The objectives of this study were to investigate the incidence of high-risk genotypes of human papillomavirus (HPV) in tumours of patients with oropharyngeal squamous cell carcinoma (OPSCC) during an ...18-year period in Eastern Denmark.
In this population-based, consecutive, semi-national registry study, all patients diagnosed with OPSCC from 2000 to 2017 in Eastern Denmark were evaluated at head and neck oncological departments at public university hospitals. Analyses included tumour characteristics (HPV-positive HPV+ versus HPV-negative HPV–), age-adjusted incidence rates (AAIRs), average annual percentage change (AAPC) of OPSCC, and patient demographics. All HPV+ cases from 2011 to 2017 were genotyped.
In total, 55% of 2169 OPSCC cases were HPV+. HPV16, HPV33, HPV35 or other types were found in 86%, 7.4%, 3.4% and 3.2% of cases, respectively. The AAIR per 100,000 of all OPSCCs was 1.8 in 2000, which increased to 5.1 in 2017 (HPV+: threefold increase, HPV–: twofold increase). The AAPC from 2000 to 2017 increased by 7% (HPV+ increased by 10% and HPV– by 4%). The median age at diagnosis for all OPSCC cases increased during the 18-year study period (HPV+: 58–61 years, p < 0.001; HPV–: 60–65 years, p < 0.001).
We report a threefold increase in OPSCC incidence during the 18-year observation period and a significant increase in median age at diagnosis. Over 93% of HPV genotypes in HPV+ OPSCC are included in current HPV vaccines except for HPV35 (4%). HPV vaccination of both sexes is advised to halt this emerging cancer epidemic.
•The current largest register-based study in Eastern Denmark of HPV-tested Oropharyngeal Squamous Cell Carcinoma (OPSCC).•All confirmed OPSCC cases (n= 2169) from 2000-2017 were included and tested for HPV DNA and p16 expression.•HPV-positive tumours had the viral DNA genotyped (n= 770) to examine high-risk genotypes.•HPV16 was the most common genotype (86%) among HPV-positive cases.•The incidence rate of OPSCC increased threefold overall, especially for HPV-positive OPSCC of the tonsils.
Full text
Available for:
GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Although there has been much success in identifying genetic variants associated with common diseases using genome-wide association studies (GWAS), it has been difficult to demonstrate which variants ...are causal and what role they have in disease. Moreover, the modest contribution that these variants make to disease risk has raised questions regarding their medical relevance. Here we have investigated a single nucleotide polymorphism (SNP) in the TNFRSF1A gene, that encodes tumour necrosis factor receptor 1 (TNFR1), which was discovered through GWAS to be associated with multiple sclerosis (MS), but not with other autoimmune conditions such as rheumatoid arthritis, psoriasis and Crohn’s disease. By analysing MS GWAS data in conjunction with the 1000 Genomes Project data we provide genetic evidence that strongly implicates this SNP, rs1800693, as the causal variant in the TNFRSF1A region. We further substantiate this through functional studies showing that the MS risk allele directs expression of a novel, soluble form of TNFR1 that can block TNF. Importantly, TNF-blocking drugs can promote onset or exacerbation of MS, but they have proven highly efficacious in the treatment of autoimmune diseases for which there is no association with rs1800693. This indicates that the clinical experience with these drugs parallels the disease association of rs1800693, and that the MS-associated TNFR1 variant mimics the effect of TNF-blocking drugs. Hence, our study demonstrates that clinical practice can be informed by comparing GWAS across common autoimmune diseases and by investigating the functional consequences of the disease-associated genetic variation.
