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Musalkova D, Piherova L, Kwasny O, Dindova Z, Stancik L, Hartmannova H, Slama O, Peckova P, Pargac J, Minarik G, Zima T, Bleyer AJ, Radina M, Pohludka M, Kmoch S. Trends in SARS-CoV-2 cycle threshold values in the Czech Republic from April 2020 to April 2022. Sci Rep 2023; 13:6156. [PMID: 37061534 PMCID: PMC10105352 DOI: 10.1038/s41598-023-32953-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 04/05/2023] [Indexed: 04/17/2023] Open
Abstract
The inability to predict the evolution of the COVID-19 epidemic hampered abilities to respond to the crisis effectively. The cycle threshold (Ct) from the standard SARS-CoV-2 quantitative reverse transcription-PCR (RT-qPCR) clinical assay is inversely proportional to the amount of SARS-CoV-2 RNA in the sample. We were interested to see if population Ct values could predict future increases in COVID-19 cases as well as subgroups that would be more likely to be affected. This information would have been extremely helpful early in the COVID-19 epidemic. We therefore conducted a retrospective analysis of demographic data and Ct values from 2,076,887 nasopharyngeal swab RT-qPCR tests that were performed at a single diagnostic laboratory in the Czech Republic from April 2020 to April 2022 and from 221,671 tests that were performed as a part of a mandatory school surveillance testing program from March 2021 to March 2022. We found that Ct values could be helpful predictive tools in the real-time management of viral epidemics. First, early measurement of Ct values would have indicated the low viral load in children, equivalent viral load in males and females, and higher viral load in older individuals. Second, rising or falling median Ct values and differences in Ct distribution indicated changes in the transmission in the population. Third, monitoring Ct values and positivity rates would have provided early evidence as to whether prevention measures are effective. Health system authorities should thus consider collecting weekly median Ct values of positively tested samples from major diagnostic laboratories for regional epidemic surveillance.
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Affiliation(s)
- Dita Musalkova
- Research Unit of Rare Diseases, Department of Paediatric and Adolescent Medicine, First Faculty of Medicine, Charles University in Prague and General University Hospital in Prague, Prague, Czech Republic
| | - Lenka Piherova
- Research Unit of Rare Diseases, Department of Paediatric and Adolescent Medicine, First Faculty of Medicine, Charles University in Prague and General University Hospital in Prague, Prague, Czech Republic
| | | | | | | | - Hana Hartmannova
- Research Unit of Rare Diseases, Department of Paediatric and Adolescent Medicine, First Faculty of Medicine, Charles University in Prague and General University Hospital in Prague, Prague, Czech Republic
| | - Otomar Slama
- Faculty of Safety Engineering, Technical University of Ostrava, Ostrava, Czech Republic
- Charles University Innovations Prague, Prague, Czech Republic
| | - Petra Peckova
- Regional Authority of the Central Bohemia Region, Prague, Czech Republic
| | | | | | - Tomas Zima
- Institute of Medical Biochemistry and Laboratory Diagnostics, General University Hospital and the First Faculty of Medicine of Charles University, Prague, Czech Republic
| | - Anthony J Bleyer
- Research Unit of Rare Diseases, Department of Paediatric and Adolescent Medicine, First Faculty of Medicine, Charles University in Prague and General University Hospital in Prague, Prague, Czech Republic
- Section on Nephrology, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | | | | | - Stanislav Kmoch
- Research Unit of Rare Diseases, Department of Paediatric and Adolescent Medicine, First Faculty of Medicine, Charles University in Prague and General University Hospital in Prague, Prague, Czech Republic.
- Medirex Group Academy, Trnava, Slovakia.
- Section on Nephrology, Wake Forest School of Medicine, Winston-Salem, NC, USA.
- GeneSpector, Prague, Czech Republic.
