Identification of tumor biomarkers for sunitinib in advanced renal cell carcinoma (RCC)

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Background: Sunitinib is a standard of care for advanced RCC. Despite efforts to identify predictive molecular markers for patient selection, none are available, likely due to multiple resistance mechanisms. Using the Total Cancer Care (TCC) database, which integrates patient clinical, molecular, and biospecimen data, we devised a tumor genomics and transcriptomics experiment to identify differences between RCC patients who derive prolonged clinical benefit from sunitinib versus those who are resistant. Methods: A discovery set of 34 RCC patients treated with sunitinib at the approved regimen were identified in the TCC database (n=16 treated for ≤6 months, having primarily discontinued for reasons other than tolerability; n=18 treated for ≥18 months). Tumor samples were analyzed by whole exome sequencing (WES) and by parallel 400-gene expression profiling. Following gene mutation identification and supervised gene expression analysis, molecular differences between the two groups were identified and tested for potential association with treatment duration. Results: Of the 34 cases identified, 24 remained for analysis following sample QC failure and clinical review (n=10 and 14 treated for ≤6 and ≥18 months, respectively). Gene expression analysis revealed a 37-gene signature associated with treatment duration: MAPK8 (JNK1) was a leading candidate biomarker (Pearson correlation with log [treatment duration]=–0.70; p=0.06 after Bonferroni multiplicity correction). Pathway-based WES analyses identified 25 potential variants of interest, none remaining statistically significant after correction. However, following genome-wide analysis, a single variant in an intronic region of ING3 was statistically associated with treatment duration (p=0.02). Conclusions: Activation of the PI3K/AKT pathway was a marker of resistance to sunitinib. In contrast, activation of the angiogenic, NOTCH, or JAK-STAT pathways was, to some degree, associated with sensitivity to therapy. However, neither VHL alteration nor lack of expression, nor alteration in chromatin-rearrangement genes, was associated with sunitinib treatment duration. These findings require further validation in a larger and independent cohort.

First Report of Apple chlorotic leaf spot virus in Hawthorn in China

Apple chlorotic leaf spot virus (ACLSV) is the type species of the genus Trichovirus in the Betaflexiviridae family (1). ACLSV is distributed worldwide in most pome and stone fruit trees of the Rosaceae family, including apple, pear, peach, plum, cherry, apricot, and hawthorn (3). In 2012, a de novo assembly of the fruit transcriptome of a hawthorn (Crataegus pinnatifida) accession maintained in the National Hawthorn Germplasm Repository at Shenyang was conducted using Illumina-based RNA-seq data, and it resulted that a 7,543 nt of the genomic sequence of ACLSV was assembled. To confirm the result of Illumina RNA-Seq analysis, nine pairs of primers were designed according to the assembled sequence of ACLSV to amplify the genomic sequence of ACLSV by RT-PCR with total RNA extracted from hawthorn leaves as template (2). The full-length sequence of the isolate of ACLSV from hawthorn assembled with the sequences of the RT-PCR fragments was also 7,543 nt (GenBank Accession No. KM207212), which shows 99.5% nucleotide identity with the sequence assembled from Illumina RNA-seq data. The isolate of ACLSV from hawthorn was named SY01, which shows about 75% nucleotide identity with the sequences of ACLSV isolated from apple (GenBank Accession No. KJ522693), peach (JN634760), and plum (M58152). The nucleotide sequences of coat protein and RNA polymerase genes of SY01 are about 83 and 88% identical with those of ACLSV isolates in GenBank, respectively. A pair of primers HF/HR (ACCGGCGTCTTTTGCAAACT/TGGGTTCCAGAGTTTGAATGCA), which amplified a 210-bp fragment, was designed according to the sequence of SY01 to detect ACLSV in hawthorns. With RT-PCR, ACLSV was detected in 6 of the 30 accessions of hawthorn, and the nucleotide identity among PCR fragments was 92%. In addition, leaves from six RT-PCR positive plants reacted positively when tested by DAS-ELISA with polyclonal antisera (X-Y Biotechnology, Shanghai, China) raised against ACLSV. These findings, representing the first report of the presence of ACLSV in hawthorn in China, illustrate the need to develop virus-free trees of hawthorn for cultivation and germplasm distribution of this important Rosaceae family plant. References: (1) E. B. Carstens. Arch. Virol. 155:133, 2010. (2) H. Dai et al. PLoS ONE 8(9):e72910, 2013. (3) A. T. Katsiani et al. Plant Pathol. 63:63, 2014.

