Frequency and spectrum of actionable pathogenic secondary findings in Taiwanese exomes

Background

Exome sequencing has recently become more readily available, and more information about incidental findings has been disclosed. However, data from East Asia are scarce. We studied the application of exome sequencing to the identification of pathogenic/likely pathogenic variants in the ACMG 59 gene list and the frequency of these variants in the Taiwanese population.

Methods

This study screened 161 Taiwanese exomes for variants from the ACMG 59 gene list. The identified variants were reviewed based on information from different databases and the available literature and classified according to the ACMG standard guidelines.

Results

We identified seven pathogenic/likely pathogenic variants in eight individuals, with five participants with autosomal recessive variants in one allele and three participants with autosomal dominant variants. Approximately 1.86% (3/161) of the Taiwanese individuals had a reportable pathogenic/likely pathogenic variant as determined by whole‐exome sequencing (WES), which was comparable to the proportions published previously in other countries. We further investigated the high carrier rate of rare variants in the ATP7B gene, which might indicate a founder effect in our population.

Conclusion

This study was the first to provide Taiwanese population data of incidental findings and emphasized a high carrier rate of candidate pathogenic/likely pathogenic variants in the ATP7B gene.

Intratumoural evolutionary landscape of high-risk prostate cancer: the PROGENY study of genomic and immune parameters

BACKGROUND

Intratumoural heterogeneity (ITH) is well recognised in prostate cancer (PC), but its role in high-risk disease is uncertain. A prospective, single-arm, translational study using targeted multiregion prostate biopsies was carried out to study genomic and T-cell ITH in clinically high-risk PC aiming to identify drivers and potential therapeutic strategies.

PATIENTS AND METHODS

Forty-nine men with elevated prostate-specific antigen and multiparametric-magnetic resonance imaging detected PC underwent image-guided multiregion transperineal biopsy. Seventy-nine tumour regions from 25 patients with PC underwent sequencing, analysis of mutations, copy number and neoepitopes combined with tumour infiltrating T-cell subset quantification.

RESULTS

We demonstrated extensive somatic nucleotide variation and somatic copy number alteration heterogeneity in high-risk PC. Overall, the mutational burden was low (0.93/Megabase), but two patients had hypermutation, with loss of mismatch repair (MMR) proteins, MSH2 and MSH6. Somatic copy number alteration burden was higher in patients with metastatic hormone-naive PC (mHNPC) than in those with high-risk localised PC (hrlPC), independent of Gleason grade. Mutations were rarely ubiquitous and mutational frequencies were similar for mHNPC and hrlPC patients. Enrichment of focal 3q26.2 and 3q21.3, regions containing putative metastasis drivers, was seen in mHNPC patients. We found evidence of parallel evolution with three separate clones containing activating mutations of β-catenin in a single patient. We demonstrated extensive intratumoural and intertumoural T-cell heterogeneity and high inflammatory infiltrate in the MMR-deficient (MMRD) patients and the patient with parallel evolution of β-catenin. Analysis of all patients with activating Wnt/β-catenin mutations demonstrated a low CD8+/FOXP3+ ratio, a potential surrogate marker of immune evasion.

CONCLUSIONS

The PROGENY (PROstate cancer GENomic heterogeneitY) study provides a diagnostic platform suitable for studying tumour ITH. Genetic aberrations in clinically high-risk PC are associated with altered patterns of immune infiltrate in tumours. Activating mutations of Wnt/β-catenin signalling pathway or MMRD could be considered as potential biomarkers for immunomodulation therapies.

CLINICAL TRIALS.GOV IDENTIFIER

NCT02022371.

Regulation of her2/neu gene-expression (review)

Transcriptional regulation of the HER2/neu protooncogene (also known as c-erbB2) has been the topic of many recent reports. The importance of these studies lies in the fact that HER2/neu overexpression occurs in about 30% of breast and ovarian cancers and to varying degrees in other cancers, including gastric, colorectal, lung, salivary, ovarian, bladder, pancreas, endometrial, cervical, oral, and prostate cancers. Furthermore, increased levels of the gene product play an important role during the neoplastic process of certain tumors. This review summarizes the recent work studying the regulation of HER2/neu expression in cells that overexpress the gene and reviews the current knowledge on general regulation of the HER2/neu promoter.

