Asem Alkhateeb

Background: The neuropeptide substance P is a potential biomarker and therapeutic target in cancer. The main objectives of this study were to investigate the expression level of substance P in different breast cancer molecular subtypes and identify its association with clinicopathological parameters of patients and with Ki-67 index.Methods: A retrospective analysis was performed for a total of 164 paraffin-embedded breast cancer tissue samples [42 Her2/neu-enriched, 40 luminal A, 42 luminal B (triple-positive) and 40 triple negative subtypes]. The tissue microarray slides containing specimens were used to determine the expression of substance p and Ki-67 by immunohistochemical staining.Results: The mean age of the cohort was 51.35 years. Twenty two percent of cases had low substance P expression levels (TS ≤ 5), while 78% had high expression levels (TS > 5). A significant association was found between SP expression level and breast cancer molecular subtype (p = 0.002), TNM stage (p = 0.034), pN stage (p = 0.013), axillary lymph node metastasis (p = 0.004), ER and PR statuses (p<0.001) and history of DCIS (p = 0.009). The average percentage of Ki-67 expression was 27.05%. When analyzed as a continuous variable, significant differences were observed between the mean Ki-67 scores and molecular subtype (p = 0.001), grade (p = 0.003), pN stage (p = 0.007), axillary lymph node metastasis (p = 0.001), and ER and PR statuses (p <0.001).Conclusion: SP is overexpressed in most of the analyzed tissues and has a negative prognostic value in the breast cancer patients. Besides substance P is a potential therapeutic target in breast cancer.

Intellectual disability is a common condition with multiple etiologies. The number of monogenic causes has increased steadily in recent years due to the implementation of next generation sequencing. Here, we describe a 2-year-old boy with global developmental delay and intellectual disability. The child had feeding difficulties since birth. He had delayed motor skills and muscular hypotonia. Brain magnetic resonance imaging revealed diffuse white matter loss and thinning of the corpus callosum. Banded karyotype and comparative genomic hybridization (CGH) array were normal. Whole exome sequencing revealed a novel de novo frameshift mutation c.3390delA (p.Lys1130Asnfs*4) in KAT6A gene (NM_006766.4). The heterozygous mutation was confirmed by Sanger sequencing in the patient and its absence in his parents. KAT6A that encodes a histone acetyltransferase has been recently found to be associated with a neurodevelopmental disorder autosomal dominant mental retardation 32 (OMIM: no. 616268). Features of this disorder are nonspecific, which makes it difficult to characterize the condition based on the clinical symptoms alone. Therefore, our findings confirm the utility of whole exome sequencing to quickly and reliably identify the etiology of such conditions.

Intellectual disability is a heterogeneous disease with many genes and mutations influencing the phenotype. Consanguineous families constitute a rich resource for the identification of rare variants causing autosomal recessive disease, due to the effects of inbreeding. Here, we examine three consanguineous Arab families, recruited in a quest to identify novel genes/mutations. All the families had multiple offspring with non-specific intellectual disability. We identified homozygosity (autozygosity) intervals in those families through SNP genotyping and whole exome sequencing, with variants filtered using Ingenuity Variant Analysis (IVA) software. The families showed heterogeneity and novel mutations in three different genes known to be associated with intellectual disability. These mutations were not found in 514 ethnically matched control chromosomes. p.G410C in WWOX, p.H530Y in RARS2, and p.I69F in C10orf2 are novel changes that affect protein function and could give new insights into the development and function of the central nervous system.