Full text
Available for:
DOBA, IJS, IZUM, KILJ, KISLJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Bacterial airway infections, predominantly caused by
P. aeruginosa
, are a major cause of mortality and morbidity of CF patients. While short insertions and deletions as well as point mutations ...occurring during infection are well studied, there is a lack of understanding of how gene loss and acquisition play roles in bacterial adaptation to the human airways. Here, we investigated
P. aeruginosa
within-host evolution with regard to gene loss and acquisition. We show that during long-term infection
P. aeruginosa
genomes tend to lose genes, in particular, genes related to virulence. This adaptive strategy allows reduction of the genome size and evasion of the host’s immune response. This knowledge is crucial to understand the basic mutational steps that, on the timescale of years, diversify lineages and adds to the identification of bacterial genetic determinants that have implications for CF disease.
ABSTRACT
Genome analyses have documented that there are differences in gene repertoire between evolutionary distant lineages of the same bacterial species; however, less is known about microevolutionary dynamics of gene loss and acquisition within bacterial lineages as they evolve over years. Here, we analyzed the genomes of 45
Pseudomonas aeruginosa
lineages evolving in the lungs of cystic fibrosis (CF) patients to identify genes that are lost or acquired during the first years of infection. On average, lineage genome content changed by 88 genes (range, 0 to 473). Genes were more often lost than acquired, and prophage genes were more variable than bacterial genes. We identified convergent loss or acquisition of the same genes across lineages, suggesting selection for loss and acquisition of certain genes in the host environment. We found that a notable proportion of such genes are associated with virulence; a trait previously shown to be important for adaptation. Furthermore, we also compared the genomes across lineages to show that the within-lineage variable genes (i.e., genes that had been lost or acquired during the infection) often belonged to genomic content not shared across all lineages. In sum, our analysis adds to the knowledge on the pace and drivers of gene loss and acquisition in bacteria evolving over years in a human host environment and provides a basis to further understand how gene loss and acquisition play roles in lineage differentiation and host adaptation.
IMPORTANCE
Bacterial airway infections, predominantly caused by
P. aeruginosa
, are a major cause of mortality and morbidity of CF patients. While short insertions and deletions as well as point mutations occurring during infection are well studied, there is a lack of understanding of how gene loss and acquisition play roles in bacterial adaptation to the human airways. Here, we investigated
P. aeruginosa
within-host evolution with regard to gene loss and acquisition. We show that during long-term infection
P. aeruginosa
genomes tend to lose genes, in particular, genes related to virulence. This adaptive strategy allows reduction of the genome size and evasion of the host’s immune response. This knowledge is crucial to understand the basic mutational steps that, on the timescale of years, diversify lineages and adds to the identification of bacterial genetic determinants that have implications for CF disease.
The aim was to explore whether the incidence of tonsillar squamous cell carcinomas (TSCCs) increased in Eastern Denmark, 2000–2010, and whether human papillomavirus (HPV) could explain the increase, ...and to assess the association of HPV prevalence with gender, age, and origin (i.e., the certainty of tonsillar tumor origin). We applied HPV DNA PCR and p16 immunohistochemistry to all TSCCs registered in the Danish Head and Neck Cancer Group (DAHANCA) and in the Danish Pathology Data Bank (n = 632). Pathologists reviewed and subdivided the tumors into two groups: specified and nonspecified TSCCs. Approximately 10% of HPV‐positive tumors was genotyped by amplicon next‐generation sequencing. The overall crude incidence of TSCCs increased significantly (2.7% per year) and was explained by an increasing incidence of HPV‐positive TSCCs (4.9% per year). The overall HPV prevalence was 58%, with HPV16 being the predominant HPV type. In multivariate analysis, the HPV prevalence was associated with age (<55 vs. >60 years) (OR, 1.72; 95% CI 1.13–2.63) and origin (nonspecified vs. specified TSCCs) (OR, 0.15; 95% CI 0.11–0.22). The association of HPV prevalence with origin increased over time in specified TSCCs (OR per year, 1.10; 95% CI 1.01–1.19), whereas no change over time was observed among nonspecified TSCCs (OR per year, 0.99; 95% CI 0.90–1.08). In conclusion, the observed increase in the number of HPV‐positive TSCCs can explain the increasing number of TSCCs in Eastern Denmark, 2000–2010. HPV prevalence was associated with younger age (<55 years) and a high certainty of tonsillar tumor origin.
