Bioinformatic analysis of KIT juxtamembrane domain mutations in Syrian GIST patients: jigsaw puzzle completed.

BACKGROUND: The huge number of detected somatic KIT mutations highlights the necessity of in silico analyses that are almost absent in the relevant medical literature. The aim of this study is to report the mutation spectrum analysis of exon 11 encoding the juxtamembrane (JM) domain of the KIT gene in a group of Syrian GIST patients. METHODS: Forty-eight formalin-fixed paraffin-embedded GIST tissue samples, collected between 2006 and 2016, were retrieved from the pathological archives and analyzed for KIT exon 11 mutations by DNA sequencing. Structural/functional impact of detected variants was predicted using several bioinformatic tools. RESULTS: Twenty-one different variants have been detected in intron 10, exon 11, and intron 11 of the KIT gene, eight of which were novel changes. Mutations in exon 11 of the KIT gene were detected in 28 of 48 (58.3%) GIST patients and predicted to be pathogenic and cancer promoting. Specifically, age above 60 was very significantly associated with the negative selection of deletion mutations (p = .007), a phenomenon that points to deletion severity. CONCLUSIONS: Six bioinformatic tools have proved efficient in predicting the impact of detected KIT variations in view of published structural, experimental, and clinical findings.

EBV Plasma Epstein-Barr Virus (EBV) DNA as a Biomarker for Diagnosis of EBV-positive Hodgkin Lymphoma in Syria.

INTRODUCTION: Epstein Barr Virus - positive Hodgkin lymphoma is defined by the presence of Epstein-Barr virus (EBV) in tumor cells. EBV plays an important role in the development and prognosis of Hodgkin's lymphoma. The standard way to detect EBV in Hodgkin lymphoma is immunohistochemistry stains for latent membrane protein-1 (LMP1) in tumor cells. The present study aimed to evaluate plasma Epstein-Barr virus (EBV) DNA as a noninvasive biomarker for diagnosis of EBV-positive Hodgkin lymphoma. METHODOLOGY: The study included 60 newly diagnosed patients with Hodgkin lymphoma, ranging in age from 4 to 60 years, and 55 sex and age-matched controls. (60) Formalin-fixed paraffin embedded blocks of Hodgkin lymphoma tissue samples were used to investigate the EBV by in immunohistochemistry stains for (LMP1) in tumor cells. Plasma EBV DNA was quantified by real-time quantitative polymerase chain reaction (PCR) for all Hodgkin lymphoma patients prior to therapy and for control. RESULTS: The results showed that (25/60, 41.7%) of Hodgkin lymphoma were positive for histological LMP1, whereas plasma EBV DNA was detectable (range from 1.1×103 to 1.5×104 copies/mL, median: 1.1×104 copies/mL) in all EBV-positive Hodgkin lymphoma samples (25/25). EBV DNA was undetectable in all cases of EBV-negative Hodgkin lymphoma (35/35) and all healthy control (55/55). It is worth mentioning that our results demonstrated that the EBV DNA load was high in the EBV associated Hodgkin lymphoma patients suffering poor prognostic state. CONCLUSIONS: Plasma EBV-DNA can be used as a noninvasive biomarker for diagnosis of EBV- positive Hodgkin lymphoma.

Frequency of BCR-ABL Transcript Types in Syrian CML Patients.

Background. In Syria, CML patients are started on tyrosine kinase inhibitors (TKIs) and monitored until complete molecular response is achieved. BCR-ABL mRNA transcript type is not routinely identified, contrary to the recommendations. In this study we aimed to identify the frequency of different BCR-ABL transcripts in Syrian CML patients and highlight their significance on monitoring and treatment protocols. Methods. CML patients positive for BCR-ABL transcripts by quantitative RT-PCR were enrolled. BCR-ABL transcript types were investigated using a home-made PCR method that was adapted from published protocols and optimized. The transcript types were then confirmed using a commercially available research kit. Results. Twenty-four transcripts were found in 21 patients. The most common was b2a2, followed by b3a2, b3a3, and e1a3 present solely in 12 (57.1%), 3 (14.3%), 2 (9.5%), and 1 (4.8%), respectively. Three samples (14.3%) contained dual transcripts. While b3a2 transcript was apparently associated with warning molecular response to imatinib treatment, b2a2, b3a3, and e1a3 transcripts collectively proved otherwise (P = 0.047). Conclusion. It might be advisable to identify the BCR-ABL transcript type in CML patients at diagnosis, using an empirically verified method, in order to link the detected transcript with the clinical findings, possible resistance to treatment, and appropriate monitoring methods.

Hepatitis B splice-generated protein antibodies in Syrian chronic hepatitis B patients: incidence and significance.

