Microbiome diversity in African American, European American, and Egyptian colorectal cancer patients.

Purpose: Although there is an established role for microbiome dysbiosis in the pathobiology of colorectal cancer (CRC), CRC patients of various race/ethnicities demonstrate distinct clinical behaviors. Thus, we investigated microbiome dysbiosis in Egyptian, African American (AA), and European American (EA) CRC patients. Patients and methods: CRCs and their corresponding normal tissues from Egyptian (n = 17) patients of the Alexandria University Hospital, Egypt, and tissues from AA (n = 18) and EA (n = 19) patients at the University of Alabama at Birmingham were collected. DNA was isolated from frozen tissues, and the microbiome composition was analyzed by 16S rRNA sequencing. Differential microbial abundance, diversity, and metabolic pathways were identified using linear discriminant analysis (LDA) effect size analyses. Additionally, we compared these profiles with our previously published microbiome data derived from Kenyan CRC patients. Results: Differential microbiome analysis of CRCs across all racial/ethnic groups showed dysbiosis. There were high abundances of Herbaspirillum and Staphylococcus in CRCs of Egyptians, Leptotrichia in CRCs of AAs, Flexspiria and Streptococcus in CRCs of EAs, and Akkermansia muciniphila and Prevotella nigrescens in CRCs of Kenyans (LDA score >4, adj. p-value <0.05). Functional analyses showed distinct microbial metabolic pathways in CRCs compared to normal tissues within the racial/ethnic groups. Egyptian CRCs, compared to normal tissues, showed lower l-methionine biosynthesis and higher galactose degradation pathways. Conclusions: Our findings showed altered mucosa-associated microbiome profiles of CRCs and their metabolic pathways across racial/ethnic groups. These findings provide a basis for future studies to link racial/ethnic microbiome differences with distinct clinical behaviors in CRC.

Genetic stratification reveals COL4A variants and spontaneous remission in Egyptian children with proteinuria in the first 2 years of life.

AIM: The earlier the onset of proteinuria, the higher the incidence of genetic forms. Therefore, we aimed to analyse the spectrum of monogenic proteinuria in Egyptian children presenting at age <2 years. METHODS: The results of 27-gene panel or whole-exome sequencing were correlated with phenotype and treatment outcomes in 54 patients from 45 families. RESULTS: Disease-causing variants were identified in 29/45 (64.4%) families. Mutations often occurred in three podocytopathy genes: NPHS1, NPHS2 and PLCE1 (19 families). Some showed extrarenal manifestations. Additionally, mutations were detected in 10 other genes, including novel variants of OSGEP, SGPL1 and SYNPO2. COL4A variants phenocopied isolated steroid-resistant nephrotic syndrome (2/29 families, 6.9%). NPHS2 M1L was the single most common genetic finding beyond the age of 3 months (4/18 families, 22.2%). Biopsy results did not correlate with genotypes (n = 30). On renin-angiotensin-aldosterone system antagonists alone, partial and complete remission occurred in 3/24 (12.5%) patients with monogenic proteinuria each, whereas 6.3% (1/16) achieved complete remission on immunosuppression. CONCLUSION: Genotyping is mandatory to avoid biopsies and immunosuppression when proteinuria presents at age <2 years. Even with such a presentation, COL4A genes should be included. NPHS2 M1L was prevalent in Egyptian children (4 months-2 years) with proteinuria, demonstrating precision diagnostic utility.

Expression of Enhancer of Zeste Homolog 2 (EZH2) Gene in Acute Myeloid Leukemia.

BACKGROUND: Enhancer of Zeste Homolog 2 (EZH2) is the catalytic subunit of the chromatin modifying enzyme polycomb repressive complex 2 (PRC2). As a complex, these proteins selectively silence target genes through trimethylation of histone 3 at lysine 27. EZH2 is strongly oncogenic. It has been observed in various malignancies which makes it an interesting therapeutic target. Whether it functions as a tumor suppressor or oncogene in acute leukemia is not settled. Aim of this work: This study aimed at determining the expression levels of EZH2 gene in a cohort of adult Egyptian patients newly diagnosed with acute myeloid leukemia (AML). MATERIALS AND METHODS: The present study included 45 de novo AML patients and 40 healthy subjects of matched age and sex as a control group. All study participants were subjected to complete blood count (CBC), bone marrow examination, immunophenotyping, conventional cytogenetic studies and Detection of EZH2 gene expression levels by real time quantitative polymerase chain reaction (RQ-PCR). RESULTS: EZH2 was significantly downregulated in AML patients compared to controls (p<0.001). There was no significant difference in EZH2 level when considering age, sex, bone marrow blasts count, cytogenetic studies, type or site of infection. Low EZH2 expression was associated with higher mortality (31 patients, 68.9%). CONCLUSIONS: Low EZH2 expression is prevalent in Egyptian AML patients subsequently; it is suggested to function as tumor suppressor gene rather than an oncogene. Moreover, EZH2 downregulation is associated with resistance to chemotherapy and high mortality rate.

