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McMann E, Gorski SM. Last but not least: emerging roles of the autophagy-related protein ATG4D. Autophagy 2024:1-12. [PMID: 38920354 DOI: 10.1080/15548627.2024.2369436] [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: 11/27/2023] [Revised: 06/05/2024] [Accepted: 06/13/2024] [Indexed: 06/27/2024] Open
Abstract
The evolutionarily conserved ATG4 cysteine proteases regulate macroautophagy/autophagy through the priming and deconjugation of the Atg8-family proteins. In mammals there are four ATG4 family members (ATG4A, ATG4B, ATG4C, ATG4D) but ATG4D has been relatively understudied. Heightened interest in ATG4D has been stimulated by recent links to human disease. Notably, genetic variations in human ATG4D were implicated in a heritable neurodevelopmental disorder. Genetic analyses in dogs, along with loss-of-function zebrafish and mouse models, further support a neuroprotective role for ATG4D. Here we discuss the evidence connecting ATG4D to neurological diseases and other pathologies and summarize its roles in both autophagy-dependent and autophagy-independent cellular processes.Abbrevation: ATG: autophagy related; BafA1: bafilomycin A1; BCL2: BCL2 apoptosis regulator; BH3: BCL2 homology region 3; CASP3: caspase 3; EV: extracellular vesicle; GABA: gamma aminobutyric acid; GABARAP: GABA type A receptor-associated protein; GABARAPL1: GABA type A receptor associated protein like 1; GABARAPL2: GABA type A receptor associated protein like 2; GFP: green fluorescent protein; LIR: LC3-interacting region; MAP1LC3: microtubule associated protein 1 light chain 3; MEF: mouse embryonic fibroblast; MYC: MYC proto-oncogene, bHLH transcription factor; PE: phosphatidylethanolamine; PS: phosphatidylserine; QKO: quadruple knockout; SDS-PAGE: sodium dodecyl sulfate-polyacrylamide gel; SQSTM1: sequestosome 1.
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Affiliation(s)
- Emily McMann
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, British Columbia, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Sharon M Gorski
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, British Columbia, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
- Centre for Cell Biology, Development and Disease, Simon Fraser University, Burnaby, British Columbia, Canada
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2
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Kurganovs NJ, Engedal N. To eat or not to eat: a critical review on the role of autophagy in prostate carcinogenesis and prostate cancer therapeutics. Front Pharmacol 2024; 15:1419806. [PMID: 38910881 PMCID: PMC11190189 DOI: 10.3389/fphar.2024.1419806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Accepted: 05/20/2024] [Indexed: 06/25/2024] Open
Abstract
Around 1 in 7 men will be diagnosed with prostate cancer during their lifetime. Many strides have been made in the understanding and treatment of this malignancy over the years, however, despite this; treatment resistance and disease progression remain major clinical concerns. Recent evidence indicate that autophagy can affect cancer formation, progression, and therapeutic resistance. Autophagy is an evolutionarily conserved process that can remove unnecessary or dysfunctional components of the cell as a response to metabolic or environmental stress. Due to the emerging importance of autophagy in cancer, targeting autophagy should be considered as a potential option in disease management. In this review, along with exploring the advances made on understanding the role of autophagy in prostate carcinogenesis and therapeutics, we will critically consider the conflicting evidence observed in the literature and suggest how to obtain stronger experimental evidence, as the application of current findings in clinical practice is presently not viable.