BACKGROUND: Previous studies have suggested hepatitis B splice-generated protein (HBSP), when expressed, is involved in the pathogenesis of HBV infection. OBJECTIVES: We aimed to evaluate anti-HBSP incidence and association with several HBV infection parameters in a group of Syrian chronic hepatitis B patients. PATIENTS AND METHODS: Eighty treatment-naïve HBsAg-positive adult chronic hepatitis B patients' sera were included in our prospective targeted study. Liver function, virological and histological tests results were obtained from patients' medical files. Three variants of a 20-mer HBSP-derived peptide were designed based on HBV genome sequences obtained from Syrian patients' sera (GenBank Accession No. JN257148-JN257217). Microtiter plate wells were coated with the synthetic peptides and used to detect anti-HBSP antibodies by an optimized indirect enzyme-linked immunosorbent assay (ELISA). Samples were considered positive when showed optical density (OD) values higher than the cut-off value for at least one peptide variant. RESULTS: Seven out of eighty (9%) CHB patients were positive for anti-HBSP antibodies. Mean OD values were not significantly different between HBeAg-positive and -negative patients (P > 0.05). OD values showed weak positive correlation with ALT and AST values (P < 0.05), and weak to moderate positive correlation with liver biopsy staging ranks (P < 0.05). No significant correlation was revealed with viral load values or liver biopsy grading ranks (P > 0.05). CONCLUSIONS: We introduced an anti-HBSP antibodies ELISA, designed for locally circulating HBV strains. Correlation observed of Anti-HBSP with liver fibrosis staging regardless of viral replication and liver inflammation suggests anti-HBSP antibodies as possible indicator for HBV-associated liver fibrosis.

Associação do alelo HLA-DRB1 com suscetibilidade a artrite reumatoide e gravidade da doença na Síria / HLA-DRB1 allele association with rheumatoid arthritis susceptibility and severity in Syria

INTRODUÇÃO: A artrite reumatoide (AR) é uma doença crônica multifatorial complexa. A importância do sistema de antígenos leucocitários humanos (HLA) como fator significativo de risco genético para AR foi estudada no mundo. Embora amplamente distribuídos em diferentes áreas na Síria, faltam estudos sobre o papel dos HLA. OBJETIVO: O objetivo de nosso estudo foi determinar a associação dos alelos HLA-DRB1 com a suscetibilidade a AR e sua gravidade na Síria. PACIENTES E MÉTODOS: Foram genotipados 86 pacientes com AR e 200 controles normais, usando-se reação em cadeia da polimerase com sequência de primer específico (PCR-SSP). Anticorpos anti-CCP foram determinados por ELISA. Fator reumatoide (FR), proteína C-reativa (PCR), velocidade de hemossedimentação (VHS) e o índice de atividade da doença (DAS-28) foram obtidos nos registros médicos e utilizados para avaliar a gravidade clínica dos pacientes. RESULTADOS: Os alelos HLA-DRB1 *01, *04 e *10 mostraram forte associação com suscetibilidade à doença (OR = 2,29, IC 95% = 1,11-4,75, P = 0,022; OR = 3,16, IC 95% = 2,08-4,8, P < 0,0001; e OR = 2,43, IC 95% = 1,07-5,51, P = 0,029, respectivamente), enquanto a frequência dos alelos HLA-DRB1 *11 e *13 foi significativamente mais baixa nos pacientes com AR do que nos controles (OR = 0,49, IC 95% = 0,3-0,8, P = 0,004; OR = 0,32, IC 95% = 0,15-0,69, P = 0,002, respectivamente). Os outros alelos HLA-DRB1 mostraram diferença significativa. A frequência dos anticorpos anti-CCP foi maior em pacientes epítopo compartilhado (EC) positivos do que em pacientes EC-negativos (OR = 5,5, IC 95% = 2-15,1, P = 0,00054). O índice DAS-28 de pacientes com AR não mostrou diferença significativa entre os grupos EC-negativo e EC-positivo. CONCLUSÃO: Nossos resultados indicam que os alelos HLA-DRB1 *01, *04 e *10 estão relacionados com AR, enquanto os alelos HLA-DRB1 *11 e *13 protegem a população síria contra a AR.

