learning (DL) algorithms has made exceptional progress in recent years and has become much more accessible to non-specialists with the development of ready-to-use tools. The study of oogenesis mechanisms and female reproductive success has also recently benefited from the development of efficient protocols for three-dimensional (3D) imaging of ovaries. Such datasets have a great potential for generating new quantitative data but are, however, complex to analyze due to the lack of efficient workflows for 3D image analysis. Here, we have integrated two existing open-source DL tools, Noise2Void and Cellpose, into an analysis pipeline dedicated to 3D follicular content analysis, which is available on Fiji. Our pipeline was developed on larvae and adult medaka ovaries but was also successfully applied to different types of ovaries (trout, zebrafish and mouse). Image enhancement, Cellpose segmentation and post-processing of labels enabled automatic and accurate quantification of these 3D images, which exhibited irregular fluorescent staining, low autofluorescence signal or heterogeneous follicles sizes. In the future, this pipeline will be useful for extensive cellular phenotyping in fish or mammals for developmental or toxicology studies.
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Affiliation(s)
- Manon Lesage
- INRAE, Fish Physiology and Genomics Institute, 16 Allee Henri Fabre, Rennes 35000, France
| | - Manon Thomas
- INRAE, Fish Physiology and Genomics Institute, 16 Allee Henri Fabre, Rennes 35000, France
| | - Thierry Pécot
- BIOSIT, UAR 3480 US 018, Université de Rennes, 2 rue Prof. Leon Bernard, Rennes 35042, France
| | - Tu-Ky Ly
- INERIS, UMR-I 02 SEBIO, Verneuil en Halatte 65550, France
| | | | - Remy Beaudouin
- INERIS, UMR-I 02 SEBIO, Verneuil en Halatte 65550, France
| | | | | | - Jérôme Bugeon
- INRAE, Fish Physiology and Genomics Institute, 16 Allee Henri Fabre, Rennes 35000, France
| | - Violette Thermes
- INRAE, Fish Physiology and Genomics Institute, 16 Allee Henri Fabre, Rennes 35000, France
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Abbassi-Daloii T, El Abdellaoui S, Kan HE, van den Akker E, 't Hoen PAC, Raz V, Voortman LM. Quantitative analysis of myofiber type composition in human and mouse skeletal muscles. STAR Protoc 2023; 4:102075. [PMID: 36853713 PMCID: PMC9898062 DOI: 10.1016/j.xpro.2023.102075] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 11/28/2022] [Accepted: 01/09/2023] [Indexed: 01/30/2023] Open
Abstract
Skeletal muscles are composed of different myofiber types characterized by the expression of myosin heavy chain isoforms, which can be affected by physical activity, aging, and pathological conditions. Here, we present a step-by-step high-throughput semi-automated approach for performing myofiber type quantification of entire human or mouse muscle tissue sections, including immunofluorescence staining, image acquisition, processing, and quantification. For complete details on the use and execution of this protocol, please refer to Abbassi-Daloii et al. (2022).1.
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Affiliation(s)
- Tooba Abbassi-Daloii
- Human Genetics, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Salma El Abdellaoui
- Human Genetics, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Hermien E Kan
- C.J. Gorter MRI Center, Department of Radiology, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands; Duchenne Center Netherlands, the Netherlands
| | - Erik van den Akker
- Molecular Epidemiology, Leiden University Medical Center, 2333 ZC Leiden, the Netherlands; Leiden Computational Biology Center, Leiden University Medical Center, 2333 ZC Leiden, the Netherlands; Delft Bioinformatics Lab, TU Delft, 2628 XE Delft, the Netherlands
| | - Peter A C 't Hoen
- Human Genetics, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands; Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Vered Raz
- Human Genetics, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands.
| | - Lenard M Voortman
- Cell and Chemical Biology, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands.