Growth suppression of low HER-2/neu-expressing breast cancer cell line MDA-MB-435 by tyrosine kinase inhibitor emodin

The tyrosine kinase inhibitor emodin (3-methyl-1,6,8-tridroxyanthaquinone) is known to preferentially suppress the growth of the HER-2/neu-overexpressing breast cancer cell line. In this study, emodin effectively suppressed growth of MDA-MB-435, a breast cancer cell line with low HER-2/neu expression. Since emodin is a tyrosine kinase inhibitor, we questioned whether another tyrosine kinase might play a role in the tumorigenicity of MDA-MB-435. By Western blotting with anti-phosphotyrosine antibody, we detected a 72-kDa protein which is uniquely phosphorylated on tyrosine in MDA-MB-435. The level of phosphotyrosine in the 72-kDa protein was significantly reduced by treatment with emodin. This suggests that a strong tyrosine kinase may reside in MDA-MB-435 and the 72-kDa protein serves as a substrate for the tyrosine kinase.

Rodent p53 suppresses the transforming activity of the activated Neu oncogene by modulating the Basal promoter activity of Neu

The rat neu oncogene encodes a dominant transforming oncogene. The mouse wild-type p53 suppresses the transforming activity of the neu oncogene while different p53 mutants demonstrate varying ability to repress neu-induced transformation. Suppression of neu-transforming activity is due to inhibition of transcription. Deletion analysis of the rat neu promoter shows that p53 represses the basal promoter activity of neu. Therefore, rodent p53 suppresses the transforming potential of neu by inhibiting transcription from the basal promoter of neu.

“VISA” Nanoparticles to Breast Cancer

Development of cancer gene therapy has been hampered by the fact that there are no effective cancer-specific expression vectors available, which is critical for improving therapeutic efficacy and reducing toxicity in clinics. To overcome this problem, we recently developed a safe and effective strategy fro targeting a potent pro-apoptotic gene (BikDD) to the pancreatic tumors (Xie et al. Cancer Cell, 2007). A VISA system (VP16-Gal4-WPRE integrated systemic amplifier) was engineered by using the two-step transcriptional amplification (TSTA) system and the posttranscriptional regulatory element of the woodchuck hepatitis virus (WPRE). The VISA system can boost the activity of cancer-specific promoters by an average of 600 folds compared to their basal levels. C-VISA (CCKAR-VISA) nanoparticles transcriptionally targets transgene expression effectively to pancreatic tumors in vivo. C-VISA-BikDD nanoparticles was shown to be highly effective in reducing tumor burden and increasing animal survival rate in orthotopic pancreatic cancer models which is moving into clinical trials at University of Texas M.D. Anderson Cancer Center, USA. In the current study, we identified hTERT(human telomerase reverse transcriptase), ß-cateinin, claudin-4, and FASN (fatty acid synthase) promoters as breast cancer-selective promoters, and amplified their activity to hundreds of folds greater by the “VISA” system without loss of their specificity. We further demonstrated significant antitumor activity of targeted BikDD expression driven by nanoparticles of the hTERT-VISA-BikDD vectors in Her-2-negative and -positive breast cancer cell lines and in multiple breast cancer models of living imaging by the Xenogen IVIS imaging system with limited toxicity. In addition, treatment with hTERT-VISA-BikDD nanoparticles plus lapatinib or produces evident combinational therapeutic efficacy, which is likely due to the ability of lapatinib to promote apoptosis of Her-2-overexpressing breast cancer cells. Thus, our newly developed hTERT-VISA-BikDD nanoparticles are an innovative strategy for targeted antitumor effects of both Her-2-negative and Her-2-positive breast cancer.

Citation Information: Cancer Res 2009;69(24 Suppl):Abstract nr 5159.

Suppression of mesenchymal phenotype in inflammatory breast cancer by EGFR tyrosine kinase inhibitor erlotinib: a novel approach to suppressing metastasis