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Affiliation(s)
- Natalie Jayne Kurganovs
- Autophagy in Cancer Lab, Institute for Cancer Research, Department of Tumor Biology, Oslo University Hospital, Oslo, Norway
| | - Nikolai Engedal
- Autophagy in Cancer Lab, Institute for Cancer Research, Department of Tumor Biology, Oslo University Hospital, Oslo, Norway
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3
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Qu J, Wu L, Zhang M, Kan M, Chen H, Shi Y, Wang S, Wang X, Chen F. Serum autophagy-related gene 5 level in stroke patients: correlation with CD4+ T cells and cognition impairment during a 3-year follow-up. Braz J Med Biol Res 2024; 57:e13019. [PMID: 38511768 PMCID: PMC10946239 DOI: 10.1590/1414-431x2024e13019] [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: 05/19/2023] [Accepted: 02/04/2024] [Indexed: 03/22/2024] Open
Abstract
Autophagy-related gene (ATG) 5 regulates blood lipids, chronic inflammation, CD4+ T-cell differentiation, and neuronal death and is involved in post-stroke cognitive impairment. This study aimed to explore the correlation of serum ATG5 with CD4+ T cells and cognition impairment in stroke patients. Peripheral blood was collected from 180 stroke patients for serum ATG5 and T helper (Th) 1, Th2, Th17, and regulatory T (Treg) cell detection via enzyme-linked immunosorbent assays and flow cytometry. The Mini-Mental State Examination (MMSE) scale was completed at enrollment, year (Y)1, Y2, and Y3 in stroke patients. Serum ATG5 was also measured in 50 healthy controls (HCs). Serum ATG5 was elevated in stroke patients compared to HCs (P<0.001) and was positively correlated to Th2 cells (P=0.022), Th17 cells (P<0.001), and Th17/Treg ratio (P<0.001) in stroke patients but not correlated with Th1 cells, Th1/Th2 ratio, or Treg cells (all P>0.050). Serum ATG5 (P=0.037), Th1 cells (P=0.022), Th17 cells (P=0.002), and Th17/Treg ratio (P=0.018) were elevated in stroke patients with MMSE score-identified cognition impairment vs those without cognition impairment, whereas Th2 cells, Th1/Th2 ratio, and Treg cells were not different between them (all P>0.050). Importantly, serum ATG5 was negatively linked with MMSE score at enrollment (P=0.004), Y1 (P=0.002), Y2 (P=0.014), and Y3 (P=0.001); moreover, it was positively related to 2-year (P=0.024) and 3-year (P=0.012) MMSE score decline in stroke patients. Serum ATG5 was positively correlated with Th2 and Th17 cells and estimated cognitive function decline in stroke patients.
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Affiliation(s)
- Juanjuan Qu
- Department of Emergency, Handan Central Hospital, Handan, China
| | - Linxia Wu
- Department of Emergency, Handan Central Hospital, Handan, China
| | - Meng Zhang
- Department of Emergency, Handan Central Hospital, Handan, China
| | - Minchen Kan
- Department of Emergency, Handan Central Hospital, Handan, China
| | - Huimin Chen
- Department of Emergency, Handan Central Hospital, Handan, China
| | - Yanqing Shi
- Department of Emergency, Handan Central Hospital, Handan, China
| | - Shuangyu Wang
- Department of Nephrology, Handan Central Hospital, Handan, China
| | - Xiaohua Wang
- Department of Neonatal Ward, Handan Central Hospital, Handan, China
| | - Fan Chen
- Department of Emergency, Handan Central Hospital, Handan, China
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4
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Uribe-Carretero E, Rey V, Fuentes JM, Tamargo-Gómez I. Lysosomal Dysfunction: Connecting the Dots in the Landscape of Human Diseases. BIOLOGY 2024; 13:34. [PMID: 38248465 PMCID: PMC10813815 DOI: 10.3390/biology13010034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 12/22/2023] [Accepted: 01/02/2024] [Indexed: 01/23/2024]
Abstract
Lysosomes are the main organelles responsible for the degradation of macromolecules in eukaryotic cells. Beyond their fundamental role in degradation, lysosomes are involved in different physiological processes such as autophagy, nutrient sensing, and intracellular signaling. In some circumstances, lysosomal abnormalities underlie several human pathologies with different etiologies known as known as lysosomal storage disorders (LSDs). These disorders can result from deficiencies in primary lysosomal enzymes, dysfunction of lysosomal enzyme activators, alterations in modifiers that impact lysosomal function, or changes in membrane-associated proteins, among other factors. The clinical phenotype observed in affected patients hinges on the type and location of the accumulating substrate, influenced by genetic mutations and residual enzyme activity. In this context, the scientific community is dedicated to exploring potential therapeutic approaches, striving not only to extend lifespan but also to enhance the overall quality of life for individuals afflicted with LSDs. This review provides insights into lysosomal dysfunction from a molecular perspective, particularly in the context of human diseases, and highlights recent advancements and breakthroughs in this field.
