Molecular and Genetic Medicine

With their ground-breaking clinical success, immune checkpoint inhibitors (ICIs) have opened a new chapter in cancer treatment; however, not all patients have a response to ICI treatment. Current approaches to maximizing the efficacy of ICI treatment include combining it with conventional cancer treatments and identifying biomarkers that accurately predict tumor responses to ICI agents. This mini-review introduces genomic determinants of ICI efficacy and directions for future immunogenomic studies in the era of checkpoint inhibition.

X-linked liver glycogenosis (XLG), also known as glycogen storage disease (GSD) type-IXa, is characterized by hepatomegaly, abnormal liver functions and growth retardation. This disease is a result of a deficiency of hepatic phosphorylase kinase (PHK), which plays an important role in glycogen metabolism by activating phosphorylase. We aim at identifying the genetic cause of the GSD running in a family with two affected boys, and hence develop proper management and genetic counseling. The boys presented with typical GSD signs and symptoms. The histology of the liver biopsy from the old brother showed glycogen accumulation in hepatocytes and confirmed his condition of GSD. The younger brother did not have a biopsy. Whole exome sequencing was used to analyze the genetic structure of the proband patients and their parents. Sanger sequencing was used to validate and confirm the identified mutation. The results showed that there was a known pathogenic mutation (p.E1125K) in PHKA2 gene located on chromosome Xp22, which encodes the regulatory subunit of PHK. Pedigree analysis revealed that the mother was a carrier, and the disease of both brothers was transmitted through their undiagnosed maternal grandfather. This is the first report of XLG caused by this mutation in China, and it indicated that GSD may be undiagnosed or underestimated since GSD IXa is one of the mild form of glycogenosis in terms of clinical symptoms. However, it is necessary to identify the genetic cause in order to perform effective intervention and genetic counseling.

Epidermal growth factor inhibitors are currently an essential treatment for many advance-stage epithelial cancers as colorectal and lung cancer. Although they are safe, these agents often present cutaneous adverse events that can cause dosage reduction, interruption of treatment and psychosocial discomfort. We report two cases of cutaneous toxicity in patients with solid tumors using different epidermal growth factor inhibitors.

NOP16 was the third most important mutation (6.84%) in a reduced-size cohort of 117 patients with Chronic Lymphocytic Leukemia (CLL) whose most recurrent mutations were NOTCH1 (9.4%) and SF3B1 (8.55%). In this paper we analyzed the effect of the NOP16 mutation in gene expression. The NOP16 mutation was predicted with 100% accuracy using a small-scale signature formed by the 26 genes with the highest Fisher’s Ratio. SLC39A4 (ZIP4) and WARS are the most discriminatory genes of this mutation providing a predictive accuracy of 97.4%. The Fold Change analysis also confirmed a very important role of the light (IGKV3D-11, IGKC and IGLJ3) and heavy (IGHG1) chain immunoglobulins, SOX11, CCND1 and CHL1 . This analysis also highlights the importance of several mechanisms such as the ZIP4-related apoptosis, the SOX11-CCND1 over expression relationship observed in mantle cell-lymphoma, and CHL1 down regulation and over expression of the midkine-neurite growth-promoting factor that enhances the angiogenic and proliferative activities of cancer cells in different types of solid cancers. Besides, the holdout stability analysis has shown the importance of Signaling Events of B Cell Receptor (BCR), P53 signaling, Infectious disease, and TGF-beta Receptor Signaling. The integration of the NOP16 mutation with the IgHV, NOTCH1 and SF3B1 mutations, that were previously analyzed, confirmed that these mutations only share two high discriminatory genes: IGHG1 and RGS13. These genes are involved in different mechanisms concerning signaling and the immunological system. This analysis opens novel working hypothesis for CLL treatment and prognosis.

Schizophrenia (Sz) hospitalization is on the rise for young men. There is a link between caffeine and calcium absorption. Calcium is necessary for a healthy nervous system. In this brief paper, I show that the cause of Sz increase among young men may be because of the dramatic increase of caffeine intake (Coffee) among that group. In addition, use of hallucinogens (LSD) among young men may be the sole explanation for the rise in Sz among that group. We also examine the connection between cholera and Schizophrenia. In this paper, we suggest possible causes of Sz that may warrant closer examination by researchers.

The Germ-terrain duality theory of disease states that the etiology of certain diseases/diseased states is better explained as a complex interplay between germs and the inherent anatomical/physiological integrity of the body cells.