Genome-wide identification of RNA editing in hepatocellular carcinoma

We did whole-transcriptome sequencing and whole-genome sequencing on nine pairs of Hepatocellular carcinoma (HCC) tumors and matched adjacent tissues to identify RNA editing events. We identified mean 26,982 editing sites with mean 89.5% canonical A→G edits in each sample using an improved bioinformatics pipeline. The editing rate was significantly higher in tumors than adjacent normal tissues. Comparing the difference between tumor and normal tissues of each patient, we found 7 non-synonymous tissue specific editing events including 4 tumor-specific edits and 3 normal-specific edits in the coding region, as well as 292 edits varying in editing degree. The significant expression changes of 150 genes associated with RNA editing were found in tumors, with 3 of the 4 most significant genes being cancer related. Our results show that editing might be related to higher gene expression. These findings indicate that RNA editing modification may play an important role in the development of HCC.

Genomic landscape and genetic heterogeneity in gastric adenocarcinoma revealed by whole-genome sequencing

Gastric cancer (GC) is the second most common cause of cancer-related deaths. It is known to be a heterogeneous disease with several molecular and histological subtypes. Here we perform whole-genome sequencing of 49 GCs with diffuse (N=31) and intestinal (N=18) histological subtypes and identify three mutational signatures, impacting TpT, CpG and TpCp[A/T] nucleotides. The diffuse-type GCs show significantly lower clonality and smaller numbers of somatic and structural variants compared with intestinal subtype. We further divide the diffuse subtype into one with infrequent genetic changes/low clonality and another with relatively higher clonality and mutations impacting TpT dinucleotide. Notably, we discover frequent and exclusive mutations in Ephrins and SLIT/ROBO signalling pathway genes. Overall, this study delivers new insights into the mutational heterogeneity underlying distinct histologic subtypes of GC that could have important implications for future research in the diagnosis and treatment of GC.

Abstract LB-313: Integrative genomic profiling of Asian gastric cancers identifies four subgroups with distinct pathobiology and prognosis

Gastric cancer is the 2nd most common cause of cancer related mortality and 4th most common cancer worldwide. The molecular classification of Gastric Cancers and the relevance of pre-clinical models are not well established, creating challenges in discovering novel molecularly targeted therapies. In order to address that, we conducted integrated molecular data analysis of 300 Asian Gastric tumors through the Asian Cancer Research Group (ACRG). We identified four cancer subtypes, based on RNA/DNA profiling, Lauren's histological classification (Intestinal and Diffused) and Epstein Barr Virus (EBV) status, exhibiting differential pathobiology as well as prognosis. The groups are 1) Mesenchymal subgroup characterized by Diffused tumors with hallmarks of Epithelial to Mesenchymal transition such as CDH1 loss and co-occurring with IGF2 over-expression; 2) Microsatellite instable (MSI) subgroup characterized by predominantly hypermutated Intestinal tumors (including majority of mutations in KRAS) with likely MLH1 loss through promoter methylation; 3) TP53 pathway active subgroup with Epstein-Barr virus (EBV) infection or mutated oncogenes (e.g. PIK3CA) and 4) TP53 pathway inactive characterized by p53 loss through deleterious mutations in TP53 or MDM2 amplification and further characterized by both focal amplifications in oncogenes such as HER2, EGFR, cMET, CCNE1 as well as large scale chromosomal gains and losses. The above subtypes exhibited differential prognosis with the Mesenchymal subtype displaying the worst prognosis and the MSI subtype the best prognosis among the subtypes. The subtypes and their association with prognosis were independently validated in an additional large Gastric cancer cohort (N=277).