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Musalkova D, Majer F, Kuchar L, Luksan O, Asfaw B, Vlaskova H, Storkanova G, Reboun M, Poupetova H, Jahnova H, Hulkova H, Ledvinova J, Dvorakova L, Sikora J, Jirsa M, Vanier MT, Hrebicek M. Transcript, protein, metabolite and cellular studies in skin fibroblasts demonstrate variable pathogenic impacts of NPC1 mutations. Orphanet J Rare Dis 2020; 15:85. [PMID: 32248828 PMCID: PMC7132889 DOI: 10.1186/s13023-020-01360-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 03/17/2020] [Indexed: 12/18/2022] Open
Abstract
Background Niemann-Pick type C (NP-C) is a rare neurovisceral genetic disorder caused by mutations in the NPC1 or the NPC2 gene. NPC1 is a multipass-transmembrane protein essential for egress of cholesterol from late endosomes/lysosomes. To evaluate impacts of NPC1 mutations, we examined fibroblast cultures from 26 NP-C1 patients with clinical phenotypes ranging from infantile to adult neurologic onset forms. The cells were tested with multiple assays including NPC1 mRNA expression levels and allele expression ratios, assessment of NPC1 promoter haplotypes, NPC1 protein levels, cellular cholesterol staining, localization of the mutant NPC1 proteins to lysosomes, and cholesterol/cholesteryl ester ratios. These results were correlated with phenotypes of the individual patients. Results Overall we identified 5 variant promoter haplotypes. Three of them showed reporter activity decreased down to 70% of the control sequence. None of the haplotypes were consistently associated with more severe clinical presentation of NP-C. Levels of transcripts carrying null NPC1 alleles were profoundly lower than levels of the missense variants. Low levels of the mutant NPC1 protein were identified in most samples. The protein localised to lysosomes in cultures expressing medium to normal NPC1 levels. Fibroblasts from patients with severe infantile phenotypes had higher cholesterol levels and higher cholesterol/cholesteryl ester ratios. On the contrary, cell lines from patients with juvenile and adolescent/adult phenotypes showed values comparable to controls. Conclusion No single assay fully correlated with the disease severity. However, low residual levels of NPC1 protein and high cholesterol/cholesteryl ester ratios associated with severe disease. The results suggest not only low NPC1 expression due to non-sense mediated decay or low mutant protein stability, but also dysfunction of the stable mutant NPC1 as contributors to the intracellular lipid transport defect.
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Affiliation(s)
- Dita Musalkova
- Research Unit for Rare Diseases, Department of Pediatrics and Adolescent Medicine, First Faculty of Medicine, Charles University and General University Hospital, Ke Karlovu 2, 120 00, Prague 2, Czech Republic
| | - Filip Majer
- Research Unit for Rare Diseases, Department of Pediatrics and Adolescent Medicine, First Faculty of Medicine, Charles University and General University Hospital, Ke Karlovu 2, 120 00, Prague 2, Czech Republic.
| | - Ladislav Kuchar
- Research Unit for Rare Diseases, Department of Pediatrics and Adolescent Medicine, First Faculty of Medicine, Charles University and General University Hospital, Ke Karlovu 2, 120 00, Prague 2, Czech Republic
| | - Ondrej Luksan
- Laboratory of Experimental Hepatology, Institute of Clinical and Experimental Medicine, Prague, Czech Republic
| | - Befekadu Asfaw
- Research Unit for Rare Diseases, Department of Pediatrics and Adolescent Medicine, First Faculty of Medicine, Charles University and General University Hospital, Ke Karlovu 2, 120 00, Prague 2, Czech Republic
| | - Hana Vlaskova
- Research Unit for Rare Diseases, Department of Pediatrics and Adolescent Medicine, First Faculty of Medicine, Charles University and General University Hospital, Ke Karlovu 2, 120 00, Prague 2, Czech Republic
| | - Gabriela Storkanova
- Research Unit for Rare Diseases, Department of Pediatrics and Adolescent Medicine, First Faculty of Medicine, Charles University and General University Hospital, Ke Karlovu 2, 120 00, Prague 2, Czech Republic
| | - Martin Reboun
- Research Unit for Rare Diseases, Department of Pediatrics and Adolescent Medicine, First Faculty of Medicine, Charles University and General University Hospital, Ke Karlovu 2, 120 00, Prague 2, Czech Republic
| | - Helena Poupetova
