The Genomics, Epigenomics, and Transcriptomics of HPV-Associated Oropharyngeal Cancer--Understanding the Basis of a Rapidly Evolving Disease

Human papillomavirus (HPV) has been shown to represent a major independent risk factor for head and neck squamous cell cancer, in particular for oropharyngeal carcinoma. This type of cancer is rapidly evolving in the Western world, with rising trends particularly in the young, and represents a distinct epidemiological, clinical, and molecular entity. It is the aim of this review to give a detailed description of genomic, epigenomic, transcriptomic, and posttranscriptional changes that underlie the phenotype of this deadly disease. The review will also link these changes and examine what is known about the interactions between the host genome and viral genome, and investigate changes specific for the viral genome. These data are then integrated into an updated model of HPV-induced head and neck carcinogenesis.

Abstract 3169: APOBEC-mediated cytosine deamination is a prominent mutagenic mechanism in human papillomavirus-driven cancer

APOBEC3B cytosine deaminase activity has recently emerged as a significant mutagenic factor in human cancer. APOBEC activity is induced in virally infected cells and APOBEC signature mutations occur at high frequency in cervical cancers, over 99% of which are caused by high risk variants of Human Papillomavirus (HPV). We tested the hypothesis that APOBEC-mediated mutagenesis plays a particularly important role in HPV-associated cancer by analysing head and neck squamous cell carcinoma (HNSCC), a tumor type for which exome sequence data from The Cancer Genome Atlas project are available from both HPV+ and HPV- variants. We show that HPV+ tumors express more APOBEC3B and harbor a higher proportion of APOBEC signature mutations than HPV- tumors. The APOBEC mutational signature is absent from hepatitis virus-associated hepatocellular carcinoma, indicating it is not simply a consequence of the immune response to persistent viral infection. We also uncover a strong linear relationship between APOBEC signature mutations and APOBEC-independent mutations in both HNSCC and in breast cancer, such that in high APOBEC subsets (HPV+ HNSCC and HER2-amplified breast cancer), the proportion of mutations due to APOBEC activity is consistently increased, regardless of the overall mutational burden in the tumor. Finally, HPV+ HNSCC and cervical cancer show particularly strong enrichment for APOBEC signature mutations in known cancer genes, implicating APOBEC activity as a key driver of HPV-induced transformation.

Citation Format: Stephen Henderson, Ankur Chakravarthy, Xiaoping Su, Chris Boshoff, Tim R. Fenton. APOBEC-mediated cytosine deamination is a prominent mutagenic mechanism in human papillomavirus-driven cancer. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 3169. doi:10.1158/1538-7445.AM2014-3169

A kinome-wide RNAi screen in Drosophila Glia reveals that the RIO kinases mediate cell proliferation and survival through TORC2-Akt signaling in glioblastoma

Glioblastoma, the most common primary malignant brain tumor, is incurable with current therapies. Genetic and molecular analyses demonstrate that glioblastomas frequently display mutations that activate receptor tyrosine kinase (RTK) and Pi-3 kinase (PI3K) signaling pathways. In Drosophila melanogaster, activation of RTK and PI3K pathways in glial progenitor cells creates malignant neoplastic glial tumors that display many features of human glioblastoma. In both human and Drosophila, activation of the RTK and PI3K pathways stimulates Akt signaling along with other as-yet-unknown changes that drive oncogenesis. We used this Drosophila glioblastoma model to perform a kinome-wide genetic screen for new genes required for RTK- and PI3K-dependent neoplastic transformation. Human orthologs of novel kinases uncovered by these screens were functionally assessed in mammalian glioblastoma models and human tumors. Our results revealed that the atypical kinases RIOK1 and RIOK2 are overexpressed in glioblastoma cells in an Akt-dependent manner. Moreover, we found that overexpressed RIOK2 formed a complex with RIOK1, mTor, and mTor-complex-2 components, and that overexpressed RIOK2 upregulated Akt signaling and promoted tumorigenesis in murine astrocytes. Conversely, reduced expression of RIOK1 or RIOK2 disrupted Akt signaling and caused cell cycle exit, apoptosis, and chemosensitivity in glioblastoma cells by inducing p53 activity through the RpL11-dependent ribosomal stress checkpoint. These results imply that, in glioblastoma cells, constitutive Akt signaling drives RIO kinase overexpression, which creates a feedforward loop that promotes and maintains oncogenic Akt activity through stimulation of mTor signaling. Further study of the RIO kinases as well as other kinases identified in our Drosophila screen may reveal new insights into defects underlying glioblastoma and related cancers and may reveal new therapeutic opportunities for these cancers.

