Integrated genomic analysis identifies driver genes and cisplatin-resistant progenitor phenotype in pediatric liver cancer

Pediatric liver cancers (PLCs) comprise diverse diseases affecting infants, children and adolescents. Despite overall good prognosis, PLCs display heterogeneous response to chemotherapy. Integrated genomic analysis of 126 pediatric liver tumors showed a continuum of driver mechanisms associated with patient age, including new targetable oncogenes. In 10% of hepatoblastoma patients, all before 3 years old, we identified a mosaic premalignant clonal expansion of cells altered at the 11p15.5 locus. Analysis of spatial and longitudinal heterogeneity revealed an important plasticity between 'Hepatocytic', 'Liver Progenitor' and 'Mesenchymal' molecular subgroups of hepatoblastoma. We showed that during chemotherapy, 'Liver Progenitor' cells accumulated massive loads of cisplatin-induced mutations with a specific mutational signature, leading to the development of heavily mutated relapses and metastases. Drug screening in PLC cell lines identified promising targets for cisplatin-resistant progenitor cells, validated in mouse xenograft experiments. These data provide new insights into cisplatin resistance mechanisms in PLC and suggest alternative therapies.

XAF1 as a modifier of p53 function and cancer susceptibility

Cancer risk is highly variable in carriers of the common TP53-R337H founder allele, possibly due to the influence of modifier genes. Whole-genome sequencing identified a variant in the tumor suppressor XAF1 (E134*/Glu134Ter/rs146752602) in a subset of R337H carriers. Haplotype-defining variants were verified in 203 patients with cancer, 582 relatives, and 42,438 newborns. The compound mutant haplotype was enriched in patients with cancer, conferring risk for sarcoma (P = 0.003) and subsequent malignancies (P = 0.006). Functional analyses demonstrated that wild-type XAF1 enhances transactivation of wild-type and hypomorphic TP53 variants, whereas XAF1-E134* is markedly attenuated in this activity. We propose that cosegregation of XAF1-E134* and TP53-R337H mutations leads to a more aggressive cancer phenotype than TP53-R337H alone, with implications for genetic counseling and clinical management of hypomorphic TP53 mutant carriers.

Adeno-associated virus in the liver: natural history and consequences in tumour development

OBJECTIVE

Adeno-associated virus (AAV) is a defective mono-stranded DNA virus, endemic in human population (35%-80%). Recurrent clonal AAV2 insertions are associated with the pathogenesis of rare human hepatocellular carcinoma (HCC) developed on normal liver. This study aimed to characterise the natural history of AAV infection in the liver and its consequence in tumour development.

DESIGN

Viral DNA was quantified in tumour and non-tumour liver tissues of 1461 patients. Presence of episomal form and viral mRNA expression were analysed using a DNAse/TaqMan-based assay and quantitative RT-PCR. In silico analyses using viral capture data explored viral variants and new clonal insertions.

RESULTS

AAV DNA was detected in 21% of the patients, including 8% of the tumour tissues, equally distributed in two major viral subtypes: one similar to AAV2, the other hybrid between AAV2 and AAV13 sequences. Episomal viral forms were found in 4% of the non-tumour tissues, frequently associated with viral RNA expression and human herpesvirus type 6, the candidate natural AAV helper virus. In 30 HCC, clonal AAV insertions were recurrently identified in CCNA2, CCNE1, TERT, TNFSF10, KMT2B and GLI1/INHBE. AAV insertion triggered oncogenic overexpression through multiple mechanisms that differ according to the localisation of the integration site.

CONCLUSION

We provided an integrated analysis of the wild-type AAV infection in the liver with the identification of viral genotypes, molecular forms, helper virus relationship and viral integrations. Clonal AAV insertions were positive selected during HCC development on non-cirrhotic liver challenging the notion of AAV as a non-pathogenic virus.

Non-virological factors are drivers of hepatocellular carcinoma in virosuppressed hepatitis B cirrhosis: Results of ANRS CO12 CirVir cohort