We studied the applicability of this classification in other gastrointestinal (GI) cancers and show the presence of our proposed molecular subtypes of Gastric cancer in Colorectal cancers as well thereby suggesting commonalities in biological processes that give rise to Gastric and Colorectal tumors and providing a common ground to classify GI cancers.

We also checked the presence of Gastric cancer subtypes in pre-clinical models of GI tract cancers and found that cell line panels often used for drug discovery shown an under-representation of p53 pathway active subtype, thus possibly creating challenges in translation to clinical studies.

Overall, we provide a stratification that will lay a more solid groundwork for rationally targeting Gastric Cancer by helping focus on specific altered mechanisms and/or oncogenes as well as allowing for a more rational choice of pre-clinical models in drug discovery and development.

Citation Format: Razvan Cristescu, Jeeyun Lee, Michael Nebozhyn, Amit Aggarwal, Jason Ting, Swee Seong Wong, Yong Yue, Christoph Reinhard, Kyoung Kim, Ingu Do, Hongyue Dai, Andrey Loboda. Integrative genomic profiling of Asian gastric cancers identifies four subgroups with distinct pathobiology and prognosis. [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 LB-313. doi:10.1158/1538-7445.AM2014-LB-313

The FEN1 E359K germline mutation disrupts the FEN1-WRN interaction and FEN1 GEN activity, causing aneuploidy-associated cancers

Polymorphisms and somatic mutations in Flap Endonuclease 1 (FEN1), an essential enzyme involved in DNA replication and repair, can lead to functional deficiencies of the FEN1 protein and a predisposition to cancer. We identified a FEN1 germline mutation which changed residue E359 to K in a patient whose family had a history of breast cancer. We determined that the E359K mutation, which is in the protein-protein domain of FEN1, abolished the interaction of FEN1 with Werner Syndrome protein (WRN), an interaction which is critical for resolving stalled DNA replication forks. Furthermore, although the flap endonuclease activity of FEN1 E359K was unaffected, it failed to resolve bubble structures, which requires the FEN1 gap dependent endonuclease (GEN) activity. To determine the etiological significance of E359K, we established a mouse model containing this mutation. E359K mouse embryonic fibroblasts (MEF) were more sensitive to DNA cross-linking agents that cause replication forks to stall. Cytological analysis suggested that the FEN1-WRN interaction was also required to for telomere stability; mutant cell lines had fragile telomeres, increased numbers of spontaneous chromosomal anomalies and higher frequencies of transformation. Moreover, the incidence of cancer was significantly higher in mice homozygous for FEN1 E359K than in wild-type mice, suggesting that the FEN1 E359K mutation is oncogenic.

Childhood obesity increases left-ventricular mass irrespective of blood pressure status

Adults with a left-ventricular mass index (LVMI) in grams normalized to height in meters(2.7) (LVMI g/m(2.7)) >51 g/m(2.7) are more prone to cardiovascular and cerebrovascular events. We delineated the odds for cardiac structural sequelae amongst apparently normal white and African-American (AA) children with varying body mass indices (BMI) and office blood pressures. A total of 2,071 children with normal echocardiograms were categorized into risk groups based on BMI and systolic blood pressures (SBPs). Predictors of cardiac sequelae examined were age, sex, race, and z-scores (z) for BMI, SBP, and diastolic blood pressure. Cardiac sequelae measures included (LVMI g/m(2.7)) >51 g/m(2.7), (LVMI) (g/m(2.7)) z, left atrial size (LA(ht)) (mm) z, and relative wall thickness z. Mean age was 14 ± 2 years with 56 % being male and 13 % being AA. Children were divided into "controls" (n = 1,059) and risk groups based on BMI and SBP. Odds ratio for LVMI (g/m(2.7)) > 51.0 g/m(2.7), varied from 5.3 up to 8.5 in children with increased BMI. Both increased BMI and SBP z were associated with increased LVMI (g/m(2.7)) z; however, BMI z had a stronger association. Increased BMI z and AA race were associated with greater LA(ht) (mm) z. AA controls had a nonsignificantly increased LVMI z and a significantly increased LA(ht) (mm) and RWT z. Being overweight or obese is associated with cardiac sequelae in children to the extent known to be associated with adverse outcomes in adults. Healthy AA children have unique cardiac structural differences.