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Jurberg AD, Gomes G, Seixas MR, Mermelstein C, Costa ML. Improving quantification of myotube width and nuclear/cytoplasmic ratio in myogenesis research. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2023; 230:107354. [PMID: 36682109 DOI: 10.1016/j.cmpb.2023.107354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 01/05/2023] [Accepted: 01/12/2023] [Indexed: 06/17/2023]
Abstract
BACKGROUND AND OBJECTIVE The culture of skeletal muscle cells is particularly relevant to basic biomedical research and translational medicine. The incubation of dissociated cells under controlled conditions has helped to dissect several molecular mechanisms associated with muscle cell differentiation, in addition to contributing for the evaluation of drug effects and prospective cell therapies for patients with degenerative muscle pathologies. The formation of mature multinucleated myotubes is a stepwise process involving well defined events of cell proliferation, commitment, migration, and fusion easily identified through optical microscopy methods including immunofluorescence and live cell imaging. The characterization of each step is usually based on muscle cell morphology and nuclei number, as well as the presence and intracellular location of specific cell markers. However, manual quantification of these parameters in large datasets of images is work-intensive and prone to researcher's subjectivity, mostly because of the extremely elongated cell shape of large myotubes and because myotubes are multinucleated. METHODS Here we provide two semi-automated ImageJ macros aimed to measure the width of myotubes and the nuclear/cytoplasmic localization of molecules in fluorescence images. The width measuring macro automatically determines the best angle, perpendicular to most cells, to draw a profile plot and identify and measure individual myotubes. The nuclear/cytoplasmic ratio macro compares the intensity values along lines, drawn by the user, over cytoplasm and nucleus. RESULTS We show that the macro measurements are more consistent than manual measurements by comparing with our own results and with the literature. CONCLUSIONS By relying on semi-automated muscle specific ImageJ macros, we seek to improve measurement accuracy and to alleviate the laborious routine of counting and measuring muscle cell features.
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Affiliation(s)
- Arnon Dias Jurberg
- Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro (UFRJ), RJ, Brazil; Instituto de Educação Médica (IDOMED), Campus Vista Carioca, Universidade Estácio de Sá (UNESA), RJ, Brazil
| | - Geyse Gomes
- Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro (UFRJ), RJ, Brazil
| | - Marianna Reis Seixas
- Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro (UFRJ), RJ, Brazil
| | - Claudia Mermelstein
- Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro (UFRJ), RJ, Brazil
| | - Manoel Luis Costa
- Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro (UFRJ), RJ, Brazil.
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40
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Saad J, Fomich M, Día VP, Wang T. A novel automated protocol for ice crystal segmentation analysis using Cellpose and Fiji. Cryobiology 2023; 111:1-8. [PMID: 36773632 DOI: 10.1016/j.cryobiol.2023.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 02/02/2023] [Accepted: 02/06/2023] [Indexed: 02/12/2023]
Abstract
Accurate measurement of ice crystal size is an essential step in quantitative ice recrystallization inhibition (IRI) analysis using the sucrose sandwiching assay (SSA) and splat assay (SA). Here, we introduce a novel method of measuring ice crystal size and shape using Fiji and Cellpose, an anatomical segmentation algorithm, to address the time-consuming and limited number of ice particle determination associated with the mean largest grain size measurement. This new automated approach, displaying rapid segmentation of ∼70 s per image, measures every ice crystal in an image field of view, consequently reducing bias introduced by subjectively selecting the largest crystals in an image. Consistent in determining a diverse set of crystal sizes and shapes, this method allows for the evaluation of ice crystals using Feret's diameter, a parameter that better accounts for irregular particle shape. This method provides new outputs such as standard deviation, particle size distributions of a population of ice crystals, and circularity to characterize and further provide insight into an analyte's IRI ability. Applicable to the SSA, the "shape descriptor" measurement can be used to quantify ice binding. This work presents a novel and accurate approach for ice crystal quantitative analysis.
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Affiliation(s)
- Joshua Saad
- Department of Food Science, The University of Tennessee, 2510 River Drive, Knoxville, TN, 37996-4539, USA
| | - Madison Fomich
- Department of Food Science, The University of Tennessee, 2510 River Drive, Knoxville, TN, 37996-4539, USA
| | - Vermont P Día
- Department of Food Science, The University of Tennessee, 2510 River Drive, Knoxville, TN, 37996-4539, USA
| | - Tong Wang
- Department of Food Science, The University of Tennessee, 2510 River Drive, Knoxville, TN, 37996-4539, USA.