Worldwide, hepatocellular carcinoma (HCC) occurs mainly in Asian patients with hepatitis B virus (HBV) infection. This study aimed to decipher the environmental and virological factors associated with HCC occurrence and validate risk scoring systems in a French multicentre prospective cohort of HBV cirrhotic patients. Patients with biopsy-proven Child-Pugh A viral cirrhosis included in the ANRS CO12 CirVir cohort who were HBsAg(+) without hepatitis C coinfection were selected for: (a) interview through a standardized questionnaire reporting coffee consumption and HCC familial history; (b) HBsAg quantification using baseline and sequential 2-year frozen sera; (c) baseline HBV genotype determination; and (d) assessment of risk factors and applicability of HCC risk scores (Kaplan-Meier analysis, Cox models). Among 317 patients studied (261 men, median age 53 years, past or ongoing antiviral treatment 93.3% and baseline detectable HBV DNA in 88 patients), the baseline and 2-year median HBsAg levels were 810 and 463 IU/mL, respectively. After a median follow-up of 65.2 months, 27 HCC cases were diagnosed (annual incidence: 1.6%). Three factors were independently associated with HCC occurrence: age > 50 years, platelets ≤ 150 × 10³ /mm³ and body mass index ≥ 30 kg/m² . Two out of five risk scores were validated, and the most accurate was PAGE-B at 1 year. Moreover, HCC in patients without maintained virological suppression seems more aggressive and less accessible to curative treatment. In conclusion, in French patients with HBV cirrhosis mostly virally suppressed, independent HCC risk factors were host-related (age, obesity) or linked to the severity of cirrhosis (thrombopenia), and the European PAGE-B score was the most accurate risk score.

Prognostic value of viral eradication for major adverse cardiovascular events in hepatitis C cirrhotic patients

BACKGROUND

The objective was to examine the role of a sustained virological response (SVR) on major adverse cardiovascular events (MACEs) in patients with compensated hepatitis C virus (HCV) cirrhosis.

METHODS

Patients with the following criteria were enrolled in 35 French centers: (1) biopsy-proven HCV cirrhosis; (2) Child-Pugh A; (3) positive viremia; and (4) no prior liver complication, and then prospectively followed. All patients received HCV treatment after inclusion. MACEs included stroke, myocardial infarction, ischemic heart disease, heart failure, peripheral arterial disease, cardiac arrest, and cardiovascular death. SVR, defined as negative viremia 12 weeks posttreatment, was considered as a time-dependent covariate, and its effect on MACE occurrence was assessed. The median follow up was 57.5 months, ending in December 2015.

RESULTS

Sixty-two of 878 (7.1%) patients presented a total of 79 MACEs. The main predictive baseline factors of MACEs were Asian ethnic origin, history of MACEs, arterial hypertension, diabetes mellitus, current smoking, low serum albumin level, high total bilirubin level, and low platelet count. In multivariate analysis, SVR was associated with a decreased risk of MACEs (hazard ratio=0.35, 95% CI 0.09-0.97, P=.044), whereas Asian ethnic origin, arterial hypertension, smoking, and low serum albumin level remained predictive of MACE occurrence. The 5-year survival rate was 60.1% versus 87.5% in patients who did versus those who did not present a MACE (P<.001).

CONCLUSIONS

In patients with compensated HCV-related cirrhosis, Asian ethnic origin, arterial hypertension, smoking, and low serum albumin are independent predictive factors of cardiovascular events, whereas an SVR is associated with a decreased rate of cardiovascular events.

Abstract 919: Adeno-associated virus 2 (AAV2) induces recurrent insertional mutagenesis in human hepatocellular carcinomas

Background: Hepatocellular carcinomas (HCC) are related to various etiologies including alcohol intake, obesity, hemochromatosis, hepatitis B and hepatitis C virus infection. Additional risk factors remain to be identified particularly in HCC developed without cirrhosis. We identified a fragment of Adeno-Associated Virus type 2 (AAV2, a defective DNA virus considered as non-pathogenic) inserted in an HCC genome and this result prompted us to screen a large series of HCC samples.

Methods: We screened 150 HCC and matched non-tumor liver samples for AAV2 sequences using PCR and next generation sequencing. Expression of the genes targeted by viral integration was quantified and the functional consequences of AAV2 integration within TERT promoter was analyzed in 3 HCC cell lines using luciferase assay Results: Among the 150 tumors, we identified 7 cases (5%) with a clonal AAV2 insertion whereas no clonal insertion was found in the corresponding non-tumor liver tissues. In the first HCC tumor, we identified a 208 base pairs insertion of an AAV2 fragment within the TERT (coding for the telomerase reverse transcriptase) promoter. In HCC cell lines, we demonstrated that this AAV2 insertion resulted in an increased TERT promoter activity. We next identified 6 additional clonal somatic integrations of AAV2, all occurred within known cancer driver genes, CCNA2 (4 cases), CCNE1 or TNFSF10 leading to over-expression of the targeted gene without generating chimeric viral-endogeneous functional fusion transcripts. In CCNA2 (coding for cyclin A2), the four integration sites were identified within intron 2 and AAV2 insertion ranged from 219 to 1,975bp occurring in both orientations. In CCNE1 (coding for cyclin E1), we identified a 368bp AAV2 integration within intron 4. In the remaining case, AAV2 integration occurred in the 3′ UTR of TNSFS10 (coding for the receptor TRAIL), 244 bp after the stop codon. In 6 out of the 7 tumors, the inserted AAV2 included the 3′inverse tandem region. Strikingly, almost all the tumors were developed on non-fibrotic liver (6 out of 7 cases, P&lt;0.05) without known risk factor (5 out of 7, P&lt;0.05), thus suggesting a particular pathogenic role of AAV2 in this subset of patients.