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Affiliation(s)
- Elisabet Uribe-Carretero
- Departamento de Bioquímica y Biología Molecular y Genética, Facultad de Enfermería y Terapia Ocupacional, Universidad de Extremadura, 10003 Caceres, Spain; (E.U.-C.)
- Centro de Investigación Biomédica en Red en Enfermedades Neurodegenerativa, Instituto de Salud Carlos III (CIBER-CIBERNED-ISCIII), 28029 Madrid, Spain
- Instituto Universitario de Investigación Biosanitaria de Extremadura (INUBE), 10003 Caceres, Spain
| | - Verónica Rey
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain
| | - Jose Manuel Fuentes
- Departamento de Bioquímica y Biología Molecular y Genética, Facultad de Enfermería y Terapia Ocupacional, Universidad de Extremadura, 10003 Caceres, Spain; (E.U.-C.)
- Centro de Investigación Biomédica en Red en Enfermedades Neurodegenerativa, Instituto de Salud Carlos III (CIBER-CIBERNED-ISCIII), 28029 Madrid, Spain
- Instituto Universitario de Investigación Biosanitaria de Extremadura (INUBE), 10003 Caceres, Spain
| | - Isaac Tamargo-Gómez
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain
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Liao D, Wei S, Hu J. Inhibition of miR-542-3p augments autophagy to promote diabetic corneal wound healing. EYE AND VISION (LONDON, ENGLAND) 2024; 11:3. [PMID: 38167306 PMCID: PMC10763460 DOI: 10.1186/s40662-023-00370-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 12/05/2023] [Indexed: 01/05/2024]
Abstract
BACKGROUND Autophagy has recently been shown to be critical for protecting peripheral nerve regeneration. This study explored the impact of miR-542-3p on diabetic corneal nerve regeneration and epithelial healing through the regulation of autophagy. METHODS A type 1 diabetes model was established in male mice through streptozotocin administration. Immunofluorescence staining of β-Tubulin III and sodium fluorescein staining were performed to observe corneal nerve fiber density and corneal epithelial healing, respectively. Western blotting, immunofluorescence and transmission electron microscopy were used to determine autophagy levels. Subconjunctival injection of RAPA and 3-MA altered autophagy levels; with them, we evaluated the role of autophagy in diabetic keratopathy. miRNA sequencing and bioinformatics analysis were performed to identify miRNA-mRNA networks with potential autophagy-regulating roles, and miR-542-3p was measured by quantitative real-time polymerase chain reaction (qRT-PCR). miR-542-3p antagomir was injected subconjunctivally to assess the role in diabetic corneal neuropathy. RESULTS Our data suggest that autophagy is suppressed in the diabetic corneal nerve and that activation of autophagy promotes diabetic corneal wound healing. We identified a potential autophagy-regulating miRNA-mRNA network in the diabetic trigeminal ganglion, in which miR-542-3p expression was significantly upregulated. Inhibition of miR-542-3p significantly enhanced the level of autophagy in trigeminal ganglion by upregulating ATG4D expression, thereby accelerating diabetic corneal nerve regeneration and epithelial healing. CONCLUSIONS Dysregulated autophagy is an important contributor to delayed diabetic corneal injury healing. Inhibiting miR-542-3p promotes diabetic corneal nerve regeneration and epithelial healing through autophagy activation by ATG4D.
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Affiliation(s)
- Danling Liao
- Department of Ophthalmology, Fujian Medical University Union Hospital, 29 Xinquan Road, Fuzhou, 350005, China
| | - Shijia Wei
- Department of Ophthalmology, Fujian Medical University Union Hospital, 29 Xinquan Road, Fuzhou, 350005, China
| | - Jianzhang Hu
- Department of Ophthalmology, Fujian Medical University Union Hospital, 29 Xinquan Road, Fuzhou, 350005, China.
