Impact of Inflammation-Related Genes on COVID-19: Prospective Study at Turkish Cohort.

The pandemic coronavirus disease 2019 (COVID-19) has caused a high mortality rate and poses a significant threat to the population. The disease may progress with mild symptoms or may cause the need for intensive care, depending on many factors. In this study, it was aimed to determine if there is a tendency due to genetic factors in COVID-19 patients. Ninety-four of 188 patients with mild clinical and 94 with severe clinical symptoms were included in the study. The targeted panel including coagulopathy (F2, F5), viral invasion (ACE2), and inflammation (CXCL8, IFNAR2, IFNL4, IL10, IL2, IL6, IRF7, TLR3, TLR7, TNF) related genes was performed sequenced by the next generation sequencing (NGS). The variants found were classified and univariate analyses were performed to select candidate variables for logistic model. Risk factors and variants were compared. It was revealed that the presence of 2 or more risk factors caused the disease to progress severely (p < 0.001). Heterozygous IRF7:c.1357-23dup variant had a 2.5 times higher risk for mild disease compared to severe disease. Other variants were found to be more significant in mild disease. Since polymorphic variants were not evaluated in the literature, the findings of our study could not be compared with the literature. However, as variants that may be effective in the severity of infections may differ according to ethnicity. This study has the feature of being a guide for subsequent studies to be carried out especially in Turkish population. Clinical course of the COVID-19 is likely to depend on a variety of risk factors, including age, sex, clinical status, immunology and genetic factors.

Neuromuscular disease genetics in under-represented populations: increasing data diversity.

Neuromuscular diseases (NMDs) affect ∼15 million people globally. In high income settings DNA-based diagnosis has transformed care pathways and led to gene-specific therapies. However, most affected families are in low-to-middle income countries (LMICs) with limited access to DNA-based diagnosis. Most (86%) published genetic data is derived from European ancestry. This marked genetic data inequality hampers understanding of genetic diversity and hinders accurate genetic diagnosis in all income settings. We developed a cloud-based transcontinental partnership to build diverse, deeply-phenotyped and genetically characterized cohorts to improve genetic architecture knowledge, and potentially advance diagnosis and clinical management. We connected 18 centres in Brazil, India, South Africa, Turkey, Zambia, Netherlands and the UK. We co-developed a cloud-based data solution and trained 17 international neurology fellows in clinical genomic data interpretation. Single gene and whole exome data were analysed via a bespoke bioinformatics pipeline and reviewed alongside clinical and phenotypic data in global webinars to inform genetic outcome decisions. We recruited 6001 participants in the first 43 months. Initial genetic analyses 'solved' or 'possibly solved' ∼56% probands overall. In-depth genetic data review of the four commonest clinical categories (limb girdle muscular dystrophy, inherited peripheral neuropathies, congenital myopathy/muscular dystrophies and Duchenne/Becker muscular dystrophy) delivered a ∼59% 'solved' and ∼13% 'possibly solved' outcome. Almost 29% of disease causing variants were novel, increasing diverse pathogenic variant knowledge. Unsolved participants represent a new discovery cohort. The dataset provides a large resource from under-represented populations for genetic and translational research. In conclusion, we established a remote transcontinental partnership to assess genetic architecture of NMDs across diverse populations. It supported DNA-based diagnosis, potentially enabling genetic counselling, care pathways and eligibility for gene-specific trials. Similar virtual partnerships could be adopted by other areas of global genomic neurological practice to reduce genetic data inequality and benefit patients globally.

High diagnostic yield with algorithmic molecular approach on hereditary neuropathies.

OBJECTIVE: Charcot-Marie-Tooth disease covers a group of inherited peripheral neuropathies. The aim of this study was to investigate the effect of targeted next-generation sequencing panels on the molecular diagnosis of Charcot-Marie-Tooth disease and its subtypes in routine clinical practice, and also to show the limitations and importance of next-generation sequencing in the diagnosis of Charcot-Marie-Tooth diseases. METHODS: This is a retrospective study. Three different molecular methods (multiplex ligation probe amplification, next-generation sequencing, and whole-exome sequencing) were used to detect the mutations related to Charcot-Marie-Tooth disease. RESULTS: In total, 64 patients (33 males and 31 females) with suspected Charcot-Marie-Tooth disease were analyzed for molecular etiology. In all, 25 (39%) patients were diagnosed by multiplex ligation probe amplification. With an extra 11 patients with normal PMP22 multiplex ligation probe amplification results that were consulted to our laboratory for further genetic analysis, a total of 50 patients underwent next-generation sequencing for targeted gene panels associated with Charcot-Marie-Tooth disease. Notably, 18 (36%) patients had pathogenic/likely pathogenic variants. Whole-exome sequencing was performed on five patients with normal next-generation sequencing results; the diagnostic yield by whole-exome sequencing was 80% and it was higher in the childhood group. CONCLUSION: The molecular etiology in Charcot-Marie-Tooth disease patients can be determined according to pre-test evaluation, deciding the inheritance type with pedigree analysis, the clinical phenotype, and an algorithm for the genetic analysis. The presence of patients without a molecular diagnosis in all the literature suggests that there are new genes or mechanisms waiting to be discovered in the etiology of Charcot-Marie-Tooth disease.

