Modeling Potential Autophagy Pathways in COVID-19 and Sarcoidosis
Authors: Alain Calender, Dominique Israel-Biet, Dominique Valeyre, Yves Pacheco
Journal: Trends in Immunology (2020)

Coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and mainly affects the lungs. Sarcoidosis is an autoinflammatory disease characterized by the diffusion of granulomas in the lungs and other organs. Here, we discuss how the two diseases might involve some common mechanistic cellular pathways around the regulation of autophagy. Coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and mainly affects the lungs. Sarcoidosis is an autoinflammatory disease characterized by the diffusion of granulomas in the lungs and other organs. Here, we discuss how the two diseases might involve some common mechanistic cellular pathways around the regulation of autophagy. The pandemic induced by SARS-CoV-2 (COVID-19) raises vital questions regarding the most beneficial putative therapeutic procedures that could prevent fatal aspects of acute respiratory distress syndrome (ARDS) induced by this coronavirus strain [1.Fung T.S. Liu D.X. Human coronavirus: host-pathogen interaction.Annu. Rev. Microbiol. 2019; 73: 529-557Crossref PubMed Scopus (656) Google Scholar]. The characteristics of SARS-CoV-2 infection that differ from other common respiratory lung diseases include the heterogeneity of clinical symptoms, ranging from asymptomatic presentations to a common flu, and in some cases, ARDS and multiorgan involvement. While COVID-19 is characterized by a high transmission rate and represents a major cause of mortality worldwide, understanding host–pathogen interactions at various steps of the viral life cycle is of importance, and should rely on widespread knowledge involving animal and human rare disease models. Sarcoidosis in mammals predisposes the lungs to diffuse granulomatosis; a lesion characterized by tightly formed conglomerates of lymphocytes and macrophages that fuse to form multinucleated giant cells (MGCs) [2.Grunewald J. et al.Sarcoidosis.Nat. Rev. Dis. Primers. 2019; 5: 45-57Crossref PubMed Scopus (278) Google Scholar]. Recent work reported the spontaneous formation of sarcoidosis-like granulomas in a Tsc2−/− knockout mouse model of constitutive mechanistic target of rapamycin complex (mTORC)1 activation in macrophages [3.Linke M. et al.Chronic signaling via the metabolic checkpoint kinase mTORC1 induces macrophage granuloma formation and marks sarcoidosis progression.Nat. Immunol. 2017; 18: 293-302Crossref PubMed Scopus (178) Google Scholar]. By using whole-exome sequencing of familial forms of sarcoidosis, our group identified mutations in genes encoding essential factors for autophagy regulation, for example, the mTOR and Rac1 (Ras-related C3 botulinum toxin substrate 1) molecular hubs, we posited that this predisposing state might be related to constitutional defects in the regulation of macroautophagy – a crucial process allowing the clearance of any microbial and nonmicrobial particles [4.Calender A. et al.Exome sequencing and pathogenicity-network analysis of five French families implicate mTOR signalling and autophagy in familial sarcoidosis.Eur. Respir. J. 2019; 541900430Crossref PubMed Scopus (41) Google Scholar]. Similar mechanisms have been suggested for other granulomatous and inflammatory disorders such as Crohn's disease [5.Wang T. et al.Autophagy and gastrointestinal diseases.Adv. Exp. Med. Biol. 2020; 1207: 529-556Crossref PubMed Scopus (14) Google Scholar]. Whether patients with sarcoidosis present differential susceptibility to SARS-CoV-2 infection remains unknown; however, several projects have been initiated to address this question [6.Southern B.D. Patients with interstitial lung disease and pulmonary sarcoidosis are at high risk for severe illness related to COVID-19.Cleve. Clin. J. Med. 2020; (Published online June 18, 2020. https://doi.org/10.3949/ccjm.87a.ccc026)Crossref PubMed Google Scholar]. Nevertheless, highlighting certain common processes involved in sarcoidosis and COVID-19 might be useful to further our understanding of potential mechanisms predisposing individuals to severe forms of SARS-CoV-2 infection. A large number of immunological and biochemical arguments have suggested that the deficient clearance of bacterial and/or viral, and/or inorganic particles, concomitant with various immune defects – including the occurrence of significant Th1/Th17 immune responses initiated by antigen presentation and impaired regulatory T cell functions – might be associated with human sarcoidosis [2.Grunewald J. et al.Sarcoidosis.Nat. Rev. Dis. Primers. 