Mutations of the DNA repair gene PNKP in a patient with microcephaly, seizures, and developmental delay (MCSZ) presenting with a high-grade brain tumor.

Polynucleotide Kinase-Phosphatase (PNKP) is a bifunctional enzyme that possesses both DNA 3'-phosphatase and DNA 5'-kinase activities, which are required for processing termini of single- and double-strand breaks generated by reactive oxygen species (ROS), ionizing radiation and topoisomerase I poisons. Even though PNKP is central to DNA repair, there have been no reports linking PNKP mutations in a Microcephaly, Seizures, and Developmental Delay (MSCZ) patient to cancer. Here, we characterized the biochemical significance of 2 germ-line point mutations in the PNKP gene of a 3-year old male with MSCZ who presented with a high-grade brain tumor (glioblastoma multiforme) within the cerebellum. Functional and biochemical studies demonstrated these PNKP mutations significantly diminished DNA kinase/phosphatase activities, altered its cellular distribution, caused defective repair of DNA single/double stranded breaks, and were associated with a higher propensity for oncogenic transformation. Our findings indicate that specific PNKP mutations may contribute to tumor initiation within susceptible cells in the CNS by limiting DNA damage repair and increasing rates of spontaneous mutations resulting in pediatric glioma associated driver mutations such as ATRX and TP53.

Metagenomics Versus Metatranscriptomics of the Murine Gut Microbiome for Assessing Microbial Metabolism During Inflammation.

Shotgun metagenomics studies have improved our understanding of microbial population dynamics and have revealed significant contributions of microbes to gut homeostasis. They also allow in silico inference of the metagenome. While they link the microbiome with metabolic abnormalities associated with disease phenotypes, they do not capture microbial gene expression patterns that occur in response to the multitude of stimuli that constantly ambush the gut environment. Metatranscriptomics closes that gap, but its implementation is more expensive and tedious. We assessed the metabolic perturbations associated with gut inflammation using shotgun metagenomics and metatranscriptomics. Shotgun metagenomics detected changes in abundance of bacterial taxa known to be SCFA producers, which favors gut homeostasis. Bacteria in the phylum Firmicutes were found at decreased abundance, while those in phyla Bacteroidetes and Proteobacteria were found at increased abundance. Surprisingly, inferring the coding capacity of the microbiome from shotgun metagenomics data did not result in any statistically significant difference, suggesting functional redundancy in the microbiome or poor resolution of shotgun metagenomics data to profile bacterial pathways, especially when sequencing is not very deep. Obviously, the ability of metatranscriptomics libraries to detect transcripts expressed at basal (or simply low) levels is also dependent on sequencing depth. Nevertheless, metatranscriptomics informed about contrasting roles of bacteria during inflammation. Functions involved in nutrient transport, immune suppression and regulation of tissue damage were dramatically upregulated, perhaps contributed by homeostasis-promoting bacteria. Functions ostensibly increasing bacteria pathogenesis were also found upregulated, perhaps as a consequence of increased abundance of Proteobacteria. Bacterial protein synthesis appeared downregulated. In summary, shotgun metagenomics was useful to profile bacterial population composition and taxa relative abundance, but did not inform about differential gene content associated with inflammation. Metatranscriptomics was more robust for capturing bacterial metabolism in real time. Although both approaches are complementary, it is often not possible to apply them in parallel. We hope our data will help researchers to decide which approach is more appropriate for the study of different aspects of the microbiome.

Autoimmune Hepatitis Leading to Liver Cirrhosis: A Case Report.

Autoimmune hepatitis is a rare form of chronic liver inflammation that begins as acute hepatitis and progresses to chronic liver disease. It presents with varied clinical features from acute hepatitis to chronic liver diseases like chronic viral hepatitis and alcoholic liver disease, making it difficult to diagnose in the absence of a high index of suspicion and adequate laboratory support. Autoimmune hepatitis is divided into two categories autoimmune hepatitis-1 and autoimmune hepatitis-2 based on the antibodies involved. We discuss the case of a 37-year-old woman who developed autoimmune hepatitis-1, with swelling and epigastric pain. These symptoms later progressed to liver cirrhosis leading to the death of the patient. Autoimmune hepatitis is extremely sensitive to immunosuppressive medication, it is necessary to maintain a high suspicion index for the disease because a prompt diagnosis can be an integral step toward a better prognosis of the disease. Keywords: autoimmune hepatitis; case reports; chronic hepatitis; liver cirrhosis.

Practice among Healthcare Workers Regarding the Use of Respiratory Protective Equipment during COVID-19 Pandemic in a Tertiary Care Center: A Descriptive Cross-sectional Study.

INTRODUCTION: Healthcare workers are always at the risk of exposure to different diseases like respiratory illness including COVID-19. Using appropriate face mask or respiratory protective equipment correctly can prevent transmission of diseases from and to healthcare workers while caring for patients. The study aimed to find out the practice regarding use of face masks during the COVID-19 pandemic in a tertiary care center. METHODS: A descriptive cross-sectional study was conducted at a tertiary care hospital during June-July 2020 after receiving ethical approval from the review committee regarding practice of use of face masks. Convenience sampling method was used and a sample size of 162 was taken. Descriptive statistical analysis was done. Point estimate at 95% Confidence Interval was calculated along with frequency and proportion for binary data. RESULTS: Among 162 participants, 123 (75.9%) knew the correct way of using the masks (72.5-79.3 at 95% Confidence Interval). CONCLUSIONS: In this study regarding practice of use of face masks, most of the healthcare workers knew the correct way of using masks and practised hygiene before and after using masks.

Role of polynucleotide kinase/phosphatase in mitochondrial DNA repair.

Mutations in mitochondrial DNA (mtDNA) are implicated in a broad range of human diseases and in aging. Compared to nuclear DNA, mtDNA is more highly exposed to oxidative damage due to its proximity to the respiratory chain and the lack of protection afforded by chromatin-associated proteins. While repair of oxidative damage to the bases in mtDNA through the base excision repair pathway has been well studied, the repair of oxidatively induced strand breaks in mtDNA has been less thoroughly examined. Polynucleotide kinase/phosphatase (PNKP) processes strand-break termini to render them chemically compatible for the subsequent action of DNA polymerases and ligases. Here, we demonstrate that functionally active full-length PNKP is present in mitochondria as well as nuclei. Downregulation of PNKP results in an accumulation of strand breaks in mtDNA of hydrogen peroxide-treated cells. Full restoration of repair of the H(2)O(2)-induced strand breaks in mitochondria requires both the kinase and phosphatase activities of PNKP. We also demonstrate that PNKP contains a mitochondrial-targeting signal close to the C-terminus of the protein. We further show that PNKP associates with the mitochondrial protein mitofilin. Interaction with mitofilin may serve to translocate PNKP into mitochondria.