HLA-based banking of induced pluripotent stem cells in Saudi Arabia.

BACKGROUND: Human iPSCs' derivation and use in clinical studies are transforming medicine. Yet, there is a high cost and long waiting time associated with autologous iPS-based cellular therapy, and the genetic engineering of hypo-immunogenic iPS cell lines is hampered with numerous hurdles. Therefore, it is increasingly interesting to create cell stocks based on HLA haplotype distribution in a given population. This study aimed to assess the potential of HLA-based iPS banking for the Saudi population. METHODS: In this study, we interrogated the HLA database of the Saudi Stem Cell Donor Registry (SSCDR), containing high-resolution HLA genotype data from 64,315 registered Saudi donors at the time of analysis. This database was considered to be a representative sample of the Saudi population. The most frequent HLA haplotypes in the Saudi population were determined, and an in-house developed iterative algorithm was used to identify their HLA matching percentages in the SSCDR database and cumulative coverage. Subsequently, to develop a clinically relevant protocol for iPSCs generation, and to illustrate the applicability of the concept of HLA-based banking for cell therapy purposes, the first HLA-based iPS cell line in Saudi Arabia was generated. Clinically relevant methods were employed to generate the two iPS clones from a homozygous donor for the most prevalent HLA haplotype in the Saudi population. The generated lines were then assessed for pluripotency markers, and their ability to differentiate into all three germ layers, beating cardiomyocytes, and neural progenitors was examined. Additionally, the genetic stability of the HLA-iPS cell lines was verified by comparing the mutational burden in the clones and the original blood sample, using whole-genome sequencing. The standards set by the American College of Medical Genetics and Genomics (ACMG) were used to determine the clinical significance of identified variants. RESULTS: The analysis revealed that the establishment of only 13 iPSC lines would match 30% of the Saudi population, 39 lines would attain 50% coverage, and 596 lines would be necessary for over 90% coverage. The proof-of-concept HLA-iPSCs, which cover 6.1% of the Saudi population, successfully demonstrated pluripotency and the ability to differentiate into various cell types including beating cardiomyocytes and neuronal progenitors. The comprehensive genetic analysis corroborated that all identified variants in the derived iPSCs were inherently present in the original donor sample and were classified as benign according to the standards set by the ACMG. CONCLUSIONS: Our study sets a road map for introducing iPS-based cell therapy in the Kingdom of Saudi Arabia. It underscores the pragmatic approach of HLA-based iPSC banking which circumvents the limitations of autologous iPS-based cellular therapies. The successful generation and validation of iPSC lines based on the most prevalent HLA haplotype in the Saudi population signify a promising step toward broadening the accessibility and applicability of stem cell therapies and regenerative medicine in Saudi Arabia.

Cycle Threshold Value as a Predictor of Severity and Intensive Care Unit Admission for Children Presenting to the Emergency Department With COVID-19: A Single-Center Experience From Saudi Arabia.

INTRODUCTION: The alarming infection rates of COVID-19 and variability in disease severity and outcome created the need for a prognostic marker to predict disease severity, prioritize services, and assist in clinical decision-making. The cycle threshold (Ct) value was hypothesized to be inversely correlated with viral load and subsequently disease severity. Therefore, it gained clinical interest and was an important topic for research. In this study, we aimed to determine the accuracy of the Ct value as a predictor of clinical severity in children presenting to the emergency department with COVID-19. Specifically, we aimed to compare the relationship between clinical severity among patients with high vs. low Ct values as well as to assess the correlation between the mean Ct value with the mean number of symptoms. METHODS: This is a single-center retrospective cohort study. Data were obtained from the electronic medical record software of King Abdulaziz Medical City in Jeddah, Saudi Arabia. The present study included randomly selected COVID-19 cases aged ≥1 months to 18 years who presented to the emergency department between March 2020 and May 2021. Collected clinical data were matched with laboratory data at the time of diagnosis to examine the association between Ct values and clinical factors. RESULTS: A total of 191 COVID-19 PCR-positive children were included with an overall mean Ct value of 11.5, a median of 10, and a highest Ct value of 25. The mean age of the patients was 95 months. More than half (51.35%) of the patients were admitted to the hospital, while 2.09% were admitted to the intensive care unit and one patient (0.52%) died. There was no significant association between Ct values and demographics or clinical characteristics of the patients. CONCLUSION: We demonstrated a lack of association between SARS-CoV-2 Ct value detected in nasopharyngeal swabs with disease severity, number of symptoms, oxygen requirement, intensive care unit admission, or length of hospital stay in the pediatric population presenting to the emergency department with COVID-19. This finding does not support the routine reporting of Ct values to aid clinicians in making clinical and patient-management decisions for COVID-19 patients or guide infection control or public health decisions. Further studies confirming our observations are needed.

