In vivo transcriptomic profiling using cell encapsulation identifies effector pathways of systemic aging
Abstract
Sustained exposure to a young systemic environment rejuvenates aged organisms and promotes cellular function. However, due to the intrinsic complexity of tissues it remains challenging to pinpoint niche-independent effects of circulating factors on specific cell populations. Here we describe a method for the encapsulation of human and mouse skeletal muscle progenitors in diffusible polyethersulfone hollow fiber capsules that can be used to profile systemic aging in vivo independent of heterogeneous short-range tissue interactions. We observed that circulating long-range signaling factors in the old systemic environment lead to an activation of Myc and E2F transcription factors, induce senescence and suppress myogenic differentiation. Importantly, in vitro profiling using young and old serum in 2D culture does not capture all pathways deregulated in encapsulated cells in aged mice. Thus, in vivo transcriptomic profiling using cell encapsulation allows for the characterization of effector pathways of systemic aging with unparalleled accuracy.
Data availability
The data discussed in this publication have been deposited in NCBI's Gene Expression Omnibus (GEO). GEO Series accession numbers are GSE111401, GSE81096 and GSE193665.
-
In Vivo Transcriptomic Profiling using Cell Encapsulation Identifies Effector Pathways of Systemic AgingNCBI Gene Expression Omnibus, GSE111401.
-
In Vivo Transcriptomic Profiling using Cell Encapsulation Identifies Effector Pathways of Systemic AgingNCBI Gene Expression Omnibus, GSE193665.
Article and author information
Author details
Funding
Canadian Institutes of Health Research (PJT-162442)
- C Florian Bentzinger
Association Française contre les Myopathies (AFM)
- Pura Muñoz-Cánoves
MWRF (MWRF)
- Pura Muñoz-Cánoves
Maria de Maeztu Unit of Excellence award to UPF (MDM-2014-0370)
- Pura Muñoz-Cánoves
Severo Ochoa Center of Excellence award to the CNIC (SEV-2015-0505)
- Pura Muñoz-Cánoves
Severo Ochoa FPI predoctoral fellowship (SEV-2015-0505-17-1))
- Xiaotong Hong
National Science and Research Council of Canada (RGPIN-2017-05490)
- C Florian Bentzinger
Fonds de Recherche du Québec - Santé (Dossiers 296357,34813,and 36789)
- C Florian Bentzinger
Centre de Recherche Médicale de l'Université de Sherbrooke (CRMUS Chair)
- C Florian Bentzinger
European Research Council (ERC-2016-AdG-741966)
- Pura Muñoz-Cánoves
La Caixa Foundation (La Caixa-HEALTH-HR17-00040)
- Pura Muñoz-Cánoves
Muscular Dystrophy Association (MDA)
- Pura Muñoz-Cánoves
H2020 (UPGRADE-H2020-825825)
- Pura Muñoz-Cánoves
Programa Estatal de Investigacion (RTI2018-096068-B-I00)
- Pura Muñoz-Cánoves
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Reviewing Editor
- Veronica Galvan, UT Health San Antonio, United States
Ethics
Animal experimentation: This study was performed in accordance with the Swiss regulation on animal experimentation and the European Community Council directive (86/609/EEC) for the care and use of laboratory animals. Experiments were approved by the Vaud cantonal authorities under license VD3085, and by the Animal Care and Ethics Committee of the Spanish National Cardiovascular Research Center (CNIC) and regional authorities.
Version history
- Preprint posted: March 9, 2020 (view preprint)
- Received: March 30, 2020
- Accepted: February 28, 2022
- Accepted Manuscript published: March 4, 2022 (version 1)
- Accepted Manuscript updated: March 7, 2022 (version 2)
- Version of Record published: March 16, 2022 (version 3)
Copyright
© 2022, Mashinchian et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
Metrics
-
- 2,140
- views
-
- 312
- downloads
-
- 1
- citations
Views, downloads and citations are aggregated across all versions of this paper published by eLife.
Download links
Downloads (link to download the article as PDF)
Open citations (links to open the citations from this article in various online reference manager services)
Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)
Further reading
-
- Cell Biology
Elastic cartilage constitutes a major component of the external ear, which functions to guide sound to the middle and inner ears. Defects in auricle development cause congenital microtia, which affects hearing and appearance in patients. Mutations in several genes have been implicated in microtia development, yet, the pathogenesis of this disorder remains incompletely understood. Here, we show that Prrx1 genetically marks auricular chondrocytes in adult mice. Interestingly, BMP-Smad1/5/9 signaling in chondrocytes is increasingly activated from the proximal to distal segments of the ear, which is associated with a decrease in chondrocyte regenerative activity. Ablation of Bmpr1a in auricular chondrocytes led to chondrocyte atrophy and microtia development at the distal part. Transcriptome analysis revealed that Bmpr1a deficiency caused a switch from the chondrogenic program to the osteogenic program, accompanied by enhanced protein kinase A activation, likely through increased expression of Adcy5/8. Inhibition of PKA blocked chondrocyte-to-osteoblast transformation and microtia development. Moreover, analysis of single-cell RNA-seq of human microtia samples uncovered enriched gene expression in the PKA pathway and chondrocyte-to-osteoblast transformation process. These findings suggest that auricle cartilage is actively maintained by BMP signaling, which maintains chondrocyte identity by suppressing osteogenic differentiation.
-
- Cancer Biology
- Cell Biology
Internalization from the cell membrane and endosomal trafficking of receptor tyrosine kinases (RTKs) are important regulators of signaling in normal cells that can frequently be disrupted in cancer. The adrenal tumor pheochromocytoma (PCC) can be caused by activating mutations of the rearranged during transfection (RET) receptor tyrosine kinase, or inactivation of TMEM127, a transmembrane tumor suppressor implicated in trafficking of endosomal cargos. However, the role of aberrant receptor trafficking in PCC is not well understood. Here, we show that loss of TMEM127 causes wildtype RET protein accumulation on the cell surface, where increased receptor density facilitates constitutive ligand-independent activity and downstream signaling, driving cell proliferation. Loss of TMEM127 altered normal cell membrane organization and recruitment and stabilization of membrane protein complexes, impaired assembly, and maturation of clathrin-coated pits, and reduced internalization and degradation of cell surface RET. In addition to RTKs, TMEM127 depletion also promoted surface accumulation of several other transmembrane proteins, suggesting it may cause global defects in surface protein activity and function. Together, our data identify TMEM127 as an important determinant of membrane organization including membrane protein diffusability and protein complex assembly and provide a novel paradigm for oncogenesis in PCC where altered membrane dynamics promotes cell surface accumulation and constitutive activity of growth factor receptors to drive aberrant signaling and promote transformation.