Abstract #2042

Background: Inflammatory breast cancer (IBC) is a rare subtype well known for its propensity for rapid metastasis. The cause of this rapid metastasis in IBC is unknown. An immunohistochemical analysis of 44 cases of IBC showed HER2 overexpression in 48% of patients and epidermal growth factor receptor (EGFR) overexpression in 30% of patients. EGFR overexpression was the only poor prognostic factor: the 5-year overall survival rate was significantly lower for women with EGFR-positive disease than for women with EGFR-negative disease (P=0.01). HER2 overexpression was not a prognostic factor. The association between EGFR overexpression and increased risk of death indicated that EGFR may represent a potential therapeutic target in IBC. We hypothesized that suppression of the EGFR pathway inhibits proliferation and metastasis of IBC.
 Methods: SUM149 IBC cells, which express low levels of HER2 and high levels of EGFR, were treated with siRNA against EGFR and with the EGFR tyrosine kinase inhibitor erlotinib.
 Results: EGFR siRNA knockdown (but not non-targeting siRNA control) inhibited the proliferation of SUM149 cells. SUM149 cells were sensitive to EGFR tyrosine kinase inhibitor erlotinib in a 2-dimensional (2-D) culture system (median inhibitory concentration [IC50] = 0.90 µM). When we activated ERK by transfecting constitutively active MEK1 in SUM149 cells, the cells showed more resistance to erlotinib. Moreover, ERK siRNA knockdown sensitized SUM149 cells to erlotinib. Further, when we cultured the SUM149 cells in matrigel by using the 3-D culture system (100% matrigel in the bottom layer and cultured medium with 5% FBS and 2% matrigel in the top layer), erlotinib treatment changed the molecular phenotype of SUM149 cells from mesenchymal (a phenotype characterized by low beta-catenin expression and high vimentin and fibronectin expression) to epithelial (recovery of beta-catenin to the sites of cell-cell contacts; downregulation of fibronectin). This reversal of the mesenchymal phenotype, a hallmark of inhibition of epithelial-to-mesenchymal transition (EMT), was ERK dependent. Interestingly, the erlotinib concentration that inhibited the mesenchymal phenotype (0.1 mcM) was one log lower than the concentration that inhibited proliferation (1 mcM).
 Conclusion: Inhibition of tumor growth and EMT in SUM149 IBC cell lines is dependent on the ERK pathway through the EGFR pathway. The erlotinib dose needed to produce an anti-mesenchymal effect is much lower than the cytotoxic dose. Thus, we speculate ERK pathway to be important in inhibiting metastasis in IBC. We are currently investigating the effects of erlotinib in a xenograft model of IBC. Our study provides a rationale for developing novel treatment strategies targeting the EGFR and ERK pathways to inhibit the growth and metastasis of IBC.

Citation Information: Cancer Res 2009;69(2 Suppl):Abstract nr 2042.

Modeling, analysis, and validation of a novel HIV integrase structure provide insights into the binding modes of potent integrase inhibitors

It has been shown that L-731988, a potent integrase inhibitor, targets a conformation of the integrase enzyme formed when complexed to viral DNA, with the 3'-end dinucleotide already cleaved. It has also been shown that diketo acid inhibitors bind to the strand transfer complex of integrase and are competitive with the host target DNA. However, published X-ray structures of HIV integrase do not include the DNA; thus, there is a need to develop a model representing the strand transfer complex. In this study, we have constructed an active-site model of the HIV-1 integrase complexed with viral DNA using the crystal structure of DNA-bound transposase and have identified a binding mode for inhibitors. This proposed binding mechanism for integrase inhibitors involves interaction with a specific Mg(2+) in the active site, accentuated by a hydrophobic interaction in a cavity formed by a flexible loop upon DNA binding. We further validated the integrase active-site model by selectively mutating key residues predicted to play an important role in the binding of inhibitors. Thus, we have a binding model that is applicable to a wide range of potent integrase inhibitors and is consistent with the available resistant mutation data.

Role of mitochondria in neuronal cell death induced by oxidative stress; neuroprotection by Coenzyme Q10

Neuronal cells depend on mitochondrial oxidative phosphorylation for most of their energy needs and therefore are at a particular risk for oxidative stress. Mitochondria play an important role in energy production and oxidative stress-induced apoptosis. In the present study, we have demonstrated that external oxidative stress induces mitochondrial dysfunction leading to increased ROS generation and ultimately apoptotic cell death in neuronal cells. Furthermore, we have investigated the role of Coenzyme Q10 as a neuroprotective agent. Coenzyme Q10 is a component of the mitochondrial respiratory chain and a potent anti-oxidant. Our results indicate that total cellular ROS generation was inhibited by Coenzyme Q10. Further, pre-treatment with Coenzyme Q10 maintained mitochondrial membrane potential during oxidative stress and reduced the amount of mitochondrial ROS generation. Our study suggests that water-soluble Coenzyme Q10 acts by stabilizing the mitochondrial membrane when neuronal cells are subjected to oxidative stress. Therefore, Coenzyme Q10 has the potential to be used as a therapeutic intervention for neurodegenerative diseases.