2019; 5: 45-57Crossref PubMed Scopus (278) Google Scholar]. Accordingly, human viruses, including coronaviruses and herpes viruses, might take advantage of autophagy processes by bypassing certain regulatory mechanisms of the latter – for example, from the initial steps of autophagosome formation, to further autophagosome fusion with lysosomes, to proteolytic degradation by lysosomal proteases – thus evolving various strategies to either escape or inhibit host cell defenses [1.Fung T.S. Liu D.X. Human coronavirus: host-pathogen interaction.Annu. Rev. Microbiol. 2019; 73: 529-557Crossref PubMed Scopus (656) Google Scholar]. There is a strong, but finely regulated, interaction between autophagy, programmed cell death, and apoptosis. Cell entry of SARS-CoV-1 and -2 depends on binding of viral spike (S) proteins to cellular receptors such as angiotensin-converting enzyme (ACE)2, expressed on mucosal and bronchial cells in humans, in concert with the serine protease transmembrane protease serine 2, mediating S protein cleavage (S1+S2) and maturation [1.Fung T.S. Liu D.X. Human coronavirus: host-pathogen interaction.Annu. Rev. Microbiol. 2019; 73: 529-557Crossref PubMed Scopus (656) Google Scholar]. Of note, SARS-CoV-2 protein has a high affinity for human ACE2, a membrane-bound peptidase highly expressed in the heart, lungs, and digestive and renal tracts; this molecular interaction leads to a membrane fusion process and further formation of syncytia with multinucleated alveolar epithelial cells (Figure 1) [7.Musarrat F. et al.The anti-HIV drug nelfinavir mesylate (Viracept) is a potent inhibitor of cell fusion caused by the SARSCoV-2 spike (S) glycoprotein warranting further evaluation as an antiviral against COVID-19 infections.J. Med. Virol. 2020; (Published online May 6, 2020. https://doi.org/10.1002/jmv.25985)Crossref PubMed Scopus (124) Google Scholar]. Nevertheless, pathological examination of lung biopsy tissues from COVID-19 patients has shown the presence of inflammatory clusters including mononuclear MGCs and CD4+ T lymphocytes, an observation reminiscent of MGCs in sarcoidosis [8.Tian S. et al.Pulmonary pathology of early-phase 2019 novel coronavirus (COVID-19) pneumonia in two patients with lung cancer.J. Thorac. Oncol. 2020; 15: 700-704Abstract Full Text Full Text PDF PubMed Scopus (1039) Google Scholar]. Moreover, in both sarcoidosis and COVID-19 patients, alveolar lymphocytosis and lymphopenia have been observed in certain cases and considered as potential predictive indicators of a severe course for the two diseases [1.Fung T.S. Liu D.X. Human coronavirus: host-pathogen interaction.Annu. Rev. Microbiol. 2019; 73: 529-557Crossref PubMed Scopus (656) Google Scholar,2.Grunewald J. et al.Sarcoidosis.Nat. Rev. Dis. Primers. 2019; 5: 45-57Crossref PubMed Scopus (278) Google Scholar]. Relevant to our discussion, SARS-CoV-2 downregulates ACE2 by carrying the receptor with it in the cell during infection, leading to increased concentrations of angiotensinogen II and its degradation products, which at high amounts, stimulate apoptosis and are negative regulators of autophagy [1.Fung T.S. Liu D.X. Human coronavirus: host-pathogen interaction.Annu. Rev. Microbiol. 2019; 73: 529-557Crossref PubMed Scopus (656) Google Scholar]. In sarcoidosis, the renin–angiotensin system remains a research focus given that certain ACE2 polymorphisms have been implicated in the progression of pulmonary sarcoidosis [1.Fung T.S. Liu D.X. Human coronavirus: host-pathogen interaction.Annu. Rev. Microbiol. 