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Penniman CM, Bhardwaj G, Nowers CJ, Brown CU, Junck TL, Boyer CK, Jena J, Fuqua JD, Lira VA, O'Neill BT. Loss of FoxOs in muscle increases strength and mitochondrial function during aging. J Cachexia Sarcopenia Muscle 2023; 14:243-259. [PMID: 36442857 PMCID: PMC9891940 DOI: 10.1002/jcsm.13124] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 10/13/2022] [Accepted: 10/25/2022] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Muscle mitochondrial decline is associated with aging-related muscle weakness and insulin resistance. FoxO transcription factors are targets of insulin action and deletion of FoxOs improves mitochondrial function in diabetes. However, disruptions in proteostasis and autophagy are hallmarks of aging and the effect of chronic inhibition of FoxOs in aged muscle is unknown. This study investigated the role of FoxOs in regulating muscle strength and mitochondrial function with age. METHODS We measured muscle strength, cross-sectional area, muscle fibre-type, markers of protein synthesis/degradation, central nuclei, glucose/insulin tolerance, and mitochondrial bioenergetics in 4.5-month (Young) and 22-24-month-old (Aged) muscle-specific FoxO1/3/4 triple KO (TKO) and littermate control (Ctrl) mice. RESULTS Lean mass was increased in Aged TKO compared with both Aged Ctrl and younger groups by 26-33% (P < 0.01). Muscle strength, measured by max force of tibialis anterior (TA) contraction, was 20% lower in Aged Ctrl compared with Young Ctrls (P < 0.01) but was not decreased in Aged TKOs. Increased muscle strength in Young and Aged TKO was associated with 18-48% increased muscle weights compared with Ctrls (P < 0.01). Muscle cross-sectional analysis of TA, soleus, and plantaris revealed increases in fibre size distribution and a 2.5-10-fold increase in central nuclei in Young and Aged TKO mice, without histologic signs of muscle damage. Age-dependent increases in Gadd45a and Ube4a expression as well accumulation of K48 polyubiquitinated proteins were observed in quad and TA but were prevented by FoxO deletion. Young and Aged TKO muscle showed minimal changes in autophagy flux and no accumulation of autophagosomes compared with Ctrl groups. Increased strength in Young and Aged TKO was associated with a 10-20% increase in muscle mitochondrial respiration using glutamate/malate/succinate compared with controls (P < 0.05). OXPHOS subunit expression and complex I activity were decreased 16-34% in Aged Ctrl compared with Young Ctrl but were prevented in Aged TKO. Both Aged Ctrl and Aged TKO showed impaired glucose tolerance by 33% compared to young groups (P < 0.05) indicating improved strength and mitochondrial respiration are not due to improved glycemia. CONCLUSIONS FoxO deletion increases muscle strength even during aging. Deletion of FoxOs maintains muscle strength in part by mild suppression of atrophic pathways, including inhibition of Gadd45a and Ube4a expression, without accumulation of autophagosomes in muscle. Deletion of FoxOs also improved mitochondrial function by maintenance of OXPHOS in both young and aged TKO.
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Affiliation(s)
- Christie M Penniman
- Fraternal Order of Eagles Diabetes Research Center and Division of Endocrinology and Metabolism, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, 52242, Iowa City, Iowa, USA
| | - Gourav Bhardwaj
- Fraternal Order of Eagles Diabetes Research Center and Division of Endocrinology and Metabolism, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, 52242, Iowa City, Iowa, USA
| | - Colette J Nowers
- Fraternal Order of Eagles Diabetes Research Center and Division of Endocrinology and Metabolism, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, 52242, Iowa City, Iowa, USA
| | - Chandler U Brown
- Fraternal Order of Eagles Diabetes Research Center and Division of Endocrinology and Metabolism, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, 52242, Iowa City, Iowa, USA
| | - Taylor L Junck
- Fraternal Order of Eagles Diabetes Research Center and Division of Endocrinology and Metabolism, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, 52242, Iowa City, Iowa, USA
| | - Cierra K Boyer
- Fraternal Order of Eagles Diabetes Research Center and Division of Endocrinology and Metabolism, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, 52242, Iowa City, Iowa, USA
| | - Jayashree Jena
- Fraternal Order of Eagles Diabetes Research Center and Division of Endocrinology and Metabolism, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, 52242, Iowa City, Iowa, USA
| | - Jordan D Fuqua
- Fraternal Order of Eagles Diabetes Research Center and Department of Health and Human Physiology, College of Liberal Arts and Sciences, University of Iowa, Iowa City, Iowa, USA
| | - Vitor A Lira
- Fraternal Order of Eagles Diabetes Research Center and Department of Health and Human Physiology, College of Liberal Arts and Sciences, University of Iowa, Iowa City, Iowa, USA
| | - Brian T O'Neill
- Fraternal Order of Eagles Diabetes Research Center and Division of Endocrinology and Metabolism, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, 52242, Iowa City, Iowa, USA.,Veterans Affairs Health Care System, 52242, Iowa City, Iowa, USA
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42
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Characterization of Stress Granule Protein Turnover in Neuronal Progenitor Cells Using Correlative STED and NanoSIMS Imaging. Int J Mol Sci 2023; 24:ijms24032546. [PMID: 36768868 PMCID: PMC9917160 DOI: 10.3390/ijms24032546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 01/18/2023] [Accepted: 01/23/2023] [Indexed: 01/31/2023] Open
Abstract
Stress granules (SGs) are stress-induced biomolecular condensates which originate primarily from inactivated RNA translation machinery and translation initiation factors. SG formation is an important defensive mechanism for cell survival, while its dysfunction has been linked to neurodegenerative diseases. However, the molecular mechanisms of SG assembly and disassembly, as well as their impacts on cellular recovery, are not fully understood. More thorough investigations into the molecular dynamics of SG pathways are required to understand the pathophysiological roles of SGs in cellular systems. Here, we characterize the SG and cytoplasmic protein turnover in neuronal progenitor cells (NPCs) under stressed and non-stressed conditions using correlative STED and NanoSIMS imaging. We incubate NPCs with isotopically labelled (15N) leucine and stress them with the ER stressor thapsigargin (TG). A correlation of STED and NanoSIMS allows the localization of individual SGs (using STED), and their protein turnover can then be extracted based on the 15N/14N ratio (using NanoSIMS). We found that TG-induced SGs, which are highly dynamic domains, recruit their constituents predominantly from the cytoplasm. Moreover, ER stress impairs the total cellular protein turnover regimen, and this impairment is not restored after the commonly proceeded stress recovery period.