Prenatal exome sequencing and chromosomal microarray analysis in fetal structural anomalies in a highly consanguineous population reveals a propensity of ciliopathy genes causing multisystem phenotypes.

Fetal abnormalities are detected in 3% of all pregnancies and are responsible for approximately 20% of all perinatal deaths. Chromosomal microarray analysis (CMA) and exome sequencing (ES) are widely used in prenatal settings for molecular genetic diagnostics with variable diagnostic yields. In this study, we aimed to determine the diagnostic yield of trio-ES in detecting the cause of fetal abnormalities within a highly consanguineous population. In families with a history of congenital anomalies, a total of 119 fetuses with structural anomalies were recruited and DNA from invasive samples were used together with parental DNA samples for trio-ES and CMA. Data were analysed to determine possible underlying genetic disorders associated with observed fetal phenotypes. The cohort had a known consanguinity of 81%. Trio-ES led to diagnostic molecular genetic findings in 59 fetuses (with pathogenic/likely pathogenic variants) most with multisystem or renal abnormalities. CMA detected chromosomal abnormalities compatible with the fetal phenotype in another 7 cases. Monogenic ciliopathy disorders with an autosomal recessive inheritance were the predominant cause of multisystem fetal anomalies (24/59 cases, 40.7%) with loss of function variants representing the vast majority of molecular genetic abnormalities. Heterozygous de novo pathogenic variants were found in four fetuses. A total of 23 novel variants predicted to be associated with the phenotype were detected. Prenatal trio-ES and CMA detected likely causative molecular genetic defects in a total of 55% of families with fetal anomalies confirming the diagnostic utility of trio-ES and CMA as first-line genetic test in the prenatal diagnosis of multisystem fetal anomalies including ciliopathy syndromes.

A Novel Variant of Adenosine Deaminase 2 Deficiency Presented With Chronic Thrombocytopenia, Anemia, and Early-Onset Stroke.

Deficiency of adenosine deaminase 2 (DADA2) is a rare recessive disorder caused by the bi-allelic loss-of-function pathogenic variants in the ADA2 gene (MIM: 607575, also known as CECR1, cat eye syndrome chromosome region, candidate 1). Based on the Human Gene Mutation Database (HGMD®), 53 different disease-causing variants have been identified in this gene to date. This case report aims to describe a new vasculitis, autoinflammation, immunodeficiency, and hematologic defects syndrome (VAIHS) case caused by a novel pathogenic variant. A four-year-old boy was referred to our hospital with anemia, thrombocytopenia, and stroke, but no skin manifestations. The patient had a significant phenotypic overlap with VAIHS. Molecular genetic analysis via whole exome sequencing identified a homozygous deleterious variant in ADA2. To our knowledge, the identified variant has never been described in the literature. Screening for ADA2 pathogenic variants should be considered in the differential diagnosis of pediatric patients manifesting with chronic thrombocytopenia or early-onset stroke for an accurate diagnosis and appropriate treatment choices.

A Novel Variant in the AGPS Gene Causes the Rare Rhizomelic Chondrodysplasia Punctata Type 3: A Case Report.

Rhizomelic chondrodysplasia punctata (RCDP) is a devastating medical condition for patients and their families. It is a rare peroxisomal autosomal recessive disorder. It was recognized clinically with skeletal abnormalities and intellectual disabilities mainly due to plasmalogen deficiency. Here, we report a case of a 16-day-old girl who was referred to King Abdulaziz Medical City Jeddah, Saudi Arabia because of dysmorphic features. Her growth parameters were below the 3rd centile with short proximal long bones and multiple joint contractures in the extremities. The radiographs showed rhizomelic and shortening of both humeri and femurs. Moreover, punctate ossification was identified in the upper spine, humeri around the shoulders, and femurs around the knees. We observed other classical features, and the genetic testing confirmed the diagnosis of RCDP type 3. Although RCDP is a rare condition, it is a distressing burden necessitating early diagnosis and a holistic approach for management.

