Rania Darwish

BACKGROUND: Inborn errors of immunity (IEI) are a group of heterogeneous disorders with geographic and ethnic diversities. Although IEI are common in Egypt, genetic diagnosis is limited due to financial restrictions. This study aims to characterize the genetic spectrum of IEI patients in Egypt and highlights the adaptation of the molecular diagnostic methods to a resource-limited setting.

METHODS: Genetic material from 504 patients was studied, and proper diagnosis was achieved in 282 patients from 246 families. Mutational analysis was done by Sanger sequencing, next-generation sequencing (NGS) targeting customized genes panels, and whole-exome sequencing (WES) according to the patients' phenotypes and availability of genetic testing.

RESULTS: A total of 194 variants involving 72 different genes were detected with RAG1/2 genes being the most encountered followed by DOCK8, CYBA, LRBA, NCF1, and JAK3. Autosomal recessive (AR) inheritance was detected in 233/282 patients (82.6%), X-linked (XL) recessive inheritance in 32/282 patients (11.3%), and autosomal dominant (AD) inheritance in 18/282 patients (6.4%), reflecting the impact of consanguineous marriages on the prevalence of different modes of inheritance and the distribution of the various IEI disorders.

CONCLUSION: The study showed that a combination of Sanger sequencing in selected patients associated with targeted NGS or WES in other patients is an effective diagnostic strategy for IEI diagnosis in countries with limited diagnostic resources. Molecular testing can be used to validate other nonexpensive laboratory techniques that help to reach definitive diagnosis and help in genetic counseling and taking proper therapeutic decisions including stem cell transplantation or gene therapy.

BACKGROUND: Paediatric cardiomyopathy is a progressive, often lethal disorder and the most common cause of heart failure in children. Despite its severe outcomes, the genetic aetiology is still poorly characterised. High-throughput sequencing offers a great opportunity for a better understanding of the genetic causes of cardiomyopathy.

AIM: The current study aimed to elucidate the genetic background of cardiomyopathy in Egyptian children.

METHODS: This hospital-based study involved 68 patients; 58 idiopathic primary dilated cardiomyopathy and 10 left ventricular noncompaction cardiomyopathy. Cardiomyopathy-associated genes were investigated using targeted next-generation sequencing.

RESULTS: Consanguinity was positive in 53 and 70% of dilated cardiomyopathy and left ventricular noncompaction cardiomyopathy patients, respectively. Positive family history of cardiomyopathy was present in 28% of dilated cardiomyopathy and 10% of the left ventricular noncompaction cardiomyopathy patients. In 25 patients, 29 rare variants were detected; 2 likely pathogenic variants in TNNI3 and TTN and 27 variants of uncertain significance explaining 2.9% of patients.

CONCLUSIONS: The low genetic detection rate suggests that novel genes or variants might underlie paediatric cardiomyopathy in Egypt, especially with the high burden of consanguinity. Being the first national and regional report, our study could be a reference for future genetic testing in Egyptian cardiomyopathy children. Genome-wide tests (whole exome/genome sequencing) might be more suitable than the targeted sequencing to investigate the primary cardiomyopathy patients. Molecular characterisation of cardiomyopathies in different ethnicities will allow for global comparative studies that could result in understanding the pathophysiology and heterogeneity of cardiomyopathies.

Paediatric cardiomyopathy is a progressive and often lethal disorder and the most common cause of heart failure in children. Despite their severe outcomes, their genetic etiology is still poorly characterised. The current study aimed at uncovering the genetic background of idiopathic primary hypertrophic cardiomyopathy in a cohort of Egyptian children using targeted next-generation sequencing. The study included 24 patients (15 males and 9 females) presented to the cardiomyopathy clinic of Cairo University Children's Hospital with a median age of 2.75 (0.5-14) years. Consanguinity was positive in 62.5% of patients. A family history of hypertrophic cardiomyopathy was present in 20.8% of patients. Ten rare variants were detected in eight patients; two pathogenic variants (8.3%) in MBPC3 and MYH7, and eight variants of uncertain significance in MYBPC3, TTN, VCL, MYL2, CSRP3, and RBM20.Here, we report on the first national study in Egypt that analysed sarcomeric and non-sarcomeric variants in a cohort of idiopathic paediatric hypertrophic cardiomyopathy patients using next-generation sequencing. The current pilot study suggests that paediatric hypertrophic cardiomyopathy in Egypt might have a particular genetic background, especially with the high burden of consanguinity. Including the genetic testing in the routine diagnostic service is important for a better understanding of the pathophysiology of the disease, proper patient management, and at-risk detection. Genome-wide tests (whole exome/genome sequencing) might be better than the targeted sequencing approach to test primary hypertrophic cardiomyopathy patients in addition to its ability for the identification of novel genetic causes.