Prognostic Significance of Long Non Coding RNA ANRIL and SNHG14 in Acute Myeloid Leukemia.

BACKGROUND: Long non-coding RNAs (lnRNAs) play a pivotal role in various malignancies including AML. Therefore, we decided to study both lnRNA ANRIL and lnRNA SNHG14 gene expressions in patients with AML to better understand their role in AML risk development, clinical presentation, and prognosis. METHODS: The current prospective study included two hundred participants, 100 AML patients and 100 control subjects. Bone marrow analysis was made to all patients, in addition to gene expression molecular testing of both lnRNA ANRIL and lnRNA SNHG14. RESULTS: Both lnRNA SNHG14 and lnRNA ANRIL showed high expression levels in AML bone marrow samples compared to non-AML subjects and were remarkably associated with lower Complete Remission (OR: 3.449, 95% CI: 1.324-8.985, p=0.011 for ANRIL and OR: 3.955, 95% CI: 1.510-10.356, p=0.005 for SNHG14), Relapse Free Survival (HR=3.504, 95%CI: 1.662-7.387, p=0.001 for ANRIL and HR=4.094, 95%CI: 1.849-9.067, p=0.001 for SNHG14) and Overall Survival (HR=3.353, 95%CI: 1.434-7.839, p=0.005 for ANRIL and HR=3.094, 95%CI: 1.277-7.494, p=0.012 for SNHG14), favouring poor prognostic significance in AML. CONCLUSION: This suggests that both lnRNA ANRIL and lnRNA SNHG14 could be used in the future as prognostic biomarkers to help in treatment decisions and follow up of AML patients.

Evaluation of Sigma metric approach for monitoring the performance of automated analyzers in hematology unit of Alexandria Main University Hospital.

INTRODUCTION: Sigma metric offers a quantitative framework for evaluating process performance in clinical laboratories. This study aimed to evaluate the analytical performance of automated analyzers in hematology unit of Alexandria Main University Hospital using the sigma metric approach. MATERIALS AND METHODS: Quality control data were collected for 6 months, and sigma value was calculated from hematology analyzers SYSMEX (XN 1000, XT 1800i), ADVIA (2120i, 2120), and coagulation analyzers SYSMEX CA 1500 (3610, 6336). RESULTS: For the normal control level, satisfactory mean sigma value ≥3 was observed for all of the studied parameters by all analyzers. For the high control level, red blood cell count by ADVIA 2120, and hematocrit by ADVIA (2120i and 2120) performed poorly with a mean sigma value <3. For the low control level, red blood cell count by ADVIA (2120i and 2120), hemoglobin by ADVIA 2120, hematocrit by ADVIA (2120i and 2120) and SYSMEX XN 1000, platelet count by the SYSMEX XT 1800i also performed poorly with a mean sigma value <3. Satisfactory mean sigma value of ≥3 was observed for prothrombin time and activated partial thromboplastin time for both normal and pathological control levels and analyzers. CONCLUSION: Sigma metrics can be used as a guide to make QC strategy and plan QC frequency and can facilitate the comparison of the same assay performance across multiple systems. Harmonization for TEa source is recommended to standardize sigma value calculation.

Modulation of Memory B Cell Phenotypes and Toll-Like Receptor-7 in Chronic Hepatitis C Virus Infection During Direct-Acting Antiviral Interferon-Free Therapy: Correlation with Interleukin-7.