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Tamargo-Gómez I, Martínez-García GG, Suárez MF, Mayoral P, Bretones G, Astudillo A, Prieto-Lloret J, Sveen C, Fueyo A, Engedal N, López-Otín C, Mariño G. Analysis of ATG4C function in vivo. Autophagy 2023; 19:2912-2933. [PMID: 37459465 PMCID: PMC10549197 DOI: 10.1080/15548627.2023.2234799] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 06/23/2023] [Accepted: 07/05/2023] [Indexed: 08/17/2023] Open
Abstract
ABBREVIATIONS ATG4 (autophagy related 4 cysteine peptidase); ATG4A (autophagy related 4A cysteine peptidase); ATG4B (autophagy related 4B cysteine peptidase); ATG4C (autophagy related 4C cysteine peptidase); ATG4D (autophagy related 4D cysteine peptidase); Atg8 (autophagy related 8); GABARAP (GABA type A receptor-associated protein); GABARAPL1(GABA type A receptor-associated protein like 1); GABARAPL2 (GABA type A receptor-associated protein like 2); MAP1LC3A/LC3A (microtubule associated protein 1 light chain 3 alpha); MAP1LC3B/LC3B (microtubule associated protein 1 light chain 3 beta); mATG8 (mammalian Atg8); PE (phosphatidylethanolamine); PS (phosphatydylserine); SQSTM1/p62 (sequestosome 1).
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Affiliation(s)
- Isaac Tamargo-Gómez
- Departamento de Biología Funcional, Facultad de Medicina, Universidad de Oviedo, Oviedo, Spain
- Instituto Universitario de Oncología (IUOPA), Oviedo, Spain
- Instituto de Investigación Sanitaria Del Principado de Asturias (ISPA), Oviedo, Spain
| | - Gemma G. Martínez-García
- Departamento de Biología Funcional, Facultad de Medicina, Universidad de Oviedo, Oviedo, Spain
- Instituto Universitario de Oncología (IUOPA), Oviedo, Spain
- Instituto de Investigación Sanitaria Del Principado de Asturias (ISPA), Oviedo, Spain
| | - María F. Suárez
- Instituto de Investigación Sanitaria Del Principado de Asturias (ISPA), Oviedo, Spain
| | - Pablo Mayoral
- Departamento de Bioquímica y Biología Molecular, Universidad de Oviedo, Spain
| | - Gabriel Bretones
- Instituto Universitario de Oncología (IUOPA), Oviedo, Spain
- Departamento de Bioquímica y Biología Molecular, Universidad de Oviedo, Spain
| | - Aurora Astudillo
- Instituto Universitario de Oncología (IUOPA), Oviedo, Spain
- Instituto de Investigación Sanitaria Del Principado de Asturias (ISPA), Oviedo, Spain
- Biobanco Del Principado de Asturias (BBPA_ISPA_IUOPA), Registro Nacional de Biobancos PT20/161, Oviedo, Spain
| | - Jesús Prieto-Lloret
- Departamento de Bioquímica y Biología Molecular y Fisiología, Facultad de Medicina, Universidad de Valladolid. Instituto de Biología y Genética Molecular-CSIC, Valladolid, Spain
| | - Christina Sveen
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Montebello, Norway
| | - Antonio Fueyo
- Departamento de Biología Funcional, Facultad de Medicina, Universidad de Oviedo, Oviedo, Spain
- Instituto Universitario de Oncología (IUOPA), Oviedo, Spain
- Instituto de Investigación Sanitaria Del Principado de Asturias (ISPA), Oviedo, Spain
| | - Nikolai Engedal
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Montebello, Norway
| | - Carlos López-Otín
- Instituto Universitario de Oncología (IUOPA), Oviedo, Spain
- Instituto de Investigación Sanitaria Del Principado de Asturias (ISPA), Oviedo, Spain
- Departamento de Bioquímica y Biología Molecular, Universidad de Oviedo, Spain
| | - Guillermo Mariño
- Departamento de Biología Funcional, Facultad de Medicina, Universidad de Oviedo, Oviedo, Spain
- Instituto Universitario de Oncología (IUOPA), Oviedo, Spain
- Instituto de Investigación Sanitaria Del Principado de Asturias (ISPA), Oviedo, Spain
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7
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Nieto-Torres JL, Zaretski S, Liu T, Adams PD, Hansen M. Post-translational modifications of ATG8 proteins - an emerging mechanism of autophagy control. J Cell Sci 2023; 136:jcs259725. [PMID: 37589340 PMCID: PMC10445744 DOI: 10.1242/jcs.259725] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/18/2023] Open
Abstract
Autophagy is a recycling mechanism involved in cellular homeostasis with key implications for health and disease. The conjugation of the ATG8 family proteins, which includes LC3B (also known as MAP1LC3B), to autophagosome membranes, constitutes a hallmark of the canonical autophagy process. After ATG8 proteins are conjugated to the autophagosome membranes via lipidation, they orchestrate a plethora of protein-protein interactions that support key steps of the autophagy process. These include binding to cargo receptors to allow cargo recruitment, association with proteins implicated in autophagosome transport and autophagosome-lysosome fusion. How these diverse and critical protein-protein interactions are regulated is still not well understood. Recent reports have highlighted crucial roles for post-translational modifications of ATG8 proteins in the regulation of ATG8 functions and the autophagy process. This Review summarizes the main post-translational regulatory events discovered to date to influence the autophagy process, mostly described in mammalian cells, including ubiquitylation, acetylation, lipidation and phosphorylation, as well as their known contributions to the autophagy process, physiology and disease.