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Misquitta NS, Ravel-Chapuis A, Jasmin BJ. Combinatorial treatment with exercise and AICAR potentiates the rescue of myotonic dystrophy type 1 mouse muscles in a sex-specific manner. Hum Mol Genet 2023; 32:551-566. [PMID: 36048859 DOI: 10.1093/hmg/ddac222] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 08/18/2022] [Accepted: 08/30/2022] [Indexed: 02/07/2023] Open
Abstract
Targeting AMP-activated protein kinase (AMPK) is emerging as a promising strategy for treating myotonic dystrophy type 1 (DM1), the most prevalent form of adult-onset muscular dystrophy. We previously demonstrated that 5-aminomidazole-4-carboxamide-1-β-D-ribofuranoside (AICAR) and exercise, two potent AMPK activators, improve disease features in DM1 mouse skeletal muscles. Here, we employed a combinatorial approach with these AMPK activators and examined their joint impact on disease severity in male and female DM1 mice. Our data reveal that swimming exercise additively enhances the effect of AICAR in mitigating the nuclear accumulation of toxic CUGexp RNA foci. In addition, our findings show a trend towards an enhanced reversal of MBNL1 sequestration and correction in pathogenic alternative splicing events. Our results further demonstrate that the combinatorial impact of exercise and AICAR promotes muscle fiber hypertrophy in DM1 skeletal muscle. Importantly, these improvements occur in a sex-specific manner with greater benefits observed in female DM1 mice. Our findings demonstrate that combining AMPK-activating interventions may prove optimal for rescuing the DM1 muscle phenotype and uncover important sex differences in the response to AMPK-based therapeutic strategies in DM1 mice.
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Affiliation(s)
- Naomi S Misquitta
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada.,The Eric J. Poulin Centre for Neuromuscular Disease, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Aymeric Ravel-Chapuis
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada.,The Eric J. Poulin Centre for Neuromuscular Disease, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Bernard J Jasmin
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada.,The Eric J. Poulin Centre for Neuromuscular Disease, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
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Dubuisson N, Versele R, Planchon C, Selvais CM, Noel L, Abou-Samra M, Davis-López de Carrizosa MA. Histological Methods to Assess Skeletal Muscle Degeneration and Regeneration in Duchenne Muscular Dystrophy. Int J Mol Sci 2022; 23:16080. [PMID: 36555721 PMCID: PMC9786356 DOI: 10.3390/ijms232416080] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 12/09/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022] Open
Abstract
Duchenne muscular dystrophy (DMD) is a progressive disease caused by the loss of function of the protein dystrophin. This protein contributes to the stabilisation of striated cells during contraction, as it anchors the cytoskeleton with components of the extracellular matrix through the dystrophin-associated protein complex (DAPC). Moreover, absence of the functional protein affects the expression and function of proteins within the DAPC, leading to molecular events responsible for myofibre damage, muscle weakening, disability and, eventually, premature death. Presently, there is no cure for DMD, but different treatments help manage some of the symptoms. Advances in genetic and exon-skipping therapies are the most promising intervention, the safety and efficiency of which are tested in animal models. In addition to in vivo functional tests, ex vivo molecular evaluation aids assess to what extent the therapy has contributed to the regenerative process. In this regard, the later advances in microscopy and image acquisition systems and the current expansion of antibodies for immunohistological evaluation together with the development of different spectrum fluorescent dyes have made histology a crucial tool. Nevertheless, the complexity of the molecular events that take place in dystrophic muscles, together with the rise of a multitude of markers for each of the phases of the process, makes the histological assessment a challenging task. Therefore, here, we summarise and explain the rationale behind different histological techniques used in the literature to assess degeneration and regeneration in the field of dystrophinopathies, focusing especially on those related to DMD.