INTRODUCTION: Rheumatoid arthritis (RA) is a complex multifactorial chronic disease. The importance of human leukocyte antigen as a major genetic risk factor for RA was studied worldwide. Although it is widely distributed in different Syrian areas, studies of human leukocyte antigen (HLA) alleles' role are absent. OBJECTIVE: The aim of our study was to determine the association of HLA-DRB1 alleles with the susceptibility and severity of RA in Syria. PATIENTS AND METHODS: Eightysix RA patients and 200 healthy controls from Syria were genotyped using polymerase chain reaction with sequencespecific primer (PCR-SSP). Anti-CCP antibodies were measured by ELISA. Rheumatoid factor (RF), C-reactive protein (CRP), erythrocyte sedimentation rate (ESR), and disease activity score 28 (DAS-28) values were obtained from patients' medical records. DAS-28 was used to assess the clinical severity of the patients. RESULTS: The HLA-DRB1*01, *04, and *10 frequencies showed a strong association with the disease susceptibility (OR = 2.29, 95% CI = 1.11-4.75, P = 0.022; OR = 3.16, 95% CI = 2.0 -4.8, P < 0.0001; OR = 2.43, 95% CI = 1.07-5.51, P = 0.029 respectively), while the frequencies of HLA-DRB1*11, and *13 were signifi cantly lower in RA patients than in controls (OR = 0.49, 95% CI = 0.3-0.8, P = 0.004; OR = 0.32, 95% CI = 0.15-0.69, P = 0.002, respectively). The other HLA-DRB1 alleles showed no signifi cant difference. The frequency of anti-CCP antibodies was higher in shared epitope (SE) positive patients compared with SE-negative patients (OR = 5.5, 95% CI = 2-15.1, P = 0.00054). DAS-28 of RA patients didn't show signifi cant difference between the SE negative and the SE positive groups. CONCLUSION: Our results indicate that HLA-DRB1*01, *04, and *10 alleles are related with RA, while HLA-DRB1*11 and *13 protect against RA in the Syrian population.

The subgingival microbiota of Papillon-Lefèvre syndrome.

BACKGROUND: There is little information about the microbiologic profiles of periodontal lesions in Papillon-Lefèvre syndrome (PLS) and the significance of bacteria in the pathogenesis of periodontitis in these patients. This comprehensive analysis of the subgingival microbiota in patients with PLS used 16S ribosomal RNA (rRNA) clonal analysis and the 16S rRNA-based Human Oral Microbe Identification Microarray (HOMIM). METHODS: Thirteen patients with PLS from seven unrelated families volunteered for this microbiologic study. Subgingival plaque was collected with sterile paper points from multiple sites with ≥5 mm probing depth, and whole genomic DNA was extracted. The 16S rRNA genes were amplified, cloned, and sequenced. The samples were then probed for ≈300 predominant oral bacterial species using the HOMIM. RESULTS: The most commonly detected phylotypes in the clonal analysis were Gemella morbillorum, Gemella haemolysans, Granulicatella adiacens, Lachnospiraceae OT 100 (EI074), Parvimonas micra, Selenomonas noxia, and Veillonella parvula. As a group, streptococci were commonly detected in these individuals. In the HOMIM analysis, a total of 170 bacterial species/phylotypes were detected, with a range of 40 to 80 species per patient with PLS. Of these, 12 bacterial species were detected in medium to high levels in ≥50% of the individuals. The high-frequency strains were clustered into eight groups: Aggregatibacter actinomycetemcomitans, Campylobacter spp., Capnocytophaga granulosa, G. morbillorum, P. micra, Porphyromonas endodontalis, Streptococcus spp., and Tannerella forsythia. CONCLUSIONS: The subgingival microbiota in PLS is diverse. Periodontal pathogens commonly associated with chronic and aggressive periodontitis and opportunistic pathogens may be associated with the development of severe periodontitis in patients with PLS.

Are human herpes viruses associated with autoimmune thyroid disease?

INTRODUCTION: Autoimmune diseases are complex diseases with genetic, endogenous and environmental etiologies. Viral infections have been postulated as one of the factors that may be the trigger of autoimmune diseases. METHODOLOGY: Thyroid peroxidase (TPO) and thyroglobulin (TG) antibodies were measured before thyroidectomy in 100 subjects by chemiluminescence method, 50 of whom were autoimmune thyroid diseases (AITD) patients and 50 of whom were multinodular goiter (MNG) patients used as a control group. Fresh thyroid samples were collected from all 100 subjects after thyroidectomy to investigate the DNAs of herpes simplex viruses types 1 and 2 (HSV-1, HSV-2), Varicella Zoster virus (VZV), Epstein-Barr virus (EBV), Cytomegalovirus (CMV) and human herpes virus type 6 (HHV-6) by PCR. RESULTS: The DNA of HSV-1, HSV-2, VZV, EBV, CMV and HHV-6 were detected in neither the patient group nor in the control group. The mean values of anti-TPO and anti-TG antibodies ranged within 9.5-2000 units/ml (527.8 ± 617.4) and 108-5000 units/ml (1458.2 ± 1774.1) in the AITD patients group, respectively. A statistically significant difference of the mean level of anti-TPO and anti-TG antibodies among the two groups was found (p value < 0.05). CONCLUSIONS: The possible role of human herpes viruses in the pathogenesis of AITD is not supported by our study; hence our raised question stays open for more investigation on more patients and in different parts of the country using different sizes and sites of biopsies.