Background: Recurrent aphthous stomatitis (RAS) is an inflammatory disease induced by genetic and environmental factors. Toll‐like receptor (TLR) and CD86 are essential components for innate immunity and cellular immune response. We aimed to determine whether inheritance of specific TLR2, TLR4and CD86 gene polymorphisms are associated with RAS.Methods: Ninety‐six patients with RAS and 153 controls were studied. Eight SNPs were genotyped using PCR–RFLP technique; four in TLR2 gene: rs4696480, rs3804100, rs121917864, rs5743708; three in TLR4 gene: rs10759931, rs4986790 rs1927911; and one in CD86 gene rs17281995. Association was assessed by logistic regression analysis. Linkage disequilibrium (LD) was assessed using the Haploview program.Results: Significant increase in inheritance of A allele (OR = 1.6, P = 0.01) and AA genotype (OR = 3.89, P = 0.01) of TLR4 rs10759931 was observed in cases. TLR4rs1927911 C allele and CC genotype were also increased (OR = 1.60 and 2.78 respectively); however, this was not statistically significant (P = 0.02 and 0.03 respectively). TLR2 and CD86 did not show association with RAS.Conclusions: This is the first study to investigate the association of TLR and CD86 with RAS. We found a significant association between TLR4 rs10759931 polymorphism and RAS. Confirmatory studies in other populations and functional investigations are needed to determine the role of TLR4 in RAS.

DNA Hypermethylation of Cell Cycle (p15 and p16) and Apoptotic (p14, p53, DAPK and TMS1) Genes in Peripheral Blood of Leukemia Patients p14;p15;p16;p53;DAPK;TMS1;DNA methylation;chronic leukemia;acute leukemia; Aberrant DNA methylation of tumor suppressor genes has been reported in all major types of leukemia with potential involvement in the inactivation of regulatory cell cycle and apoptosis genes. However, most of the previous reports did not show the extent of concurrent methylation of multiple genes in the four leukemia types. Here, we analyzed six key genes (p14, p15, p16, p53, DAPK and TMS1) for DNA methylation using methylation specific PCR to analyze peripheral blood of 78 leukemia patients (24 CML, 25 CLL, 12 AML, and 17 ALL) and 24 healthy volunteers. In CML, methylation was detected for p15 (11%), p16 (9%), p53 (23%) and DAPK (23%), in CLL, p14 (25%), p15 (19%), p16 (12%), p53 (17%) and DAPK (36%), in AML, p14 (8%), p15 (45%), p53 (9%) and DAPK (17%) and in ALL, p15 (14%), p16 (8%), and p53 (8%). This study highlighted an essential role of DAPK methylation in chronic leukemia in contrast to p15 methylation in the acute cases, whereas TMS1 hypermethylation was absent in all cases. Furthermore, hypermethylation of multiple genes per patient was observed, with obvious selectiveness in the 9p21 chromosomal region genes (p14, p15 and p16). Interestingly, methylation of p15 increased the risk of methylation in p53, and vice versa, by five folds (p=0.03) indicating possible synergistic epigenetic disruption of different phases of the cell cycle or between the cell cycle and apoptosis. The investigation of multiple relationships between methylated genes might shed light on tumor specific inactivation of the cell cycle and apoptotic pathways.

Objectives: Recurrent aphthous stomatitis (RAS) is a common oral inflammatory disease induced by genetic and environmental factors. Gelatinases (MMP‐2 and MMP‐9) and their natural inhibitor TIMP‐1 are active players in the inflammatory process. We aimed to determine whether inheritance of specific MMP‐2, MMP‐9, or TIMP‐1 gene polymorphisms is associated with RAS susceptibility.Subjects and methods: Ninety‐six RAS patients and 153 healthy controls were studied. Five polymorphisms were genotyped: rs17576, rs3918242, and rs11697325 in MMP‐9, MMP‐2 rs2285053, and TIMP‐1 rs6609533. Association was assessed by logistic regression analysis after adjustment for confounding factors. Linkage disequilibrium (LD) was assessed using the Haploview program.Results: MMP‐9 rs11697325 was significantly associated with RAS, with an increase in the AA genotype in patients, determined using χ² analysis (OR = 2.3, P = 0.006) and adjusted regression analysis (OR = 3.1, P = 0.009). MMP‐9 rs11697325 and rs17576 showed strong LD (D' = 0.95), with an increase in the AA haplotype (P = 0.023) and a decrease in the GA haplotype (P = 0.015) in patients.Conclusions: This is the first study to investigate the association of MMPs or TIMP‐1 with RAS. We found a significant association between MMP‐9 rs11697325 polymorphisms and RAS. Confirmatory studies in other populations and functional investigations are needed to determine the role of these genes in RAS.