Glioblastomas, the most common primary brain tumor, harbor mutations in receptor tyrosine kinases (RTKs), such as EGFR, and components of the Pi-3 kinase (PI3K) signaling pathway. However, the genes that act downstream of RTK and PI3K signaling to drive glioblastoma remain unclear. To investigate the genetic and molecular basis of this disease, we created a glioblastoma model in the fruit fly Drosophila melanogaster. To identify new genes involved in glioblastoma development, we performed a screen for the genes required for tumor cell proliferation using our Drosophila glioblastoma model and then functionally assessed the activity of human versions of novel genes identified in this screen. Our results revealed that the RIO kinases become overexpressed in human glioblastomas but not in normal human glial or neuronal cells. We found that overexpression of the RIO kinases promotes and maintains signals that drive tumor cell proliferation and survival in RTK- and PI3K-dependent human glioblastoma, and reduction of RIO kinase expression decreased proliferation and prompted cell death and chemosensitivity in glioblastoma cells. Therefore, disruption of the RIO kinases may provide new therapeutic opportunities to target glioblastoma and other RTK- or PI3K-dependent cancers.

Functions and regulation of the 70kDa ribosomal S6 kinases

The 70kDa ribosomal protein S6 kinases, S6K1 and S6K2 are two highly homologous serine/threonine kinases that are activated in response to growth factors, cytokines and nutrients. The S6 kinases have been linked to diverse cellular processes, including protein synthesis, mRNA processing, glucose homeostasis, cell growth and survival. Studies in model organisms have highlighted the roles that S6K activity plays in a number of pathologies, including obesity, diabetes, ageing and cancer. The importance of S6K function in human diseases has led to the development of S6K-specific inhibitors by a number of companies, offering the promise of improved tools with which to study these enzymes and potentially the effective targeting of deregulated S6K signalling in patients. Here we review the current literature on the role of S6Ks in the regulation of cell growth, survival and proliferation downstream of various signalling pathways and how their dysregulation contributes to the pathogenesis of human diseases.

S6K1 is acetylated at lysine 516 in response to growth factor stimulation

The 70kDa ribosomal protein S6 kinase 1 (S6K1) plays important roles in the regulation of protein synthesis, cell growth and metabolism. S6K1 is activated by the phosphorylation of multiple serine and threonine residues in response to stimulation by a variety of growth factors and cytokines. In addition to phosphorylation, we have recently shown that S6K1 is also targeted by lysine acetylation. Here, using tandem mass spectrometry we have mapped acetylation of S6K1 to lysine 516, a site close to the C-terminus of the kinase that is highly conserved amongst vertebrate S6K1 orthologues. Using acetyl-specific K516 antibodies, we show that acetylation of endogenous S6K1 at this site is potently induced upon growth factor stimulation. Although S6K1 acetylation and phosphorylation are both induced by growth factor stimulation, these events appear to be functionally independent. Indeed, experiments using inhibitors of S6K1 activation and exposure of cells to various stresses indicate that S6K1 acetylation can occur in the absence of phosphorylation and vice versa. We propose that K516 acetylation may serve to modulate important kinase-independent functions of S6K1 in response to growth factor signalling.

Histone acetyltransferases interact with and acetylate p70 ribosomal S6 kinases in vitro and in vivo

The 70kDa ribosomal protein S6 kinases (S6K1 and S6K2) play important roles in the regulation of protein synthesis, cell growth and survival. S6Ks are activated in response to mitogen stimulation and nutrient sufficiency by the phosphorylation of conserved serine and threonine residues. Here we show for the first time, that in addition to phosphorylation, S6Ks are also targeted by lysine acetylation. Following mitogen stimulation, S6Ks interact with the p300 and p300/CBP-associated factor (PCAF) acetyltransferases. S6Ks can be acetylated by p300 and PCAF in vitro and S6K acetylation is detected in cells expressing p300. Furthermore, it appears that the acetylation sites targeted by p300 lie within the divergent C-terminal regulatory domains of both S6K1 and S6K2. Acetylation of S6K1 and 2 is increased upon the inhibition of class I/II histone deacetylases (HDACs) by trichostatin-A, while the enhancement of S6K1 acetylation by nicotinamide suggests the additional involvement of sirtuin deacetylases in S6K deacetylation. Both expression of p300 and HDAC inhibition cause increases in S6K protein levels, and we have shown that S6K2 is stabilized in cells treated with HDAC inhibitors. The finding that S6Ks are targeted by histone acetyltransferases uncovers a novel mode of crosstalk between mitogenic signalling pathways and the transcriptional machinery and reveals additional complexity in the regulation of S6K function.