What's new?
Are throat cancers on the rise in Denmark, as in other Western populations? These authors analyzed samples from the Danish Head and Neck Cancer Group, making this the largest non‐selected cohort of tonsillar cancer cases studied to date. They found that during the years 2000–2010, the rate of tonsillar cancer increased, and that HPV could be to blame. The incidence of HPV‐positive cancers rose over the study period, with most of the HPV‐positive cancers harboring HPV‐16. When they classified the tumors by whether they originated in the tonsillar tissue, they found that tumor origin was the strongest predictor of HPV status; specified tonsillar tumors contained HPV more often than those appearing to have originated elsewhere.
Full text
Available for:
BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SAZU, SBCE, SBMB, UL, UM, UPUK
species are increasingly being detected in patients with cystic fibrosis (CF), and this emerging pathogen is associated with antibiotic resistance and more-severe disease outcomes. Nonetheless, ...little is known about the extent of transmission and antibiotic resistance development in
infections. We sequenced the genomes of 101
clinical isolates (identified as
based on matrix-assister laser desorption ionization-time of flight MALDI-TOF or API N20 typing) collected from 51 patients with CF-the largest longitudinal data set to date. We performed phylogenetic analysis on the genomes and combined this with epidemiological and antibiotic resistance data to identify patient-to-patient transmission and the development of antibiotic resistance. We confirmed that the MALDI-TOF or API N20 method was not sufficient for
species-level typing and that the population of
isolates was composed of five different species, among which
accounted for 52% of infections. Most patients were infected by unique
clone types; nonetheless, suspected patient-to-patient transmission cases identified by shared clone types were observed in 35% (
= 18) of patients. In 15 of 16 cases, the suspected transmissions were further supported by genome- or clinic visit-based epidemiological analysis. Finally, we found that resistance developed over time. We show that whole-genome sequencing (WGS) is essential for
species typing and identification of patient-to-patient transmission, which was revealed for
,
, and, for the first time,
Furthermore, we show that the development of antibiotic resistance is associated with chronic
infections. Our findings emphasize that transmission and antibiotic resistance should be considered in future treatment strategies.
Localized mRNAs are transported to sites of local protein synthesis in large ribonucleoprotein (RNP) granules, but their molecular composition is incompletely understood. Insulin-like growth factor ...II mRNA-binding protein (IMP) zip code-binding proteins participate in mRNA localization, and in motile cells IMP-containing granules are dispersed around the nucleus and in cellular protrusions. We isolated the IMP1-containing RNP granules and found that they represent a unique RNP entity distinct from neuronal hStaufen and/or fragile X mental retardation protein granules, processing bodies, and stress granules. Granules were 100–300 nm in diameter and consisted of IMPs, 40 S ribosomal subunits, shuttling heterologous nuclear RNPs, poly(A)-binding proteins, and mRNAs. Moreover granules contained CBP80 and factors belonging to the exon junction complex and lacked eIF4E, eIF4G, and 60 S ribosomal subunits, indicating that embodied mRNAs are not translated. Granules embodied mRNAs corresponding to about 3% of the human embryonic kidney 293 mRNA transcriptome. Messenger RNAs encoding proteins participating in the secretory pathway and endoplasmic reticulum-associated quality control, as well as ubiquitin-dependent metabolism, were enriched in the granules, reinforcing the concept of RNP granules as post-transcriptional operons.
