Novel Presentation of Major Histocompatibility Complex Class II Deficiency with Hemophagocytic Lymphohistiocytosis.

PURPOSE: Major histocompatibility complex (MHC) class II deficiency is one of the combined immune deficiency disorders caused by defects in the MHC class II regulatory genes leading to abnormal T cells development and function. Therefore, patients mainly present with increased susceptibility to infections, diarrhea, and failure to thrive. In this report, we present one MHC class II deficient patient with a novel presentation with Hemophagocytic Lymphohistiocytosis (HLH). METHODS: Immunophenotyping of lymphocyte subpopulations and HLA-DR expression was assess by flow cytometry. Gene mutational analysis was performed by whole exome and Sanger sequencing. RESULTS: We reported a 7-year-old girl, who was diagnosed at age of 2 years with MHC class II deficiency by genetic testing and flow cytometry. Two years later, she developed disseminated BCGitis which was treated with proper antimicrobial agents. At the age of 7 years, she presented with clinical features fulfilling 6 diagnostic criteria of HLH including evidence of hemophagocytic activity in bone marrow aspiration. Accordingly, the diagnosis of HLH was established and the patient was started on IV Dexamethasone, Anakinra and IVIG. Eventually, patient started to improve and was discharged in good condition. Few months later, the patient was readmitted with severe pneumonia and sepsis leading to death. CONCLUSION: Patients with MHC class II deficiency might present with disseminated BCGitis especially if the patient has severe T cell lymphopenia. Additionally, this immune defect might be added to the list of inborn errors of immunity that can be complicated with HLH.

Risk factors predicting disease severity and mortality in coronavirus disease 2019 Saudi Arabian patients.

CONTEXT: Coronavirus disease 2019 (COVID-19) became a global pandemic that may be associated with significant associated risk factors. AIMS: The aim of this study was to evaluate the factors predisposing risk to death in COVID-19 patients. SETTINGS AND DESIGN: This is a retrospective study that presents the demographic, clinical presentation, and laboratory findings on our patients to determine risk factors contributing to their COVID-19 outcome. METHODS: We used logistic regression (odds ratios) to examine associations between clinical findings and risk of death in COVID-19 patients. All analyses were done using STATA 15. RESULTS: A total of 206 COVID-19 patients were investigated, 28 of them died, and 178 survived. Expired patients were older (74.04 ± 14.45 vs. 55.56 ± 18.41 in those who survived) and mainly of male gender (75% vs. 42% in those who survived). The following factors were strong predictors of death: hypertension (OR: 5.48, 95% CI: 2.10-13.59, P < 0.001), cardiac disease (OR: 5.08, 95% CI: 1.88-13.74, P = 0.001), and hospital admission (OR: 39.75, 95% CI: 5.28-299.12, P < 0.001). In addition, blood group B was more frequent in expired patients (OR: 2.27, 95% CI: 0.78-5.95, P = 0.065). CONCLUSIONS: Our work adds to the current knowledge about the factors predisposing to death in COVID-19 patient. In our cohort, expired patients were of older age and male gender plus they were more likely to have hypertension, cardiac disease, and hospital severe disease. These factors might be used to evaluate risk of death in patients recently diagnosed of COVID-19.

Isolation and Establishment of a Highly Proliferative, Cancer Stem Cell-Like, and Naturally Immortalized Triple-Negative Breast Cancer Cell Line, KAIMRC2.

In vitro studies of a disease are key to any in vivo investigation in understanding the disease and developing new therapy regimens. Immortalized cancer cell lines are the best and easiest model for studying cancer in vitro. Here, we report the establishment of a naturally immortalized highly tumorigenic and triple-negative breast cancer cell line, KAIMRC2. This cell line is derived from a Saudi Arabian female breast cancer patient with invasive ductal carcinoma. Immunocytochemistry showed a significant ratio of the KAIMRC2 cells' expressing key breast epithelial and cancer stem cells (CSCs) markers, including CD47, CD133, CD49f, CD44, and ALDH-1A1. Gene and protein expression analysis showed overexpression of ABC transporter and AKT-PI3Kinase as well as JAK/STAT signaling pathways. In contrast, the absence of the tumor suppressor genes p53 and p73 may explain their high proliferative index. The mice model also confirmed the tumorigenic potential of the KAIMRC2 cell line, and drug tolerance studies revealed few very potent candidates. Our results confirmed an aggressive phenotype with metastatic potential and cancer stem cell-like characteristics of the KAIMR2 cell line. Furthermore, we have also presented potent small molecule inhibitors, especially Ryuvidine, that can be further developed, alone or in synergy with other potent inhibitors, to target multiple cancer-related pathways.