Using the LMS method to calculate z-scores for the Fenton preterm infant growth chart

OBJECTIVES

The use of exact percentiles and z-scores permit optimal assessment of infants' growth. In addition, z-scores allow the precise description of size outside of the 3rd and 97th percentiles of a growth reference. To calculate percentiles and z-scores, health professionals require the LMS parameters (Lambda for the skew, Mu for the median, and Sigma for the generalized coefficient of variation; Cole, 1990). The objective of this study was to calculate the LMS parameters for the Fenton preterm growth chart (2003).

DESIGN

Secondary data analysis of the Fenton preterm growth chart data.

METHODS

The Cole methods were used to produce the LMS parameters and to smooth the L parameter. New percentiles were generated from the smooth LMS parameters, which were then compared with the original growth chart percentiles.

RESULTS

The maximum differences between the original percentile curves and the percentile curves generated from the LMS parameters were: for weight; a difference of 66 g (2.9%) at 32 weeks along the 90th percentile; for head circumference; some differences of 0.3 cm (0.6-1.0%); and for length; a difference of 0.5 cm (1.6%) at 22 weeks on the 97th percentile.

CONCLUSION

The percentile curves generated from the smoothed LMS parameters for the Fenton growth chart are similar to the original curves. These LMS parameters for the Fenton preterm growth chart facilitate the calculation of z-scores, which will permit the more precise assessment of growth of infants who are born preterm.

Higher versus lower protein intake in formula-fed low birth weight infants

BACKGROUND

The ideal quantity of dietary protein for formula-fed low birth weight infants < 2.5 kilograms is still a matter of controversy and debate. In premature infants, the protein intake must be sufficient to achieve normal growth without negative effects such as acidosis, uremia, and elevated levels of circulating amino acids (e.g. phenylalanine levels). This systematic review evaluates the benefits and risks of higher (>= 3.0 g/kg/day) versus lower (< 3.0 g/kg/day) protein intakes during the initial hospital stay of formula-fed preterm infants < 2.5 kilograms.

OBJECTIVES

To determine whether higher (>= 3.0 g/kg/day) versus lower (< 3.0 g/kg/day) protein intakes during the initial hospital stay of formula-fed preterm infants < 2.5 kilograms result in improved growth and neurodevelopmental outcomes without evidence of short and long-term morbidity.

SEARCH STRATEGY

Two review authors searched MEDLINE (1966 - May 2005), CINAHL (1982 - May 2005), PubMed (1966 - May 2005), EMBASE (1980 - May 2005), the Cochrane Central Register of Controlled Trials (CENTRAL, The Cochrane Library, Issue 2, 2005), abstracts, conferences and symposia proceedings from Society of Pediatric Research, and American Academy of Pediatrics. Cross references were reviewed independently for additional relevant titles and abstracts for articles up to fifty years old.

SELECTION CRITERIA

Randomized controlled trials contrasting levels of formula protein intakes as low (< 3.0 g/kg/day), high (=> 3.0 g/kg/day but < 4.0 g/kg/day), or very high protein intake (=> 4.0 g/kg/day) during hospitalization of neonates less than 2.5 kilograms at birth who were formula-fed. Studies were not included if infants received partial parenteral nutrition during the study period or were fed formula as a supplement to human milk. Given the small number of studies that met all inclusion criteria, studies in which nutrients other than protein also varied (> 10% relative difference) were added in a post-facto analysis.

DATA COLLECTION AND ANALYSIS

Two review authors used standard methods of the Cochrane Collaboration and of the Cochrane Neonatal Review Group to independently assess trial eligibility and quality, and extracted data. In a 3-arm trial where two groups fell within the same predesignated protein intake group, weighted means and pooled standard deviations were calculated.

MAIN RESULTS

The literature search identified 37 studies, of which five met all the inclusion criteria. All five studies compared low (< 3.0 g/kg/day) to high protein intakes (=> 3.0 g/kg/day but < 4.0 g/kg/day). The overall analysis revealed an improved weight gain (WMD 2.36 g/kg/day, 95% CI 1.31, 3.40) and higher nitrogen accretion (WMD 143.7 mg/kg/day, 95% CI 128.7, 158.8) in infants receiving formula with higher protein content while other nutrients were kept constant. None of the studies reported IQ or Bayley scores at 18 months or later. No significant differences were seen in rates of necrotizing enterocolitis, sepsis or diarrhea. Of three studies included in the post-facto analysis, only one could be included in the meta-analysis. The post-facto analysis revealed further improvement in all growth parameters in infants receiving formula with higher protein content (weight gain: WMD 2.53 g/kg/day, 95% CI 1.62, 3.45, linear growth: WMD 0.16 cm/week, 95% CI 0.03, 0.30, and head growth: WMD 0.23, 95% CI 0.12, 0.35). There was no significant difference (WMD 0.25, 95% CI -0.20, 0.70) in the concentration of plasma phenylalanine between the high and low protein intake groups. One study (Goldman 1969) in the post-facto analysis documented a significantly increased incidence of low IQ scores, below 90, in infants of birth weight less than 1300 grams who received a very high protein intake (6 to 7.2 g/kg/day).