BACKGROUND: Human pegivirus (HPgV) is structurally similar to hepatitis C virus (HCV) and was discovered 20 years ago. Its distribution, natural history and exact rule of this viral group in human hosts remain unclear. Our aim was to determine, by deep next-generation sequencing (NGS), the entire genome sequence of HPgV that was discovered in an Egyptian patient while analyzing HCV sequence from the same patient. We also inspected whether the co-infection of HCV and HPgV will affect the patient response to HCV viral treatment. To the best of our knowledge, this is the first report for a newly isolated HPgV in an Egyptian patient who is co-infected with HCV.

CASE PRESENTATION: The deep Next Generation Sequencing (NGS) technique was used to detect HCV sequence in hepatitis C patient's plasma. The results revealed the presence of HPgV with HCV. This co-infection was confirmed using conventional PCR of the HPgV 5' untranslated region. The patient was then subjected to direct-acting-antiviral treatment (DAA). At the end of the treatment, the patient showed a good response to the HCV treatment (i.e., no HCV-RNA was detected in the plasma), while the HPgV-RNA was still detected. Sequence alignment and phylogenetic analyses demonstrated that the detected HPgV was a novel isolate and was not previously published.

CONCLUSION: We report a new variant of HPgV in a patient suffering from hepatitis C viral infection.

Tumor necrosis factor related apoptosis-inducing ligand (TRAIL) plays an important role in many cancers including hepatocellular carcinoma (HCC). The aim of this study is to investigate the association of the DR4 polymorphisms C626G (Thr209Arg, rs20575) and A683C (Glu228Ala, rs20576) with the occurrence of HCC in Egyptian patients chronically infected with HCV. The study included 80 patients with HCV-related HCC (group 1) and 80 patients with HCV-related liver cirrhosis (group 2) who are naïve to treatment. Clinical and laboratory data were recorded. Genotyping of TRAIL receptor DR4 polymorphism C626G rs20575 and A683C rs20576 SNP was done by Real-Time PCR using taqman probes technology. The mean age of HCC patients was 57.6 ± 8.4 years with 62 patients (77.5%) were males. While group 2 mean age was 49.5 ± 10.29 years with 50% were males. The frequency distribution of rs20575 genotypes showed a statistically significant difference between the two studied groups (P = 0.02), the carriers of the C allele were 2.01 times more likely to develop HCC than the carriers of the G allele (P = 0.003), while no significant difference in rs20576 genotypes distribution was found between the studied groups (P = 0.680). On combining the carriers of C allele of rs20575 and the carriers of A allele of rs20576, a significant difference was detected (P > 0.001) with 2.85 higher risk of HCC development in patients who carried both genetic risk alleles simultaneously. The significant difference in DR4 polymorphisms among HCC and cirrhotic patients suggests their role as potential risk factors of HCC development.

We investigated the association of the Osteopontin (OPN) (rs9138 and rs1126616) polymorphisms with colorectal cancer (CRC). One hundred CRC patients and 112 healthy individuals were subjected to OPN (rs9138 and rs1126616) genotyping and measurement of OPN protein plasma level. The C allele of OPN rs1126616 and the CC haplotype were significantly higher in CRC patient (p = 0.036, 0.003, respectively). In females, the C allele of OPN rs9318 (A/C) polymorphism was significantly associated with increased CRC risk (p = 0.036). The plasma OPN level >104.35 ng/mL was significantly associated with CRC. Our findings suggest a significant role played by OPN (rs9138 and rs1126616) in colorectal carcinogenesis.

The present study aimed at evaluating the role of
IL-1β −511 promoter and IL-1β +3953 exon 5 gene polymorphisms
in the risk of developing rheumatoid arthritis
(RA) and its correlation to disease activity in Egyptian
patients. Thirty-two patients having RA as defined by
American College of Rheumatology and 20 healthy control
subjects were included. All were subjected to DNA analysis
for IL-1β −511and IL-1β +3953 gene polymorphisms using
PCR-RFLP technique with restriction enzymes AvaI and
TaqI, respectively. No special pattern of association could
be detected either between IL-1β −511 and +3953 gene
polymorphisms and disease susceptibility or between the
polymorphisms and the disease activity parameters represented
by disease activity score 28 (DAS 28), ESR, and
number of swollen and tender joints. Allele distribution
failed as well to detect any association with either disease
susceptibility or activity; however, a trend towards positive
association involving IL-1β −511 C allele was observed (P=
0.054). Our results suggest that IL-1β −511 and IL-1β +3953
gene polymorphisms do not influence the susceptibility to
acquire RA in our population with no relation to disease
activity. The complex role of the genetic factors in RA and
the magnitude of the effects will require further thorough
confirmations in other populations and on larger samples to
acknowledge this issue.