Activating transcription factor 6 (ATF6), a key regulator of the unfolded protein
response, plays a key role in endoplasmic reticulum function and protein homeostasis.
Variants of ATF6 that abrogate transcriptional activity cause morphologic and molecular
defects in cones, clinically manifesting as the human vision loss disease achromatopsia
(ACHM). ATF6 is expressed in all retinal cells. However, the effect of disease-associated
ATF6 variants on other retinal cell types remains unclear. Herein, this was investigated
by analyzing bulk RNA-sequencing transcriptomes from retinal organoids generated from
patients with ACHM, carrying homozygous loss-of-function ATF6 variants. Marked dysregulation
in mitochondrial respiratory complex gene expression and disrupted mitochondrial morphology
in ACHM retinal organoids were identified. This indicated that loss of ATF6 leads
to previously unappreciated mitochondrial defects in the retina. Next, gene expression
from control and ACHM retinal organoids were compared with transcriptome profiles
of seven major retinal cell types generated from recent single-cell transcriptomic
maps of nondiseased human retina. This indicated pronounced down-regulation of cone
genes and up-regulation in Müller glia genes, with no significant effects on other
retinal cells. Overall, the current analysis of ACHM patient retinal organoids identified
new cellular and molecular phenotypes in addition to cone dysfunction: activation
of Müller cells, increased endoplasmic reticulum stress, disrupted mitochondrial structure,
and elevated respiratory chain activity gene expression.
Graphical abstract
Graphical Abstract
To read this article in full you will need to make a payment
Purchase one-time access:
Academic & Personal: 24 hour online accessCorporate R&D Professionals: 24 hour online accessOne-time access price info
- For academic or personal research use, select 'Academic and Personal'
- For corporate R&D use, select 'Corporate R&D Professionals'
Subscribe:
Subscribe to The American Journal of PathologyAlready a print subscriber? Claim online access
Already an online subscriber? Sign in
Register: Create an account
Institutional Access: Sign in to ScienceDirect
References
- The cone dysfunction syndromes.Br J Ophthalmol. 2016; 100: 115-121
- Achromatopsia: clinical features, molecular genetics, animal models and therapeutic options.Ophthalmic Genet. 2018; 39: 149-157
- Mutations in the CNGB3 gene encoding the beta-subunit of the cone photoreceptor cGMP-gated channel are responsible for achromatopsia (ACHM3) linked to chromosome 8q21.Hum Mol Genet. 2000; 9: 2107-2116
- Total colour blindness is caused by mutations in the gene encoding the alpha-subunit of the cone photoreceptor cGMP-gated cation channel.Nat Genet. 1998; 19: 257-259
- Mutations in the cone photoreceptor G-protein alpha-subunit gene GNAT2 in patients with achromatopsia.Am J Hum Genet. 2002; 71: 422-425
- A nonsense mutation in PDE6H causes autosomal-recessive incomplete achromatopsia.Am J Hum Genet. 2012; 91: 527-532
- A homologous genetic basis of the murine cpfl1 mutant and human achromatopsia linked to mutations in the PDE6C gene.Proc Natl Acad Sci U S A. 2009; 106: 19581-19586
- Mutation of ATF6 causes autosomal recessive achromatopsia.Hum Genet. 2015; 134: 941-950
- Mutations in the unfolded protein response regulator ATF6 cause the cone dysfunction disorder achromatopsia.Nat Genet. 2015; 47: 757-765
- Autosomal recessive cone-rod dystrophy can be caused by mutations in the ATF6 gene.Eur J Hum Genet. 2017; 25: 1210-1216
- ATF6 is mutated in early onset photoreceptor degeneration with macular involvement.Invest Ophthalmol Vis Sci. 2015; 56: 3889-3895
- Multiexon deletion alleles of ATF6 linked to achromatopsia.JCI Insight. 2020; 5: e136041