Conclusion: Infection by AAV2, that is very frequent the general population (around 30 to 60% of individuals), is involved in the pathogenesis of rare human HCC by recurrent somatic integration in cancer driver genes challenging its safety as a vector for gene therapy.

Citation Format: Shalini Datta, Jean-Charles Nault, Andrea Franconi, Sandrine Imbeaud, Maxime Mallet, Gabrielle Couchy, Eric Letouze, Camilla Pilati, Benjamin Verret, Jean-Frédéric Blanc, Charles Balabaud, Julien Calderaro, Alexis Laurent, Mélanie Letexier, Paulette Bioulac-Sage, Fabien Calvo, Jessica Zucman-Rossi. Adeno-associated virus 2 (AAV2) induces recurrent insertional mutagenesis in human hepatocellular carcinomas. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 919. doi:10.1158/1538-7445.AM2015-919

Prognostic value of chromosomal imbalancies and the colon gene expression signatures in rectal cancer

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Background: Some studies have suggested colon and rectal cancer as two different entities when considering DNA mutations or chromosomal imbalances. We therefore wondered if two colon gene expression signatures could predict specific survival. We also tested the influence of chromosomal imbalancies on prognosis in rectal cancer.

Methods: Between 1998-2001 a series of 94 patients (pts) with rectal adenocarcinoma (T1-2-3 M0) were treated with preoperative radiotherapy (RT) with or without concurrent chemotherapy (CT) (78 pts) or with curative RT alone using contact X Ray therapy (CXRT) (18 pts). High-throughput analysis of genomic imbalancies and DNA expression were performed within the frame of the Carte d’Identité des Tumeurs (CIT) programme of Ligue du Cancer- France. Biostatistical analysis were performed and correlated with metastasis-free survival (MFS) and specific survival (SS). Coloprint and Oncotype DX colon signatures were tested on this cohort.

Results: The median survival of the 96 patients was 105 months. The overall specific survival rate at 8 years was 75% for the preoperative group and 65 % for the RT alone group. Overall the rate of distant metastases was 30 % at 8 years (26 pts). A validated biopsy specimen was analysed in 67 pts for DNA expression and for genomic imbalances. Deletion of 8p and 1p36-35 correlated with MFS (p=0.001 and p=0.02 respectively) and SS (p=0.0002 and p=0.008 respectively). Multivariate analysis identified -8p as an independent prognostic factor of MFS (p=0.004) and SS (p=0.003). Validation of this deletion on an independent cohort is on-going. Regarding mRNA profile analysis, no stable consensus could identify clusters that accurately separate patients of bad and good SS or MFS, whatever the method used (28 methods of clustering). Coloprint signature could discriminate patients with the worst prognosis (SS: p<0.05) whereas Oncotype DX colon signature did not (SS: p=0.4).

Conclusions: By analysing this series of patients from a single center we have been able for the first time in rectal cancer to identify -8p as an independent prognostic factor of MFS and SS. mRNA analysis suggest that colon and rectal cancer may not always share the same DNA expression profile.

Modular α-Helical Mimetics with Antiviral Activity against Respiratory Syncitial Virus

A 13-residue peptide sequence from a respiratory syncitial virus fusion protein was constrained in an alpha-helical conformation by fusing two back-to-back cyclic alpha-turn mimetics. The resulting peptide, Ac-(3-->7; 8-->12)-bicyclo-FP[KDEFD][KSIRD]V-NH(2), was highly alpha-helical in water by CD and NMR spectroscopy, correctly positioning crucial binding residues (F488, I491, V493) on one face of the helix and side chain-side chain linkers on a noninteracting face of the helix. This compound displayed potent activity in both a recombinant fusion assay and an RSV antiviral assay (IC(50) = 36 nM) and demonstrates for the first time that back-to-back modular alpha-helix mimetics can produce functional antagonists of important protein-protein interactions.