Crystallographic modeling of the PNPT1:c.1453A>G variant as a cause of mitochondrial dysfunction and autosomal recessive deafness; expanding the neuroimaging and clinical features.

Deficiency of the proteins involved in oxidative phosphorylation (OXPHOS) can lead to mitochondrial dysfunction. Polyribonucleotide nucleotidyltransferase 1 (PNPT1) is one of the genes involved in the OXPHOS and encodes the mitochondrial polynucleotide phosphorylase (PNPase) which is implicated in RNA-processing exoribonuclease activity. Herein, we report a 34-month-old boy who presented with global developmental delay, muscular hypotonia, hearing impairment, and movement disorders including chorea and dystonia. Mitochondrial genome sequencing and whole-exome sequencing (WES) were performed and a variant in PNPT1:c.1453A>G; p. (Met485Val) was identified. A number of patient's neurologic problems had been already reported in previous studies, however, lower limbs spasticity and bulbar dysfunction were novel phenotypic findings. In addition, delayed myelination during infancy, progressive basal ganglia atrophy, and brain stem abnormal signals including transverse pontine fibers and superior colliculus involvement were also novel neuroimaging findings in this case. Different crystallographic modeling and stereochemical analysis of the c.1453A>G; p. (Met485Val) variant showed this variant affects the active site of the protein and disrupts the normal protein function.

Methylation Assessment of Two DKK2 and DKK4 Genes in Oral Squamous Cell Carcinoma Patients.

BACKGROUND: Oral squamous cell carcinoma (OSCC) is one of the most important types of oral malignancies. DKK gene family members as well as DKK2/4 have critical roles in regulation of Wnt signaling as one of the main determining pathway in oral carcinogenesis. This study aimed to identify promoter methylation status of DKK2/4 genes to provide possible biomarkers for early detection and treatment of OSCC patients. METHODS: A case control study was performed on 31 fresh tissues obtained from oral cavity of patients affected by OSCC and 31 fresh corresponding tissues from normal healthy controls in Tehran and, between the years of 2016-2018. Purified DNA from tissue samples was subjected to bisulfite treatment and then methylation specific polymerase chain reaction (MSP-PCR) was carried out on treated DNA samples. RESULTS: DKK4 promoter was methylated in none of OSCC samples while it was methylated in 16.1% of healthy controls. 16.1% of OSCC samples were detected to be semimethylated and 22.6% of healthy normal samples were methylated for DKK2 promoter gene. Meaningful difference was found in DKK4 promoter methylation among OSCC patients and healthy controls. Significant correlation was found between DKK4 promoter methylation and tumor grade. The age of all enrolled samples was demonstrated to have strong effect on promoter methylation of studied genes. CONCLUSION: Hypomethylation of DKK2 and DKK4 genes in higher grades of OSCC samples may indicate the pivotal role of their expression in tumor cells invasion and progression through modulation of Wnt signaling pathway. Further study required to determine simultaneous expression of those genes and Wnt signaling elements at mRNA and protein levels.

The First Comprehensive Cohort of the Duchenne Muscular Dystrophy in Iranian Population: Mutation Spectrum of 314 Patients and Identifying Two Novel Nonsense Mutations.

Mutations in the dystrophin gene could cause Duchenne muscular dystrophy (DMD), which is the most common muscular disorder in pediatrics. Considering the growing evidence on appropriateness of gene therapies for DMD, precise genetic diagnosis seems essential. Hence, we conducted a study to determine mutational patterns in Iranian children with DMD. To detect all probable large mutations in the dystrophin gene, 314 DMD patients were evaluated using the multiplex ligation-dependent probe amplification (MLPA). Subjects who were MLPA-negative underwent the next generation sequencing (NGS) to identify potential point mutations. MLPA detected deletions (79.93%) and duplications (5.41%) along the dystrophin gene of 268 patients. Distribution of large mutations was heterogeneous and followed hotspot pattern throughout the gene. From 46 patients who were MLPA-negative, 43 exhibited point mutations including nonsense in 7.64%, frameshifts in 4.77%, splicing in 0.96%, and missense variations in 0.32% of participants. Most of the point mutations were located between exons 19 and 40. In three patients (1%), no mutation was found using either MLPA or NGS. Two subjects had novel nonsense mutations (L1675X and E1199X) in their dystrophin gene, which were considered as the possible reason for elimination of major domains of the gene. The results of this study provided invaluable information regarding the distribution of various large and small mutations in Iranian individuals with DMD. Besides, the novel nonsense mutations L1675X and E1199X were identified within the highly conserved residues, leading to elimination of significant domains of the dystrophin gene.

Expanding the clinical and neuroimaging features of NKX6-2-related hereditary spastic ataxia type 8.

Pathogenic variants in NKX6-2 gene causing autosomal recessive spastic ataxia type 8 with hypomyelinating leukodystrophy have been reported in few families around the world. In this study, we performed Whole Exome Sequencing and identified a novel missense variant, c.501C > G; p.(Phe167Leu), in two affected siblings with main manifestations of global developmental delay, motor regression, hypotonia, clonus in lower limbs and muscle bulk atrophy especially in the upper limbs, spasticity and contracture, scoliosis, hip dislocation, oculomotor apraxia, horizontal and vertical nystagmus. In addition, wrist and foot drop due to peripheral axonal neuropathy were observed in these patients as a new clinical finding and cerebellar white matter involvement in brain Magnetic Resonance Imaging (MRI) as new imaging finding. Therefore, we expanded the manifestations of NKX6-2-related disorders in this manuscript.

Novel in-frame deletion in MFSD8 gene revealed by trio whole exome sequencing in an Iranian affected with neuronal ceroid lipofuscinosis type 7: a case report.