A novel gene in early childhood diabetes: EDEM2 silencing decreases SLC2A2 and PXD1 expression, leading to impaired insulin secretion.

Monogenic diabetes is a rare type of diabetes resulting from mutations in a single gene. To date, most cases remain genetically unexplained, posing a challenge for accurate diabetes treatment, which leads to on a molecular diagnosis. Therefore, a trio exome scan was performed in a lean, nonsyndromic Caucasian girl with diabetes onset at 2½ years who was negative for autoantibodies. The lean father had diabetes from age 11 years. A novel heterozygous mutation in EDEM2, c.1271G > A; p.Arg424His, was found in the proband and father. Downregulation of Edem2 in rat RIN-m ß-cells resulted in a decrease in insulin genes Ins1 to 67.9% (p = 0.006) and Ins2 to 16.8% (p < 0.001) and reduced insulin secretion by 60.4% (p = 0.0003). Real-time PCR revealed a major disruption of endocrine pancreas-specific genes, including Glut2 and Pxd1, with mRNA suppression to 54% (p < 0.001) and 85.7% (p = 0.01), respectively. No other expression changes related to stress or apoptotic genes were observed. Extended clinical follow-up involving ten family members showed that two healthy individuals carried the same mutation with no sign of diabetes in the clinical screen except for a slight increase in IA-2 antibody in one of them, suggesting incomplete penetrance. In conclusion, we describe EDEM2 as a likely/potential novel diabetes gene, in which inhibition in vitro reduces the expression of ß-cell genes involved in the glucose-stimulated insulin secretion (GSIS) pathway, leading to an overall suppression of insulin secretion but not apoptosis.

Late-onset multiple venous malformations confined to the upper limb: link to somatic MAP3K3 mutations.

Venous (cavernous) malformations are commonly seen in the upper limb. Almost all venous malformations are congenital. They may be sporadic, familial, or syndromic. Late-onset, multiple venous malformations confined to the upper limb are rare. Lesions present after puberty. All previously reported cases were located subcutaneously and were small in size. The condition is non-hereditary and non-syndromic. We present a unique series of eight patients with this rare condition. Unique features included the presence of large malformations (up to 20 cm in diameter) and the presence of subfascial lesions causing nerve compression. Surgical excision was curative. Mutational analysis in one patient identified a novel somatic MAP3K3 gene mutation (c.1723T > C, p.Tyr 575 His) in the affected veins. The encoded MAP3K3 protein is known to accelerate the RAS pathway of cellular proliferation.Level of evidence: IV.

Exome sequencing revealed DNA variants in NCOR1, IGF2BP1, SGLT2 and NEK11 as potential novel causes of ketotic hypoglycemia in children.

Unexplained or idiopathic ketotic hypoglycemia (KH) is the most common type of hypoglycemia in children. The diagnosis is based on the exclusion of routine hormonal and metabolic causes of hypoglycemia. We aimed to identify novel genes that cause KH, as this may lead to a more targeted treatment. Deep phenotyping of ten preschool age at onset KH patients (boys, n = 5; girls, n = 5) was performed followed by trio exome sequencing and comprehensive bioinformatics analysis. Data analysis revealed four novel candidate genes: (1) NCOR1 in a patient with KH, iron deficiency and loose stools; (2) IGF2BP1 in a proband with KH, short stature and delayed bone age; (3) SLC5A2 in a proband with KH, intermittent glucosuria and extremely elevated p-GLP-1; and (4) NEK11 in a proband with ketotic hypoglycemia and liver affliction. These genes are associated with different metabolic processes, such as gluconeogenesis, translational regulation, and glucose transport. In conclusion, WES identified DNA variants in four different genes as potential novel causes of IKH, suggesting that IKH is a heterogeneous disorder that can be split into several novel diseases: NCOR1-KH, IGF2BP1-KH, SGLT2-KH or familial renal glucosuria KH, and NEK11-KH. Precision medicine treatment based on exome sequencing may lead to advances in the management of IKH.

A novel interstitial deletion of chromosome 2q21.1-q23.3: Case report and literature review.

