A telomere-targeting drug depletes cancer initiating cells and promotes anti-tumor immunity in small cell lung cancer

There are few effective treatments for small cell lung cancer (SCLC) underscoring the need for innovative therapeutic approaches. This study focuses on exploiting telomerase, a critical SCLC dependency as a therapeutic target. A prominent characteristic of SCLC is their reliance on telomerase activity, a key enzyme essential for their continuous proliferation. Here we utilize a nucleoside analog, 6-Thio-2'-deoxyguanosine (6TdG) currently in phase II clinical trials, that is preferentially incorporated by telomerase into telomeres leading to telomere dysfunction. Using preclinical mouse and human derived models we find low intermittent doses of 6TdG inhibit tumor growth and reduce metastatic burden. Anti-tumor efficacy correlates with a reduction in a subpopulation of cancer initiating like cells (CICs) identified by their expression of L1CAM/CD133 and highest telomerase activity. 6TdG treatment also leads to activation of innate and adaptive anti-tumor responses. Mechanistically, 6TdG depletes CICs and induces type-I interferon signaling leading to tumor immune visibility by activating tumor cell STING signaling. We also observe increased sensitivity to irradiation after 6TdG treatment in both syngeneic and humanized SCLC xenograft models both of which are dependent on the presence of host immune cells. This study underscores the immune-enhancing and metastasis-reducing effects of 6TdG, employing a range of complementary in vitro and in vivo SCLC preclinical models providing a potential therapeutic approach to SCLC.

Inhibition of Karyopherin β1-Mediated Nuclear Import Disrupts Oncogenic Lineage-Defining Transcription Factor Activity in Small Cell Lung Cancer

Genomic studies support the classification of small cell lung cancer (SCLC) into subtypes based on the expression of lineage-defining transcription factors ASCL1 and NEUROD1, which together are expressed in ∼86% of SCLC. ASCL1 and NEUROD1 activate SCLC oncogene expression, drive distinct transcriptional programs, and maintain the in vitro growth and oncogenic properties of ASCL1 or NEUROD1-expressing SCLC. ASCL1 is also required for tumor formation in SCLC mouse models. A strategy to inhibit the activity of these oncogenic drivers may therefore provide both a targeted therapy for the predominant SCLC subtypes and a tool to investigate the underlying lineage plasticity of established SCLC tumors. However, there are no known agents that inhibit ASCL1 or NEUROD1 function. In this study, we identify a novel strategy to pharmacologically target ASCL1 and NEUROD1 activity in SCLC by exploiting the nuclear localization required for the function of these transcription factors. Karyopherin β1 (KPNB1) was identified as a nuclear import receptor for both ASCL1 and NEUROD1 in SCLC, and inhibition of KPNB1 led to impaired ASCL1 and NEUROD1 nuclear accumulation and transcriptional activity. Pharmacologic targeting of KPNB1 preferentially disrupted the growth of ASCL1+ and NEUROD1+ SCLC cells in vitro and suppressed ASCL1+ tumor growth in vivo, an effect mediated by a combination of impaired ASCL1 downstream target expression, cell-cycle activity, and proteostasis. These findings broaden the support for targeting nuclear transport as an anticancer therapeutic strategy and have implications for targeting lineage-transcription factors in tumors beyond SCLC.

SIGNIFICANCE

The identification of KPNB1 as a nuclear import receptor for lineage-defining transcription factors in SCLC reveals a viable therapeutic strategy for cancer treatment.

Cell-autonomous immune gene expression is repressed in pulmonary neuroendocrine cells and small cell lung cancer

Small cell lung cancer (SCLC) is classified as a high-grade neuroendocrine (NE) tumor, but a subset of SCLC has been termed “variant” due to the loss of NE characteristics. In this study, we computed NE scores for patient-derived SCLC cell lines and xenografts, as well as human tumors. We aligned NE properties with transcription factor-defined molecular subtypes. Then we investigated the different immune phenotypes associated with high and low NE scores. We found repression of immune response genes as a shared feature between classic SCLC and pulmonary neuroendocrine cells of the healthy lung. With loss of NE fate, variant SCLC tumors regain cell-autonomous immune gene expression and exhibit higher tumor-immune interactions. Pan-cancer analysis revealed this NE lineage-specific immune phenotype in other cancers. Additionally, we observed MHC I re-expression in SCLC upon development of chemoresistance. These findings may help guide the design of treatment regimens in SCLC.

Ling Cai et al. used transcriptomic profiling data of healthy lung, patient-derived small cell lung cancer cell lines, xenografts, and primary tumors to examine a link between neuroendocrine (NE) signatures and immune gene expression. Their findings suggest that cell-autonomous immune gene repression is a shared feature between healthy and tumor cells of NE lineage and may influence tumor-immune cell interaction and response to immunotherapy.

