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1.
Science ; 376(6595): eabn6020, 2022 05 20.
Article in English | MEDLINE | ID: covidwho-1861569

ABSTRACT

The detyrosination-tyrosination cycle involves the removal and religation of the C-terminal tyrosine of α-tubulin and is implicated in cognitive, cardiac, and mitotic defects. The vasohibin-small vasohibin-binding protein (SVBP) complex underlies much, but not all, detyrosination. We used haploid genetic screens to identify an unannotated protein, microtubule associated tyrosine carboxypeptidase (MATCAP), as a remaining detyrosinating enzyme. X-ray crystallography and cryo-electron microscopy structures established MATCAP's cleaving mechanism, substrate specificity, and microtubule recognition. Paradoxically, whereas abrogation of tyrosine religation is lethal in mice, codeletion of MATCAP and SVBP is not. Although viable, defective detyrosination caused microcephaly, associated with proliferative defects during neurogenesis, and abnormal behavior. Thus, MATCAP is a missing component of the detyrosination-tyrosination cycle, revealing the importance of this modification in brain formation.


Subject(s)
Carboxypeptidases , Microtubule-Associated Proteins , Microtubules , Protein Processing, Post-Translational , Tubulin , Tyrosine , Animals , Carboxypeptidases/genetics , Cryoelectron Microscopy , Crystallography, X-Ray , Humans , Mice , Microtubule-Associated Proteins/chemistry , Microtubule-Associated Proteins/genetics , Microtubules/chemistry , Tubulin/chemistry , Tyrosine/chemistry
3.
Eur J Med Res ; 26(1): 75, 2021 Jul 13.
Article in English | MEDLINE | ID: covidwho-1309928

ABSTRACT

BACKGROUND: The aim of this study was to evaluate the expression of four up/down-regulated inflammatory miRNAs and their mRNA targets in the serum samples of COVID-19 patients with different grades. Also, we investigated the relative expression of these miRNAs and mRNAs during hospitalization. METHODS: In this cross-sectional study, 5 mL of blood sample were taken from COVID-19 patients with different grades and during hospitalization from several health centers of Yazd, Tehran, and Zahedan province of Iran from December 20, 2020 to March 2, 2021. The relative expression of miRNAs and mRNAs was evaluated by q-PCR. RESULTS: We found that the relative expression of hsa-miR-31-3p, hsa-miR-29a-3p, and hsa-miR-126-3p was significantly decreased and the relative expression of their mRNA targets (ZMYM5, COL5A3, and CAMSAP1) was significantly increased with the increase of disease grade. Conversely, the relative expression of hsa-miR-17-3p was significantly increased and its mRNA target (DICER1) was significantly decreased with the increase of disease grade. This pattern was exactly seen during hospitalization of COVID-19 patients who did not respond to treatment. In COVID-19 patients who responded to treatment, the expression of selected miRNAs and their mRNA targets returned to the normal level. A negative significant correlation was seen between (1) the expression of hsa-miR-31-3p and ZMYM5, (2) hsa-miR-29a-3p and COL5A3, (3) hsa-miR-126-3p and CAMSAP1, and (4) hsa-miR-17-3p and DICER1 in COVID-19 patients with any grade (P < 0.05) and during hospitalization. CONCLUSIONS: In this study, we gained a more accurate understanding of the expression of up/down-regulated inflammatory miRNAs in the blood of COVID-19 patients. The obtained data may help us in the diagnosis and prognosis of COVID-19. TRIAL REGISTRATION: The ethics committee of Zahedan University of Medical Sciences, Zahedan, Iran. (Ethical Code: IR.ZAUMS.REC.1399.316) was registered for this project.


Subject(s)
COVID-19/genetics , Gene Expression Profiling , MicroRNAs/genetics , RNA, Messenger/genetics , COVID-19/blood , COVID-19/virology , Carrier Proteins/genetics , Collagen/genetics , Cross-Sectional Studies , DEAD-box RNA Helicases/genetics , Hospitalization/statistics & numerical data , Humans , Iran , Microtubule-Associated Proteins/genetics , Nuclear Proteins/genetics , Ribonuclease III/genetics , SARS-CoV-2/physiology , Severity of Illness Index
4.
J Med Virol ; 93(8): 5182-5187, 2021 08.
Article in English | MEDLINE | ID: covidwho-1298501