BACKGROUND: Interstitial deletions of 2q are rare. Those that have been reported show varying clinical manifestations according to the size of the deletion and the genomic region involved. METHOD AND RESULTS: We describe a preterm male harboring a novel interstitial deletion encompassing the 2q21.2-q23.3 region of 2q, a deletion that has not been described previously. The patient had multiple congenital anomalies including agenesis of the corpus callosum, congenital cardiac defects, bilateral hydronephrosis, spontaneous intestinal perforation, hypospadias and cryptorchidism, sacral dimple and rocker-bottom feet. Array comparative genomic hybridization (aCGH) analysis revealed a de novo >18 Mb deletion at 2q21.1-q23.3, a region that included (605802, 611472 and 604593) OMIM genes. CONCLUSION: To the best of our knowledge this is the first report of a de novo interstitial deletion at 2q21.1-q23.3 in which haploinsufficiency of dose-sensitive genes is shown to contribute to the patient's phenotype.

De Novo Variants in TAOK1 Cause Neurodevelopmental Disorders.

De novo variants represent a significant cause of neurodevelopmental delay and intellectual disability. A genetic basis can be identified in only half of individuals who have neurodevelopmental disorders (NDDs); this indicates that additional causes need to be elucidated. We compared the frequency of de novo variants in patient-parent trios with (n = 2,030) versus without (n = 2,755) NDDs. We identified de novo variants in TAOK1 (thousand and one [TAO] amino acid kinase 1), which encodes the serine/threonine-protein kinase TAO1, in three individuals with NDDs but not in persons who did not have NDDs. Through further screening and the use of GeneMatcher, five additional individuals with NDDs were found to have de novo variants. All eight variants were absent from gnomAD (Genome Aggregation Database). The variant carriers shared a non-specific phenotype of developmental delay, and six individuals had additional muscular hypotonia. We established a fibroblast line of one mutation carrier, and we demonstrated that reduced mRNA levels of TAOK1 could be increased upon cycloheximide treatment. These results indicate nonsense-mediated mRNA decay. Further, there was neither detectable phosphorylated TAO1 kinase nor phosphorylated tau in these cells, and mitochondrial morphology was altered. Knockdown of the ortholog gene Tao1 (Tao, CG14217) in Drosophila resulted in delayed early development. The majority of the Tao1-knockdown flies did not survive beyond the third instar larval stage. When compared to control flies, Tao1 knockdown flies revealed changed morphology of the ventral nerve cord and the neuromuscular junctions as well as a decreased number of endings (boutons). Furthermore, mitochondria in mutant flies showed altered distribution and decreased size in axons of motor neurons. Thus, we provide compelling evidence that de novo variants in TAOK1 cause NDDs.

Analysis of CCR5 gene polymorphisms in 321 healthy Saudis using Next Generation Sequencing.

AIMS: To investigate the extent of CCR5 polymorphism in the healthy Saudi population. METHOD: A total of 321 healthy Saudi individuals were sequenced using the ion Ampliseq™ Exome kit (Life Technologies, USA) on genomic DNA following manufacturer's protocol. Whole Exome Sequencing (WES) reads were aligned to the human reference genome (hg19 build) with Torrent Suite Software (v5.0.2) and the variants were called using the Torrent Variant Caller plugin (v5.0) and imported into Ion Reporter Server (v5.0) for the annotation. CCR5 coding exons variants were filtered and checked against the NHLBI GO Exome Sequencing Project (NHLBI), NCBI Reference dbSNPs database, 1000 genomes and Exome Aggregation Consortium datasets (ExAC). RESULTS: A total of 475 variants were identified. Table 1 shows polymorphisms/mutations detected within exons that introduced an amino acid change, deletion or copy number variants (CNV). Three mutations are predicted to influence CCR5 function, including the 32bp deletion (Rs333). Four polymorphisms were detected, plus two CNV. CONCLUSIONS: This is the first report on sequencing the full CCR5 gene using NGS in the Saudi population. Here we demonstrate seven polymorphisms/mutations that were reported before. All were detected within very low frequency including the delta 32 mutation. However, we report for the first time copy number variants at two CCR5 gene locations; 45072265 and 38591712.

Two novel homozygous missense mutations in the GDF5 gene cause brachydactyly type C.

Mutations of the GDF5 gene cause a variable phenotype including brachydactyly type C. A review of the literature showed that it is caused either by heterozygous frameshift mutations within the prodomain or heterozygous missense/nonsense mutations within the active domain. Only a single patient with a homozygous mutation (c.517A > G, which predicts p. Met173Val) has been reported in this disorder. In this paper, we report two children with novel homozygous missense mutations in the GDF5 gene associated with brachydactyly type C: one mutation was within the region coding for the prodomain (c.608C > A, which predicts p.Thr203Asn) and the other was within the region coding for the active domain (c.1456 G > A, which predicts p.Val486Met). The genotype-phenotype correlations in the mutational spectrum of the GDF5 gene are discussed.

