Guy Lampe

Genomic catastrophes frequently arise in esophageal adenocarcinoma and drive tumorigenesis

Oesophageal adenocarcinoma (EAC) incidence is rapidly increasing in Western countries. A better understanding of EAC underpins efforts to improve early detection and treatment outcomes. While large EAC exome sequencing efforts to date have found recurrent loss-of-function mutations, oncogenic driving events have been underrepresented. Here we use a combination of whole-genome sequencing (WGS) and single-nucleotide polymorphism-array profiling to show that genomic catastrophes are frequent in EAC, with almost a third (32%, n = 40/123) undergoing chromothriptic events. WGS of 22 EAC cases show that catastrophes may lead to oncogene amplification through chromothripsis-derived double-minute chromosome formation (MYC and MDM2) or breakage-fusion-bridge (KRAS, MDM2 and RFC3). Telomere shortening is more prominent in EACs bearing localized complex rearrangements. Mutational signature analysis also confirms that extreme genomic instability in EAC can be driven by somatic BRCA2 mutations. These findings suggest that genomic catastrophes have a significant role in the malignant transformation of EAC.

ELF score ≥9.8 indicates advanced hepatic fibrosis and is influenced by age, steatosis and histological activity

There is increasing need to identify individuals with advanced liver fibrosis, who are at risk of complications such as hepatocellular carcinoma. The commercially available enhanced liver fibrosis (ELF) test provides a non‐invasive assessment of fibrosis severity. This study was designed to determine the diagnostic accuracy of the manufacturers cut‐off value (≥9.8) in identifying advanced fibrosis.

Genome-wide analysis of esophageal adenocarcinoma yields specific copy number aberrations that correlate with prognosis

The incidence of esophageal adenocarcinoma (EAC) has been increasing rapidly for the past 3 decades in Western (Caucasian) populations. Curative treatment is based around esophagectomy, which has a major impact on quality of life. For those suitable for treatment with curative intent, 5‐year survival is ∼30%. More accurate prognostic tools are therefore needed, and copy number aberrations (CNAs) may offer the ability to act as prospective biomarkers in this regard. We performed a genome‐wide examination of CNAs in 54 samples of EAC using single‐nucleotide polymorphism (SNP) arrays. Our aims were to describe frequent regions of CNA, to define driver CNAs, and to identify CNAs that correlated with survival. Regions of frequent amplification included oncogenes such as EGFR, MYC, KLF12, and ERBB2, while frequently deleted regions included tumor suppressor genes such as CDKN2A/B, PTPRD, FHIT, and SMAD4. The genomic identification of significant targets in cancer (GISTIC) algorithm identified 24 regions of gain and 28 regions of loss that were likely to contain driver changes. We discovered 61 genes in five regions that, when stratified by CNA type (gain or loss), correlated with a statistically significant difference in survival. Pathway analysis of the genes residing in both the GISTIC and prognostic regions showed they were significantly enriched for cancer‐related networks. Finally, we discovered that copy‐neutral loss of heterozygosity is a frequent mechanism of CNA in genes currently targetable by chemotherapy, potentially leading to under‐reporting of cases suitable for such treatment.

Human papillomavirus status and p16INK4A expression in patients with mucosal squamous cell carcinoma of the head and neck in Queensland, Australia

BACKGROUND The last decade has seen changes in the epidemiology of mucosal squamous cell carcinomas of the head and neck (HNSCCs), with increasing numbers of cases attributable to human papillomavirus (HPV) infection. We sought to determine the prevalence of HPV and p16(INK4a) expression in Australian HNSCC patients and to identify predictors of HPV-positivity. METHODS We recruited 248 HNSCC patients with histologically confirmed primary SCC of the oropharynx, oral cavity, hypopharynx or larynx diagnosed between 2004 and 2010. All patients completed a questionnaire. Clinical data were abstracted from medical records. HPV presence in paraffin-embedded tumours was determined by PCR, and expression of p16(INK4a), p21(WAF1), p53, pRB, cyclin D1, and Ki67 by immunohistochemistry. RESULTS Fifty (20%) patients were HPV-positive, 63 (28%) overexpressed p16(INK4a), and 44 (19%) were positive for HPV and p16(INK4a) (high concordance between HPV-positivity and p16(INK4a) status, κ=0.72). HPV-16 was most common (84%), followed by HPV-18 (10%), HPV-33 (4%) and HPV-69 (2%). HPV and p16(INK4a) prevalence was highest for SCCs of the oropharynx, followed by hypopharynx, larynx and oral cavity (HPV and p16(INK4a)p<0.0001). HPV prevalence and p16(INK4a)-overexpression were significantly higher in younger than older patients (HPV p=0.001; p16 (INK4a)p=0.003). Heavy smokers had lower HPV prevalence than non- or moderate smokers (p=0.017). Gender and alcohol consumption were not associated with HPV or p16(INK4a) status. HPV-positive tumours had significantly lower cyclin D1 and higher p21(WAF1) expression than HPV-negative tumours. CONCLUSION HPV prevalence and p16(INK4a)-overexpression were highest in oropharyngeal tumours, younger patients, and non-smokers.