- Characterization of retinal structure in ATF6-associated achromatopsia.Invest Ophthalmol Vis Sci. 2019; 60: 2631-2640
- Achromatopsia mutations target sequential steps of ATF6 activation.Proc Natl Acad Sci U S A. 2017; 114: 400-405
- Mammalian transcription factor ATF6 is synthesized as a transmembrane protein and activated by proteolysis in response to endoplasmic reticulum stress.Mol Biol Cell. 1999; 10: 3787-3799
- Underglycosylation of ATF6 as a novel sensing mechanism for activation of the unfolded protein response.J Biol Chem. 2004; 279: 11354-11363
- The unfolded protein response: from stress pathway to homeostatic regulation.Science. 2011; 334: 1081-1086
- Reduction of disulfide bridges in the lumenal domain of ATF6 in response to glucose starvation.Cell Struct Funct. 2006; 31: 127-134
- OsTGAP1, a bZIP transcription factor, coordinately regulates the inductive production of diterpenoid phytoalexins in rice.J Biol Chem. 2009; 284: 26510-26518
- ER stress induces cleavage of membrane-bound ATF6 by the same proteases that process SREBPs.Mol Cell. 2000; 6: 1355-1364
- Stable binding of ATF6 to BiP in the endoplasmic reticulum stress response.Mol Cell Biol. 2005; 25: 921-932
- Activation of ATF6 and an ATF6 DNA binding site by the endoplasmic reticulum stress response.J Biol Chem. 2000; 275: 27013-27020
- Endoplasmic reticulum stress in human photoreceptor diseases.Brain Res. 2016; 1648: 538-541
- Protein misfolding in the endoplasmic reticulum as a conduit to human disease.Nature. 2016; 529: 326-335
- The neuronal organization of the retina.Neuron. 2012; 76: 266-280
Kolb H, Nelson R, Fernandez E, Jones B: Webvision: The Organization of the Retina and Visual System. Salt Lake City, UT: University of Utah Health Sciences Center, 2022. Available at: http://webvision.med.utah.edu (accessed June 3, 2022)
- Müller cells in the healthy and diseased retina.Prog Retin Eye Res. 2006; 25: 397-424
- Müller glial cell reprogramming and retina regeneration.Nat Rev Neurosci. 2014; 15: 431-442
- ATF6 is essential for human cone photoreceptor development.Proc Natl Acad Sci U S A. 2021; 118 (e2103196118)
- Single-nuclei RNA-seq on human retinal tissue provides improved transcriptome profiling.Nat Commun. 2019; 10: 5743
- Single-cell transcriptomic atlas of the human retina identifies cell types associated with age-related macular degeneration.Nat Commun. 2019; 10: 4902
- Cell types of the human retina and its organoids at single-cell resolution.Cell. 2020; 182: 1623-1640.e34
- The unfolded protein response regulator ATF6 promotes mesodermal differentiation.Sci Signal. 2018; 11: eaan5785
- Generation of three-dimensional retinal tissue with functional photoreceptors from human iPSCs.Nat Commun. 2014; 5: 4047
- The immunocytochemical localization of connexin 36 at rod and cone gap junctions in the guinea pig retina.Eur J Neurosci. 2003; 18: 2925-2934
- Pathway enrichment analysis and visualization of omics data using g:Profiler, GSEA, Cytoscape and EnrichmentMap.Nat Protoc. 2019; 14: 482-517
- Cytoscape: a software environment for integrated models of biomolecular interaction networks.Genome Res. 2003; 13: 2498-2504
- Molecular signatures database (MSigDB) 3.0.Bioinformatics. 2011; 27: 1739-1740
- Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles.Proc Natl Acad Sci U S A. 2005; 102: 15545-15550
- XBP-1 regulates a subset of endoplasmic reticulum resident chaperone genes in the unfolded protein response.Mol Cell Biol. 2003; 23: 7448-7459
- Genetics of mitochondrial diseases: identifying mutations to help diagnosis.eBioMedicine. 2020; 56: 102784
- g:Profiler: a web server for functional enrichment analysis and conversions of gene lists (2019 update).Nucleic Acids Res. 2019; 47: W191-W198
- Gene ontology: tool for the unification of biology.Nat Genet. 2000; 25: 25-29
- The reactome pathway knowledgebase.Nucleic Acids Res. 2020; 48: D498-D503
