TERT promoter mutations and telomere length in adult malignant gliomas and recurrences.

In this report on 303 gliomas we show the highest frequency of TERT promoter mutations in gliobastomas (80%) followed by oligodendrogliomas (70%) and astrocytomas (39%). We observed positive association between TERT promoter and IDH mutations in oligodendroglial tumors (OR = 26.3; 95% CI 2.5-250.2) and inverse association in primary glioblastomas (OR = 0.13; 95% CI 0.03-0.58). Tumors with TERT promoter mutations compared to those without showed increased TERT transcription; we also showed difference in the transcription levels due to the two main mutations. Tumors with TERT promoter mutations had shorter telomeres than those without. The patients with only TERT promoter mutations showed worst survival (median survival 14.6 months) and patients with both IDH and TERT promoter mutations showed best survival (246.5 months). In patients with astrocytoma, the TERT promoter mutations only associated with poor survival (P < 0.0001); IDH mutations and 1p/19q deletions associated with increased survival (P = 0.0004). TERT promoter mutations in low grade gliomas associated with reduced progression free survival (HR 10.2; 95% CI 1.9 - 55.9). While our data affirm the role of TERT promoter mutations in glial tumors, effects on transcription and telomere length emphasise the importance of telomere biology in disease genesis and outcome

Pancreatic Cancer Susceptibility Loci and Their Role in Survival

Pancreatic cancer has one of the worst mortality rates of all cancers. Little is known about its etiology, particularly regarding inherited risk. The PanScan project, a genome-wide association study, identified several common polymorphisms affecting pancreatic cancer susceptibility. Single nucleotide polymorphisms (SNPs) in ABO, sonic hedgehog (SHH), telomerase reverse transcriptase (TERT), nuclear receptor subfamily 5, group A, member 2 (NR5A2) were found to be associated with pancreatic cancer risk. Moreover the scan identified loci on chromosomes 13q22.1 and 15q14, to which no known genes or other functional elements are mapped. We sought to replicate these observations in two additional, independent populations (from Germany and the UK), and also evaluate the possible impact of these SNPs on patient survival. We genotyped 15 SNPs in 690 cases of pancreatic ductal adenocarcinoma (PDAC) and in 1277 healthy controls. We replicated several associations between SNPs and PDAC risk. Furthermore we found that SNP rs8028529 was weakly associated with a better overall survival (OS) in both populations. We have also found that NR5A2 rs12029406_T allele was associated with a shorter survival in the German population. In conclusion, we found that rs8028529 could be, if these results are replicated, a promising marker for both risk and prognosis for this lethal disease

The evaluation of acoustic characteristic performance on natural sound absorbing materials from cogon grass waste

In the past few decades, synthetic fibers are been used widely in the field of sound absorption due to their superior characteristics such as durable and chemical resistant. However, there are several disadvantages of synthetic fibers such as non-biodegradability and hazards to the health of human. In this research, the natural sound absorber from cogon grass was investigated. The objective of the research was to evaluate the performance of cogon grass physical characteristics on its acoustical behavior, to evaluate the effect of sodium hydroxide (NaOH) treatment times on physical and acoustical characteristics of cogon grass, to investigate the decay effects after it was left over for twelve months and lastly to compare and verify the acoustical results with theoretical models based on (Delany-Bazley and Miki Model). The measurement of acoustical characteristics which are sound absorption coefficient (SAC) and noise reduction coefficient (NRC) were done by using impedance tube method (ITM). The samples of cogon grass were tested in a way of the untreated and treated with NaOH in varied soaked hours which are one, two, three, four and five hours. Scanning electron microscope (SEM) and density kit were used to investigate physical characteristics. The research confirmed that physical characteristics of tortuosity and airflow resistivity values tend to increase with the increment of treatment times, but the density and porosity tend to decrease. Untreated samples were tested with varied thicknesses of 10, 20, 30, 40 and 50mm. The results show SAC value increases when the thickness of the sample was increased. Treated samples results show the least treated sample (1 hour) reached the maximum SAC value and indicated the highest value of NRC which is 0.50. The results also show a reduction in sound absorption value after the samples were left for twelve months. Verification parts demonstrated that Delany-Bazley and Miki Model can predict approximately pattern compared with ITM results because of the theoretical models are developed by a simple empirical model approach. Overall, cogon grass samples have the good characteristics to be an acoustic material component