Genome-wide association study of chronic hepatitis B virus infection reveals a novel candidate risk allele on 11q22.3.

BACKGROUND: Hepatitis B virus (HBV) affects millions of people worldwide. While some people are able to clear the virus following the first encounter, those who develop chronic infection manifest remarkable clinical heterogeneity that ranges from asymptomatic carrier state to cirrhosis and hepatocellular carcinoma. Despite extensive studies, little is known about genetic host factors that influence the outcome of chronic HBV infection. Thus, we conducted this study to investigate the genetic risk of developing active liver disease among chronic carriers of HBV. METHODS: In this study, we conducted a genome-wide association study (GWAS) on a cohort of patients with chronic HBV infection. RESULTS: One particular SNP that is 16 kb upstream of Ferredoxin 1 was found to have an association with complicated chronic HBV infection (cirrhosis and hepatocellular carcinoma) that reached GWAS significance, and was successfully validated on an independent set of samples. CONCLUSIONS: This first GWAS in an Arab population further demonstrates the utility of this approach in elucidating the genetic risk of HBV infection-related complications and highlights the advantage of conducting GWAS in different ethnicities to achieve that goal.

Novel point mutations and mutational complexes in the enhancer II, core promoter and precore regions of hepatitis B virus genotype D1 associated with hepatocellular carcinoma in Saudi Arabia.

In this study, a cohort of 182 patients [55 hepatocellular carcinoma (HCC) and 127 non-HCC] infected with hepatitis B virus (HBV) in Saudi Arabia was investigated to study the relationship between sequence variation in the enhancer II (EnhII), basal core promoter (BCP) and precore regions of HBV genotype D (HBV/D) and the risk of HCC. HBV genotypes were determined by sequencing analysis and/or enzyme-linked immunosorbent assay. Variations in the EnhII, BCP and precore regions were compared between 107 non-HCC and 45 HCC patients infected with HBV/D, followed by age-matched analysis of 40 cases versus equal number of controls. Age and male gender were significantly associated with HCC (p = 0.0001 and p = 0.03, respectively). Serological markers such as aspartate aminotransferase, albumin and anti-HBe were significantly associated with HCC (p = 0.0001 for all), whereas HBeAg positivity was associated with non-HCC (p = 0.0001). The most prevalent HBV genotype was HBV/D (94%), followed by HBV/E (4%), HBV/A (1.6%) and HBV/C (0.5%). For HBV/D1, genomic mutations associated with HCC were T1673/G1679, G1727, C1741, C1761, A1757/T1764/G1766, T1773, T1773/G1775 and C1909. Age- and gender-adjusted stepwise logistic regression analysis indicated that mutations G1727 [odds ratio (OR) = 18.3; 95% confidence interval (CI) = 2.8-118.4; p = 0.002], A1757/T1764/G1766 (OR = 4.7; 95% CI = 1.3-17.2; p = 0.01) and T1773 (OR = 14.06; 95% CI = 2.3-84.8; p = 0.004) are independent predictors of HCC development. These results implicate novel individual and combination patterns of mutations in the X/precore region of HBV/D1 as predictors of HCC. Risk stratification based on these mutation complexes would be useful in determining high-risk patients and improving diagnostic and treatment strategies for HBV/D1.

The unclassified variant: c.2044AD>G, p.T682A (het.) in exon 12 of the GLI3 gene in a patient with oral-facial-digital syndrome type II (Mohr syndrome) phenotype.

The gene mutation for oral-facial digital syndrome type II (Mohr syndrome) is unknown. We describe a Saudi female infant with Mohr syndrome. An unclassified variant: c.2044 A>G, p.T682A in exon 12 of the GLI3 gene in a heterozygous state was identified in the infant. Mutation Taster (http://www.mutationtaster.org) considers this variant as "disease causing". However, when the unaffected parents were tested, the father was found to have the same variant, also in a heterozygous state. Hence, the pathogenic role of this variant seems unlikely; although apparent non-penetrance remains a possibility.

HCV genotypes among 1013 Saudi nationals: a multicenter study.