The Enhanced liver fibrosis score is associated with clinical outcomes and disease progression in patients with chronic liver disease

Current tools for risk stratification of chronic liver disease subjects are limited. We aimed to determine whether the serum‐based ELF (Enhanced Liver Fibrosis) test predicted liver‐related clinical outcomes, or progression to advanced liver disease, and to compare the performance of ELF to liver biopsy and non‐invasive algorithms.

Severe acute liver injury associated with lumiracoxib.

Backgound and Aim:  Significant elevations in liver transaminases were noted in some patients during pre‐marketing clinical trials with lumiracoxib, a selective COX‐2 inhibitor. It was withdrawn from the Australian market in August 2007, because of an association with severe liver injury. We describe in detail three cases of severe liver injury in patients taking lumiracoxib

Identification of the CIMP-like subtype and aberrant methylation of members of the chromosomal segregation and spindle assembly pathways in esophageal adenocarcinoma

Summary This study describes the esophageal cancer methylation landscape and its impact on gene expression. Genes aberrantly methylated suggest a mechanism that could lead to genomic instability and chromothripsis. A CpG island methylator phenotype-like subtype with potentially worse clinical outcome was also identified.

Multiplex serum protein analysis identifies novel biomarkers of advanced fibrosis in patients with chronic liver disease with the potential to improve diagnostic accuracy of established biomarkers

Background and Aims Non-invasive markers of liver fibrosis are urgently required, especially for use in non-specialist settings. The aim of this study was to identify novel serum biomarkers of advanced fibrosis. Methods We performed an unbiased screen of 120 serum analytes including cytokines, chemokines and proteases in 70 patients (35 without fibrosis, 35 with cirrhosis on biopsy), and selected a panel of 44 candidate biomarkers, which were subsequently measured in a mixed-etiology cohort of 432 patients with known serum HA, PIIINP and TIMP1 (which comprise the validated Enhanced Liver Fibrosis (ELF) test). Multivariate logistic regression modelling was used to generate models for the prediction of advanced or significant fibrosis (METAVIR ≥F3 and ≥F2, respectively); in addition to identifying biomarkers of disease activity and steatohepatitis. Results Seventeen analytes were significantly differentially expressed between patients with no advanced fibrosis and patients with advanced fibrosis, the most significant being hyaluronic acid (HA) and matrix metalloproteinase (MMP) 7 (p = 2.9E-41 and p = 1.0E-26, respectively). The optimal model for the prediction of advanced fibrosis comprised HA, MMP7, MMP1, alphafetoprotein (AFP) and the AST to platelet ratio index (APRI). We demonstrate enhanced diagnostic accuracy (AUROC = 0.938) compared to a model comprising HA, PIIINP and TIMP1 alone (ELF) (AUROC = 0.898, p<0.0001, De Long’s test). Conclusions We have identified novel serum biomarkers of advanced liver fibrosis, which have the potential to enhance the diagnostic accuracy of established biomarkers. Our data suggest MMP7 is a valuable indicator of advanced fibrosis and may play a role in liver fibrogenesis.

Khat-associated hepatitis

We report a case of khat-associated hepatitis in a 32-year-old Somali man living in Australia. This is the first case of hepatoxicity related to khat ingestion reported in Australia.

Is Alpha-B Crystallin an Independent Marker for Prognosis in Lung Cancer?

BACKGROUND Alpha B-crystallin (CRYAB) is an oncogene that increases tumour survival by promoting angiogenesis and preventing apoptosis. CRYAB is an independent prognostic marker in epithelial tumours including head and neck squamous cell carcinoma and breast cancer where it is predictive of nodal status and associated with poor outcome. We explored the role of CRYAB in non-small-cell lung cancer (NSCLC). METHODS Immunohistochemical analysis was performed on 50 samples. Following staining with anti-alpha-B crystallin antibody, a blinded pathologist scored samples for nuclear (N) and cytoplasmic (C) staining intensity. Analysis was performed using Coxs proportional hazards model. RESULTS There were 32 adenocarcinomas and 18 squamous cell carcinomas. The median tumour size was T2, grade 2 moderately differentiated, and 10 patients had nodal spread. Recurrence was seen in 22 patients (46%). Mortality was 48%, with median time to mortality 871 days. N staining was detected in eight samples (16%), and C staining in 20 (40%), with both N and C staining positive in five (10%). Staining for CRYAB predicted neither recurrence (N stain p=0.78, C stain p=0.38) nor mortality (N stain p=0.86, C stain p=0.66). CONCLUSION CRYAB did not predict outcomes in patients treated for NSCLC. Larger studies are required to validate this finding.