AUTHORS' CONCLUSIONS

This systematic review suggests that higher protein intake (=> 3.0 g/kg/day but < 4.0 g/kg/day) from formula accelerates weight gain. Based on increased nitrogen accretion rates, this most likely indicates an increase in lean body mass. Although accelerated weight gain is considered to be a positive effect, increase in other outcome measures examined may represent a negative or ambivalent effect. These include elevated blood urea nitrogen levels and increased metabolic acidosis. Limited information was available regarding the impact of higher formula protein intakes on long term outcomes such as neurodevelopmental abnormalities. As determined in this review, existing research literature on this topic is not adequate to make specific recommendations regarding the provision of very high protein intake (> 4.0 g/kg/day) from formula.

A novel higher plant protein tyrosine phosphatase interacts with SNF1-related protein kinases via a KIS (kinase interaction sequence) domain

A novel protein phosphatase in Arabidopsis thaliana was identified by database searching. This protein, designated AtPTPKIS1, contains a protein tyrosine phosphatase (PTP) catalytic domain and a kinase interaction sequence (KIS) domain. It is predicted to interact with plant SNF1-related kinases (SnRKs), representing central regulators of metabolic and stress responses. AtPTPKIS1 has close homologues in other plant species, both dicots and monocots, but is not found in other kingdoms. The tomato homologue of AtPTPKIS1 was expressed as a recombinant protein and shown to hydrolyse a generic phosphatase substrate, and phosphotyrosine residues in synthetic peptides. The KIS domain of AtPTPKIS1 was shown to interact with the plant SnRK AKIN11 both in vivo in the yeast two-hybrid system, and in vitro in a GST-fusion 'pull down' assay. The genomes of Arabidopsis and other plants contain further predicted proteins related to AtPTPKIS1, which could also interact with SnRKs and act in novel regulatory and signalling pathways.

Breast milk supplementation for preterm infants: parental preferences and postdischarge lactation duration

Breast milk supplementation is frequently used to improve preterm infant growth and to achieve satisfactory intakes of minerals and vitamins. In the North American market there are commercial preparations: two powders and a liquid. The nutritional data available suggest these products are similar and their utilization is based on healthcare team choice. Parental perception about supplementation has not been previously evaluated although parental attitudes are known to impact on lactation success. The objectives of this paper are to determine parental preference and breastfeeding duration for very-low-birth-weight infants given commercial breast milk enrichment products. The study design is a randomized clinical trial with parental interviews. Sixty-three families with 71 infants were enrolled. Parents expressed their preference for the addition of a powder over a liquid preparation (p<0.01). Those mothers whose infants received the liquid enrichment had a shorter lactation relative to their goal, compared with the mothers of the infants who received the powder (p = 0.017). Parents prefer a powder product for breast milk supplementation and this choice positively impacts on the duration of breastfeeding for very-low-birth-weight infants.

Serum triglycerides of breast milk-fed very-low-birth-weight infants

Normative triglyceride levels were obtained from eighty-five infants weighing < 1500 g. At least 80% of their nutritional intake was their own mother's breast milk. Triglyceride levels did not correlate with birth weight, gestational age, volume of milk fed, age in days, or use of milk fortifier. The 95th percentile triglyceride value was 2.5 mmol/L. Assuming that breast milk-fed infants have triglyceride in the normal range, the acceptable limit of triglyceride values in very-low-birth-weight infants receiving i.v. lipids could be revised upward to 2.5 mmol/L.

Twin pregnancy: the distribution of maternal weight gain of non-smoking normal weight women

We documented the pattern and distribution of weight gain through twin pregnancies of healthy non-smoking women with good birth outcomes. The mean birthweight was 2621 g and the mean gestational age at delivery was 37.6 weeks. As few of the women were weighed after 34 weeks, the weight gain graph was drawn to this point. The sample was separated into subgroups based on birthweights and gender of the infants. Weight gains, parity, income, first measured weight, BMI and Apgars were not different between the subgroups. The only difference between those with infants that were small for gestational age (SGA), over 3 kg, or intermediate in weight was gestational age. For the groups divided by infant gender, the only differences were maternal age and infant birthweight. The mean, median and 80% confidence limits for weight gain at 34 weeks were 14.1, 13.6, and between 8.5 and 19.4 kg, respectively. There was a wide range of weight gained by these women carrying twin pregnancies.