- Research Unit for Rare Diseases, Department of Pediatrics and Adolescent Medicine, First Faculty of Medicine, Charles University and General University Hospital, Ke Karlovu 2, 120 00, Prague 2, Czech Republic
| | - Helena Jahnova
- Research Unit for Rare Diseases, Department of Pediatrics and Adolescent Medicine, First Faculty of Medicine, Charles University and General University Hospital, Ke Karlovu 2, 120 00, Prague 2, Czech Republic
| | - Helena Hulkova
- Research Unit for Rare Diseases, Department of Pediatrics and Adolescent Medicine, First Faculty of Medicine, Charles University and General University Hospital, Ke Karlovu 2, 120 00, Prague 2, Czech Republic
| | - Jana Ledvinova
- Research Unit for Rare Diseases, Department of Pediatrics and Adolescent Medicine, First Faculty of Medicine, Charles University and General University Hospital, Ke Karlovu 2, 120 00, Prague 2, Czech Republic
| | - Lenka Dvorakova
- Research Unit for Rare Diseases, Department of Pediatrics and Adolescent Medicine, First Faculty of Medicine, Charles University and General University Hospital, Ke Karlovu 2, 120 00, Prague 2, Czech Republic
| | - Jakub Sikora
- Research Unit for Rare Diseases, Department of Pediatrics and Adolescent Medicine, First Faculty of Medicine, Charles University and General University Hospital, Ke Karlovu 2, 120 00, Prague 2, Czech Republic
| | - Milan Jirsa
- Laboratory of Experimental Hepatology, Institute of Clinical and Experimental Medicine, Prague, Czech Republic
| | - Marie T Vanier
- INSERM U820, Lyon, France.,Laboratoire Gillet-Mérieux, Lyon University Hospitals (HCL), Lyon, France
| | - Martin Hrebicek
- Research Unit for Rare Diseases, Department of Pediatrics and Adolescent Medicine, First Faculty of Medicine, Charles University and General University Hospital, Ke Karlovu 2, 120 00, Prague 2, Czech Republic.
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Richtrova E, Mrazova LS, Musalkova D, Luksan O, Stolnaya L, Minks J, Lukas J, Dvorakova L, Jirsa M, Hrebicek M. HGSNAT has a TATA-less promoter with multiple starts of transcription. Gene 2016; 592:36-42. [PMID: 27452122 DOI: 10.1016/j.gene.2016.07.051] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Revised: 07/08/2016] [Accepted: 07/21/2016] [Indexed: 11/15/2022]
Abstract
Acetyl-CoA:α-glucosaminide N-acetyltransferase (N-acetyltransferase) is a lysosomal membrane enzyme that catalyzes a key step in the lysosomal degradation of heparan sulfate. Its deficiency causes Sanfilippo syndrome type IIIC (Mucopolysaccharidosis type IIIC, MPS IIIC). Here we characterize the promoter region of HGSNAT, the gene encoding N-acetyltransferase, which is located in the pericentromeric region of chromosome 8. We show that HGSNAT transcription is driven by a TATA-less promoter whose key elements are contained within the 1054bp region upstream of exon 1. About 400 bases of the region's 3'-prime end overlap with an unmethylated CpG island. Reduced reporter activities from promoter serial deletion constructs suggested strong regulatory elements at positions -101 to -20bp and -1073 to -716bp of the downstream initiation codon (DS-ATG). Targeted mutagenesis of the first Specificity protein 1-A (Sp1-A) of the six in silico-predicted Sp1 sites in the region flanking the major transcription start sites (TSSs, +50/-101) led to a 55% decrease of reporter activity, while inactivation of each of Sp1-B and Sp1-C resulted in its almost two-fold increase. The binding of Sp1 to the region was confirmed by chromatin immunoprecipitation (ChIP). Overall, this confirms that Sp1 is important for regulation of the HGSNAT promoter. Promoter fragments in antisense orientation (constructs pGL4 -20/-1305 and pGL4 +50/-1305) led to reporter activities of about 50% of the pGL4 -1305/-20 activity, implying divergent initiation of transcription at the promoter. We identified two main TSSs at positions +1 and -15 from DS-ATG using Rapid amplification of cDNA ends (5'RACE). Transcripts initiating at the TSSs thus contain only DS-ATG. Five patients from our MPS IIIC cohort (n=23) carried the rs4523300 promoter variant and one the rs149596192 promoter variant. Both variants lowered the expression of the reporter down to 68% and 59%, respectively. However, white blood cell (WBC) N-acetyltransferase activities in individuals carrying the variants did not significantly differ from homozygotes for the wild-type alleles, suggesting only a partial impact of transcriptional regulation on N-acetyltransferase activities in vivo.