Oxidative stress-induced apoptosis in dividing fibroblasts involves activation of p38 MAP kinase and over-expression of Bax: resistance of quiescent cells to oxidative stress

Oxidative stress has been postulated to be involved in aging and age-related degenerative diseases. Cell death as a result of oxidative stress plays an important role in the age related diseases. Using human diploid fibroblasts (HDF) as model to study the mechanism of cell death induced by oxidative stress, a condition was standardized to induce apoptosis in the early passage sub-confluent HDFs by a brief exposure of cells to 250 microM hydrogen peroxide. It was observed that p38 MAP kinase (MAPK) was activated soon after the treatment followed by over-expression of Bax protein in cells undergoing apoptosis. An interesting finding of the present study is that the confluent, quiescent HDFs were resistant to cell death under identical condition of oxidative stress. The contact-inhibited quiescent HDFs exhibited increased glutathione level following H(2)O(2)-treatment, did not activate p38 MAP kinase, or over-express Bax, and were resistant to cell death. These findings indicated that there was a correlation between the cell cycle and sensitivity to oxidative stress. This is the first report to our knowledge that describes a relationship between the quiescence state and anti-oxidative defense. Furthermore, our results also suggest that the p38MAPK activation-Bax expression pathway might be involved in apoptosis induced by oxidative stress.

Sequence analysis and expression of a cDNA clone encoding a 98-kDa allergen in Dermatophagoides farinae

BACKGROUND

The important dust mite allergens identified to date are of molecular weights ranging from 14 to 60 kDa. Our previous protein study indicated that the 98-kDa native paramyosin in Dermatophagoides farinae mite showed IgE reactivity with 82% of the mite-sensitive asthmatic patients suggesting that it is a novel major mite allergen. This study described the isolation and characterization of the cDNA clone encoding the 98-kDa mite allergen.

METHODS

A Dermatophagoides farinae cDNA library was constructed in lambda ZAPII vector and the library was immunoscreened with a monoclonal antibody 642. The cDNA insert was sub-cloned into M13 sequencing vector for single-stranded sequencing. The whole cDNA insert was expressed in pGEX-2T Escherichia coli expression system as a fusion protein with GST. The allergenicity of the recombinant peptides was tested by skin tests and IgE immunoassay. The IgE and IgG immunoassays were performed with sera from 20 mite-allergic patients.

RESULTS

The cDNA clone Df642 was 2134 bp long, coding for a polypeptide of 711 amino acid residues. Protein sequence analysis and alignment confirmed that the deduced polypeptide is a mite paramyosin which is truncated slightly at the N- and C-terminuses. In vivo skin tests and in vitro IgE-binding study showed that 62% (13/21) and 50% (10/20) of the mite-sensitive asthmatic patients reacted positively with the recombinant Dermatophagoides farinae paramyosin, respectively.

CONCLUSION

The study indicated that 98-kDa mite paramyosin is an important allergen.

Robustness of group testing in the estimation of proportions

In binomial group testing, unlike one-at-a-time testing, the test unit consists of a group of individuals, and each group is declared to be defective or nondefective. A defective group is one that is presumed to include one or more defective (e.g., infected, positive) individuals and a nondefective group to contain only nondefective individuals. The usual binomial model considers the individuals being grouped as independent and identically distributed Bernoulli random variables. Under the binomial model and presuming that groups are tested and classified without error, it has been shown that, when the proportion of defective individuals is low, group testing is often preferable to individual testing for identifying infected individuals and for estimating proportions of defectives. We discuss the robustness of group testing for estimating proportions when the underlying assumptions of (i) no testing errors and (ii) independent individuals are violated. To evaluate the effect of these model violations, two dilution-effect models and a serial correlation model are considered. Group testing proved to be quite robust to serial correlation. In the presence of a dilution effect, smaller group sizes should be used, but most of the benefits of group testing can still be realized.

Importance of ribosomal frameshifting for human immunodeficiency virus type 1 particle assembly and replication

The recent development and use of protease inhibitors have demonstrated the essential role that combination therapy will play in the treatment of individuals infected with the human immunodeficiency virus type 1 (HIV-1). Past clinical experience suggests that due to the appearance of resistant HIV-1 variants, additional therapeutics will be required in the future. To identify new options for combination therapy, it is of paramount importance to pursue novel targets for drug development. Ribosomal frameshifting is one potential target that has not been fully explored. Data presented here demonstrate that small molecules can stimulate frameshifting, leading to an imbalance in the ratio of Gag to Gag-Pol and inhibiting HIV-1 replication at what appears to be the point of viral particle assembly. Thus, we propose that frameshifting represents a new target for the identification of novel anti-HIV-1 therapeutics.