Familial hypercholesterolemia (FH) is an autosomal dominant disorder most commonly caused by mutations in the gene for the Low-Density Lipoprotein (LDL) receptor (LDLR), but about 5% of patients in the UK with a clinical diagnosis of FH have a mutation in the gene for apolipoprotein B (APOB). This disorder is called Familial Defective APOB-100 (FDB), and while plasma total- and LDL-cholesterol levels overlap between patients with FDB and those with LDLR mutations, usually those with FDB present with a milder form of the disease, especially in homozygous FDB compared to LDLR mutation-caused FH. The most common mutation in APOB is p.(Arg3527Gln), but another APOB mutation p.(Arg3527Trp) has previously been identified in a family of South Asian origin. Here we describe a consanguineous marriage of parents of South Asian origin with both homozygous and heterozygous offspring with the APOB p.(Arg3527Trp) mutation. The mean untreated levels of LDL-cholesterol in the three heterozygous, Father and Mother (age 45 years) and a girl (age 9 years) were 5.5 mmol/l, 4.5 mmol/l, and 4.2 mmol/l respectively, while the mean untreated levels of LDL-cholesterol in the two homozygous boys (age 15 years and 11 years) were 6.2 mmol/l and 7.0 mmol/l respectively and this was reduced by ~30% on statin treatment. This confirms the milder phenotype and good response to statin therapy even for homozygous FDB.

Clinicians have been facing an enormous challenge of treating infections caused by multiple drug resistant (MDR) pathogens since long. The latest and most alarming of such challenge is the emergence of New Delhi Metallo-β-Lactamase-type 1 (NDM-1) producing clinical isolates. NDM-1 is a metallo β-lactamase that confers resistance to all β-lactam antibiotics including carbapenems generally regarded as last resort to treat infections. NDM-1 is part of a huge conjugative plasmid blaNDM capable of rapid dissemination via horizontal gene transfer, transposition and recombination. Therefore, it has become a matter of global concern now as these pathogens have surpassed all geographical barriers and are threatening the public health all over the world. In addition to this, NDM-1 gene coexists with other resistance determinants such as other MBLs or porin mutations. Plasmid also carries genes conferring resistance to other antibiotic classes such as 16S RMTases, qcr, or mcr-1 gene imparting resistance to aminoglycosides, fluroquinolones and colistin respectively making current therapeutic recourse ineffective. If not addressed immediately, this resistance and its dissemination will bring us to a therapeutic dead end. In the present review, we have discussed the global spread of NDM-1 and its variants, its structural challenges that currently limit inhibitor drug designing, along with focusing some light on immediate measures that can be adapted at healthcare facilities with review of recent pharmacologic agents under research effective against NDM-1.

The proline rich domain of the P53 tumor suppressor protein is necessary for the induction of apoptosis. A common polymorphism, Proline-72-Arginine, alters structural and biological properties of P53 . The Arginine allele has been suggested as a risk factor for breast cancer. We investigate by association and segregation studies, the role of Arg72 allele as a risk factor in sporadic and familial breast cancer in Senegalese women. Eighty patients diagnosed with breast cancer followed up at the Curie Institute in Dakar, and eighty-five healthy controls without known cancer, were recruited after informed consent. For each individual, DNA was extracted from whole blood and codon 72 polymorphism genotyped by PCR-RFLP. Our results showed an increased risk for patients carrying Arg/ Arg and Arg/Pro genotypes compared to those carrying Pro/Pro (p<0.03). Similarly, the Arg allele was associated with an increased risk (p<0.03). The codon 72 of P53 might be involved in susceptibility to breast cancer.

Despite the many advancements in Liver Transplantation (LT), mortality in patients with hepatic failure remains high, and to date, many patients die while awaiting LT. The Molecular Adsorbent Recirculating System (MARS®) is an extracorporeal liver support system intended to provide short-term metabolic detoxification, often as a vital bridge to LT. We report the case of a 41-year-old non-Hispanic White male who developed worsening multi-factorial encephalopathy in the setting of decompensated alcoholic cirrhosis. He continued to deteriorate despite supportive medical therapy, and extensive investigation for alternative causes of encephalopathy aside from hepatic was unrevealing; as a result, there was concern that his encephalopathy was due to irreversible causes from which he may not recover appropriately following LT. We herein: i) describe the implementation of MARS as a diagnostic intervention for encephalopathy of uncertain etiology in a patient with end stage liver disease who, on the basis of prompt psychomotor improvement, underwent LT 19 days post-MARS implementation with an excellent clinical outcome and thus ii) propose the use of extracorporeal liver support not only as a short-term bridge but also as a diagnostic (and potentially therapeutic) measure in cases of cryptogenic encephalopathy, particularly in the setting of advanced liver disease.