Establishing best practices and guidance in population modeling: an experience with an internal population pharmacokinetic analysis guidance

This tutorial describes the development of a population pharmacokinetic (Pop PK) analysis guidance within Pfizer, which strives for improved consistency and efficiency, and a more systematic approach to model building. General recommendations from the Pfizer internal guidance and a suggested workflow for Pop PK model building are discussed. A description is also provided for mechanisms by which conflicting opinions were captured and resolved across the organization to arrive at the final guidance.

CPT: Pharmacometrics & Systems Pharmacology (2013) 2, e51; doi:10.1038/psp.2013.26; advance online publication 3 July 2013

Whole-genome sequencing identifies recurrent mutations in hepatocellular carcinoma

Hepatocellular carcinoma (HCC) is one of the most deadly cancers worldwide and has no effective treatment, yet the molecular basis of hepatocarcinogenesis remains largely unknown. Here we report findings from a whole-genome sequencing (WGS) study of 88 matched HCC tumor/normal pairs, 81 of which are Hepatitis B virus (HBV) positive, seeking to identify genetically altered genes and pathways implicated in HBV-associated HCC. We find beta-catenin to be the most frequently mutated oncogene (15.9%) and TP53 the most frequently mutated tumor suppressor (35.2%). The Wnt/beta-catenin and JAK/STAT pathways, altered in 62.5% and 45.5% of cases, respectively, are likely to act as two major oncogenic drivers in HCC. This study also identifies several prevalent and potentially actionable mutations, including activating mutations of Janus kinase 1 (JAK1), in 9.1% of patients and provides a path toward therapeutic intervention of the disease.

Abstract LB-229: Whole genome sequencing reveals genetic landscape of hepatocellular carcinoma

Hepatocellular carcinoma (HCC) is one of the most deadly cancers worldwide and has no effective treatment, yet the molecular basis of hepatocarcinogenesis remains largely unknown. Here we report findings from a whole genome sequencing (WGS) study of 88 matched HCC tumour/normal pairs, 81 of which are HBV positive, seeking to identify genetically altered genes and pathways implicated in HBV-associated HCC. We find β-catenin to be the most frequently mutated oncogene (15.9%) and TP53 the most frequently mutated tumour suppressor (35.2%). The Wnt/β-catenin pathway, altered in 62.5% of cases, is likely to act as the major oncogenic driver in HCC. TP53 alterations appear to cause increased levels of genomic arrangement and chromosomal instability. We identified chromothripsis in 5 HCC genomes (5.7%) recurrently affecting chromosomal arms 1q and 8q. We also identified recurrent HBV integration events at the known and putative cancer-related genes such as TERT, MLL4 and CCNE1, which showed upregulated gene expression in tumour versus normal tissue. The frequently altered genes and pathways in HCC reflect classical cancer hallmarks. This study identified several prevalent and actionable mutations that provide a path towards therapeutic intervention of the disease.

Citation Format: Mao Mao, Hancheng Zheng, Zhengyan Kan, Jiangchun Xu, Xiao Liu, Shuyu Li, Thomas Barber, Zhuolin Gong, Huan Gao, Ke Hao, Melinda Willard, Robert Hauptschein, Paul Rejto, Julio Fernandez, Guan Wang, Qinghui Zhang, Bo Wang, Ronghua Chen, Jian Wang, Nikki Lee, Wei Zhou, Zhao Lin, Zhiyu Peng, Kang Yi, Shengpei Chen, Lin Li, Xiaomei Fan, Jie Yang, Rui Ye, Jia Ju, Kai Wang, Heather Estrella, Shibing Deng, Ping Wei, Ming Qiu, Isabella Wulur, Jiangang Liu, Mariam Ehsani, Chunsheng Zhang, Andrey Loboda, Wing Kin Sung, Amit Aggarwal, Ronnie Poon, Sheung Tat Fan, Jun Wang, James Hardwick, Christoph Reinhard, Hongyue Dai, Yingrui Li, John Luk. Whole genome sequencing reveals genetic landscape of hepatocellular carcinoma. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr LB-229. doi:10.1158/1538-7445.AM2013-LB-229