High diagnostic yield with algorithmic molecular approach on hereditary neuropathies

SUMMARY OBJECTIVE: Charcot-Marie-Tooth disease covers a group of inherited peripheral neuropathies. The aim of this study was to investigate the effect of targeted next-generation sequencing panels on the molecular diagnosis of Charcot-Marie-Tooth disease and its subtypes in routine clinical practice, and also to show the limitations and importance of next-generation sequencing in the diagnosis of Charcot-Marie-Tooth diseases. METHODS: This is a retrospective study. Three different molecular methods (multiplex ligation probe amplification, next-generation sequencing, and whole-exome sequencing) were used to detect the mutations related to Charcot-Marie-Tooth disease. RESULTS: In total, 64 patients (33 males and 31 females) with suspected Charcot-Marie-Tooth disease were analyzed for molecular etiology. In all, 25 (39%) patients were diagnosed by multiplex ligation probe amplification. With an extra 11 patients with normal PMP22 multiplex ligation probe amplification results that were consulted to our laboratory for further genetic analysis, a total of 50 patients underwent next-generation sequencing for targeted gene panels associated with Charcot-Marie-Tooth disease. Notably, 18 (36%) patients had pathogenic/likely pathogenic variants. Whole-exome sequencing was performed on five patients with normal next-generation sequencing results; the diagnostic yield by whole-exome sequencing was 80% and it was higher in the childhood group. CONCLUSION: The molecular etiology in Charcot-Marie-Tooth disease patients can be determined according to pre-test evaluation, deciding the inheritance type with pedigree analysis, the clinical phenotype, and an algorithm for the genetic analysis. The presence of patients without a molecular diagnosis in all the literature suggests that there are new genes or mechanisms waiting to be discovered in the etiology of Charcot-Marie-Tooth disease.

Relationship between asthma and IL-17 gene polymorphism in a Turkish population.

BACKGROUND: Asthma is a prevalent chronic obstructive disease of the airways. AIMS: The aim of our study was to investigate the relationship between asthma and IL-17F gene 74488 T > C, IL-17A gene -197G > A, and IL17A gene -737C > T polymorphisms in Turkish population. METHODS: In our study, peripheral blood samples collected from a total of 127 subjects, with 65 in the patient group and 62 in the control group, were analyzed for IL-17F gene 74488 T > C, IL-17A gene -197G > A, and IL17A gene -737C > T polymorphisms using next-generation sequencing. RESULTS: There was no statistically significant relationship between IL-17A gene -197G > A and IL-17A gene -737C > T polymorphisms and the risk of developing asthma. It was found that the risk of developing asthma was 2.9-fold higher in individuals with a C allele in the IL-17F gene 7488 T > C polymorphic site than the individuals with a T allele. It was shown that ATT and GCT haplotype carriers had a greater disease risk compared with the GTT haplotype carriers. CONCLUSIONS: In conclusion, IL-17F gene 7488 T > C polymorphism was found to be associated with asthma in the Turkish population. The IL-17 gene should be further investigated as a potential candidate gene in predicting asthma susceptibility and in the treatment of asthma.

The effectiveness of anti-interleukin-1 therapy on subclinical inflammation parameters during the attack-free period in familial Mediterranean fever patients: A case-control study.

BACKGROUND: : Anti IL-1 therapy is useful in suppressing attacks in FMF patients with colchicine resistance, however, it is not certain whether subclinical inflammation can sufficiently be inhibited with anti-IL-1 therapy in FMF patients with amyloidosis. METHODS: Forty-six FMF patients receiving anti-interleukin-1 therapy and 36 healthy control patients were compared in terms of laboratory parameters. Also, FMF patients were further divided into two groups; those with amyloidosis and those without it, and these subgroups were compared to each other in terms of clinical and laboratory findings. RESULTS: In comparison between the FMF and healthy control groups, erythrocyte sedimentation rate (ESR), C-reactive protein (CRP) level, and red cell distribution width (RDW) level were detected to be higher and hemoglobin level lower in the patient group. Within the FMF patient group, the ESR, CRP, fibrinogen, RDW, and NLR values were significantly higher in the subgroup with amyloidosis in comparison to the subgroup without amyloidosis. DISCUSSION: Anti-interleukin-1 therapy could not fully suppress the subclinical inflammatory parameters when compared to healthy individuals.