Abstract 2664: Identification of two small molecules with small cell lung cancer growth inhibition response profiles different from etoposide/topotecan

Small Cell Lung Cancer (SCLC) is an aggressive, highly metastatic cancer with an overall 5-year survival rate of <5% whose treatment has not changed in the past 20 years and has been designated by the US Congress and the National Cancer Institute as a “recalcitrant cancer.” SCLCs are characterized by high initial response rates to chemotherapy (platin + etoposide) and radiation therapy but relapse is almost universal within 1 year. A NCI screen of 526 clinical or clinical investigational agents in 63 SCLC lines found large response phenotype differences (Polley, JNCI (2016) 108(10): djw122) but, in general, SCLC lines were either “sensitive” or “resistant” to all drugs tested and there was no correlation with tumor molecular biomarkers, or prior chemotherapy treatment. Thus, new drugs are needed (preferably with tumor associated molecular biomarkers) that have different profiles than available agents. As part of an NCI Cancer Treatment Discovery and Development Network (CTD2N) consortium we have screened large chemical libraries and identified chemical compounds that kill subsets of non-small cell lung cancers (NSCLCs) but not normal lung epithelial cells thus displaying a “therapeutic window” and tumor specificity. We first tested 116 of these compounds against 4 SCLC lines and found 30 that displayed dose dependent SCLC toxicity. We have so far tested 2 (SW034510, SW140154) compounds against a panel of 22 SCLC lines, which were also in the NCI screen, along with etoposide and topotecan as comparators, using 8-point dose response curves, for effect on SCLC growth inhibition. The SCLC lines (all with p53 and Rb mutations) were also phenotyped for expression of Myc family members (c-, N-, and L-), lineage transcription factors ASCL1 and NeuroD1 and neuroendocrine mRNAs. As found by Polley et al, etoposide and topotecan response phenotypes were correlated with each other (r2 = 0.7). By contrast, our two compounds, SW034510 and SW140154, response phenotypes did not correlate with etoposide/topotecan (r2 values of <0.08, and 0.1 respectively) and did not correlate with each other. Both agents cause cell death as assessed by the CellTox Green Assay suggesting efficacy across the ASCL1/NeuroD1, Myc family expression profiles. Cleaved caspase-3 western blot shows SW034510 causes caspase induced apoptosis. Cell cycle analysis suggests SW140154 causes a G1 cell cycle arrest. SARM1 gene expression anti-correlates with SW140154 IC50s. In conclusion, starting with chemical compounds that have selectivity for NSCLC, we have identified two new chemical compounds with specificity for subsets of NSCLC over normal lung epithelial cells, and which also inhibit the growth/kill subsets of SCLC in patterns different from the established therapy. Thus, these two new compounds provide potentially new therapeutic opportunities for SCLC patients resistant to current chemotherapies.

Citation Format: Allison A. Mootz, Michael Peyton, Paul Yenerall, Kimberley Avila, Kenneth Huffman, Tomohiro Haruki, Mahboubeh Papari-Zareei, Victor Stastny, Luc Girard, Elizabeth McMillan, Michael Roth, John MacMillan, Bruce Posner, Michael White, Gazdar Adi, John Minna. Identification of two small molecules with small cell lung cancer growth inhibition response profiles different from etoposide/topotecan [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2664.

Small cell lung cancer tumors and preclinical models display heterogeneity of neuroendocrine phenotypes

Background

Small cell lung cancer (SCLC) is a deadly, high grade neuroendocrine (NE) tumor without recognized morphologic heterogeneity. However, over 30 years ago we described a SCLC subtype with "variant" morphology which did not express some NE markers and exhibited more aggressive growth.

Methods

To quantitate NE properties of SCLCs, we developed a 50-gene expression-based NE score that could be applied to human SCLC tumors and cell lines, and genetically engineered mouse (GEM) models. We identified high and low NE subtypes of SCLC in all of our sample types, and characterized their properties.

Results

We found that 16% of human SCLC tumors and 10% of SCLC cell lines were of the low NE subtype, as well as cell lines from the GEM model. High NE SCLC lines grew as non-adherent floating aggregates or spheroids while Low NE lines had morphologic features of the variant subtype and grew as loosely attached cells. While the high NE subtype expressed one of the NE lineage master transcription factors ASCL1 or NEUROD1, together with NKX2-1, the entire range of NE markers, and lacked expression of the neuronal and NE repressor REST, the low NE subtype had lost expression of most NE markers, ASCL1, NEUROD1 and NKX2-1 and expressed REST. The low NE subtype had undergone epithelial mesenchymal transition (EMT) and had activated the Notch, Hippo and TGFβ pathways and MYC oncogene . Importantly, the high and low NE group of SCLC lines had similar gene expression profiles as their SCLC tumor counterparts.