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Affiliation(s)
- Nicolas Dubuisson
- Endocrinology, Diabetes and Nutrition Unit, Institute of Experimental and Clinical Research, Medical Sector, Université Catholique de Louvain (UCLouvain), Avenue Hippocrate 55, 1200 Brussels, Belgium
- Neuromuscular Reference Center, Cliniques Universitaires Saint-Luc (CUSL), Avenue Hippocrate 10, 1200 Brussels, Belgium
| | - Romain Versele
- Endocrinology, Diabetes and Nutrition Unit, Institute of Experimental and Clinical Research, Medical Sector, Université Catholique de Louvain (UCLouvain), Avenue Hippocrate 55, 1200 Brussels, Belgium
| | - Chloé Planchon
- Endocrinology, Diabetes and Nutrition Unit, Institute of Experimental and Clinical Research, Medical Sector, Université Catholique de Louvain (UCLouvain), Avenue Hippocrate 55, 1200 Brussels, Belgium
| | - Camille M. Selvais
- Endocrinology, Diabetes and Nutrition Unit, Institute of Experimental and Clinical Research, Medical Sector, Université Catholique de Louvain (UCLouvain), Avenue Hippocrate 55, 1200 Brussels, Belgium
| | - Laurence Noel
- Endocrinology, Diabetes and Nutrition Unit, Institute of Experimental and Clinical Research, Medical Sector, Université Catholique de Louvain (UCLouvain), Avenue Hippocrate 55, 1200 Brussels, Belgium
| | - Michel Abou-Samra
- Endocrinology, Diabetes and Nutrition Unit, Institute of Experimental and Clinical Research, Medical Sector, Université Catholique de Louvain (UCLouvain), Avenue Hippocrate 55, 1200 Brussels, Belgium
| | - María A. Davis-López de Carrizosa
- Endocrinology, Diabetes and Nutrition Unit, Institute of Experimental and Clinical Research, Medical Sector, Université Catholique de Louvain (UCLouvain), Avenue Hippocrate 55, 1200 Brussels, Belgium
- Departamento de Fisiología, Facultad de Biología, Universidad de Sevilla, 41012 Seville, Spain
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Reinbigler M, Cosette J, Guesmia Z, Jimenez S, Fetita C, Brunet E, Stockholm D. Artificial intelligence workflow quantifying muscle features on Hematoxylin-Eosin stained sections reveals dystrophic phenotype amelioration upon treatment. Sci Rep 2022; 12:19913. [PMID: 36402802 PMCID: PMC9675753 DOI: 10.1038/s41598-022-24139-z] [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: 06/20/2022] [Accepted: 11/10/2022] [Indexed: 11/21/2022] Open
Abstract
Cell segmentation is a key step for a wide variety of biological investigations, especially in the context of muscle science. Currently, automated methods still struggle to perform skeletal muscle fiber quantification on Hematoxylin-Eosin (HE) stained histopathological whole slide images due to low contrast. On the other hand, the Deep Learning algorithm Cellpose offers new perspectives considering its increasing adoption for segmentation of a wide range of cells. Combining two open-source tools, Cellpose and QuPath, we developed MyoSOTHES, an automated Myofibers Segmentation wOrkflow Tuned for HE Staining. MyoSOTHES enables solving segmentation inconsistencies encountered by default Cellpose model in presence of large range size cells and provides information related to muscle Feret's diameter distribution and Centrally Nucleated Fibers, thus depicting muscle health and treatment effects. MyoSOTHES achieves high quality segmentation compared to baseline workflow with a detection F1-score increasing from 0.801 to 0.919 and a Root Mean Square Error (RMSE) on diameter improved by 31%. MyoSOTHES was validated on an animal study featuring gene transfer in [Formula: see text]-Sarcoglycanopathy, for which dose-response effect is visible and conclusions drawn are consistent with those previously published. MyoSOTHES thus paves the way for wide quantification of HE stained muscle sections and retrospective analysis of HE labeled slices used in laboratories for decades.