The effectiveness of anti-interleukin-1 therapy on subclinical inflammation parameters during the attack-free period in familial Mediterranean fever patients: A case-control study.

Background/aim: Anti IL-1 therapy is useful in suppressing attacks in FMF patients with colchicine resistance, however, it is not certain whether subclinical inflammation can sufficiently be inhibited with anti-IL-1 therapy in FMF patients with amyloidosis. Materials and methods: Forty-six FMF patients receiving anti-interleukin-1 therapy and 36 healthy control patients were compared in terms of laboratory parameters. Also, FMF patients were further divided into two groups; those with amyloidosis and those without it, and these subgroups were compared to each other in terms of clinical and laboratory findings. Results: In comparison between the FMF and healthy control groups, erythrocyte sedimentation rate (ESR), C-reactive protein (CRP) level, and red cell distribution width (RDW) level were detected to be higher and hemoglobin level lower in the patient group. Within the FMF patient group, the ESR, CRP, fibrinogen, RDW, and NLR values were significantly higher in the subgroup with amyloidosis in comparison to the subgroup without amyloidosis. Conclusion: Anti-interleukin-1 therapy could not fully suppress the subclinical inflammatory parameters when compared to healthy individuals.

The increased expression of Piezo1 and Piezo2 ion channels in human and mouse bladder carcinoma.

BACKGROUND: Piezo1/2, a mechanically activated ion channel, is believed to play an important role in bladder carcinogenesis process. Piezo1/2 expression has not been previously reported in urinary bladder carcinoma, and little is known about its significance in bladder carcinogenesis. OBJECTIVES: In our study, we aimed to evaluate the Piezo1 and Piezo2 expression as developmental in mouse bladder tissue and bladder cancer tissue of mice and humans. MATERIAL AND METHODS: The detection of developmental expression was performed on P0-P90 days in bladder tissue of Balb/c strain mice. Mice were divided into bladder cancer (n = 40) and control groups (n = 10). Bladder cancer in mice was created by using N-butyl-N-(4-hydroxybutyl)nitrosamine (BBN). In the study, 60 human subjects were included, whose normal tissues were used as controls. After the histopathological evaluation, the expression of Piezo1/2 genes was examined by reverse transcription polymerase chain reaction (RT-PCR) and immunohistochemistry in tumor and normal tissues. RESULTS: In developmental period of the mice, Piezo1 expression increased on days 21 and 90, whereas Piezo2 expression increased on day 7 and decreased on day 90 in mouse bladder tissues. There was a significant increase in the expression of Piezo1/2 in both cancer groups compared to the control group. Piezo1 expression was significantly increased at tumor size, stage and grade. Piezo2 expression was upregulated in high grade tumors in human subjects. CONCLUSIONS: The developmental changes of Piezo expression on specific days demonstrate the role of these channels in bladder cancer development. The dysfunction of Piezo1/2 expression may contribute to the carcinogenesis of bladder cancer by causing proliferative changes and angiogenesis. The expression of Piezo1/2 can provide new prognostic information for disease progression.

Potential role of melastatin-related transient receptor potential cation channel subfamily M gene expression in the pathogenesis of urinary bladder cancer.

Urinary bladder cancer is one of the most common malignancies of the urinary tract. Ion channels and calcium homeostasis are involved in almost all basic cellular mechanisms. The transient receptor potential cation channel subfamily M (TRPM) takes its name from the melastatin protein, which is classified as potential tumor suppressor. To the best of our knowledge, there have been no previous studies in the literature investigating the role of these ion channels in bladder cancer. The present study aimed to determine whether bladder cancer is associated with mRNA expression levels of TRPM ion channel genes, and whether there is the potential to conduct further studies to establish novel treatment modalities. The present study included a total of 47 subjects, of whom 40 were bladder cancer patients and 7 were controls. Following the histopathological evaluation for bladder carcinoma, the mRNA and protein expression of TRPM were examined by reverse transcription-quantitative polymerase chain reaction (RT-qPCR) and immunohistochemistry in tumor and normal tissues, in order to determine whether there is a difference in the expression of these channels in tumor and normal tissues. Immunoreactivity for TRPM2, TRPM4, TRPM7 and TRPM8 was observed in epithelial bladder cells in the two groups. RT-qPCR revealed a significant increase in TRPM7 expression in bladder cancer tissue compared to the controls (healthy bladder tissue), whereas no differences in TRPM2 or TRPM4 expression levels were observed. There were significant reductions in the expression levels of TRPM5 and TRPM8 in bladder cancer tissues. In the present study, the effects of TRP ion channels on the formation of bladder cancer was investigated. This study is instructive for TRPM2, TRPM4, TRPM5, TRPM7 and TRPM8 and their therapeutic role in bladder cancer. The results support the fact that these gens can be novel targets and can also be tested for during the treatment of bladder cancer.