ABSTRACT

Infections due to human herpesvirus 6 (HHV-6) are frequent during early childhood. Usually, they have a favorable clinical course. Conversely, HHV-6 congenital infections occur in about 1% of neonates and may present with more severe clinical pictures. HHV-6 can be found in lung tissues and bronchoalveolar lavage (BAL) samples from patients with pneumonia and in immunocompromised patients can cause mild to severe pneumonia. In neonates, the role of HHV-6 in the genesis of severe pneumonia is poorly defined still now. We describe a healthy infant with a late-onset (15 days of life) severe interstitial pneumonia and heavy HHV-6 genome load, persistently detected in its BAL fluid. The baby underwent high-frequency oscillatory ventilation, hydroxychloroquine, steroids, and ganciclovir for 6 weeks and at 9 months she died. Next-generation sequencing of genes known to cause neonatal respiratory insufficiency revealed the presence of a "probably pathogenetic" heterozygous variant in the autosomal recessive DRC1 gene, a heterozygous variant of unknown significance (VUS) in the autosomal recessive RSPH9 gene, and a heterozygous VUS in the autosomal recessive MUC5B gene. HHV-6 infection should be considered in the differential diagnosis of late-onset severe respiratory distress in neonates and the co-occurrence of genetic predisposing factors or modifiers should be tested by specific molecular techniques. The intensity of HHV-6 genome load in BAL fluid could be an indicator of the response to antiviral therapy.


Subject(s)
Genetic Predisposition to Disease/genetics , Lung Diseases, Interstitial/genetics , Roseolovirus Infections/genetics , Cytoskeletal Proteins/genetics , Fatal Outcome , Female , Genetic Variation , Herpesvirus 6, Human/genetics , Herpesvirus 6, Human/isolation & purification , Heterozygote , Humans , Infant, Newborn , Lung Diseases, Interstitial/therapy , Lung Diseases, Interstitial/virology , Microtubule-Associated Proteins/genetics , Mucin-5B/genetics , Pneumonia, Viral/genetics , Pneumonia, Viral/therapy , Pneumonia, Viral/virology , Roseolovirus Infections/therapy , Roseolovirus Infections/virology , Viral Load
5.
Sci Signal ; 14(675)2021 03 23.
Article in English | MEDLINE | ID: covidwho-1186203

ABSTRACT

Nicotinic acid adenine dinucleotide phosphate (NAADP) is a second messenger that releases Ca2+ from acidic organelles through the activation of two-pore channels (TPCs) to regulate endolysosomal trafficking events. NAADP action is mediated by NAADP-binding protein(s) of unknown identity that confer NAADP sensitivity to TPCs. Here, we used a "clickable" NAADP-based photoprobe to isolate human NAADP-binding proteins and identified Jupiter microtubule-associated homolog 2 (JPT2) as a TPC accessory protein required for endogenous NAADP-evoked Ca2+ signaling. JPT2 was also required for the translocation of a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pseudovirus through the endolysosomal system. Thus, JPT2 is a component of the NAADP receptor complex that is essential for TPC-dependent Ca2+ signaling and control of coronaviral entry.


Subject(s)
COVID-19/metabolism , COVID-19/virology , Calcium Signaling/physiology , Microtubule-Associated Proteins/metabolism , NADP/analogs & derivatives , SARS-CoV-2/physiology , Affinity Labels , Animals , Calcium Channels/metabolism , Carrier Proteins/metabolism , Click Chemistry/methods , Gene Knockdown Techniques , HEK293 Cells , Humans , Microtubule-Associated Proteins/antagonists & inhibitors , Microtubule-Associated Proteins/genetics , NADP/metabolism , Recombinant Proteins/genetics , Recombinant Proteins/metabolism , Second Messenger Systems/physiology , Transcriptome , Virus Internalization
6.
Eur J Hum Genet ; 29(6): 1019-1026, 2021 06.
Article in English | MEDLINE | ID: covidwho-1111983

ABSTRACT

Germline variants in genes involved in SARS-CoV-2 cell entry and in host innate immune responses to viruses may influence the susceptibility to infection. This study used whole-genome analyses of lung tissue to identify polymorphisms acting as expression quantitative trait loci (eQTLs) for 60 genes of relevance to SARS-CoV-2 infection susceptibility. The expression of genes with confirmed or possible roles in viral entry-replication and in host antiviral responses was studied in the non-diseased lung tissue of 408 lung adenocarcinoma patients. No gene was differently expressed by sex, but APOBEC3H levels were higher and PARP12 levels lower in older individuals. A total of 125 cis-eQTLs (false discovery rate < 0.05) was found to modulate mRNA expression of 15 genes (ABO, ANPEP, AP2A2, APOBEC3D, APOBEC3G, BSG, CLEC4G, DDX58, DPP4, FURIN, FYCO1, RAB14, SERINC3, TRIM5, ZCRB1). eQTLs regulating ABO and FYCO1 were found in COVID-19 susceptibility loci. No trans-eQTLs were identified. Genetic control of the expression of these 15 genes, which encode putative virus receptors, proteins required for vesicle trafficking, enzymes that interfere with viral replication, and other restriction factors, may underlie interindividual differences in risk or severity of infection with SARS-CoV-2 or other viruses.