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Affiliation(s)
- Jose L. Nieto-Torres
- Sanford Burnham Prebys Medical Discovery Institute, Program of Development, Aging, and Regeneration, La Jolla, CA 92037, USA
- Department of Biomedical Sciences, School of Health Sciences and Veterinary, Universidad Cardenal Herrera-CEU, CEU Universities, 46113 Moncada, Spain
| | - Sviatlana Zaretski
- Sanford Burnham Prebys Medical Discovery Institute, Program of Development, Aging, and Regeneration, La Jolla, CA 92037, USA
| | - Tianhui Liu
- Sanford Burnham Prebys Medical Discovery Institute, Program of Development, Aging, and Regeneration, La Jolla, CA 92037, USA
| | - Peter D. Adams
- Sanford Burnham Prebys Medical Discovery Institute, Program of Development, Aging, and Regeneration, La Jolla, CA 92037, USA
| | - Malene Hansen
- Sanford Burnham Prebys Medical Discovery Institute, Program of Development, Aging, and Regeneration, La Jolla, CA 92037, USA
- The Buck Institute for Aging Research, Novato, CA 94945, USA
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8
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Morimoto M, Bhambhani V, Gazzaz N, Davids M, Sathiyaseelan P, Macnamara EF, Lange J, Lehman A, Zerfas PM, Murphy JL, Acosta MT, Wang C, Alderman E, Reichert S, Thurm A, Adams DR, Introne WJ, Gorski SM, Boerkoel CF, Gahl WA, Tifft CJ, Malicdan MCV, Baldridge D, Bale J, Bamshad M, Barbouth D, Bayrak-Toydemir P, Beck A, Beggs AH, Behrens E, Bejerano G, Bellen HJ, Bennett J, Berg-Rood B, Bernstein JA, Berry GT, Bican A, Bivona S, Blue E, Bohnsack J, Bonner D, Botto L, Boyd B, Briere LC, Brokamp E, Brown G, Burke EA, Burrage LC, Butte MJ, Byers P, Byrd WE, Carey J, Carrasquillo O, Cassini T, Chang TCP, Chanprasert S, Chao HT, Clark GD, Coakley TR, Cobban LA, Cogan JD, Coggins M, Cole FS, Colley HA, Cooper CM, Cope H, Craigen WJ, Crouse AB, Cunningham M, D’Souza P, Dai H, Dasari S, Davis J, Dayal JG, Dell’Angelica EC, Dipple K, Doherty D, Dorrani N, Doss AL, Douine ED, Duncan L, Earl D, Eckstein DJ, Emrick LT, Eng CM, Esteves C, Falk M, Fieg EL, Fisher PG, Fogel BL, Forghani I, Glass I, Gochuico B, Goddard PC, Godfrey RA, Golden-Grant K, Grajewski A, Gutierrez I, Hadley D, Hahn S, Halley MC, Hamid R, Hassey K, Hayes N, High F, Hing A, Hisama FM, Holm IA, Hom J, Horike-Pyne M, Huang A, Hutchison S, Introne WJ, Isasi R, Izumi K, Jamal F, Jarvik GP, Jarvik J, Jayadev S, Jean-Marie O, Jobanputra V, Karaviti L, Kennedy J, Ketkar S, Kiley D, Kilich G, Kobren SN, Kohane IS, Kohler JN, Korrick S, Kozuira M, Krakow D, Krasnewich DM, Kravets E, Lalani SR, Lam B, Lam C, Lanpher BC, Lanza IR, LeBlanc K, Lee BH, Levitt R, Lewis RA, Liu P, Liu XZ, Longo N, Loo SK, Loscalzo J, Maas RL, MacRae CA, Maduro VV, Mahoney R, Mak BC, Mamounas LA, Manolio TA, Mao R, Maravilla K, Marom R, Marth G, Martin BA, Martin MG, Martínez-Agosto JA, Marwaha S, McCauley J, McConkie-Rosell A, McCray AT, McGee E, Mefford H, Merritt JL, Might M, Mirzaa G, Morava E, Moretti P, Nakano-Okuno M, Nelson SF, Newman JH, Nicholas