In recent years, limited reports of epidermal growth factor receptor mutations in pulmonary large cell neuroendocrine tumors have implicated potential therapeutic targets in a tumor which has historically been treated with platinum based chemotherapy. We report partial response in metastatic large cell neuroendocrine tumor with an EGFR mutation. Moreover, targeted next generation sequencing analysis upon disease progression identified possible resistance pathways in EGFR and PIK3CA which parallels observations in adenocarcinoma of the lung. New therapeutic strategies may be need to be developed overcome resistance.

This report discusses the case of a twenty-eight years old male patient reported in our tertiary care skin institute for the treatment of post-traumatic scar revision on his left heel following a history of road side accident one year back. The treatment of this patient is based on the principle of regenerative surgery where body’s own tissues and fluids are utilized for healing and repair. The intention of combining three procedures was to induce repeated injuries on scarred skin and give appropriate direction for wound repair in presence of PRP released growth factors. Eventually by the end of third session, the patients started perceiving touch and pain sensation which led to complete healing of trophic ulcers and prevented risk of osteomyelitis to underlying bone. Author strongly believes that no amount of external agents can ever match our body’s own healing potential; all it needs is a little support, right nutrition and the direction to work in.

Juvenile nasopharyngeal angiofibroma (JNA), a rare type of tumor that occurs most frequently in adolescent males, is difficult to treat. The relationship between JNA and certain biomolecules has been the subject of a great deal of research conducted over a long period. This review summarizes the research on the etiopathogenesis of JNA.

Background: Cucurbitaceae family is one of the best genetically assorted accumulations of restorative plants in the plant kingdom. Previous studies have suggested that Citrullus colocynthis (L.) Schrad. plant parts (root, stem, leaf, fruits, and seeds) have been utilized in the traditional system of medicine. Pharmacological activities reported for this plant include antioxidant activity, antimicrobial activity, anti-diabetic activity, anti-hyperlipidemic activity. The antidiarrheal activity of hydroalcoholic extract of fruits of this plant is reported for the first time in the present study.
Objective: To evaluate the anti-diarrheal activity of Citrullus colocynthis (L.) Schrad. (Cucurbitaceae) in experimentally induced diarrhea in Wistar rats.
Materials and methods: Hydroalcoholic extract of fruits of Citrullus colocynthis was examined for its acute toxicity on rats, in order to establish the safe doses. Castor oil induced diarrhea model and gastrointestinal motility test using barium sulfate milk were done to assess the antidiarrheal activity of plant extracts. Extract of Citrullus colocynthisat the dose of 50 mg/kg, 100 mg/kg and per se group (100 mg/kg) were used in Wistar rats of either sex. Loperamide (2 mg/kg) was taken as a standard drug in both the models.
Results: Phytochemical analysis showed the presence of phenols, alkaloids, terpenoids, flavonoids, saponins, cardiac glycosides, steroids, tannins, and carbohydrates. The acute toxicity studies revealed that extract is relatively safe when given orally; no death was recorded at a dose of 2000 mg/kg. The dose of 100 mg/kg (P<0.001) and 50 mg/kg (P<0.01) of plant fruit extract significantly reduced defecation frequency in 6 h and also increased the latency time which showed similar effects as produced in loperamide treated group. Both doses of fruit extract and loperamide reduced the gastrointestinal motility in Wistar rats significantly (P<0.001).
Conclusion: The hydroalcoholic extract of fruits of Citrullus colocynthis showed significant antidiarrheal activity and supports its use as a complementary and alternative medicine for treatment of diarrhea.

Background: It has shown that congenital color vision deficiency (CVD) has different prevalence and patterns in various ethnic groups and geographical areas. Perception of color have significant role in routine daily life. The children with color vision defects may have problems in detecting colors in schools, color posters and slides which may lead to failure in exam as well as in the daily learning activities. So, this present study is aimed to find out the prevalence of CVD in children living in high altitudes of Nepal.
Methods: A total of 423 children including 217 males and 206 females between ages 11-15 years were examined for congenital CVD in children of high altitudes (2500meter above sea-level) of Sindhupalchowk and Dolakha districts of Nepal. Each subject was shown the plates of Ishihara for color vision under normal day light at distance of 75 cm and the duration given for them to see was 5 seconds.
Results: Children’s color vision was tested using Ishihara’s 38 Plates edition. Among 217 boys, 24 (11.05%) were color deficient. Among 206 girls, 5 (2.42%) were color deficient.
Conclusion: The trends of color vision deficiency in high altitudes showed the need of more and more research on CVD in children and make them aware about the problem that might be faced by them in near future.