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

Studies on conformational stability of the ectodomain of influenza virus hemagglutinin

Das Hüllglykoprotein Hämagglutinin (HA) von Influenzavirus ist verantwortlich sowohl für die Bindung als auch für die nachfolgende Fusion der viralen Hülle mit der endosomalen Membran. Eine Analyse der 3D Struktur der HA-Ektodomaine zeigt, dass die Stabilität des Proteins sowohl durch kovalente als auch durch nicht-kovalente Wechselwirkungen bedingt ist. Die Konformationsänderung von HA bei saurem pH-Wert weißt auf eine mögliche Rolle von Protonierungseffekten auf ionisierbare Aminosäuren hin. Untersuchungen zur Bedeutung geladener Aminosäuren und Salzbrücken für die Struktur des HA wurden auf der Grundlage von ‚site directed mutagenesis’ durchgeführt. Der Einfluss der Mutationen auf die Konformationsänderung und die Fusionsaktivität von HA wurden durch einen Proteinase K-Assay bzw. Fluoreszenzmikroskopie erfasst. Die Ergebnisse beider Methoden wurden miteinander korreliert. Abgesehen von der Mutante R109E zeigten Wildtyp-HA und alle anderen Mutanten eine vergleichbare Oberflächenexpression. Die beobachteten Unterschiede in der pH-Abhängigkeit der Konformationumwandlung zwischen Wildtyp-HA und HA-Mutanten zeigen, daß eine Zerstörung von Salzbrücken und ggf. eine Erhöhung der elektrostatischen Abstoßung an den betrachteten Kontakstellen sehr wahrscheinlich eine Herabsetzung der energetischen Barriere der Konformationsumwandlung verursacht. Dieser Ergebnisse erklären die molekularen Grundlagen des erhöhten pH-Schwellwertes der HA-Konformationsumwandlung von Amantadin-resistenten Influenzaviren. Im Gegensatz wurde für Mutanten, die die Stabilität von HA erhöhten, keine Konformationsumwandlung bei einem pH-Wert beobachtet, der typisch für die Konformationumwandlung von Wildtyp-HA war. Aminosäuren, die denen dieser stabiliserenden Mutationen entsprachen, wurden in einer natürlichen Influenzavirusvariante – A/JPN/305/57 – gefunden. Die Bedeutung von Ladungen für die Stabilität der HA-Ektodomaine wird dadurch unterstrichen, dass eine Konservierung einer positiven Ladung und insbesondere eines Argininrestes in der Position 109 (Nummerierung auf der Basis von HA X31) für alle Influenzaviren A und B gefunden wurde. Die Ergebnisse der Arbeit zeigen, dass sehr wahrscheinlich eine komplexe Salzbrücke an der Kontaktfläche zwischen HA1 und HA2 für alle Influenzaviren A evolutionär konserviert ist.Hemagglutinin (HA), a major envelope glycoprotein is responsible for fusing viral and endosomal membranes during influenza virus entry. The analysis of 3D crystal structure of the HA ectodomain shows that the stability of protein is maintained by both non-covalent and covalent interactions. The conformational change of HA at low pH indicates a role for protonation effects of the ionisable amino acids. Structural investigations were done using “site directed mutagenesis” in order to conceive the importance of charged amino acids and more emphatically the involvement of salt bridges. The effect of mutations on the conformational change and fusion activity was probed by proteinase K assay and fluorescence microscopy respectively. It was observed that HA-wt and all the mutants except R109E showed comparable surface expression. The difference in pH threshold between the HA-wt and the mutants showed that breakage of salt bridge and further incorporation of repulsion at the considered interfaces would lower the energy barrier requirements for the conformational change. The results explain the molecular basis of the higher pH threshold for naturally occurring amantadine resistant mutants. On the other hand, mutants designed to stabilise the HA were resistant to conformational changes at those pH values which typically trigger the conformational change of HA-wt. Coincidentally these mutations were found to be existing in the natural variant of H2 Japan subtype (A/JPN/305/57). Interestingly, the study shows that a positive charge and, more specifically, an Arg residue at position 109 (numbering based on X-31 strain) is conserved in all of the influenza A and B viruses underlining the relevance of electrostatic interactions for the HA stability. Aptly a complex salt bridge at the interface of HA1 and HA2 is probably conserved evolutionarily in all the members of influenza A virus

TERT promoter mutations in cancer development.