Full text
Available for:
GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Lack of IGF2 in mice results in diminished embryonic growth due to diminished cell proliferation. Here we show that mouse embryonic fibroblasts lacking the RNA-binding protein IMP1 (IGF2 mRNA-binding ...protein 1) have defective splicing and translation of IGF2 mRNAs, markedly reduced IGF2 polypeptide production, and diminished proliferation. The proliferation of the IMP1-null fibroblasts can be restored to wild-type levels by IGF2 in vitro or by re-expression of IMP1, which corrects the defects in IGF2 RNA splicing and translation. The ability of IMP1 to correct these defects is dependent on IMP1 phosphorylation at Ser181, which is catalyzed cotranslationally by mTOR complex 2 (mTORC2). Phosphorylation strongly enhances IMP1 binding to the IGF2-leader 3 5' untranslated region, which is absolutely required to enable IGF2-leader 3 mRNA translational initiation by internal ribosomal entry. These findings uncover a new mechanism by which mTOR regulates organismal growth by promoting IGF2 production in the mouse embryo through mTORC2-catalyzed cotranslational IMP1/IMP3 phosphorylation. Inasmuch as TORC2 is activated by association with ribosomes, the present results indicate that mTORC2-catalyzed cotranslational protein phosphorylation is a core function of this complex.
Recent genome-wide association (GWA) studies of type 2 diabetes (T2D) have implicated IGF2 mRNA-binding protein 2 (IMP2/IGF2BP2) as one of the several factors in the etiology of late onset diabetes. ...IMP2 belongs to a family of oncofetal mRNA-binding proteins implicated in RNA localization, stability, and translation that are essential for normal embryonic growth and development. This review provides a background to the IMP protein family with an emphasis on human IMP2, followed by a closer look at the GWA studies to evaluate the significance, if any, of the proposed correlation between IMP2 and T2D.
Oncofetal RNA‐binding IMPs have been implicated in mRNA localization, nuclear export, turnover and translational control. To depict the cellular actions of IMPs, we performed a loss‐of‐function ...analysis, which showed that IMPs are necessary for proper cell adhesion, cytoplasmic spreading and invadopodia formation. Loss of IMPs was associated with a coordinate downregulation of mRNAs encoding extracellular matrix and adhesion proteins. The transcripts were present in IMP RNP granules, implying that IMPs were directly involved in the post‐transcriptional control of the transcripts. In particular, we show that a 5.0 kb CD44 mRNA contained multiple IMP‐binding sites in its 3′UTR, and following IMP depletion this species became unstable. Direct knockdown of the CD44 transcript mimicked the effect of IMPs on invadopodia, and we infer that CD44 mRNA stabilization may be involved in IMP‐mediated invadopodia formation. Taken together, our results indicate that RNA‐binding proteins exert profound effects on cellular adhesion and invasion during development and cancer formation.
Full text
Available for:
FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SAZU, SBCE, SBMB, UL, UM, UPUK
In chronic lymphocytic leukemia,
mutations and deletion of chromosome 17p are well-characterized biomarkers associated with poor progression-free and overall survival following chemoimmunotherapy. ...Patients harboring low burden
mutations with variant allele frequencies of 0.3-15% have been shown to have similar dismal outcome as those with high burden mutations. We here describe a highly sensitive deep targeted next-generation sequencing assay allowing for the detection of
mutations as low as 0.2% variant allele frequency. Within a consecutive, single center cohort of 290 newly diagnosed patients with chronic lymphocytic leukemia, deletion of chromosome 17p was the only
aberration significantly associated with shorter overall survival and treatment-free survival. We were unable to demonstrate any impact of
mutations, whether high burden (variant allele frequency >10%) or low burden (variant allele frequency ≤10%), in the absence of deletion of chromosome 17p. In addition, the impact of high burden
aberration (deletion of chromosome 17p and/or
mutation with variant allele frequency >10%) was only evident for patients with IGHV unmutated status; no impact of
aberrations on outcome was seen for patients with IGHV mutated status. In 61 patients at time of treatment, the prognostic impact of
mutations over 1% variant allele frequency could be confirmed. This study furthers the identification of a clinical significant limit of detection for robust
mutation analysis in chronic lymphocytic leukemia. Multicenter studies are needed for validation of ultra-sensitive
mutation assays in order to define and implement a technical as well as a clinical lower limit of detection.
PDF