Focal epithelial hyperplasia associated with human papillomavirus 13 and common human leukocyte antigen alleles in a Turkish family.

BACKGROUND: Focal epithelial hyperplasia (FEH) is a rare and benign papillomatous disease of the oral cavity, which is closely associated with human papillomavirus (HPV) type 13 and 32. Genetic susceptibility to HPV infections are supported by recent studies involving the human leukocyte antigen system (HLA). In this report, we aimed to determine the clinicopathological features of a Turkish family with FEH and to detect the shared HLA DR and DQ types. METHODS: HPV DNA typing of tissue samples and HLA determination from blood samples of four family members were performed by polymerase chain reaction. RESULTS: Histopathological examination of all patients revealed acanthotic papillomatous epidermis, koilocytes, apoptotic keratinocytes, and mitosoid bodies. HPV13 was detected by polymerase chain reaction. HLA DQA1*0501, HLA DQB1*0302, and HLA DRB1*11 alleles were common in all family members. HLA DRB1*04 was detected in three of them. CONCLUSION: This report is the first step for the investigation of involvement of HLA types in the pathogenesis of Turkish patients with FEH.

Phenotype 2 familial mediterranean fever: evaluation of 22 case series and review of the literature on phenotype 2 FMF.

Familial Mediterranean fever (FMF) is an autosomal recessive autoimmune disorder characterized by recurrent bouts of fever and serosal inflammation. FMF may be complicated by AA-type amyloidosis, worsening the prognosis, with associated renal failure in some patients. Complication rate varies with race, being as high as 60% in Turks and as low as 2% in Armenians. In a few cases of patients with FMF (phenotype 2), amyloid nephropathy may be the presenting manifestation. This study included 420 patients who were admitted to the Nephrology and Rheumatology Departments of Atatürk Education and Research Hospital with unexplained proteinuria/nephrotic syndrome. The initial screening test for amyloidosis was the presence of significant proteinuria (300 mg/24 h). All MEFV gene exons were screened for causative mutations by direct DNA sequencing to check for any mutations. There were 22 phenotype 2 FMF patients with 27 allelic variants. The most prevalent allelic variants were M694V (10/27, 37%) and E148Q (7/27, 26%). Phenotype 2 FMF is not as rare as it was thought before; this should be kept in mind for all patients with unexplained proteinuria and/or acute phase response in high-risk ethnic groups for FMF.

Concomitance of Gitelman syndrome and familial Mediterranean fever: a rare case presentation.

We report a case that has Gitelman syndrome (GS) and familial Mediterranean fever (FMF) presenting with recurrent arthritis of right knee and heel pain. Investigations showed hypokalemia and hypomagnesemia with urinary magnesium wasting. Genetic analysis revealed the presence of heterozygous E148Q mutation in the MEFV gene. Management with potassium, magnesium supplements, spironolactone for GS, and colchicine for FMF resulted in a significant improvement in symptoms. To the best of our knowledge, this is the first report of association between GS and FMF. Further studies are needed to identify if there is an association between these two diseases and the genes responsible for these diseases.

Low plasma vitamin D levels in patients with familial Mediterranean fever.

Familial Mediterranean fever (FMF) is an autosomal recessive, inherited autoinflammatory disease characterized by recurrent, self-limited attacks of fever and inflammation of serosal surfaces. There is an explosion of the data regarding inflammatory markers in FMF and clinical effects of chronic inflammation on the disease presentation. Vitamin D (vit D) is the common denomination of a group of sterols with a crucial role in phospho-calcium metabolism. There are some data about the importance of vit D in the initiation and propogation of a range of autoimmune diseases. The aim of the present study was to determine whether vit D deficiency is present in patients with FMF compared with healthy individuals. The study group included 99 patients with diagnosis of FMF attended to our outpatient Rheumatology and Nephrology Clinics of Atatürk Education and Research Hospital. The control group comprised 51 age- and sex-matched healthy people selected from hospital staff. Serum baseline 25-hydroxy vit D levels were measured by HPLC method using an Agilent 1100 Liquid Chromatograph. We found significantly lower serum 25-hydroxy vit D levels among FMF patients compared with matched controls and a high prevalence of vit D deficiency. This study demonstrated that vit D deficiency is frequent in patients with FMF than the healthy controls. It is convenient to look for vit D deficiency and to correct vit D nutritional status in FMF patients.