Bi-allelic pathogenic variants in NDUFC2 cause early-onset Leigh syndrome and stalled biogenesis of complex I.

Leigh syndrome is a progressive neurodegenerative disorder, most commonly observed in paediatric mitochondrial disease, and is often associated with pathogenic variants in complex I structural subunits or assembly factors resulting in isolated respiratory chain complex I deficiency. Clinical heterogeneity has been reported, but key diagnostic findings are developmental regression, elevated lactate and characteristic neuroimaging abnormalities. Here, we describe three affected children from two unrelated families who presented with Leigh syndrome due to homozygous variants (c.346_*7del and c.173A>T p.His58Leu) in NDUFC2, encoding a complex I subunit. Biochemical and functional investigation of subjects' fibroblasts confirmed a severe defect in complex I activity, subunit expression and assembly. Lentiviral transduction of subjects' fibroblasts with wild-type NDUFC2 cDNA increased complex I assembly supporting the association of the identified NDUFC2 variants with mitochondrial pathology. Complexome profiling confirmed a loss of NDUFC2 and defective complex I assembly, revealing aberrant assembly intermediates suggestive of stalled biogenesis of the complex I holoenzyme and indicating a crucial role for NDUFC2 in the assembly of the membrane arm of complex I, particularly the ND2 module.

Clinical, molecular, and biochemical delineation of asparagine synthetase deficiency in Saudi cohort.

PURPOSE: Asparagine synthetase deficiency (ASNSD) is a rare neurometabolic disease. Patients may not demonstrate low asparagine levels, which highlights the advantage of molecular over biochemical testing in the initial work-up of ASNSD. We aimed to further delineate the ASNSD variant and phenotypic spectrum and determine the value of biochemical testing as a frontline investigation in ASNSD. METHODS: We retrospectively collected the clinical and molecular information on 13 families with ASNSD from the major metabolic clinics in Saudi Arabia. RESULTS: The major phenotypes included congenital microcephaly (100%), facial dysmorphism (100%), global developmental delay (100%), brain abnormalities (100%), spasticity (86%), and infantile-onset seizures (93%). Additional unreported phenotypes included umbilical hernia, osteopenia, eczema, lung hypoplasia, and hearing loss. Overall, seven homozygous variants accounted for ASNSD. The p.Tyr398Cys and p.Asn75Ile variants accounted for 54% of the cases. The clinical sensitivity and specificity of the proposed biochemical analysis of cerebrospinal fluid (CSF) for the detection of patients with ASNSD were 83% and 98%, respectively. CONCLUSION: Our study describes the largest reported ASNSD cohort with clinical, molecular, and biochemical characterization. Taking into consideration the suboptimal sensitivity of biochemical screening, the delineation of the phenotype variant spectrum is of diagnostic utility for accurate diagnosis, prognosis, counseling, and carrier screening.

Majewski dwarfism type II: an atypical neuroradiological presentation with a novel variant in the PCNT gene.

Microcephalic osteodysplastic primordial dwarfism syndrome II (MOPDII) is microcephalic primordial dwarfism and is a very rare form of disproportionate short stature. This disorder shares common features with other forms of microcephalic primordial dwarfism, including severe prenatal and postnatal growth retardation with marked microcephaly. However, it includes characteristic skeletal dysplasia, abnormal dentition and increased risk for cerebrovascular diseases. Recent reports added more features, including café-au-lait lesions, cutis marmorata, astigmatism, Moyamoya disease, insulin resistance, obesity, abnormal skin pigmentation and acanthosis nigricans around the neck. Clearly, the more MOPDII reports that are produced, the more information will be added to the spectrum of MOPDII features that can improve our understanding of this disorder. In this paper, we reported a new case of MOPDII with more severe clinical features, earlier onset of common features, in addition to a homozygous novel variant in the PCNT gene.