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Affiliation(s)
- Eva Richtrova
- Institute of Inherited Metabolic Disorders, First Faculty of Medicine, Charles University in Prague and General University Hospital in Prague, Ke Karlovu 2, Prague 120 08, Czech Republic.
| | - Lenka S Mrazova
- Institute of Inherited Metabolic Disorders, First Faculty of Medicine, Charles University in Prague and General University Hospital in Prague, Ke Karlovu 2, Prague 120 08, Czech Republic.
| | - Dita Musalkova
- Institute of Inherited Metabolic Disorders, First Faculty of Medicine, Charles University in Prague and General University Hospital in Prague, Ke Karlovu 2, Prague 120 08, Czech Republic.
| | - Ondrej Luksan
- Laboratory of Experimental Hepatology, Institute of Clinical and Experimental Medicine, Vídeňská 1958/9, Prague 140 21, Czech Republic.
| | - Larisa Stolnaya
- Institute of Inherited Metabolic Disorders, First Faculty of Medicine, Charles University in Prague and General University Hospital in Prague, Ke Karlovu 2, Prague 120 08, Czech Republic.
| | - Jakub Minks
- Institute of Inherited Metabolic Disorders, First Faculty of Medicine, Charles University in Prague and General University Hospital in Prague, Ke Karlovu 2, Prague 120 08, Czech Republic.
| | - Jan Lukas
- Institute of Inherited Metabolic Disorders, First Faculty of Medicine, Charles University in Prague and General University Hospital in Prague, Ke Karlovu 2, Prague 120 08, Czech Republic.
| | - Lenka Dvorakova
- Institute of Inherited Metabolic Disorders, First Faculty of Medicine, Charles University in Prague and General University Hospital in Prague, Ke Karlovu 2, Prague 120 08, Czech Republic.
| | - Milan Jirsa
- Laboratory of Experimental Hepatology, Institute of Clinical and Experimental Medicine, Vídeňská 1958/9, Prague 140 21, Czech Republic.
| | - Martin Hrebicek
- Institute of Inherited Metabolic Disorders, First Faculty of Medicine, Charles University in Prague and General University Hospital in Prague, Ke Karlovu 2, Prague 120 08, Czech Republic.
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Kostalova E, Pavelka K, Vlaskova H, Musalkova D, Stiburkova B. Corrigendum to “Hyperuricemia and gout due to deficiency of hypoxanthine–guanine phosphoribosyltransferase in female carriers: New insight to differential diagnosis” [Clin. Chim. Acta 440 (2015) 214–217]. Clin Chim Acta 2015. [DOI: 10.1016/j.cca.2015.04.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Kostalova E, Pavelka K, Vlaskova H, Musalkova D, Stiburkova B. Hyperuricemia and gout due to deficiency of hypoxanthine-guanine phosphoribosyltransferase in female carriers: New insight to differential diagnosis. Clin Chim Acta 2014; 440:214-7. [PMID: 25476133 DOI: 10.1016/j.cca.2014.11.026] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Revised: 11/25/2014] [Accepted: 11/25/2014] [Indexed: 11/28/2022]
Abstract
BACKGROUND X-linked hypoxanthine-guanine phosphoribosyltransferase (HPRT) deficiency in an inherited disorder of purine metabolism is usually associated with the clinical manifestations of hyperuricemia. A variable spectrum of neurological involvement occurs predominantly in males. Females are usually asymptomatic. Carrier status cannot be confirmed by biochemical and enzymatic methods reliably. METHODS We studied clinical, biochemical and molecular genetic characteristics of Czech families with hyperuricemia and HPRT deficiency. We analyzed age at diagnosis, clinical symptoms, uricemia, urinary hypoxanthine and xanthine, HPRT activity in erythrocytes, mutation in the HPRT1 gene, X-inactivation, and major urate transporters. RESULTS A mutation in the HPRT1 gene in family A was confirmed in one boy and four females. Three females with hyperuricemia had normal excretion of purine. One female was normouricemic. An 8-month-old boy with neurological symptoms showed hyperuricemia, increased excretion of urinary hypoxanthine and xanthine and a very low HPRT activity in erythrocytes. We have found three other unrelated female carriers with hyperuricemia and normal excretion of hypoxanthine and xanthine among other families with HPRT deficiency. CONCLUSIONS HPRT deficiency needs to be considered in females with hyperuricemia with normal excretion of purine metabolites. Familiar hyperuricemia and/or nonfamiliar gout should always be further investigated, especially in children.