Conclusions

SCLC tumors and cell lines can exhibit distinct inter-tumor heterogeneity with respect to expression of NE features. Loss of NE expression results in major alterations in morphology, growth characteristics, and molecular properties. These findings have major clinical implications as the two subtypes are predicted to have very different responses to targeted therapies.

A comprehensively characterized cell line panel highly representative of clinical ovarian high-grade serous carcinomas

Recent literature suggests that most widely used ovarian cancer (OVCA) cell models do not recapitulate the molecular features of clinical tumors. To address this limitation, we generated 18 cell lines and 3 corresponding patient-derived xenografts predominantly from high-grade serous carcinoma (HGSOC) peritoneal effusions. Comprehensive genomic characterization and comparison of each model to its parental tumor demonstrated a high degree of molecular similarity. Our characterization included whole exome-sequencing and copy number profiling for cell lines, xenografts, and matched non-malignant tissues, and DNA methylation, gene expression, and spectral karyotyping for a subset of specimens. Compared to the Cancer Genome Atlas (TCGA), our models more closely resembled HGSOC than any other tumor type, justifying their validity as OVCA models. Our meticulously characterized models provide a crucial resource for the OVCA research community that will advance translational findings and ultimately lead to clinical applications.

Validation of SCT Methylation as a Hallmark Biomarker for Lung Cancers

INTRODUCTION

The human secretin gene (SCT) encodes secretin, a hormone with limited tissue distribution. Analysis of the 450k methylation array data in The Cancer Genome Atlas (TCGA) indicated that the SCT promoter region is differentially hypermethylated in lung cancer. Our purpose was to validate SCT methylation as a potential biomarker for lung cancer.

METHODS

We analyzed data from TCGA and developed and applied SCT-specific bisulfite DNA sequencing and quantitative methylation-specific polymerase chain reaction assays.

RESULTS

The analyses of TCGA 450K data for 801 samples showed that SCT hypermethylation has an area under the curve (AUC) value greater than 0.98 that can be used to distinguish lung adenocarcinomas or squamous cell carcinomas from nonmalignant lung tissue. Bisulfite sequencing of lung cancer cell lines and normal blood cells allowed us to confirm that SCT methylation is highly discriminative. By applying a quantitative methylation-specific polymerase chain reaction assay, we found that SCT hypermethylation is frequently detected in all major subtypes of malignant non-small cell lung cancer (AUC = 0.92, n = 108) and small cell lung cancer (AUC = 0.93, n = 40) but is less frequent in lung carcinoids (AUC = 0.54, n = 20). SCT hypermethylation appeared in samples of lung carcinoma in situ during multistage pathogenesis and increased in invasive samples. Further analyses of TCGA 450k data showed that SCT hypermethylation is highly discriminative in most other types of malignant tumors but less frequent in low-grade malignant tumors. The only normal tissue with a high level of methylation was the placenta.

CONCLUSIONS

Our findings demonstrated that SCT methylation is a highly discriminative biomarker for lung and other malignant tumors, is less frequent in low-grade malignant tumors (including lung carcinoids), and appears at the carcinoma in situ stage.

Abstract 225: Assessing and enriching human tumor cell content in patient-derived cancer xenografts and co-cultures

Purpose: To develop a robust real-time PCR-based assay with improved accuracy for quantifying the relative fractions of human and mouse DNA in heterogeneous samples such as patient-derived cancer xenografts or cultures. Background: Patient derived mouse xenografts (PDXs), or irradiated mouse fibroblast conditionally reprogrammed cancer cultures (CRCs) provide valuable resources for studying cancers, but as mouse tissue in heterogeneous samples can significantly confound downstream functional and molecular assays (such as next-generation sequencing) it is important to determine the fraction of mouse DNA in mixed samples. Methods: Using an approach different from a previously reported PCR assay (Alcoser SY et al BMC Biotech 2011, 11:124), we established a Taqman real-time PCR assay employing mouse- and human-specific primers that amplified the same chromosomal region of PTGER2 on human chromosome 14q22.1 and mouse chromosome 14 22.68 cM. We also developed a method to enrich human tumor cells from PDXs using enzymatic digestion with Liberase (Roche), followed by differential centrifugation and adherence. Results: Utilizing serial dilutions of heterogeneous DNA mixtures of mouse spleen DNA and normal human white blood cell DNA at varied DNA ratios we demonstrated the assay to be linear (Pearson r = 0.9984, human DNA; r = 0.9998, mouse DNA; p<0.0001) and sensitive (>6.4 pg DNA/reaction). The assay was evaluated in 66 samples of human tumors (lung, ovary, neuroblastoma, colon, pancreas, stomach and melanoma) including 25 PDXs before and after tumor cell enrichment, 12 non-enriched PDXs, 2 CRC-derived xenografts and 2 CRCs. Of the PDXs 28 were subcutaneous tumors and 9 were malignant ascites. A wide range of human:mouse DNA ratios were found from zero to 99% among all samples, with two PDXs and 2 CRC-derived xenografts lacking detectable human DNA. The highest human cell fractions were in the malignant ascites samples. Of the enriched samples, 18 of 25 (72%) showed tumor cell enrichment of 2 to 71-fold as compared with the value of matching non-enriched PDX. Conclusions: We developed a robust real-time PCR assay for measuring the relative fraction of species-specific DNA in human:mouse heterogenous samples. The human:mouse DNA ratios in PDX samples varied widely and the human tumor cell populations in PDXs can be effectively enriched in vitro. Assessing human tumor cell content with this assay will facilitate molecular studies with PDXs and mouse-human cocultivated cells.