A very rare form of autosomal dominant progressive myoclonus epilepsy caused by a novel variant in the PRICKLE1 gene.

PURPOSE: Progressive myoclonus epilepsy (PME) comprises a group of heterogeneous disorders defined by the combination of action myoclonus, epileptic seizures, and progressive neurologic deterioration. Neurologic deterioration may include progressive cognitive decline, ataxia, neuropathy, and myopathy. A number of genes have been identified to cause either isolated PME or diseases that manifest PME. We report a Saudi family with a very rare form of autosomal dominant PME. METHODS: We included two patients from Saudi Arabia with a presumptive clinical diagnosis of PME. The patients were from a family with an affected mother I-2 and two affected siblings proband II-3 and II-4 (a girl and a boy). RESULTS: Genetic analysis revealed a single variant in the PRICKLE1 gene NM_153026.2: c.251 G > A (p.Arg84Gln). Segregation study was performed using DNA from the parents and two sisters. The same variant was identified in one affected parent (the mother I-2) and the two unaffected sisters II-1 and II-2 while it was absent from the unaffected father I-1. CONCLUSION: This gene was linked to both autosomal dominant and autosomal recessive PME. To our best knowledge, this is the first report that demonstrates a single PRICKLE1 pathogenic variant segregating with PME in one family. The novel variant identified in this family has never been previously reported as a disease-causing variant. The presence of the same variant in the unaffected individuals may suggest that heterozygous mutations in the PRICKLE1 gene have incomplete penetrance. Further research is needed to elucidate the penetrance of heterozygous mutations in the PRICKLE1 gene.

A case of atypical systemic primary carnitine deficiency in Saudi Arabia.

Systemic primary carnitine deficiency (SPCD) is an autosomal recessive inborn error of fatty acid metabolism caused by a defect in the transporter responsible for moving carnitine across plasma membrane. The clinical features of SPCD vary widely based on the age of onset and organs involved. During infancy, patients might show episodes of hypoketotic hypoglycemia, hepatomegaly, elevated transaminases, and hyperammonemia. Skeletal myopathy, elevated creatine kinase, and cardiomyopathy are the main manifestations in children with SPCD, while in adults, the disorder is usually manifested as cardiomyopathy, arrhythmias, or fatigability. Here, we report a 5-year-old boy with SPCD that presented as dilated cardiomyopathy with atypical features, such as anemia, respiratory distress, and proximal muscle weakness. This report supports considering carnitine deficiency treatment in the work-up of unexplained pediatric dilated cardiomyopathy.

Biallelic inactivating variants in the GTPBP2 gene cause a neurodevelopmental disorder with severe intellectual disability.

Congenital neurological disorders are genetically highly heterogeneous. Rare forms of hereditary neurological disorders are still difficult to be adequately diagnosed. Pertinent studies, especially when reporting only single families, need independent confirmation. We present three unrelated families in which whole-exome sequencing identified the homozygous non-sense variants c.430[C>T];[C>T] p.(Arg144*), c.1219[C>T];[C>T] p.(Gln407*) and c.1408[C>T];[C>T] p.(Arg470*) in GTPBP2. Their clinical presentations include early onset and apparently non-progressive motor and cognitive impairment, and thereby overlap with findings in a recently described family harbouring a homozygous GTPBP2 splice site variant. Notable differences include structural brain abnormalities (e.g., agenesis of the corpus callosum, exclusive to our patients), and evidence for brain iron accumulation (exclusive to the previously described family). This report confirms pathogenicity of biallelic GTPBP2 inactivation and broadens the phenotypic spectrum. It also underlines that a potential involvement of brain iron accumulation needs clarification. Further patients will have to be identified and characterised in order to fully define the core features of GTPBP2-associated neurological disorder, but future approaches to molecular diagnosis of neurodevelopmental disorders should implement GTPBP2.

Retrospective study of prenatal ultrasound findings in newborns with a Noonan spectrum disorder.