Concordance of KRAS mutation detection between Illumina next generation gene sequencing (NGS) and CLIA-approved, clinical assays in metastatic colorectal cancer (mCRC)

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Background: It is well known that KRAS mutations limit the efficacy of anti-EGFR therapy in patients with mCRC. Therefore, accurate testing of KRAS is needed to ensure that appropriate patients receive anti-EFGR therapy. Most clinical institutions conduct KRAS testing in CLIA approved labs using standard DNA sequencing methods. The purpose of this study is to correlate KRAS mutation detection by Illumina KRAS gene sequencing to standard KRAS testing performed with CLIA. Methods: We analyzed tumor samples collected from 471 patients between 1998-2010. Patients were chosen randomly based on availability of sufficient tissue for DNA extraction. We performed targeted exome sequencing using an Illumina NGS platform with 50-100X coverage of KRAS. The BWA/GATK pipeline was used to identify variants and indels. Because matched normal samples were not available for comparison to identify somatic mutations, filtering of normal variants was performed using 1000 Genomes. Variants identified in 1000 Genomes with an MAF < 0.01 were filtered. Results: Out of 471 patients, 83 pts had KRAS testing done both by exome sequencing & CLIA approved labs. The concordance rate between the two testing methods was 89%. 39 pts (47%) were KRAS mutation negative (wild type) and 35 pts (46%) harbored KRAS mutation as determined by both methods. Of these, 31 pts had codon 12 mutations and 4 pts had codon 13 mutations. However, 6 pts (7%) were found to have no KRAS mutation using CLIA but were found to have KRAS mutations by NGS (two had A146V mutations, the others had Q61 mutations). In addition, 3 pts (4%) were KRAS mutants using CLIA but wild type by NGS. Thus, 10% of samples tested showed a discrepancy in outcome between the NGS & CLIA testing. Conclusions: Standard DNA sequencing methods (CLIA) was able to identify a majority of the KRAS mutants detected by NGS. However 10% of patients had either false positive or false negative results. The main explanation for this discrepancy is that CLIA approved labs generally only test for codons 12 & 13. The clinical role for NGS in tumor KRAS mutation detection should be further investigated to ensure that patients with mCRC receive appropriate therapy.

In vitro chemosensitivity assay of ascites in epithelial ovarian cancer

OBJECTIVE

This study aimed to investigate the predictive value of 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay for chemosensitivity test in ascites.

MATERIALS AND METHODS

The relationship of the in vitro sensitivity results and the clinicopathological characteristics, objective response rates (ORRs) of chemotherapy, and time to progression (TTP) were retrospectively analyzed in 120 epithelial ovarian cancer (EOC) patients. The clinical response criterion was based on the Response Evaluation Criteria in Solid Tumors (RECIST) standard. The log-rank test and Kaplan-Meier curve were used to estimate TTP.

RESULTS

MTT assays revealed that tumor cells from ascites of primary and type II EOC were more sensitive to paclitaxel (PTX) and carboplatin (CBDCA) than relapse (p = 0.01 and p < 0.01, respectively) and type I (p = 0.03, p = 0.02, respectively) EOC. p53 positive expression and Ki67 high expression were associated with high PTX (p = 0.01 and p < 0.01, respectively) and CBDCA (p = 0.03 and p < 0.01, respectively) sensitivity. Ki67 weak positive immunostaining was associated with topotecan (p < 0.01), gemcitabine (p < 0.01), and doxorubicin (p < 0.01) resistance. Chemosensitivity to CBDCA/PTX was associated with the ORR ofneo-adjuvant (p = 0.03) and adjuvant (p = 0.02) chemotherapy. The MTT assay results of ascites were consistent with the clinical response (p = 0.04) and TTP (p = 0.04) in patients with platinum-resistant relapse EOC tumors.