BACKGROUND: The neuronal ceroid lipofuscinoses are a group of neurodegenerative, lysosomal storage disorders. They are inherited as an autosomal recessive pattern with the exception of adult neuronal ceroid lipofuscinosis, which can be inherited in either an autosomal recessive or an autosomal dominant manner. The neuronal ceroid lipofuscinoses are characterized by accumulation of autofluorescent lipopigments in the cells and one of the most important pathological manifestations is ceroid accumulation in the lysosomes. Various types of neuronal ceroid lipofuscinoses are categorized based on the clinical manifestations and the genes involved. Accumulatively, 15 different genes have been found so far to be implicated in the pathogenesis of at least nine different types of neuronal ceroid lipofuscinoses, which result in similar pathological and clinical manifestations. CASE PRESENTATION: A 5-year-old Iranian boy affected by a neurodegenerative disorder with speech problems, lack of concentration, walking disability at age of 4 years leading to quadriplegia, spontaneous laughing, hidden seizure, clumsiness, psychomotor delay, and vision deterioration at age of 5 years, which could be the consequence of macular dystrophy, was referred to us for genetic testing. Trio whole exome sequencing, Sanger validation, and segregation analysis discovered a novel in-frame small deletion c.325_339del (p.Val109_Ile113del) in MFSD8 gene associated with neuronal ceroid lipofuscinosis type 7. CONCLUSIONS: The deletion found in this patient affects the exon 5 of this gene which is the region encoding transmembrane domain. Sequencing analysis in this family has shown that the index is homozygous for 15 base pairs in-frame deletion, his uncle has normal homozygous, and his parents are heterozygous. This pattern of mutation inheritance and the signs and symptoms observed in the affected male of this family are compatible with what is described in the literature for neuronal ceroid lipofuscinosis type 7 and, therefore, suggest that the MFSD8 gene deletion found in this study is most probably the cause of disease in this family.

Pharmacogenetics and Personalized Medicine in Pancreatic Cancer.

 Pancreatic cancer (PC) is a progressive, fatal disease with a high degree of malignancy. More than 40000 peoplediefrom this cancer annually in the United States. As a multifactorial condition, PC has a complex nature, and there are several genes and signalingpathwaysimplicated in PC pathogenesis and progression. There are diffèrent mutations in master genesincludingtumorsuppressors and oncogenesthat lead to Pancreaticintraepithelialneoplasia (PanIN) whichis the mostcommon non-invasive precursorlesion of pancreatic cancer. These mutations influence directly or indirectly the cycle of Pharmacodynamics profile. Interactions between genetics and drug metabolism could be considered as one of the most important insights in the personalized medicine and targeted therapy based on the genetic profile of each affected person. In this literature, we will discuss pathogenesis and susceptibility to PC, pharmacogenetics and personalized medicine in pancreatic cancer and scrutinized the most important genes, variations and signaling pathways that influence individualized therapy of PC.

Cancer/Testis Antigens: Expression, Regulation, Tumor Invasion, and Use in Immunotherapy of Cancers.

UNLABELLED: Cancer/testis antigens (CTAs) are named based on their expression pattern that is restricted in a number of normal and abnormal tissues. Tumor cells frequently express antigens whose expression is typically restricted to germ cells. Their unique expression pattern is guaranteed by precise epigenetic regulatory mechanisms. Because of their tumor-limited, high immunogenicity, and biased expression, discovery of these molecules provides unprecedented opportunities for further research and clinical development in the field of cancer diagnosis and immunotherapy. Evolving evidence reveals that a number of CTAs stimulate epithelial mesenchymal transition (EMT) and generation of cancer stem-like cells, intensifying metastasis, invasion, and tumorigenesis. Based on these features, CTAs attract attention to be considered as ideal targets for developing several clinical trials, many of them concentrating on CTA vaccine therapy. According to recent practical clinical interest, more characterizations of CTA regulation are identified. CTA expression has been demonstrated in a variety of human cancer tissues, and some of them have been found to elicit humoral and/or cellular immune responses in cancer patients. CTAs are brilliant targets for anticancer drug discovery, targeted tumor therapy, and diagnostic biomarkers, furthermore, valued genes in the study of immunotherapy, promoting tumorigenesis, and malignant progression. This review outlines and categorizes our current understanding of the complex and biased process of CTAs mRNA and protein expression in cancer, and supplies the most recent information on their regulation and function. Besides, a concise synopsis of the major clinical trials involving CTAs, as therapeutic avenues, is discussed. ABBREVIATIONS: AIRE: autoimmune regulator; cAMP: cyclic adenosine 3',5'-cyclic monophosphate; CEA: carcinoembryonic antigen; CML: chronic myeloid leukemia; CREB: cyclicamp response element binding; CSCs: cancer stem cells; CTAs: cancer/testis antigens; CTL: cytotoxic T lymphocyte; DCs: dendritic cells; EMT: epithelial-mesenchymal transition; ERK: extracellular signal-regulated kinase; ESCC: esophageal squamous cell carcinoma; ETS: E26 transformation-specific; His: histidine; HLA: human leukocyte antigen; HNSCC: head and neck squamous cell carcinoma; IFN-γ: interferon-γ; IHC: Immunohistochemistry; IL-7: Interleukin7; MHC: major histocompatibility complex; MMP2: matrix metalloproteinase 2; mTECs: medullary thymus epithelial cells; MUC1: mucin 1; NSCLC: non-small cell lung cancer; PRAME: preferentially expressed antigen in melanoma; RDA: representational difference analysis; SEREX: serological analysis of cDNA expression; SSX: synovial sarcoma X chromosome; TAAs: tumor-associated antigens; TCR: T-cell receptor; TCGA: The Cancer Genome Atlas; TGF-ß: transforming growth factor-ß.