BACKGROUND AND OBJECTIVES: Hepatitis C virus (HCV) genotype (G) knowledge is essential for determining type, duration and rate of response to antiviral therapy, possible route of HCV transmission, and future vaccine development. Our aim was to study HCV genotypes and to provide precise data on genotype distribution in both genders and different age groups amongst Saudi patients. DESIGN AND SETTING: Genotype data from molecular laboratories at four different tertiary care hospitals in Riyadh from January 2006 until December 2010 were collected and analyzed. PATIENTS AND METHODS: Consecutive data on genotype, sex and age was collected from 1013 Saudi patients. Genotyping was done by selective hybridization of amplicons to HCV genotype-specific oligonucleotides. RESULTS: We found G1 in 262 patients (25.9%), G2 in 44 (4.4 %), G3 in 29 (2.9 %), G4 in 608 (60%), and 3 patients (0.3%) each of G5 and G6. In addition, 64 (6.3%) patients had mixed genotypes, mostly G4 and G1. On subtyping in 191 G1 patients, 67 (35.1%) were G1a, and 124 (64.9 %) G1b. Age distribution showed that 18 (1.7%) were 0-20 years, 173 (17.1 %) 21-40 years, 521 (51.4%) 41-60 years and 301(29.7%) > 60 years. There was no significant difference in frequency of G1, G3 and G4 among the two genders. CONCLUSION: G1 and G4 are the predominant genotypes in Saudi patients infected with HCV (85.9%), with a similar distribution among the two sexes and no significant changes in genotype distribution over the past decade.

Efficacy and safety of treatment of hepatitis C virus infection in renal transplant recipients.

AIM: To assess the efficacy and safety of combined pegylated interferon and ribavirin therapy in hepatitis C virus (HCV) infection in renal transplant recipients. METHODS: This is a retrospective chart review of post renal transplant patients who were positive for anti-HCV and HCV-RNA, and who have received treatment with combination of pegylated interferon and ribavirin between October 2003 and December 2008. Only patients with stable graft function and absence of evidence of cirrhosis and who received the therapy for continuous 48 wk were included. Nineteen patients (13 male and 6 female) were identified and included. The patient's complete blood count, liver and kidney profile, and calculated glomerular filtration rate (GFR) were monitored every 6-8 wk while on treatment. HCV-RNA was tested at 12 wk for early virological response, at 48 wk for end of treatment response (ETR), and then retested at 24, and 48 wk after completion of therapy for sustained virological response (SVR). Liver biopsies were obtained before treatment from all patients and graft kidney biopsies were performed as required. RESULTS: Of the entire cohort, 9 patients (47.4%) showed an ETR and 8 had SVR (42.1%). Of the 8 patients with abnormal alanine aminotransferase (ALT) levels at baseline, 78.9% had their ALT normalized (including the virological non responders). ALT was normal in all responders at the end of therapy and at 24 wk post therapy (100%). Only one patient (5.3%) developed an increase in creatinine and decline in GFR from baseline towards the end of treatment. This patient's kidney biopsy revealed borderline rejection. There was no impact on response by HCV-genotype, initial HCV RNA load, age or sex of the patient or duration post transplant before commencement of therapy. All patients tolerated treatment in the same way as non-transplant with no unusual or increased occurrence of side effects. CONCLUSION: The combination of pegylated interferon and ribavirin is effective in suppressing HCV-RNA, with a low risk of graft rejection or failure in HCV infected renal transplant recipients.

Prevalence of mixed hepatitis C virus (HCV) genotypes among recently diagnosed dialysis patients with HCV infection.

Hepatitis C virus (HCV) infection is considered a major health problem recognized globally. HCV is a major cause of chronic liver disease that may lead to cirrhosis and hepatocellular carcinoma. The aim of this study was to investigate the prevalence of multiple (mixed) HCV genotypes in Saudi patients recently diagnosed with HCV infection and their association with various clinical risk factors. We examined a total of 1,292 newly diagnosed HCV-positive cases between January 2006 and July 2009 at the Molecular Pathology Laboratory, King Abdulaziz Medical City, Riyadh. The clinical and laboratory data of the study patients were collected. The HCV-RNA viral load and its genotyping were carried out with RT-PCR technology to assist in the follow-up and management of HCV-infected patients undergoing antiviral therapy. Twenty-two patients (1.7%) were found to have mixed HCV genotypes; of them, mixed genotypes associated with genotype-4 were seen in 19 patients (86%), mixed genotypes associated with genotype-1 were found in 68.4%, with genotype-3 in 26.3% and with genotype-2 in 5.3%. Additionally, mixed genotypes associated with genotype-1 were seen in three cases (13.6%); they were associated with genotype-2 in two (66.7%) and with genotype-5 in one patient (33.3%). In conclusion, the prevalence rate of mixed HCV genotypes in the cohort of the newly infected Saudi patients was 1.7%, with genotype-4 being the most frequent genotype encountered.