Human telomerase reverse transcriptase (TERT) encodes a rate-limiting catalytic subunit of telomerase that maintains genomic integrity. TERT expression is mostly repressed in somatic cells with exception of proliferative cells in self-renewing tissues and cancer. Immortality associated with cancer cells has been attributed to telomerase over-expression. The precise mechanism behind the TERT activation in cancers has mostly remained unknown. The newly described germline and recurrent somatic mutations in melanoma and other cancers in the TERT promoter that create de novo E-twenty six/ternary complex factors (Ets/TCF) binding sites, provide an insight into the possible cause of tumor-specific increased TERT expression. In this review we discuss the discovery and possible implications of the TERT promoter mutations in melanoma and other cancers

Mapping of deletion breakpoints at the CDKN2A locus in melanoma: detection of MTAP-ANRIL fusion transcripts.

Genomic locus at chromosome 9p21 that contains the CDKN2A and CDKN2B tumor suppressor genes is inactivated through mutations, deletions and promoter methylation in multiple human cancers. Additionally, the locus encodes an anti-sense RNA (ANRIL). Both hemizygous and homozygous deletions at the locus targeting multiple genes are fairly common in different cancers. We in this study investigated breakpoints in five melanoma cell lines, derived from metastasized tumors, with previously identified homozygous deletions using array comparative genomic hybridization (aCGH). For breakpoint mapping, we used primer approximation multiplex PCR (PAMP) and inverse PCR techniques. Our results showed that three cell lines carried complex rearrangements. In two other cell lines, with focal deletions of 141 kb and 181 kb, we identified fusion gene products, involving MTAP and ANRIL. We also confirmed the complex rearrangements and focal deletions in DNA from tumor tissues corresponding to three cell lines. The rapid amplification of 3'cDNA ends (3'RACE) carried out on transcripts resulted in identification of three isoforms of MTAP-ANRIL fusion gene. Screening of cDNA from 64 melanoma cell lines resulted in detection of fusion transcripts in 13 (20%) cell lines that involved exons 4-7 of the MTAP and exon 2 or 5 of the ANRIL genes. We also detected fusion transcripts involving MTAP and ANRIL in two of the seven primary melanoma tumors with focal deletion at the locus. The results from the study, besides identifying complex rearrangements involving CDKN2A locus, show frequent occurrence of fusion transcripts involving MTAP and ANRIL genes

TERT promoter mutations in melanoma render TERT expression dependent on MAPK pathway activation

The mechanism of telomerase re-activation in cancer had remained elusive until the discovery of frequent mutations in the promoter of the TERT gene that encodes the catalytic reverse transcriptase subunit of telomerase. We investigated the regulation of TERT expression in melanoma cell lines and our results show that promoter mutations render TERT expression dependent on MAPK activation due to oncogenic BRAF or NRAS mutations. Mutations in the TERT promoter create binding sites for ETS transcription factors. ETS1, expressed in melanoma cell lines, undergoes activating phosphorylation by ERK at Thr38 residue as a consequence of constitutively activated MAPK pathway. We demonstrate that ETS1 binds on the mutated TERT promoter leading to the re-expression of the gene. The inhibition of ETS1 resulted in reduced TERT expression. We provide evidence that the TERT promoter mutations provide a direct link between TERT expression and MAPK pathway activation due to BRAF or NRAS mutations via the transcription factor ETS1.7335312753136COORDENAÇÃO DE APERFEIÇOAMENTO DE PESSOAL DE NÍVEL SUPERIOR - CAPESSem informaçã