2019; 73: 529-557Crossref PubMed Scopus (656) Google Scholar]. Furthermore, molecular and bioinformatics studies have shown that the SARS-CoV-2 spike protein can also bind to the glucose-regulated protein 78 or heat shock 70 kD protein 5 cell-surface receptor, known to activate autophagy through the AMP kinase–mTOR pathway [9.Ibrahim I.M. et al.COVID-19 spike-host cell receptor GRP78 binding site prediction.J. Infect. 2020; 80: 554-562Abstract Full Text Full Text PDF PubMed Scopus (393) Google Scholar]. Indeed, the spike protein of coronaviruses is considered to be the main driving force for host cell recognition. Under homeostatic conditions in rat liver and human fibroblasts, SARS-CoV-2 RNA and proteins are found in the vesicular system, driven by the endoplasmic reticulum (ER), and then joining autophagosomes associated with lysosomes and the lytic autophagic process. Different cellular receptors such as Toll-like receptor 3 and retinoic acid inducible gene 1 – closely related to autophagy activation in mammalian granulocyte and macrophage models – have been implicated in innate immunity response to RNA virus infections – for example, coronavirus, measles virus, hepatitis viruses, and influenza virus infections [10.Crosse K.M. et al.Interferon-stimulated genes as enhancers of antiviral innate immune signaling.J. Innate Immun. 2018; 10: 85-93Crossref PubMed Scopus (114) Google Scholar]. In sarcoidosis, 1–10% of patients develop opportunistic infections, mostly related to fungi – for example, Aspergillus sp., Cryptococcus neoformans, and mycobacteria; they can also develop progressive multifocal leukoencephalopathy due to opportunistic polyomavirus infection [11.Jamilloux Y. et al.The spectrum of opportunistic diseases complicating sarcoidosis.Autoimmun. Rev. 2015; 14: 64-74Crossref PubMed Scopus (45) Google Scholar]. These clinical observations raise the question of what the sensitivity of patients with sarcoidosis to respiratory viral disease is, such as that induced by SARS-CoV-2 infection (COVID-19) – presently being explored in several international projects [6.Southern B.D. Patients with interstitial lung disease and pulmonary sarcoidosis are at high risk for severe illness related to COVID-19.Cleve. Clin. J. Med. 2020; (Published online June 18, 2020. https://doi.org/10.3949/ccjm.87a.ccc026)Crossref PubMed Google Scholar]. These studies take into account current treatments and pulmonary status of patients. We hypothesize that the defect in autophagy observed in sarcoidosis patients might also decrease the traffic of viral RNA into vesicles for viral infections, similar to what might be observed for nanoparticles in experimental mouse models. We highlight the possibility that genetic predisposition involving pathogenic variants in genes encoding regulating factors of autophagy might contribute – at least in part – to the deleterious clinical evolution of COVID-19 in a significant proportion of individuals devoid of comorbidities. However, this possibility remains to be robustly tested. Nevertheless, we posit that furthering such knowledge may be vital for either preventing severe and irreversible lung lesions, and/or adapting candidate therapies in the most progressive forms of SARS-CoV-2 infection. This also raises the question of what these genetic susceptibilities to COVID-19 forms might be, as these might be related to various stages of SARS-CoV-2 infection, thus calling for a definition of all steps of host–pathogen interactions at the protein level during this type of infection. Clearly, the substratum of host–pathogen interactions must be related to the genetic background of individuals, thus contributing to the diversity of clinical expression. This is the reason why we argue that it will be relevant to test pharmacological agents capable of modulating regulatory hubs of autophagy. Many of these compounds have strong immunosuppressive effects and are therefore considered deleterious to treating infectious diseases. Certain mTOR or Rac1 inhibitors derived respectively from rapamycin and azathioprine activate autophagy, and are considered as alternative therapies in severe/specific forms of sarcoidosis [1.Fung T.S. Liu D.X. Human coronavirus: host-pathogen interaction.Annu. Rev. Microbiol. 