Nutrition and growth analysis of very low birth weight infants

The growth and nutrition of 220 very low birth weight infants were reviewed after comprehensive data on all infants in the hospital were entered into the Neonatal Intensive Care Unit Audit Data Base for 2 years prospectively. Fluid and energy (parenteral and oral) intakes were compared in four birth weight categories (1, less than or equal to 750 g; 2, 751 to 1000 g; 3, 1001 to 1250 g; 4, 1251 to 1500 g). Parenteral nutrition was the major source of first nutrition for the small infants, but seldom did it alone provide adequate nutrition for very low birth weight infants. The age of the first nutrition (parenteral and/or oral nutrition other than dextrose) decreased with increasing birth weight. The age of the first oral feedings was later for the infants of the lower birth weights but enteral feeding became the major nutrition for all weight categories by the second week of life. During the first 50 days the infants accumulated a deficit of 3780 to 5460 kJ relative to their estimated need of 504 kJ/kg per day, with the smaller infants accumulating a significantly larger deficit. The growth of infants appropriate for gestational age and of infants small for gestational age differed from each other and from the commonly used graph of Dancis et al (J Pediatr. 1948;33:570-572).

Development of colonic sodium transport in early childhood and its regulation by aldosterone

Aldosterone is important in the regulation of sodium conservation by both kidney and colon. In the very preterm neonate marked urinary salt wasting occurs because of immature renal tubular function, but little is known of the ontogeny of colonic transport processes. Using an in vivo rectal dialysis technique, we have shown that in the human infant the colon has well developed salt conserving mechanisms from early in the last trimester of gestation and that aldosterone is an important regulatory hormone. Sodium transport mechanisms in the colon appear to develop before those in the kidney and it is possible that the colon is the major organ of sodium conservation in the preterm neonate.

Maternal insecurity and failure to thrive in Asian children

Four Asian babies were investigated because they failed to thrive. In all four cases the failure to thrive was a result of the mother's social isolation and inability to communicate, and to the father's refusal to accept that there was a problem in the family.

Air embolism in ventilated very low birthweight infants

Five cases of air embolism in ventilated very low birthweight infants are reported. In all cases the outcome was fatal with the babies dying at about 15 hours of age.

Stress analysis of vasoconstriction at arterial branch sites

The object of the research was to estimate wall stresses caused by vasoconstriction at arterial branches. The basic procedure was a combination of experimental strain measurement and analytical stress analysis. Segments of canine renal arteries were perfused and stimulated to constrict with dopamine hydrochloride and norepinephrine. Surface wall deformation was measured with a stereo-photographic technique. A plane stress finite element analysis was used to calculate wall stresses based on the experimentally derived deformations. The major result of the study was to demonstrate tensile stresses, and in some cases biaxial tension, in contracting vessels. Peak stresses in the apex of the acute angle of the branches were approximately three times unpenetrated hoop stress in the parent vessels. The results imply that constriction at a branch site may be capable of generating sufficient wall tension to tear arterial tissue, and that smooth muscle reactivity is important with respect to the etiology of cerebral aneurysms and the clinical management of acute branch site pathology.

Defective jejunal brush-border Na+/H+ exchange: a cause of congenital secretory diarrhoea

In a child with congenital secretory diarrhoea, jejunal perfusion studies showed net water and electrolyte secretion and suggested a defect in sodium/proton exchange. A technique was developed for investigation of such exchange in brush-border membrane vesicles from jejunal biopsy specimens. Vesicles from control specimens displayed proton-gradient-dependent sodium uptake, whereas those from the patient did not. These findings, as well as pointing to a cause of congenital secretory diarrhoea, confirm the existence and importance of jejunal sodium/proton exchange in man.

Collapse and viscoelasticity of diseased human arteries

A laboratory study of the hydrostatic collapse of diseased tibial arteries demonstrated hysteresis in the pressure-flow behaviour which resembled that seen in the stress-strain relations of the arterial tissue. The pressures at which the vessels collapsed were found to be considerably lower than expected on the basis of theoretical elastic models. Also, the pressures at which the vessels reopened were consistently lower than the pressures at which they collapsed. These findings were explained on the basis of viscoelasticity. The difference between collapse and opening pressure may provide insight into the mechanical properties of vessels, and a clue to errors in non-invasive measurements of blood pressure which depend upon collapse of arteries.