Citation Format: Yu-An Zhang, Victor Stastny, Mahboubeh Papari-Zareei, Heather Davidson, Boning Gao, Brenda Timmons, Jingsheng Yan, C Patrick Reynolds, John D. Minna, Adi F. Gazdar. Assessing and enriching human tumor cell content in patient-derived cancer xenografts and co-cultures. [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 225. doi:10.1158/1538-7445.AM2015-225

Abstract 5605: Spectral karyotyping characterization of ovarian adenocarcinomas and corresponding cell lines and xenografts

Ovarian cancer is the 9th leading cancer and the 5th cause of cancer deaths in women in the USA. To understand tumor biology, identify oncogenic driver pathways and verify response to drugs, numerous in vitro (cell lines) and in vivo (xenograft in mouse) models have been developed and extensively used. In this study, we aimed to cytogenetically characterize ovarian carcinomas and their respective in vitro and in vivo models to investigate how representative the models are of their originating source.

Ascitic fluid was collected from 10 women with previously untreated high grade serous papillary adenocarcinomas of the ovary that presented with malignant ascites (stage 3). Ascitic fluid was subjected to differential centrifugation and plating to enrich for the tumor cell population (TCP). The TCP cells were cultured and considered permanent cell lines (CLP) when grew continuously without evidence of a non-malignant component and could be recovered from cryopreservation. TCP cells were also inoculated intraperitoneally into athymic nude mice and tumors harvested and cryopreserved (XCP). Eight pairs of TCP and CLP and two triplets of TCP, CLP and XCP specimens were characterized by spectral karyotyping (SKY), for a total of 22 specimens.

Highly rearranged karyotypes were detected in all specimens. All matched pairs and triplets were obviously related, sharing most of the structural (SA) and numerical (NA) abnormalities identified. Numerous examples of evolution from simple to complex chromosomal rearrangements and of multiple rearrangements originating from a single breakpoint were detected. For 9 patients, TCP and CLP specimens had the same ploidy level (near-2n in 4, near-3n in 3 and near 4n in 2); for one patient, the ploidy changed from near-2n (TCP) to near-4n (CLP). The 2 xenografts had same ploidy as their matched TCP and CLP specimens. In individual analyses, specific SA accounted for <10% of total SA in 8 specimens, for 10-30% in 8 and for >30% in 6. Specific NA accounted for <10% of total NA in 13 specimens, for 10-30% in 6 and for >30% in 3. In the TCP-CLP analyses, 3 pairs were very similar, differing by <10% of specific abnormalities; 5 pairs differed by 10-30% and 2 pairs by >30%. Higher frequency of abnormalities was detected in the TCP specimen for 4 pairs, and in the CLP for 3 pairs. One xenograft was very similar to both TCP and CLP, while the other was closer to the CLP.

In conclusion, the ovarian adenocarcinomas were highly rearranged chromosomally and highly heterogeneous. In vitro (CLP) and in vivo (XCP) models maintained a core of the TCP's SA and NA but also displayed unique events, quantitatively and qualitatively variable in distinct tumors, indicating evidence of ex vivo tumor cell selection or progression events. These findings have implications for using established tumor models in research, as well as for potentially identifying the driver rearrangements in specific tumors.

Citation Format: Marileila Varella-Garcia, Isabel M. Bernal, Sakshi Mahale, Evelyn M. Musselwhite, Victor Stastny, Mahboubeh Papari-Zareei, Jayanthi Lea, Tito Woodburn, Patrick Reynolds, Adi F. Gazdar. Spectral karyotyping characterization of ovarian adenocarcinomas and corresponding cell lines and xenografts. [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 5605. doi:10.1158/1538-7445.AM2014-5605

Methylation analysis in spontaneous sputum for lung cancer diagnosis

OBJECTIVES

Lung cancer is the most fatal cancer in the developed world due to presence of metastases at time of diagnosis. The aim of this study is to examine DNA hypermethylation in sputum compared to sputum cytology for the diagnosis of lung cancer. A novel risk analysis is introduced, using the distinction between diagnostic and risk markers.