Subject(s)
ABO Blood-Group System/genetics , COVID-19/genetics , Galactosyltransferases/genetics , Genetic Predisposition to Disease , Microtubule-Associated Proteins/genetics , COVID-19/virology , Gene Expression Regulation/genetics , Humans , Immunity, Innate/genetics , Lung/metabolism , Lung/pathology , Polymorphism, Genetic , Quantitative Trait Loci/genetics , Receptors, Virus/genetics , SARS-CoV-2/genetics , SARS-CoV-2/pathogenicity
7.
Sci Rep ; 10(1): 22303, 2020 12 18.
Article in English | MEDLINE | ID: covidwho-989953

ABSTRACT

The increasing body of literature describing the role of host factors in COVID-19 pathogenesis demonstrates the need to combine diverse, multi-omic data to evaluate and substantiate the most robust evidence and inform development of therapies. Here we present a dynamic ranking of host genes implicated in human betacoronavirus infection (SARS-CoV-2, SARS-CoV, MERS-CoV, seasonal coronaviruses). We conducted an extensive systematic review of experiments identifying potential host factors. Gene lists from diverse sources were integrated using Meta-Analysis by Information Content (MAIC). This previously described algorithm uses data-driven gene list weightings to produce a comprehensive ranked list of implicated host genes. From 32 datasets, the top ranked gene was PPIA, encoding cyclophilin A, a druggable target using cyclosporine. Other highly-ranked genes included proposed prognostic factors (CXCL10, CD4, CD3E) and investigational therapeutic targets (IL1A) for COVID-19. Gene rankings also inform the interpretation of COVID-19 GWAS results, implicating FYCO1 over other nearby genes in a disease-associated locus on chromosome 3. Researchers can search and review the gene rankings and the contribution of different experimental methods to gene rank at https://baillielab.net/maic/covid19 . As new data are published we will regularly update the list of genes as a resource to inform and prioritise future studies.


Subject(s)
COVID-19/epidemiology , COVID-19/genetics , Algorithms , CD3 Complex/genetics , CD4 Antigens/genetics , Chemokine CXCL10/genetics , Computational Biology , Cyclophilin A/genetics , Cyclosporine/pharmacology , Databases, Genetic , Genome-Wide Association Study , Genomics , Humans , Immune System , Immunogenetics , Inflammation , Interleukin-1alpha/genetics , Microtubule-Associated Proteins/genetics , Proteomics
8.
FEBS J ; 287(17): 3672-3676, 2020 09.
Article in English | MEDLINE | ID: covidwho-960854

ABSTRACT

The novel coronavirus SARS-CoV-2 is the causative agent of the global coronavirus disease 2019 (COVID-19) outbreak. In addition to pneumonia, other COVID-19-associated symptoms have been reported, including loss of smell (anosmia). However, the connection between infection with coronavirus and anosmia remains enigmatic. It has been reported that defects in olfactory cilia lead to anosmia. In this Viewpoint, we summarize transmission electron microscopic studies of cilia in virus-infected cells. In the human nasal epithelium, coronavirus infects the ciliated cells and causes deciliation. Research has shown that viruses such as influenza and Sendai attach to the ciliary membrane. The Sendai virus enters cilia by fusing its viral membrane with the ciliary membrane. A recent study on SARS-CoV-2-human protein-protein interactions revealed that the viral nonstructural protein Nsp13 interacts with the centrosome components, providing a potential molecular link. The mucociliary escalator removes inhaled pathogenic particles and functions as the first line of protection mechanism against viral infection in the human airway. Thus, future investigation into the virus-cilium interface will help further the battle against COVID-19.


Subject(s)
Anosmia/metabolism , COVID-19/metabolism , Centrosome/virology , Cilia/virology , Nasal Mucosa/virology , SARS-CoV-2/pathogenicity , Viral Nonstructural Proteins/metabolism , Anosmia/complications , Anosmia/physiopathology , Anosmia/virology , COVID-19/complications , COVID-19/physiopathology , COVID-19/virology , Centrosome/metabolism , Centrosome/ultrastructure , Cilia/metabolism , Cilia/ultrastructure , Host-Pathogen Interactions/genetics , Humans , Methyltransferases/genetics , Methyltransferases/metabolism , Microtubule-Associated Proteins/genetics , Microtubule-Associated Proteins/metabolism , Nasal Mucosa/metabolism , Nasal Mucosa/ultrastructure , Orthomyxoviridae/metabolism , Orthomyxoviridae/pathogenicity , Protein Binding , RNA Helicases/genetics , RNA Helicases/metabolism , SARS-CoV-2/metabolism , Sendai virus/metabolism , Sendai virus/pathogenicity , Severity of Illness Index , Smell/physiology , Viral Nonstructural Proteins/genetics
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