- Integration of biological networks and gene expression data using Cytoscape.Nat Protoc. 2007; 2: 2366-2382
- Rod outer segment disk shedding in rat retina: relationship to cyclic lighting.Science. 1976; 194: 1071-1074
- Phototransduction influences metabolic flux and nucleotide metabolism in mouse retina.J Biol Chem. 2016; 291: 4698-4710
- Daily mitochondrial dynamics in cone photoreceptors.Proc Natl Acad Sci U S A. 2020; 117: 28816-28827
- Photoreceptor inner segments in monkey and human retina: mitochondrial density, optics, and regional variation.Vis Neurosci. 2002; 19: 395-407
- ER stress and its functional link to mitochondria: role in cell survival and death.Cold Spring Harb Perspect Biol. 2011; 3: a004424
- Stress-responsive regulation of mitochondria through the ER unfolded protein response.Trends Endocrinol Metab. 2014; 25: 528-537
- Functional and morphological impact of ER stress on mitochondria.J Cell Physiol. 2013; 228: 1802-1818
- Mitophagy: mechanisms, pathophysiological roles, and analysis.Biol Chem. 2012; 393: 547-564
- Autophagy regulates endoplasmic reticulum stress in ischemic preconditioning.Autophagy. 2012; 8: 310-325
- Mice conditionally lacking the Wolfram gene in pancreatic islet beta cells exhibit diabetes as a result of enhanced endoplasmic reticulum stress and apoptosis.Diabetologia. 2005; 48: 2313-2321
- Measuring ER stress and the unfolded protein response using mammalian tissue culture system.Methods Enzymol. 2011; 490: 71-92
- Deconvoluting stress-responsive proteostasis signaling pathways for pharmacologic activation using targeted RNA sequencing.ACS Chem Biol. 2019; 14: 784-795
- ATF6alpha induces XBP1-independent expansion of the endoplasmic reticulum.J Cell Sci. 2009; 122: 1626-1636
- ATF6alpha optimizes long-term endoplasmic reticulum function to protect cells from chronic stress.Dev Cell. 2007; 13: 351-364
- Implication of specific retinal cell-type involvement and gene expression changes in AMD progression using integrative analysis of single-cell and bulk RNA-seq profiling.Sci Rep. 2021; 11: 15612
- Differential contributions of ATF6 and XBP1 to the activation of endoplasmic reticulum stress-responsive cis-acting elements ERSE, UPRE and ERSE-II.J Biochem. 2004; 136: 343-350
- Transcriptional induction of mammalian ER quality control proteins is mediated by single or combined action of ATF6alpha and XBP1.Dev Cell. 2007; 13: 365-376
- Stress-independent activation of XBP1s and/or ATF6 reveals three functionally diverse ER proteostasis environments.Cell Rep. 2013; 3: 1279-1292
- ATF6 is required for efficient rhodopsin clearance and retinal homeostasis in the P23H rho retinitis pigmentosa mouse model.Sci Rep. 2021; 11: 16356
- ERAD: the long road to destruction.Nat Cell Biol. 2005; 7: 766-772
- Ubiquitin-dependent protein degradation at the endoplasmic reticulum and nuclear envelope.Semin Cell Dev Biol. 2019; 93: 111-124
- Endoplasmic reticulum-mitochondria contacts: function of the junction.Nat Rev Mol Cell Biol. 2012; 13: 607-625
- Here, there, and everywhere: the importance of ER membrane contact sites.Science. 2018; 361: eaan5835
- Endoplasmic reticulum-mitochondrial contactology: structure and signaling functions.Trends Cell Biol. 2018; 28: 523-540
- The endoplasmic reticulum stress response in neuroprogressive diseases: emerging pathophysiological role and translational implications.Mol Neurobiol. 2018; 55: 8765-8787
- The role of endoplasmic reticulum stress in neurodegenerative disease.Apoptosis. 2017; 22: 1-26
- Upregulated function of mitochondria-associated ER membranes in Alzheimer disease.EMBO J. 2012; 31: 4106-4123
- Endoplasmic reticulum-mitochondria crosstalk and beta-cell destruction in type 1 diabetes.Front Immunol. 2021; 12: 669492
- Physiology of the choroidal vascular bed.Int Ophthalmol. 1983; 6: 101-107