METHODS

Two independent sets were randomly composed from a prospectively collected sputum bank (Set 1: n = 98 lung cancer patients, n = 90 controls; Set 2: n = 60 lung cancer patients, n = 445 controls). Sputum cytology was performed for all samples. The following DNA hypermethylation markers were tested in both sets: RASSF1A, APC and cytoglobin (CYGB). Two statistical analyses were conducted: multivariate logistic regression and a risk classification model based on post-test probabilities.

RESULTS

In multivariate analysis, RASSF1A was the best of the three markers in discriminating lung cancer cases from controls in both sets (sensitivity 41-52%, specificity 94-96%). The risk model showed that 36% of lung cancer patients were defined as "high risk" (≥ 60% chance on lung cancer) based on RASSF1A hypermethylation in Set 1. The model was reproducible in Set 2. Risk markers (APC, CYGB) have less diagnostic value. Sensitivity of cytology for lung cancer diagnosis was 22%. RASSF1A hypermethylation yielded a sensitivity of 45%. The combined sensitivity for RASSF1A with cytological diagnosis increased to 52% with similar specificity (94%).

CONCLUSION

In a diagnostic setting, hypermethylation analysis in sputum is possible when a diagnostic marker is used. However, risk markers are insufficient for this purpose.

Abstract LB-146: A study of p16 inactivation in lung cancer cell lines and tumor samples with a meta-analysis of the literature

Introduction: p16 inactivation is a common genetic alteration in lung adenocarcinoma and is often inactivated by homozygous deletion (HD) or methylation of promoter, or rarely by point mutation. While p16 methylation was reported to be linked to KRAS mutation and smoking, the association between specific p16 inactivation mechanism and other common genetic changes and smoking status remains controversial. In this study, we examined all of the three p16 inactivation mechanisms and correlated them with other common genetic chanes in lung adenocarcinoma: EGFR, KRAS, and LKB1, and smoking status. We also performed a meta-analysis to study the effect of smoking on p16 inactivation. Methods: We examined 40 cell lines and 45 tumor samples from patients with primary NSCLC, mostly adenocarcinoma. SNP and qPCR were used to detect HD. Methylation was determined by MSP analysis and mutation was identified by sequencing. We performed the meta-analysis by using Woolf's test to identify heterogeneity and followed by using a random-effect model. Results: The cell lines and tumor samples demonstrated similar results. No statistical differences were found between the two groups and the data were hence combined for analysis. p16 inactivation occurred at similar frequencies (54-57%) regardless of mutational status of EGFR, KRAS and LKB1 but the major mechanism of inactivation varied. Multivariate analysis showed that LKB1 inactivation was associated with p16 HD; p16 methylation was linked to KRAS mutation but was mutually exclusive with EGFR mutation. No significant association was established between any p16 inactivation mechanism and smoking status based on our data. HD was found to be the major mechanism of p16 inactivation among both smokers and never smokers although the rate of p16 methylation was higher in smokers. The result of our meta-analysis showed that p16 methylation was associated with smoking. The results from the literature were homogenous and the overall odds ratio from the meta-analysis was 2.01, which is significant at 0.05 level. Conclusions: p16 inactivation is a common event in lung adenocarcinoma and the inactivation mechanism of p16 is associated with other genetic changes and smoking status. Meta-analysis confirmed the association between p16 methylation and smoking. Our results indicate the presence of different pathways via p16 inactivation in the development of lung adenocarcinoma.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr LB-146. doi:1538-7445.AM2012-LB-146

Frequent detection of infectious xenotropic murine leukemia virus (XMLV) in human cultures established from mouse xenografts

PURPOSE

To investigate the frequency of xenotropic murine leukemia virus (MLV) presence in human cell lines established from mouse xenografts and to search for the evidence of horizontal viral spread to other cell lines.

RESULTS

Six of 23 (26%) mouse DNA free xenograft cultures were strongly positive for MLV and their sequences had greater than 99% homology to known MLV strains. Four of five available supernatant fluids from these viral positive cultures were strongly positive for RT activity. Three of these supernatant fluids were studied to confirm the infectivity of the released virions for other human culture cells. Of the 78 non-xenograft derived cell lines maintained in the xenograft culture-containing facilities, 13 (17%) were positive for MLV, including XMRV, a virus strain first identified in human tissues. By contrast, all 50 cultures maintained in a xenograft culture-free facility were negative for viral sequences.