Effects of estrogen receptor expression on growth and transformation of cells overexpressing neu

The mechanism by which breast cancers progress to hormone independence does not always require the loss of estrogen receptor(ER) expression or function. Cellular alterations that disturb the normal pathway of estrogen-regulated growth may contribute to a state of hormone independence. We and others have described an inverse relationship between estrogen stimulation of ER(+) breast cancer cell lines and their expression of neu. Amplification and overexpression of neu are known to enhance cellular transformation and increase the metastatic potential of cancer cells. Clinically, they are also correlated with more aggressive tumor phenotypes. Therefore, expression of neu may represent a key regulatory point in estrogenic control of cellular growth and transformation. In this communication we demonstrate that the presence of E2/ER can repress transformation of NIH/3T3 cells by the neu oncogene. Furthermore, we have investigated the effects of E2/ER on growth and transformation of an ER(+), neu-overexpressing breast cancer cell line. We report that the presence of E2/ER in these cells leads to repression of the transformed phenotype (as measured by anchorage-independent growth) while stimulating cellular proliferation (in monolayer culture) and propose a model for the role of neu in progression to hormone independence based on these results.

Characterization and localized expression of the laminin binding protein/p40 (LBP/p40) gene during sea urchin development

We have isolated and characterized the expression of a cDNA clone from the sea urchin Strongylocentrotus purpuratus that encodes a protein very similar to LBP/p40, originally identified as a nonintegrin, 67-kDa laminin binding protein. The deduced amino acid sequence of the protein, which we call spLBP/p40, shows significant similarity with the LBP/p40 from other sources, although significant divergence does occur at the carboxyl end. The S. purpuratus mRNA is present as a maternal transcript and its level remains constant until activation of zygotic transcription at the hatching blastula stage, whereupon the total spLBP/p40 increases through the pluteus larval stage. Adult tissues also contain the spLBP/p40 mRNA. Both maternal and zygotic transcripts are translated as determined by their presence in polysomes. Immunoblot analysis using an antibody raised against a recombinant fusion protein indicates that the concentration of the spLBP/p40 protein remains constant during development despite the postblastula increase in mRNA concentration. However, the spatial distribution of the protein changes from a uniform, intracellular distribution in all cells of cleavage and blastula stages to localized, elevated levels in cells of the gut, primary mesenchyme, and oral epithelium of prism larvae. The distribution of spLBP/p40 mRNA at different developmental stages, analyzed by in situ hybridization, reflects that of the protein. Our results argue against a laminin binding function for this protein; instead they place the spLBP/p40 gene in a class of previously described sea urchin genes involved in growth and proliferation.

Suppressed autophosphorylation and tyrosine kinase-activity in revertant cell-lines expressing rat Neu oncogene

The revertants of neu oncogene-transformed cell lines, neu-R1 and neu-R2, have been shown previously to be phenotypically and morphologically nontransformed, yet both expressed the rat neu oncogene. In both cell lines the rat neu lacked significant tyrosine phosphorylation. We show that the intrinsic tyrosine kinase activity of neu-encoded p185 protein of both revertants was suppressed as well, and the p185 neu protein contained extracellular conformational changes that may inhibit receptor activity. Five other revertant cell lines that lost neu upon reversion were transfected with a rat neu oncogenic construct. They remained nontransforned but expressed the oncogene. Like neu-R1 and neu-R2, the transfectants expressed p185 that lacked receptor tyrosine phosphorylation. The inability of neu to induce transformation in these cell lines may be through a common mechanism that suppresses receptor autophosphorylation and tyrosine kinase activity.

Her2 Neu overexpression counteracts the growth effects of C-myc in breast-cancer cells

Amplification and overexpression of the c-myc gene and/or the HER2/neu gene are common events in many human breast cancers. Studying the effects of increasing c-myc expression in breast cancer cell lines, we found that the anchorage-dependent growth rate of cells overexpressing HER2/neu is not affected by increased c-myc expression, whereas enhanced expression of c-myc in cells that do not overexpress HER2/neu can slow that growth rate. Increased c-myc expression did not affect anchorage-independent growth in soft agarose in any of the cells, and it slowed the anchorage-dependent growth of only those cells that do not overexpress HER2/neu, suggesting that HER2/neu overexpression may counteract the anchorage-dependent growth inhibition mediated by c-myc.

The microfocus assay system (mfas) - a simple quantitative assay to identify inhibitory drugs targeted against specific oncogenes

We have developed an assay, the microfocus assay system (MFAS), that enables the quantitative assessment of anticancer drugs and their ability to specifically target and inhibit cellular oncogenes. Analysis of three chemotherapeutic reagents showed a differential negative effect against the ability of transformed cells containing either the oncogenic rat neu, human H-ras, or v-mos oncogene to form transformed foci on a background of normal fibroblasts. Though these drugs have not been examined previously for targeting against specific oncogenes, our results with the MFAS indicate preferential inhibitory effects against cells transformed with different oncogenes. Therefore, the MFAS should enable the large scale screening of anti-cancer drugs specifically targeted against known oncogenes and provide a quantitative measurement of their effectiveness.