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Affiliation(s)
- Marie Reinbigler
- grid.508893.fTélécom SudParis, Institut Polytechnique de Paris, 91120 Palaiseau, France
| | - Jérémie Cosette
- grid.419946.70000 0004 0641 2700Généthon, 91000 Evry, France
| | - Zoheir Guesmia
- grid.419946.70000 0004 0641 2700Généthon, 91000 Evry, France ,grid.418250.a0000 0001 0308 8843Centre de Recherche en Myologie, UMR-S 974, Institut de Myologie, 75000 Paris, France
| | - Simon Jimenez
- grid.419946.70000 0004 0641 2700Généthon, 91000 Evry, France
| | - Catalin Fetita
- grid.508893.fTélécom SudParis, Institut Polytechnique de Paris, 91120 Palaiseau, France
| | - Elisabeth Brunet
- grid.508893.fTélécom SudParis, Institut Polytechnique de Paris, 91120 Palaiseau, France
| | - Daniel Stockholm
- grid.419946.70000 0004 0641 2700Généthon, 91000 Evry, France ,grid.424469.90000 0001 2195 5365École Pratique des Hautes Études, PSL University, 75000 Paris, France
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Gómez-Oca R, Edelweiss E, Djeddi S, Gerbier M, Massana-Muñoz X, Oulad-Abdelghani M, Crucifix C, Spiegelhalter C, Messaddeq N, Poussin-Courmontagne P, Koebel P, Cowling BS, Laporte J. Differential impact of ubiquitous and muscle dynamin 2 isoforms in muscle physiology and centronuclear myopathy. Nat Commun 2022; 13:6849. [PMID: 36369230 PMCID: PMC9652393 DOI: 10.1038/s41467-022-34490-4] [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: 09/06/2021] [Accepted: 10/27/2022] [Indexed: 11/13/2022] Open
Abstract
Dynamin 2 mechanoenzyme is a key regulator of membrane remodeling and gain-of-function mutations in its gene cause centronuclear myopathies. Here, we investigate the functions of dynamin 2 isoforms and their associated phenotypes and, specifically, the ubiquitous and muscle-specific dynamin 2 isoforms expressed in skeletal muscle. In cell-based assays, we show that a centronuclear myopathy-related mutation in the ubiquitous but not the muscle-specific dynamin 2 isoform causes increased membrane fission. In vivo, overexpressing the ubiquitous dynamin 2 isoform correlates with severe forms of centronuclear myopathy, while overexpressing the muscle-specific isoform leads to hallmarks seen in milder cases of the disease. Previous mouse studies suggested that reduction of the total dynamin 2 pool could be therapeutic for centronuclear myopathies. Here, dynamin 2 splice switching from muscle-specific to ubiquitous dynamin 2 aggravated the phenotype of a severe X-linked form of centronuclear myopathy caused by loss-of-function of the MTM1 phosphatase, supporting the importance of targeting the ubiquitous isoform for efficient therapy in muscle. Our results highlight that the ubiquitous and not the muscle-specific dynamin 2 isoform is the main modifier contributing to centronuclear myopathy pathology.
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Affiliation(s)
- Raquel Gómez-Oca
- grid.420255.40000 0004 0638 2716Dpt Translational Medicine, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U1258, Université de Strasbourg, CNRS UMR7104 Illkirch, France ,Dynacure, Illkirch, France
| | - Evelina Edelweiss
- grid.420255.40000 0004 0638 2716Dpt Translational Medicine, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U1258, Université de Strasbourg, CNRS UMR7104 Illkirch, France
| | - Sarah Djeddi
- grid.420255.40000 0004 0638 2716Dpt Translational Medicine, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U1258, Université de Strasbourg, CNRS UMR7104 Illkirch, France
| | | | - Xènia Massana-Muñoz
- grid.420255.40000 0004 0638 2716Dpt Translational Medicine, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U1258, Université de Strasbourg, CNRS UMR7104 Illkirch, France
| | - Mustapha Oulad-Abdelghani
- grid.420255.40000 0004 0638 2716Core platforms, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U1258, Université de Strasbourg, CNRS UMR7104 Illkirch, France
| | - Corinne Crucifix
- grid.420255.40000 0004 0638 2716Integrated Structural Biology platform, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U1258, Université de Strasbourg, CNRS UMR7104 Illkirch, France
| | - Coralie Spiegelhalter
- grid.420255.40000 0004 0638 2716Core platforms, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U1258, Université de Strasbourg, CNRS UMR7104 Illkirch, France
| | - Nadia Messaddeq
- grid.420255.40000 0004 0638 2716Core platforms, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U1258, Université de Strasbourg, CNRS UMR7104 Illkirch, France
| | - Pierre Poussin-Courmontagne
- grid.420255.40000 0004 0638 2716Integrated Structural Biology platform, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U1258, Université de Strasbourg, CNRS UMR7104 Illkirch, France
| | - Pascale Koebel
- grid.420255.40000 0004 0638 2716Core platforms, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U1258, Université de Strasbourg, CNRS UMR7104 Illkirch, France
| | | | - Jocelyn Laporte
- grid.420255.40000 0004 0638 2716Dpt Translational Medicine, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U1258, Université de Strasbourg, CNRS UMR7104 Illkirch, France