METHODOLOGY

We examined xenograft tumor cell lines from seven independent laboratories and 128 non-xenografted tumor cell lines. Cell line DNA was examined for mouse DNA contamination, and by 3 Taqman qPCR assays targeting the gag, env or pol regions of MLV. Sequencing was used for viral strain identification. Supernatant fluids were tested for reverse transcriptase (RT) activity.

CONCLUSIONS

Human cultures derived after mouse xenografting frequently contain and release highly infectious xenotropic MLV viruses. Laboratories working with xenograft-derived human cultures should be aware of the risk of contamination with potentially biohazardous human-tropic mouse viruses and their horizontal spread to other cultures.

Abstract 4292: Frequent detection of xenotropic murine leukemia virus (XMLV) strains including XMRV in human cultures established from mouse xenografts

Purpose: To investigate the frequency of XMLV in human cell lines from xenografts and for evidence of horizontal spread to other cell lines. Background: The mouse genome contains multiple integrated copies of type C murine leukemia viruses including xenotropic strains (XMLV) capable of growth in human and other foreign species. XMLV has been detected in sporadic human cultures established after murine xenografting. Sequences, usually partial, of a XMLV related virus (XMRV) have been reported in prostate cancer and the chronic fatigue syndrome. Methodology: We examined 27 human cell lines established after murine xenografting in six independent laboratories. We also examined an additional 127 non-xenografted cell lines maintained in the same cell culture facilities. Cell line DNA was examined for presence of a human and mouse housekeeping gene, and by three Taqman qPCR assays targeting the gag, pol or env regions of MLV including specificity to XMRV, most MLV or all known XMLV strains, respectively. For virus positive samples we performed additional sequencing for strain identification and tested supernatant fluids for reverse transcriptase activity. Results: Three of the 27 cell lines from xenografts were found to contain mouse DNA and were excluded from further study. Seven of the remaining 24 cultures (29%) were strongly positive by either two or all three viral probes. At least five strains of XMLV were identified and some cultures contained multiple strains. These strains included XMRV and the N417 strain we originally identified from a small cell lung cancer xenograft-derived culture. Of six available supernantant fluids from viral positive cultures, five were strongly positive for reverse transcriptase activity, indicating release of potentially infectious viral particles (estimated range of 2.9×102 to 8.2×105 vp/ul). Of the 127 non-xenograft derived cell lines maintained in the cell culture facilities, 12 (9.5%) were also positive by at least two viral probes and all four corresponding supernatant fluids tested were positive for reverse transcriptase activity. Conclusions: Human cell lines derived after murine xenografting frequently contain full length sequences of several XMLV strains including XMRV. Infected cultures release large numbers of potentially infectious virus particles. Other human cell lines maintained in the same facility are at risk of cross contamination. The data also suggest that XMRV is, in all probability, a stain of XMLV present in the mouse genome. Laboratories working with xenograft-derived human cultures should be aware of the risk of contamination with a human tropic murine virus of unknown biological significance and of the possibility of horizontal spread to other cultures.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 4292. doi:10.1158/1538-7445.AM2011-4292

Cytoglobin, the newest member of the globin family, functions as a tumor suppressor gene

Cytoglobin (CYGB) is a recently discovered vertebrate globin distantly related to myoglobin with unknown function. CYGB is assigned to chromosomal region 17q25, which is frequently lost in multiple malignancies. Previous studies failed to detect evidence for mutations in the CYGB gene. Recent studies provided preliminary evidence for increased methylation of the gene in lung cancer. Our study was aimed at investigating the role of CYGB as a tumor suppressor gene. By nested methylation-specific DNA sequencing analysis of lung and breast cancer cell lines and bronchial and mammary epithelial cell lines, we identified that methylation of a 110-bp CpG-rich segment of the CYGB promoter was correlated with gene silencing. We specifically targeted this sequence and developed a quantitative methylation-specific PCR assay, suitable for high-throughput analysis. We showed that the tumor specificity of CYGB methylation in discriminating patients with and without lung cancer, using biopsies and sputum samples. We further showed the tumor specificity of this assay with multiple other epithelial and hematologic malignancies. To show tumor suppressor activity of CYGB, we performed the following: (a) RNA interference-mediated knockdown of CYGB gene on colony formation in a CYGB expression-positive lung cancer cell line, resulting in increased colony formation; (b) enforced gene expression in CYGB expression-negative lung and breast cancer cell lines, reducing colony formation; and (c) identification of potential proximate targets down-stream of the CYGB genes. Our data constitute the first direct functional evidence for CYGB, the newest member of the globin family, as a tumor suppressor gene.