Background: Growth hormone (GH) therapy has long been suspected to induce obstructive sleep apnea (OSA) in children and adults. Moreover, reports about GH-associated sudden death in children with Prader-Willi syndrome (PWS) have prompted concerns about GH worsening sleep apnea. Previous studies have supported routine polysomnography for children with PWS prior to starting GH treatments, regardless of clinical history. However, there are no established guidelines recommending routine polysomnography (PSG) prior to the commencement of GH therapy in other pediatric patients.
Case description: We report a case of a 15-year-old young man with intractable headaches, referred to the sleep clinic to rule out any sleep-related variables. After an initial non-significant (mild snoring) sleep study, the patient returned with worsening snoring about one year after starting GH therapy for concerns of short stature.
Results: A second polysomnogram revealed that his obstructive apnea-hypopnea index had risen dramatically from baseline. His symptoms resolved after tonsillectomy and adenoidectomy.
Conclusion: This interesting case highlights the need for caution with any patient eligible for GH therapy. We recommend additional research to look in the development of definitive guidelines regarding the indications for polysomnography for patients with idiopathic short stature and non-significant initial sleep history—particularly before and during the administration of GH therapy.

The recent improvements in the outcomes of patients with acute lymphoblastic leukemia reflect the progress in the field of diagnostics and the achievements in therapeutic interventions. In particular, the availability of more advanced technology in the cytogenetic and molecular laboratories has resulted in the stratification of patients into specific risk groups and thus several novel agents as well as targeted therapies have been introduced. Additionally, precision medicine will be applicable in the near future and thus the recent developments will facilitate the provision of safer modalities of therapy that may ultimately yield not only higher responses but also improved survival rates.

This review represents a recent update on the role of various cytogenetic assays and molecular techniques in patients with acute lymphoblastic leukemia. It is composed of a number of sections including: history of cytogenetics, disease etiology and pathophysiology, utilization of various cytogenetic assays diagnostically, disease-specific cytogenetic and molecular abnormalities, common disease genetic subtypes, prognosis and risk stratification, refractory and relapsed disease, novel therapies, precision medicine and drug repurposing.

Cancer is the most leading cause of deaths worldwide. Despite present understanding and experimental advancements, the morbidity and mortality still remain high. Dok2 have been visualized as a key player in multiple biological processes as inflammation, differentiation, cellular migration and even as an important marker for tumor progression. Recent reports have vividly discussed the regulatory aspects and prognostic aspects of Dok2. Here, we sought to summarize the recent shreds of evidence of Dok2 involvement in carcinogenesis. Dok2 represents an attractive marker for cancer progression and represents a valuable therapeutic target.

Nicotinamide mononucleotide adenylyl transferase (NMNAT) is a key enzyme in the biosynthesis of nicotinamide adenine dinucleotide (NAD+), which is an essential molecule in cellular metabolism. Specific sequences have been described in other NMNATs, which are associated with the regulation of catalytic activity and intracellular localization. In addition, it has been observed that prokaryotic NMNATs have specific regions that could be used as possible therapeutic targets. By aligning Plasmodium falciparum (Pf) NMNAT sequences with their human orthologues (HsNMNAT), specific domains of the P. falciparum protein can be observed. PfNMNAT mutants were designed using bioinformatics software to obtain 2 mutants in order to evaluate the specific sequences of the P. falciparum enzyme. For mutant construction, t-directed mutagenesis was used to introduce changes in the wild-type maltose binding protein (MBP)-PfNMNAT clone previously obtained. The results were compared to those obtained with the wild-type protein. The experimental evidence indicates that the catalytic activity of the enzyme can be affected by transitional and transversional amino acid changes in charge and size. The study of these mutants allows an approach to studying the function and regulation of these proteins.

Understudying gene regulatory network in different plants is essential to engineer plants against biotic/abiotic stress. Here, we analyzed 5’UTR to determine which cis-acting elements present at the promoter of canola NHX1 gene, a salt responsive gene. Arabidopsis NHX1 gene sequence was searched in canola (Brassica napus) genome. The putative sequence of NHX1 gene was extracted and analyzed. Many elements were identified that some of them discussed here.