CONCLUSIONS

Evaluation of the chemosensitivity of ascites in EOC by MTT can aid the establishment of individualized clinical chemotherapeutic plans for platinum-resistant relapse patients.

Integrative analysis of a cross-loci regulation network identifies App as a gene regulating insulin secretion from pancreatic islets

Complex diseases result from molecular changes induced by multiple genetic factors and the environment. To derive a systems view of how genetic loci interact in the context of tissue-specific molecular networks, we constructed an F2 intercross comprised of >500 mice from diabetes-resistant (B6) and diabetes-susceptible (BTBR) mouse strains made genetically obese by the Leptin^ob/ob mutation (Lep^ob). High-density genotypes, diabetes-related clinical traits, and whole-transcriptome expression profiling in five tissues (white adipose, liver, pancreatic islets, hypothalamus, and gastrocnemius muscle) were determined for all mice. We performed an integrative analysis to investigate the inter-relationship among genetic factors, expression traits, and plasma insulin, a hallmark diabetes trait. Among five tissues under study, there are extensive protein–protein interactions between genes responding to different loci in adipose and pancreatic islets that potentially jointly participated in the regulation of plasma insulin. We developed a novel ranking scheme based on cross-loci protein-protein network topology and gene expression to assess each gene's potential to regulate plasma insulin. Unique candidate genes were identified in adipose tissue and islets. In islets, the Alzheimer's gene App was identified as a top candidate regulator. Islets from 17-week-old, but not 10-week-old, App knockout mice showed increased insulin secretion in response to glucose or a membrane-permeant cAMP analog, in agreement with the predictions of the network model. Our result provides a novel hypothesis on the mechanism for the connection between two aging-related diseases: Alzheimer's disease and type 2 diabetes.

Alzheimer's disease and type 2 diabetes are two common aging-related diseases. Numerous studies have shown that the two diseases are associated. However, the mechanisms of such connection are not clear. Both diseases are complex diseases that are induced by multiple genetic factors and the environment. To understand the molecular network regulated by complex genetic factors causing type 2 diabetes, we constructed an F2 intercross comprised of >500 mice from diabetes-resistant and diabetic mouse strains. We measured genotypes, clinical traits, and expression profiling in five tissues for each mouse. We then performed an integrative analysis to investigate the inter-relationship among genetic factors, expression traits, and plasma insulin, a hallmark diabetes trait, and developed a novel method for inferring key regulators for regulating plasma insulin. In islets, the Alzheimer's gene App was identified as a top candidate regulator. Islets from 17-week-old, but not 10-week-old, App knockout mice showed increased insulin secretion in response to glucose, in agreement with the predictions of the network model. Our result provides a novel hypothesis on the mechanism for the connection between two aging-related diseases: Alzheimer's disease and type 2 diabetes.

Genome-wide survey of recurrent HBV integration in hepatocellular carcinoma

To survey hepatitis B virus (HBV) integration in liver cancer genomes, we conducted massively parallel sequencing of 81 HBV-positive and 7 HBV-negative hepatocellular carcinomas (HCCs) and adjacent normal tissues. We found that HBV integration is observed more frequently in the tumors (86.4%) than in adjacent liver tissues (30.7%). Copy-number variations (CNVs) were significantly increased at HBV breakpoint locations where chromosomal instability was likely induced. Approximately 40% of HBV breakpoints within the HBV genome were located within a 1,800-bp region where the viral enhancer, X gene and core gene are located. We also identified recurrent HBV integration events (in ≥ 4 HCCs) that were validated by RNA sequencing (RNA-seq) and Sanger sequencing at the known and putative cancer-related TERT, MLL4 and CCNE1 genes, which showed upregulated gene expression in tumor versus normal tissue. We also report evidence that suggests that the number of HBV integrations is associated with patient survival.