2019; 73: 529-557Crossref PubMed Scopus (656) Google Scholar]. Chloroquine, a well-known antimalarial preventive and curative treatment, brought numerous clinical trials and was considered as a potential efficient therapeutic agent in COVID-19. Paradoxically, chloroquine inhibits autophagy by impairing autophagosome fusion with lysosomes in U2OS and HeLa cells [12.Devaux C.A. et al.New insights on the antiviral effects of chloroquine against coronavirus: what to expect for COVID-19?.Int. J. Antimicrob. Agents. 2020; 55105938Crossref PubMed Scopus (801) Google Scholar]. Of note, this antimalarial agent induces apoptosis by activating ER stress pathways and is frequently used in the treatment of skin sarcoidosis [1.Fung T.S. Liu D.X. Human coronavirus: host-pathogen interaction.Annu. Rev. Microbiol. 2019; 73: 529-557Crossref PubMed Scopus (656) Google Scholar]. Chloroquine might act at various stages of viral infection (e.g., fusion of viral envelope with host cell membranes, decreasing intraluminal acidity, post-translational modifications of viral proteins, export of viral antigens) and contribute to trigger T cell responses and/or inhibition of cytokine production, that is, interleukin (IL)-1, IL-6 and tumor necrosis factor [12.Devaux C.A. et al.New insights on the antiviral effects of chloroquine against coronavirus: what to expect for COVID-19?.Int. J. Antimicrob. Agents. 2020; 55105938Crossref PubMed Scopus (801) Google Scholar]. However, the real benefit of chloroquine remains highly controversial and warrants thorough investigation. Azithromycin, a macrolide that might be combined with chloroquine or other antiviral therapies, has been reported to downregulate mTOR in vitro in regulatory T cells from healthy human donors, and might thus potentially activate autophagy [13.Weng D. et al.Azithromycin treats diffuse panbronchiolitis by targeting T cells via inhibition of mTOR pathway.Biomed. Pharmacother. 2019; 110: 440-448Crossref PubMed Scopus (19) Google Scholar]. Rifampicin and isoniazid, commonly used for tuberculosis treatment, can also activate autophagy, as evidenced from in vitro isoniazid treatment of human hepatocarcinoma HepG2 cells, and thus, might be expected to increase microbial clearance [14.Genestet C. et al.Antituberculous drugs modulate bacterial phagolysosome avoidance and autophagy in Mycobacterium tuberculosis-infected macrophages.Tuberculosis (Edinb.). 2018; 111: 67-70Crossref PubMed Scopus (24) Google Scholar]. Such agents await robust testing. We argue that to build effective and safe therapeutic models, a combinatorial approach to treating infectious diseases (viral, bacterial, and fungal) in large populations affected by COVID-19, as well as in autoinflammatory diseases, should take into account the respective functional effects of therapeutic agents on the pathways regulating ER stress, apoptosis, and macroautophagy (xenophagy). To date, nearly 20 published reports analyzed the human SARS-CoV-2 interactome by pathway enrichment protocols and identified target genes, some of which are putatively involved in sarcoidosis or other autoinflammatory diseases [15.Sadegh S. et al.Exploring the SARS-CoV-2 virus-host-drug interactome for drug repurposing.Nat. Commun. 2020; 113518Crossref PubMed Scopus (132) Google Scholar]. We posit that rare diseases such as sarcoidosis might offer excellent models to test and adapt certain existing treatments to common infections. This work was performed in the framework of a national clinical and research group working on sarcoidosis, Group Sarcoidosis France, and is supported by grants from the Fondation Maladies Rares (France) and the French Research Ministry (INNOVARC–Direction Générale de l'Offre de Soins, DGOS, 12-027-0309). The authors declare that they have no competing interests.