OBJECTIVES: Noonan spectrum disorders (NSDs) occur in 1:1000-2500 live births. Currently, there are no guidelines for prenatal molecular genetic testing for NSDs. Recent studies recommend prenatal testing for NSDs when ultrasonography detects two or more associated abnormalities. A stronger association between ultrasound findings and NSDs would enable more informed prenatal genetic testing. METHODS: A total of 212 newborns (0-12 weeks) with prenatal ultrasound findings and a clinical suspicion of a NSD were referred for molecular genetic testing. Of these, 159/212 newborns tested had a single ultrasound abnormality and 53/212 newborns had two or more. Testing was performed by either a microarray-based resequencing assay or next generation sequencing of RAS/MAPK pathway genes associated with NSDs. Prenatal ultrasound findings in positive and negative cases were compared. RESULTS: A disease-causing variant was identified in 21.7% (46/212) of newborns tested. Of these positive cases, 67.4% (31/46) had only one ultrasound abnormality reported. The rate of detecting a disease-causing variant in cases with one ultrasound finding was 19.5% (31/159), which was not significantly different (p-value = 0.36) than that in cases with two or more ultrasound findings (28.3%; 15/53). CONCLUSIONS: Prenatal molecular testing for NSDs should be considered even in the presence of a single associated abnormal ultrasound finding. © 2016 John Wiley & Sons, Ltd.

The role of HOX genes in head and neck squamous cell carcinoma.

Recent decades have witnessed the publication of numerous studies reporting alterations in the genome and transcriptome of head and neck squamous cell carcinoma (HNSCC). Currently, the utilisation of these alterations as biomarkers and targets for therapy is limited and new, useful molecular characteristics are being sought. Many of the published HNSCC gene expression profiles demonstrate alterations in the expression of HOX genes. These are a family of Homeobox-containing genes which are involved in developmental patterning and morphogenesis in the embryo, and which are often aberrantly expressed in cancer. The 39 HOX genes found in the human genome are arranged in four paralogous groups at different chromosomal loci. These control a wide range of cellular processes, including proliferation and migration, which are relevant in the context of cancer development. In this review article, we will outline the biology of HOX genes in relation to cancer and summarise the accumulating evidence for their role in the development of HNSCC and the possibility that they could be a therapeutic target in this malignancy. We will also identify areas where our current understanding is weak to focus future work and appraise the ongoing strategies for pharmacological intervention.

The role of HOXB9 and miR-196a in head and neck squamous cell carcinoma.

BACKGROUND: Previous studies have demonstrated that a number of HOX genes, a family of transcription factors with key roles in early development, are up-regulated in head and neck squamous cell carcinoma (HNSCC) and other cancers. The loci of several Homeobox (HOX) genes also contain microRNAs (miRs), including miR-196a. METHODS: Global miR expression and expression of all 39 HOX genes in normal oral keratinocytes (NOKs), oral pre-malignant (OPM) and HNSCC cells was assessed by expression microarray and qPCR and in tissues by immunohistochemistry (IHC) and qPCR of laser microdissected (LCM) tissues. Expression of miR196a and HOXB9 was reduced using anti-miR-196a and siRNA, respectively. Expression microarray profiles of anti-miR196a and pre-miR196a transfected cells were compared to parental cells in order to identify novel targets of miR-196a. Putative miR196a targets were validated by qPCR and were confirmed as binding to the 3'UTR of miR196a by a dual luciferase reporter assay combined with mutational analysis of the miR-196a binding site. RESULTS: miR-196a and HOXB9 are highly expressed in HNSCC compared to NOKs, a pattern also seen in HNSCC tissues by HOXB9 IHC and qPCR of miR-196a in LCM tissue. Knock-down of miR-196a expression decreased HNSCC cell migration, invasion and adhesion to fibronectin, but had no effect on proliferation. Furthermore, knock-down of HOXB9 expression decreased migration, invasion and proliferation but did not alter adhesion. We identified a novel primary mRNA transcript containing HOXB9 and miR196a-1 as predicted from in-silico analysis. Expression array analysis identified a number of miR196a targets, including MAMDC2 and HOXC8. We confirmed that MAMDC2 is a novel miR-196a target using a dual luciferase reporter assay with the effect abolished on mutation of the binding site. CONCLUSIONS: These results show that miR-196a and HOXB9 are overexpressed, perhaps co-ordinately, as HNSCC develops and exert a pro-tumourigenic phenotype in HNSCC and OPM cells.