SK, Nickerson D, Nieves-Rodriguez S, Novacic D, Oglesbee D, Orengo JP, Pace L, Pak S, Pallais JC, Palmer CGS, Papp JC, Parker NH, Phillips JA, Posey JE, Potocki L, Pusey Swerdzewski BN, Quinlan A, Rao DA, Raper A, Raskind W, Renteria G, Reuter CM, Rives L, Robertson AK, Rodan LH, Rosenfeld JA, Rosenwasser N, Rossignol F, Ruzhnikov M, Sacco R, Sampson JB, Saporta M, Schaechter J, Schedl T, Schoch K, Scott DA, Scott CR, Shashi V, Shin J, Silverman EK, Sinsheimer JS, Sisco K, Smith EC, Smith KS, Solem E, Solnica-Krezel L, Solomon B, Spillmann RC, Stoler JM, Sullivan K, Sullivan JA, Sun A, Sutton S, Sweetser DA, Sybert V, Tabor HK, Tan QKG, Tan ALM, Tekin M, Telischi F, Thorson W, Toro C, Tran AA, Ungar RA, Urv TK, Vanderver A, Velinder M, Viskochil D, Vogel TP, Wahl CE, Walker M, Wallace S, Walley NM, Wambach J, Wan J, Wang LK, Wangler MF, Ward PA, Wegner D, Weisz Hubshman M, Wener M, Wenger T, Wesseling Perry K, Westerfield M, Wheeler MT, Whitlock J, Wolfe LA, Worley K, Xiao C, Yamamoto S, Yang J, Zhang Z, Zuchner S, Reichert S, Thurm A, Adams DR, Introne WJ, Gorski SM, Boerkoel CF, Gahl WA, Tifft CJ, Malicdan MCV. Bi-allelic ATG4D variants are associated with a neurodevelopmental disorder characterized by speech and motor impairment. NPJ Genom Med 2023; 8:4. [PMID: 36765070 PMCID: PMC9918471 DOI: 10.1038/s41525-022-00343-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 12/06/2022] [Indexed: 02/12/2023] Open
Abstract
Autophagy regulates the degradation of damaged organelles and protein aggregates, and is critical for neuronal development, homeostasis, and maintenance, yet few neurodevelopmental disorders have been associated with pathogenic variants in genes encoding autophagy-related proteins. We report three individuals from two unrelated families with a neurodevelopmental disorder characterized by speech and motor impairment, and similar facial characteristics. Rare, conserved, bi-allelic variants were identified in ATG4D, encoding one of four ATG4 cysteine proteases important for autophagosome biogenesis, a hallmark of autophagy. Autophagosome biogenesis and induction of autophagy were intact in cells from affected individuals. However, studies evaluating the predominant substrate of ATG4D, GABARAPL1, demonstrated that three of the four ATG4D patient variants functionally impair ATG4D activity. GABARAPL1 is cleaved or "primed" by ATG4D and an in vitro GABARAPL1 priming assay revealed decreased priming activity for three of the four ATG4D variants. Furthermore, a rescue experiment performed in an ATG4 tetra knockout cell line, in which all four ATG4 isoforms were knocked out by gene editing, showed decreased GABARAPL1 priming activity for the two ATG4D missense variants located in the cysteine protease domain required for priming, suggesting that these variants impair the function of ATG4D. The clinical, bioinformatic, and functional data suggest that bi-allelic loss-of-function variants in ATG4D contribute to the pathogenesis of this syndromic neurodevelopmental disorder.