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Jiao Y, Liang B, Yang G, Xin Q, Hong D. A simple and efficient method to quantify the cell parameters of the seed coat, embryo and silique wall in rapeseed. PLANT METHODS 2022; 18:117. [PMID: 36329545 PMCID: PMC9632141 DOI: 10.1186/s13007-022-00948-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 09/29/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Researchers interested in the seed size of rapeseed need to quantify the cell size and number of cells in the seed coat, embryo and silique wall. Scanning electron microscope-based methods have been demonstrated to be feasible but laborious and costly. After image preparation, the cell parameters are generally evaluated manually, which is time consuming and a major bottleneck for large-scale analysis. Recently, two machine learning-based algorithms, Trainable Weka Segmentation (TWS) and Cellpose, were released to overcome this long-standing problem. Moreover, the MorphoLibJ and LabelsToROIs plugins in Fiji provide user-friendly tools to deal with cell segmentation files. We attempted to verify the practicability and efficiency of these advanced tools for various types of cells in rapeseed. RESULTS We simplified the current image preparation procedure by skipping the fixation step and demonstrated the feasibility of the simplified procedure. We developed three methods to automatically process multicellular images of various tissues in rapeseed. The TWS-Fiji (TF) method combines cell detection with TWS and cell measurement with Fiji, enabling the accurate quantification of seed coat cells. The Cellpose-Fiji (CF) method, based on cell segmentation with Cellpose and quantification with Fiji, achieves good performance but exhibits systematic error. By removing border labels with MorphoLibJ and detecting regions of interest (ROIs) with LabelsToROIs, the Cellpose-MorphoLibJ-LabelsToROIs (CML) method achieves human-level performance on bright-field images of seed coat cells. Intriguingly, the CML method needs very little manual calibration, a property that makes it suitable for massive-scale image processing. Through a large-scale quantitative evaluation of seed coat cells, we demonstrated the robustness and high efficiency of the CML method at both the single-cell level and the sample level. Furthermore, we extended the application of the CML method to developing seed coat, embryo and silique wall cells and acquired highly precise and reliable results, indicating the versatility of this method for use in multiple scenarios. CONCLUSIONS The CML method is highly accurate and free of the need for manual correction. Hence, it can be applied for the low-cost, high-throughput quantification of diverse cell types in rapeseed with high efficiency. We envision that this method will facilitate the functional genomics and microphenomics studies of rapeseed and other crops.
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Affiliation(s)
- Yushun Jiao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Baoling Liang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Guangsheng Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Qiang Xin
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China.
| | - Dengfeng Hong
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.
- Hubei Hongshan Laboratory, Wuhan, China.
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Monceau A, Moutachi D, Lemaitre M, Garcia L, Trollet C, Furling D, Klein A, Ferry A. Dystrophin Restoration after Adeno-Associated Virus U7-Mediated Dmd Exon Skipping Is Modulated by Muscular Exercise in the Severe D2-Mdx Duchenne Muscular Dystrophy Murine Model. THE AMERICAN JOURNAL OF PATHOLOGY 2022; 192:1604-1618. [PMID: 36113555 DOI: 10.1016/j.ajpath.2022.07.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 07/18/2022] [Accepted: 07/29/2022] [Indexed: 06/15/2023]
Abstract
Duchenne muscular dystrophy (DMD) is a severe neuromuscular disease caused by Dmd mutations, resulting in the absence of dystrophin in skeletal muscle, and a greater susceptibility to damage during contraction (exercise). The current study evaluated whether voluntary exercise impacts a Dmd exon skipping and muscle physiology in a severe DMD murine model. D2-mdx mice were intramuscularly injected with an adeno-associated virus (AAV) U7 snRNA to correct Dmd reading frame, and allowed to voluntary run on a wheel for 1 month. Voluntary running did not induce muscle fiber regeneration, as indicated by the percentage of centronucleated fibers, Myh3 and Myh4 expression, and maximal force production, and thus possibly did not compromise the gene therapy approach. Voluntary running did not impact the number of viral genomes and the expression of U7 and Dmd 1 month after injection of AAV-U7 injected just before exercise initiation, but reduced the amount of dystrophin in dystrophin-expressing fibers from 80% to 65% of the muscle cross-sectional area. In conclusion, voluntary running did not induce muscle damage and had no drastic detrimental effect on the AAV gene therapy exon skipping approach in a severe murine DMD model. Moreover, these results suggest considering exercise as an additional element in the design and conception of future therapeutic approaches for DMD.