Globally, colorectal cancer (CRC) is the third most common cancer in men and the second most common cancer in women, accounting for an estimated 1.4 million new cases and almost 700,000 deaths in 2012. Global incidences vary 10-fold, with the highest rates occurring in developed countries (e.g., Australia, New Zealand, Europe, the United States of America [USA]) and the lowest rates occurring in Africa and South-Central Asia. Within Europe in 2008, the highest incidence of colorectal cancer was in Hungary and Denmark. The lowest incidence was in Cyprus and Greece. In Ireland an annual average of 1445 colon cancer and 606 rectal cancers was registered between 2005 and 2009. Approximately 21% of patients with CRC have metastases at diagnosis, and nearly 50% have cancers that will eventually metastasize, accounting for the high mortality rate. Patients with early stage CRC often have no symptoms, which reinforces the importance of screening. This activity briefly describes the rationale for using molecular markers in the diagnosis and prognosis of CRC.

Background: Nasopharyngeal carcinoma (NPC) is a rare form of cancer. NPC is the 4th most common cancer in Malaysia and the incidence rate for Malaysian Chinese is exceptionally high compared to other races. NPC is considered as a relatively radiosensitive tumor and patients diagnosed at early stages tend to survive longer compared to those who with advanced disease. Given that early symptoms of NPC are non-specific, and that the nasopharynx is relatively inaccessible, less invasive screening methods such as biomarker screening might be the key to improve NPC survival and management. Methodology: A matched case-control study was conducted to investigate the effect of hOGG1 Ser326Cys, ITGA2 C807T and TNF-α -308G>A polymorphisms on the risk of nasopharyngeal carcinoma and all-cause survival. hOGG1 gene encodes for a DNA glycosylase, a protein that is involved in DNA repair. ITGA2 is the alpha subunit of the transmembrane receptor integrin and is mainly responsible for cell-cell and cell-extracellular matrix interaction. TNF-α is a cytokine that is released by immune cells during inflammation. Restriction fragment length polymorphism-polymerase chain reaction (RFLP-PCR) was used to process DNA genotyping studies involving all aforementioned gene polymorphisms. Conditional logistic regression was used for the analysis of NPC risk on gene polymorphisms, controlling for cigarette smoking, salted fish and alcohol consumption. Results: Conditional logistic regression showed that NPC cases were more likely to ever consume salted fish during childhood compared to controls (OR=1.80, 95% CI=1.32-2.46, p<0.01). Individuals with previous smoking history were also at higher risk of NPC (OR=1.96, 95% CI=1.37-2.81, p<0.01). No significant difference was found between NPC cases and controls for alcohol consumption. No significant association was observed between hOGG1 Ser326Cys, ITGA2 C807T, TNF-α -308G>A polymorphisms with NPC risk. Conclusion: None of the aforementioned polymorphisms showed significant association in increasing NPC risk individually.

Background: The use of antiretroviral therapy (ART) in HIV-infected women is crucial to restore and maintain the immune system and prevent HIV transmission during pregnancy, labor, delivery and breastfeeding. Furthermore, ART reduce the risk of Mother-to-child transmission (MTCT). Therefore, ART has been associated with mitochondrial defections that could induce preeclampsia, preterm birth, low birthweight, intrauterine growth restriction (IUGR), stillbirth and sudden infant death. Objective: To evaluate the effect of antiretroviral therapy on mitochondrial defections in HIV-infected pregnant women. Methods: We searched eligible studies in MEDLINE, Scorpus and WHO Global Index Medicus. Included studies were assessing the effects of antiretroviral therapy on genetic mitochondrial diseases in HIV infected pregnant women and HIV exposed infants. JTL searched eligible studies in different databases and both JLT and JLT critically appraised included studies. Results: We found five observational studies with low risk of bias. All studies illustrated that ART increased the mean of mitochondrial defections. The results were statistically significant in all studies with P<0.05. Conclusion: Mitochondrial lesions were very common in HIV infected pregnant women and HIV exposed infants. However, further investigations are needful to strengthen this evidence.

Deafness is inherited as one of the most frequent type of neurosensory disorder. The specific physiologic mechanisms of the different types of hearing loss are still unknown. Recent studies have listed numerous causative agents for hearing loss. Genetic factors contribute to a greater extent in hearing disability. GJB2 gene is one of the most promising candidates. 35delG is the most common mutation which accounts for about 50% of all GJB2 gene mutation. After collection of data and isolation of blood, extraction of DNA was performed for each sample. Direct sequencing of GJB2 gene was performed. Primary sequencing data of the representative sample concluded that GJB2 gene is not mutated in the studied family. There are other candidates for hearing disability; further investigations are needed for assessment of other members of the selected family or other genes that are responsible for hearing loss. Human GJB2 protein was compared with that of mouse and rabbit. The data from multiple alignment shows that there is only alteration at nine different points of rabbit compared to human GJB2 protein while this variation is sixteen times when we compared human GJB2 protein sequence with that of mouse.