Differential methylation of a short CpG-rich sequence within exon 1 of TCF21 gene: a promising cancer biomarker assay

Detection of cancer cells at early stages could potentially increase survival rates in cancer patients. Aberrant promoter hypermethylation is a major mechanism for silencing tumor suppressor genes in many kinds of human cancers. A recent report from our laboratory described the use of quantitative methylation-specific PCR assays for discriminating patients with lung cancer from those without lung cancer using lung biopsies as well as sputum samples. TCF21 is known to be essential for differentiation of epithelial cells adjacent to mesenchyme. Using restriction landmark genomic scanning, a recent study identified TCF21 as candidate tumor suppressor at 6q23-q24 that is epigenetically inactivated in lung and head and neck cancers. Using DNA sequencing technique, we narrowed down a short CpG-rich segment (eight specific CpG sites in the CpG island within exon 1) of the TCF21 gene, which was unmethylated in normal lung epithelial cells but predominantly methylated in lung cancer cell lines. We specifically targeted this short CpG-rich sequence and developed a quantitative methylation-specific PCR assay suitable for high-throughput analysis. We showed the usefulness of this assay in discriminating patients with lung cancer from those without lung cancer using biopsies and sputum samples. We further showed similar applications with multiple other malignancies. Our assay might have important implications in early detection and surveillance of multiple malignancies.

Evaluation of candidate methylation markers to detect cervical neoplasia

OBJECTIVE

Studies of cervical cancer and its immediate precursor, cervical intraepithelial neoplasia 3 (CIN3), have identified genes that often show aberrant DNA methylation and therefore represent candidate early detection markers. We used quantitative PCR assays to evaluate methylation in five candidate genes (TNFRSF10C, DAPK1, SOCS3, HS3ST2 and CDH1) previously demonstrated as methylated in cervical cancer.

METHODS

In this analysis, we performed methylation assays for the five candidate genes in 45 invasive cervical cancers, 12 histologically normal cervical specimens, and 23 liquid-based cervical cytology specimens confirmed by expert review as unequivocal demonstrating cytologic high-grade squamous intraepithelial lesions, thus representing the counterparts of histologic CIN3.

RESULTS

We found hypermethylation of HS3ST2 in 93% of cancer tissues and 70% of cytology specimens interpreted as CIN3; hypermethylation of CDH1 was found in 89% of cancers and 26% of CIN3 cytology specimens. Methylation of either HS3ST2 or CDH1 was observed in 100% of cervical cancer tissues and 83% of CIN3 cytology specimens. None of the five genes showed detectable methylation in normal cervical tissues.

CONCLUSION

Our data support further evaluation of HS3ST2 and CDH1 methylation as potential markers of cervical cancer and its precursor lesions.

Application of a methylation gene panel by quantitative PCR for lung cancers

Detection of lung cancer at early stages could potentially increase survival rates. One promising approach is the application of suitable lung cancer-specific biomarkers to specimens obtained by non-invasive methods. Thus far, clinically useful biomarkers that have high sensitivity have proven elusive. Certain genes, which are involved in cellular pathways such as signal transduction, apoptosis, cell to cell communication, cell cycles and cytokine signaling are down-regulated in cancers and may be considered as potential tumor suppressor genes. Aberrant promoter hypermethylation is a major mechanism for silencing tumor suppressor genes in many kinds of human cancers. Using quantitative real time PCR, we tested 11 genes (3-OST-2, RASSF1A, DcR1, DcR2, P16, DAPK, APC, ECAD, HCAD, SOCS1, SOCS3) for levels of methylation within their promoter sequences in non-small cell lung cancers (NSCLC), adjacent non-malignant lung tissues, in peripheral blood mononuclear cells (PBMC) from cancer free patients, in sputum of cancer patients and controls. Of all the 11 genes tested 3-OST-2 showed the highest levels of promoter methylation in tumors combined with lowest levels of promoter methylation in control tissues. 3-OST-2 followed by, RASSF1A showed increased levels of methylation with advanced tumor stage (P<0.05). Thus, quantitative analysis of 3-OST-2 and RASSF1A methylation appears to be a promising biomarker assay for NSCLC and should be further explored in a clinical study. Our preliminary data on the analysis of sputum DNA specimens from cancer patients further support these observations.