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Affiliation(s)
- Alexandra Monceau
- UMRS974 INSERM, Association of Myology Institute, Myology Center of Research, UMRS974, Sorbonne Université, Paris, France
| | - Dylan Moutachi
- UMRS974 INSERM, Association of Myology Institute, Myology Center of Research, UMRS974, Sorbonne Université, Paris, France
| | | | - Luis Garcia
- U1179 INSERM, Université de Versailles Saint-Quentin-en-Yvelines, Montigny le Bretonneux, Paris, France
| | - Capucine Trollet
- UMRS974 INSERM, Association of Myology Institute, Myology Center of Research, UMRS974, Sorbonne Université, Paris, France
| | - Denis Furling
- UMRS974 INSERM, Association of Myology Institute, Myology Center of Research, UMRS974, Sorbonne Université, Paris, France
| | - Arnaud Klein
- UMRS974 INSERM, Association of Myology Institute, Myology Center of Research, UMRS974, Sorbonne Université, Paris, France
| | - Arnaud Ferry
- UMRS974 INSERM, Association of Myology Institute, Myology Center of Research, UMRS974, Sorbonne Université, Paris, France; Faculty of Science Sport, Université Paris Cité, Paris, France.
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49
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Rapid antibiotic susceptibility testing and species identification for mixed samples. Nat Commun 2022; 13:6215. [PMID: 36266330 PMCID: PMC9584937 DOI: 10.1038/s41467-022-33659-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 09/28/2022] [Indexed: 12/24/2022] Open
Abstract
Antimicrobial resistance is an increasing problem on a global scale. Rapid antibiotic susceptibility testing (AST) is urgently needed in the clinic to enable personalized prescriptions in high-resistance environments and to limit the use of broad-spectrum drugs. Current rapid phenotypic AST methods do not include species identification (ID), leaving time-consuming plating or culturing as the only available option when ID is needed to make the sensitivity call. Here we describe a method to perform phenotypic AST at the single-cell level in a microfluidic chip that allows subsequent genotyping by in situ FISH. By stratifying the phenotypic AST response on the species of individual cells, it is possible to determine the susceptibility profile for each species in a mixed sample in 2 h. In this proof-of-principle study, we demonstrate the operation with four antibiotics and mixed samples with combinations of seven species.
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50
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Yamanouchi K, Tanaka Y, Ikeda M, Kato S, Okino R, Nishi H, Hakuno F, Takahashi SI, Chambers J, Matsuwaki T, Uchida K. Macroglossia and less advanced dystrophic change in the tongue muscle of the Duchenne muscular dystrophy rat. Skelet Muscle 2022; 12:24. [PMID: 36258243 PMCID: PMC9580129 DOI: 10.1186/s13395-022-00307-7] [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: 02/21/2022] [Accepted: 10/06/2022] [Indexed: 11/25/2022] Open
Abstract
Background Duchenne muscular dystrophy (DMD) is an X-linked muscle disease caused by a complete lack of dystrophin, which stabilizes the plasma membrane of myofibers. The orofacial function is affected in an advanced stage of DMD and this often leads to an eating disorder such as dysphagia. Dysphagia is caused by multiple etiologies including decreased mastication and swallowing. Therefore, preventing the functional declines of mastication and swallowing in DMD is important to improve the patient’s quality of life. In the present study, using a rat model of DMD we generated previously, we performed analyses on the masseter and tongue muscles, both are required for proper eating function. Methods Age-related changes of the masseter and tongue muscle of DMD rats were analyzed morphometrically, histologically, and immunohistochemically. Also, transcription of cellular senescent markers, and utrophin (Utrn), a functional analog of dystrophin, was examined. Results The masseter muscle of DMD rats showed progressive dystrophic changes as observed in their hindlimb muscle, accompanied by increased transcription of p16 and p19. On the other hand, the tongue of DMD rats showed macroglossia due to hypertrophy of myofibers with less dystrophic changes. Proliferative activity was preserved in the satellite cells from the tongue muscle but was perturbed severely in those from the masseter muscle. While Utrn transcription was increased in the masseter muscle of DMD rats compared to WT rats, probably due to a compensatory mechanism, its level in the tongue muscle was comparable between WT and DMD rats and was similar to that in the masseter muscle of DMD rats. Conclusions Muscular dystrophy is less advanced in the tongue muscle compared to the masseter muscle in the DMD rat. Supplementary Information The online version contains supplementary material available at 10.1186/s13395-022-00307-7.
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Affiliation(s)
- Keitaro Yamanouchi
- Laboratory of Veterinary Physiology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.
| | - Yukie Tanaka
- Laboratory of Veterinary Physiology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Masanari Ikeda
- Laboratory of Veterinary Physiology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Shizuka Kato
- Laboratory of Veterinary Pathology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Ryosuke Okino
- Laboratory of Animal Cell Regulation, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Hiroki Nishi
- Laboratory of Animal Cell Regulation, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Fumihiko Hakuno
- Laboratory of Animal Cell Regulation, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Shin-Ichiro Takahashi
- Laboratory of Animal Cell Regulation, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - James Chambers
- Laboratory of Veterinary Pathology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Takashi Matsuwaki
- Laboratory of Veterinary Physiology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Kazuyuki Uchida
- Laboratory of Veterinary Pathology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
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