Hepatitis C virus (HCV) infection is a major worldwide problem with the highest incidence rates in Egypt. It affects B cells that serve as reservoirs for persistent HCV, resulting in phenotypic B cell alterations. Interleukin-7 (IL-7) is a cytokine with antiviral activity, important for B cell physiology. In addition, B cell-intrinsic toll-like receptor-7 (TLR7) signaling is required for optimal B cell responses during chronic viral infection, and the deficiency of TLR7 in B cells is sufficient to significantly impact antibody responses. Based on their known immunomodulatory effects, we hypothesized that direct-acting antiviral interferon-free therapy may affect TLR7 expression and the exhausted peripheral B cell compartment with the possibility of their restoration in patients who achieved a sustained virological response and their correlation to IL-7 level. This prospective study was accomplished on 80 Egyptian HCV patients and 75 controls. Frequencies of peripheral B cell subsets, TLR7 gene expression, TLR7 protein, and serum IL-7 levels were investigated by flow cytometry, quantitative polymerase chain reaction, and enzyme-linked immunosorbent assay, respectively. B cell subpopulations were exhausted and partially restored among HCV patients after receiving treatment, but not recovered with regard to activated mature or resting memory B cells. Almost all responders to direct antiviral drugs showed upregulation of TLR7 gene expression and correlated with the frequency of memory B cell, but not with IL-7. Moreover, IL-7 was not significantly different between groups although correlated with immature transitional B cells. Results may indicate the interplay between TLR7 and B cells during remission or progression of HCV. Thus, TLR7 could be used as a promising biomarker for assessment of antiviral treatment efficacy among chronically infected HCV patients, and that targeting TLR7 may be used as a potential prophylactic and/or therapeutic agent during chronic HCV as well as immune-potentiation of memory B cells.

The clinical and prognostic significance of FIS1, SPI1, PDCD7 and Ang2 expression levels in acute myeloid leukemia.

OBJECTIVES: The marked heterogeneity of acute myeloid leukemia (AML) renders precisely predicting patient prognosis extremely difficult. Genetic alterations, fusions and mutations, may result in misexpression of key genes in AML. We aimed to investigate the expression patterns of 4 novel genes; FIS1, SPI1, PDCD7 and Ang2 to determine their potential prognostic role in AML patients. METHODS: Bone marrow mononuclear cells were analyzed for of FIS1, SPI1, PDCD7 and Ang2 expression levels by real-time quantitative PCR as well as of FLT3/ITD and NPM1 mutations in 100 newly diagnosed cytogenetically normal (CN-AML) patients, and 100 non-malignant controls. RESULTS: FIS1, SPI1, PDCD7 and Ang2 were significantly overexpressed in CN-AML patients (p < 0.001). Their high expression levels were significantly associated with lower complete remission (CR) rate, shorter relapse-free survival (RFS) and overall survival (OS). On multivariate analysis, high FIS1 expression showed a significant impact on CR response after induction therapy (OR = 88.777, 95% C.I: 2.85-2765.78, p = 0.011) while high PDCD7 appeared to be an independent risk factor for RFS (HR = 5.107, 95% C.I: 1.731-15.066, p = 0.003) and OS (HR = 7.353, 95% C.I: 1.859-29.079, p = 0.004) in CN-AML patients. CONCLUSIONS: FIS1 and PDCD7 expression are considered independent risk factors and should be integrated into the current AML stratification system.

Study of the influence of heme oxygenase 1 gene single nucleotide polymorphism (rs2071746) on esophageal varices among patients with cirrhosis.

INTRODUCTION: Cirrhosis as a pathological term has some criteria known to be common in all cases of liver cirrhosis. Esophageal varices are portosystemic collaterals arising in the submucosa of the lower esophagus because of portal hypertension. Portal hypertension is defined as hepatic venous pressure gradient greater than 5 mmHg that arises often as a sequelae of mesenchymal dysfunction in a cirrhotic liver. This study was carried out on 120 personnel divided into three groups: group A included 50 cases of liver cirrhosis with esophageal varices, group B consisted of 50 cases of cirrhosis without esophageal varices, and group C had 20 healthy volunteers a control group. PATIENTS AND METHODS: DNA was extracted from the peripheral blood of the study participants. Genotyping of the HO1 413A>T promoter SNP (rs2071746) was performed using TaqMan SNP genotyping assay according to the manufacturer's protocol by RQ-PCR. RESULTS: Patients carrying T allele of HO1 promoter were found to have 5.46-fold increased risk of esophageal varices development than patients with cirrhosis carrying A allele. T allele was significantly higher in cirrhotics with esophageal varices compared with those without esophageal varices (P<0.001). Rates of esophageal varices development in patients with cirrhotic liver were 52, 40, and 8% for genotypes TT, AT, and AA, respectively. CONCLUSION: The T allele of heme oxygenase 1 gene SNP polymorphism (rs2071746) is a risk factor for esophageal varices development in cirrhotics.