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Affiliation(s)
- Eva Kostalova
- Institute of Inherited Metabolic Disorders, First Faculty of Medicine, Charles University in Prague and General University Hospital in Prague, Prague, Czech Republic
| | | | - Hana Vlaskova
- Institute of Inherited Metabolic Disorders, First Faculty of Medicine, Charles University in Prague and General University Hospital in Prague, Prague, Czech Republic
| | | | - Blanka Stiburkova
- Institute of Inherited Metabolic Disorders, First Faculty of Medicine, Charles University in Prague and General University Hospital in Prague, Prague, Czech Republic; Institute of Rheumatology, Prague, Czech Republic.
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Musalkova D, Minks J, Storkanova G, Dvorakova L, Hrebicek M. Identification of novel informative loci for DNA-based X-inactivation analysis. Blood Cells Mol Dis 2014; 54:210-6. [PMID: 25455112 DOI: 10.1016/j.bcmd.2014.10.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Revised: 02/23/2014] [Accepted: 04/23/2014] [Indexed: 01/19/2023]
Abstract
The HUMARA assay, the most common method for evaluation of X-inactivation skewing in blood cells, has been reported to be usable in only about 80% of females, emphasizing the need for alternative methods for testing of HUMARA-uninformative individuals. We conducted an in silico search for potentially polymorphic tri-to-hexanucleotide repeats in the proximity of CpG islands located in 5' regions of X-chromosome genes to design five candidate assays (numbered I, II, III, IV, and V) combining methylation-specific restriction digest with PCR amplification in a manner similar to the HUMARA assay. The results obtained by these assays in 100 healthy females were compared to X-inactivation skewing measured by the AR-MSP method which is based on methylation-specific PCR amplification of the first exon of the AR gene. On the basis of statistical evidence, three of the novel assays (II, IV, and V), which were informative in 18%, 61%, and 55% of females in the cohort, respectively, may be used as alternatives or conjointly with the HUMARA assay to improve its reliability. The three new assays were combined with the HUMARA assay into a novel X-inactivation test leading to the increase of informative females in the cohort from 67% to 96%.
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Affiliation(s)
- Dita Musalkova
- Institute of Inherited Metabolic Disorders, First Faculty of Medicine, Charles University in Prague and General University Hospital in Prague, Prague, Czech Republic
| | - Jakub Minks
- Institute of Inherited Metabolic Disorders, First Faculty of Medicine, Charles University in Prague and General University Hospital in Prague, Prague, Czech Republic
| | - Gabriela Storkanova
- Institute of Inherited Metabolic Disorders, First Faculty of Medicine, Charles University in Prague and General University Hospital in Prague, Prague, Czech Republic
| | - Lenka Dvorakova
- Institute of Inherited Metabolic Disorders, First Faculty of Medicine, Charles University in Prague and General University Hospital in Prague, Prague, Czech Republic
| | - Martin Hrebicek
- Institute of Inherited Metabolic Disorders, First Faculty of Medicine, Charles University in Prague and General University Hospital in Prague, Prague, Czech Republic.
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