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Affiliation(s)
- Marie Morimoto
- grid.94365.3d0000 0001 2297 5165National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD 20892 USA
| | - Vikas Bhambhani
- grid.418506.e0000 0004 0629 5022Department of Medical Genetics, Children’s Hospitals and Clinics of Minnesota, Minneapolis, MN 55404 USA
| | - Nour Gazzaz
- grid.17091.3e0000 0001 2288 9830Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC V6H 3N1 Canada ,grid.414137.40000 0001 0684 7788Provincial Medical Genetics Program, British Columbia Women’s and Children’s Hospital, Vancouver, BC V6H 3N1 Canada ,grid.412125.10000 0001 0619 1117Department of Pediatrics, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mariska Davids
- grid.94365.3d0000 0001 2297 5165National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD 20892 USA
| | - Paalini Sathiyaseelan
- grid.434706.20000 0004 0410 5424Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 1L3 Canada ,grid.61971.380000 0004 1936 7494Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6 Canada
| | - Ellen F. Macnamara
- grid.94365.3d0000 0001 2297 5165National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD 20892 USA
| | | | - Anna Lehman
- grid.17091.3e0000 0001 2288 9830Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC V6H 3N1 Canada
| | - Patricia M. Zerfas
- grid.94365.3d0000 0001 2297 5165Diagnostic and Research Services Branch, Office of Research Services, National Institutes of Health, Bethesda, MD 20892 USA
| | - Jennifer L. Murphy
- grid.94365.3d0000 0001 2297 5165National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD 20892 USA
| | - Maria T. Acosta
- grid.94365.3d0000 0001 2297 5165National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD 20892 USA
| | - Camille Wang
- grid.94365.3d0000 0001 2297 5165National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD 20892 USA
| | - Emily Alderman
- grid.17091.3e0000 0001 2288 9830Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC V6H 3N1 Canada ,grid.414137.40000 0001 0684 7788Provincial Medical Genetics Program, British Columbia Women’s and Children’s Hospital, Vancouver, BC V6H 3N1 Canada
| | | | - Sara Reichert
- grid.418506.e0000 0004 0629 5022Department of Medical Genetics, Children’s Hospitals and Clinics of Minnesota, Minneapolis, MN 55404 USA
| | - Audrey Thurm
- grid.94365.3d0000 0001 2297 5165Neurodevelopmental and Behavioral Phenotyping Service, Office of the Clinical Director, National Institute of Mental Health, National Institutes of Health, Bethesda, MD 20892 USA
| | - David R. Adams
- grid.94365.3d0000 0001 2297 5165National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD 20892 USA ,grid.94365.3d0000 0001 2297 5165Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892 USA
| | - Wendy J. Introne
- grid.94365.3d0000 0001 2297 5165National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD 20892 USA ,grid.94365.3d0000 0001 2297 5165Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892 USA ,grid.94365.3d0000 0001 2297 5165Human Biochemical Genetics Section, Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892 USA
| | - Sharon M. Gorski
- grid.17091.3e0000 0001 2288 9830Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC V6H 3N1 Canada ,grid.434706.20000 0004 0410 5424Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 1L3 Canada ,grid.61971.380000 0004 1936 7494Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6 Canada
| | - Cornelius F. Boerkoel
- grid.17091.3e0000 0001 2288 9830Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC V6H 3N1 Canada ,grid.414137.40000 0001 0684 7788Provincial Medical Genetics Program, British Columbia Women’s and Children’s Hospital, Vancouver, BC V6H 3N1 Canada
| | - William A. Gahl
- grid.94365.3d0000 0001 2297 5165National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD 20892 USA ,grid.94365.3d0000 0001 2297 5165Human Biochemical Genetics Section, Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892 USA
| | - Cynthia J. Tifft
- grid.94365.3d0000 0001 2297 5165National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD 20892 USA ,grid.94365.3d0000 0001 2297 5165Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892 USA
| | - May Christine V. Malicdan
- grid.94365.3d0000 0001 2297 5165National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD 20892 USA ,grid.94365.3d0000 0001 2297 5165Human Biochemical Genetics Section, Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892 USA
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9