- Oxidative damage is a potential cause of cone cell death in retinitis pigmentosa.J Cell Physiol. 2005; 203: 457-464
- Three-dimensional analysis of mouse rod and cone mitochondrial cristae architecture: bioenergetic and functional implications.Mol Vis. 2003; 9: 60-73
- The localization of glutathione peroxidase in the photoreceptor cells and the retinal pigment epithelial cells of Wistar and Royal College of Surgeons dystrophic rats.Pigment Cell Res. 1999; 12: 107-117
- An hypothesis to account for the renewal of outer segments in rod and cone photoreceptor cells: renewal as a surrogate antioxidant.Invest Ophthalmol Vis Sci. 2008; 49: 3259-3261
- Morphological and functional abnormalities in the inner retina of the rd/rd mouse.J Neurosci. 2002; 22: 5492-5504
- Müller glial cells in retinal disease.Ophthalmologica. 2012; 227: 1-19
- Up-regulation of glial fibrillary acidic protein in response to retinal injury: its potential role in glial remodeling and a comparison to vimentin expression.Int Rev Cytol. 2003; 230: 263-290
- Sigma receptor 1 modulates ER stress and Bcl2 in murine retina.Cell Tissue Res. 2014; 356: 15-27
- Unfolded protein response pathways correlatively modulate endoplasmic reticulum stress responses in rat retinal Müller cells.J Ophthalmol. 2019; 2019: 9028483
- Light- and electron-microscopic analysis of neuropeptide Y-immunoreactive amacrine cells in the guinea pig retina.Cell Tissue Res. 2001; 306: 363-371
- The transcriptome of retinal Müller glial cells.J Comp Neurol. 2008; 509: 225-238
- Loss of XBP1 leads to early-onset retinal neurodegeneration in a mouse model of type I diabetes.J Clin Med. 2019; 8: 906
- Visualization and analysis of gene expression in tissue sections by spatial transcriptomics.Science. 2016; 353: 78-82
- Rods and cones in the mouse retina, I: structural analysis using light and electron microscopy.J Comp Neurol. 1979; 188: 245-262
- The development of parafoveal and mid-peripheral human retina.Behav Brain Res. 1992; 49: 21-31
- An analysis of retinal receptor orientation, I: angular relationship of neighboring photoreceptors.Invest Ophthalmol. 1971; 10: 69-77
- A qualitative and quantitative analysis of the human fovea during development.Vis Res. 1986; 26: 847-855
- Some structural features of the fovea centralis in the human retina.Arch Ophthalmol. 1969; 82: 151-159
- Localization of Usher 1 proteins to the photoreceptor calyceal processes, which are absent from mice.J Cell Biol. 2012; 199: 381-399
- Induction of endoplasmic reticulum stress genes, BiP and chop, in genetic and environmental models of retinal degeneration.Invest Ophthalmol Vis Sci. 2012; 53: 7590-7599
- Endoplasmic reticulum stress is activated in light-induced retinal degeneration.J Neurosci Res. 2008; 86: 910-919
Article info
Publication history
Published online: December 16, 2022
Accepted:
December 5,
2022
Publication stage
In Press Journal Pre-ProofFootnotes
Supported by NIH awards P30EY026877, R01EY027735, R01AG046495, R01NS125674, R01NS088485, and CIRM DISC2-10973 (J.H.L.); VA Merit I01BX002284 (J.H.L.); and Research to Prevent Blindness Foundation (J.H.L. and M.S.D.-A.).
E.-J.L., M.S.D.-A. and H.M. contributed equally to this work.
Disclosures: None declared.
Portions of this work were presented at the American Society for Investigative Pathology (ASIP) Annual Meeting at Experimental Biology 2022, Philadelphia, PA, April 2–5, 2022, where J.H.L. delivered a lecture entitled “Proteostasis Diseases of the Eye and Brain.” J.H.L. is the 2022 recipient of the ASIP Outstanding Investigator Award, which is presented annually to a midcareer investigator with demonstrated excellence in research in experimental pathology.
Identification
Copyright
© 2022 American Society for Investigative Pathology. Published by Elsevier Inc. All rights reserved.