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Kim ML, Hardy MY, Edgington-Mitchell LE, Ramarathinam SH, Chung SZ, Russell AK, Currie I, Sleebs BE, Purcell AW, Tye-Din JA, Wicks IP. Hydroxychloroquine inhibits the mitochondrial antioxidant system in activated T cells. iScience 2021; 24:103509. [PMID: 34934928 DOI: 10.1016/j.isci.2021.103509] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 10/15/2021] [Accepted: 11/20/2021] [Indexed: 12/30/2022] Open
Abstract
Although hydroxychloroquine (HCQ) has long been used to treat autoimmune diseases, its mechanism of action remains poorly understood. In CD4 T-cells, we found that a clinically relevant concentration of HCQ inhibited the mitochondrial antioxidant system triggered by TCR crosslinking, leading to increased mitochondrial superoxide, impaired activation-induced autophagic flux, and reduced proliferation of CD4 T-cells. In antigen-presenting cells, HCQ also reduced constitutive activation of the endo-lysosomal protease legumain and toll-like receptor 9, thereby reducing cytokine production, but it had little apparent impact on constitutive antigen processing and peptide presentation. HCQ's effects did not require endo-lysosomal pH change, nor impaired autophagosome-lysosome fusion. We explored the clinical relevance of these findings in patients with celiac disease-a prototypic CD4 T-cell-mediated disease-and found that HCQ limits ex vivo antigen-specific T cell responses. We report a T-cell-intrinsic immunomodulatory effect from HCQ and suggest potential re-purposing of HCQ for celiac disease.
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Affiliation(s)
- Man Lyang Kim
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC 3052, Australia
| | - Melinda Y Hardy
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC 3052, Australia
| | - Laura E Edgington-Mitchell
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC 3052, Australia.,Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia.,Department of Oral and Maxillofacial Surgery, New York University College of Dentistry, Bluestone Center for Clinical Research, New York, NY 10010, USA
| | - Sri H Ramarathinam
- Infection and Immunity Program and The Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute Monash University, Clayton, VIC 3800, Australia
| | - Shan Zou Chung
- Infection and Immunity Program and The Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute Monash University, Clayton, VIC 3800, Australia
| | - Amy K Russell
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Iain Currie
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC 3052, Australia
| | - Brad E Sleebs
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC 3052, Australia
| | - Anthony W Purcell
- Infection and Immunity Program and The Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute Monash University, Clayton, VIC 3800, Australia
| | - Jason A Tye-Din
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC 3052, Australia.,Gastroenterology Department, Royal Melbourne Hospital, Parkville, VIC 3052, Australia
| | - Ian P Wicks
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC 3052, Australia.,Rheumatology Unit, Royal Melbourne Hospital, Parkville, VIC 3052, Australia
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10
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Tamargo-Gómez I, Martínez-García GG, Suárez MF, Fernández AF, Mariño G. ATG4D role in mAtg8s delipidation and neuroprotection. Autophagy 2021; 17:1558-1560. [PMID: 33960274 DOI: 10.1080/15548627.2021.1922979] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Affiliation(s)
- Isaac Tamargo-Gómez
- Departamento de Biología Funcional, Facultad de Medicina, Universidad de Oviedo, Oviedo, Spain.,Instituto Universitario de Oncología (IUOPA), Oviedo, Spain.,Autophagy and Metabolism Lab, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Gemma G Martínez-García
- Departamento de Biología Funcional, Facultad de Medicina, Universidad de Oviedo, Oviedo, Spain.,Instituto Universitario de Oncología (IUOPA), Oviedo, Spain.,Autophagy and Metabolism Lab, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - María F Suárez
- Autophagy and Metabolism Lab, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Alvaro F Fernández
- Instituto Universitario de Oncología (IUOPA), Oviedo, Spain.,Universidad de Oviedo, Oviedo, Spain
| | - Guillermo Mariño
- Departamento de Biología Funcional, Facultad de Medicina, Universidad de Oviedo, Oviedo, Spain.,Instituto Universitario de Oncología (IUOPA), Oviedo, Spain.,Autophagy and Metabolism Lab, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
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