Sun exposure related methylation in malignant and non-malignant skin lesions

We investigated the aberrant promoter methylation status of 12 genes in skin lesions, both malignant (basal cell carcinomas (BCCs), n=68 and squamous cell carcinomas (SCCs), n=35) and non-malignant (tags, n=58) skin lesions and compared the results of lesions from sun exposed (SE) and sun protected (SP) regions. Methylation was studied using a methylation specific PCR (MSP) and methylation of CDH1 was also measured using a semi-quantitative fluorescence based real-time MSP method. The methylation index (MI) was calculated as the methylated fraction of the genes examined. In this report, we found high frequencies of methylation of several known or suspected tumor suppressor genes in tags and skin cancers. Among the 12 genes, for the cadherin genes CDH1 and CDH3 and for two of the laminin 5 encoding genes LAMA3 and LAMC2 methylation frequencies greater than 30% were noted in one or more specimen types. We investigated whether methylation was tumor related. Surprisingly, the differences in the methylation profile of genes among the three specimen types were modest, and the MI, indicators of overall methylation frequencies, was nearly identical. However, significant differences were noted in the frequencies of methylation among the three specimen types for the genes RASSF1A (P=0.002), CDH1 (P=0.007) and one or more of three CAD genes (P=0.02). Methylation was highly significantly related to sun exposure, and sun protected specimens had little or no methylation. As methylation of CDH1 was completely SE specific we analyzed all the skin samples using a semi-quantitative real-time PCR assay for the CDH1 gene. The concordance between standard MSP and real-time MSP for all the samples (n=161) was 75% (P<0.0001). While weak signals were detected in the SP samples by real time PCR, the differences between SE and SP specimens were 148 fold for tags and 390 fold for BCCs. These differences were highly significant (P<0.0001). These findings suggest that methylation commences in UV exposed skin at a relatively early age and occurs in skin prior to the onset of recognizable preneoplastic changes.

Genomic alterations in cultured human embryonic stem cells

Cultured human embryonic stem cell (hESC) lines are an invaluable resource because they provide a uniform and stable genetic system for functional analyses and therapeutic applications. Nevertheless, these dividing cells, like other cells, probably undergo spontaneous mutation at a rate of 10(-9) per nucleotide. Because each mutant has only a few progeny, the overall biological properties of the cell culture are not altered unless a mutation provides a survival or growth advantage. Clonal evolution that leads to emergence of a dominant mutant genotype may potentially affect cellular phenotype as well. We assessed the genomic fidelity of paired early- and late-passage hESC lines in the course of tissue culture. Relative to early-passage lines, eight of nine late-passage hESC lines had one or more genomic alterations commonly observed in human cancers, including aberrations in copy number (45%), mitochondrial DNA sequence (22%) and gene promoter methylation (90%), although the latter was essentially restricted to 2 of 14 promoters examined. The observation that hESC lines maintained in vitro develop genetic and epigenetic alterations implies that periodic monitoring of these lines will be required before they are used in in vivo applications and that some late-passage hESC lines may be unusable for therapeutic purposes.

Aberrant methylation of Reprimo in human malignancies

Reprimo is a new candidate mediator of p53-mediated cell cycle arrest at the G2 phase. Loss of Reprimo gene expression accompanied by its promoter methylation was identified in pancreatic and lung cancers. Our aim was to examine the methylation status of Reprimo in a broad range of cancers. We examined Reprimo expression by RT-PCR and the DNA methylation status of the Reprimo promoter by MSP in 39 tumor cell lines. Loss or downregulation of Reprimo expression was frequent (62%), and we confirmed that transcriptional repression of Reprimo was caused by hypermethylation (overall concordance 92%). Treatment of expression-negative cells with 5-aza-2'-deoxycytidine restored Reprimo expression. We then examined aberrant methylation of Reprimo in 645 tumors representing 16 tumor types. Promoter methylation of Reprimo was found in 79% of gastric cancers, 62% of gallbladder cancers, 57% of lymphomas, 56% of colorectal cancers, 40% of esophageal adenocarcinomas, 37% of breast cancers and 31% of leukemias. Methylation frequencies in ovarian cancers, bladder cancers, cervical cancers, brain tumors, malignant mesotheliomas and pediatric tumors were lower (0-20%). Reprimo methylation was rarely detected in nonmalignant tissues (0-11%) except for gastric epithelia. While colorectal polyps were also frequently methylated (27%), chronic cholecystitis samples were infrequently methylated (4%). Furthermore, we failed to identify Reprimo mutation in colorectal and gastric cancer cell lines and 50 primary colorectal cancers. Aberrant methylation of Reprimo with loss of expression is a common event and may contribute to the pathogenesis of some types of human malignancy.

Aberrant methylation profile of human malignant mesotheliomas and its relationship to SV40 infection

Malignant mesothelioma (MM) is associated with asbestos exposure and the presence of SV40 viral sequences. Recently, we reported that SV40 infection of human mesothelial cells (HM) causes aberrant methylation of the tumor suppressor gene (TSG) RASSF1A. We investigated methylation of 12 genes by methylation-specific PCR in 63 MMs, six MM cell lines, and two foci of SV40-infected HM. Methylation percentages of the tested genes ranged from 3 to 65%. The frequencies of HPP1, RASSF1A, Cyclin D2, and RRAD methylation, and the value of the methylation index, were significantly higher in SV40 sequence-positive MMs than in SV40-negative MMs. Methylation of TMS1 and HIC-1 was associated with shortened survival. SV40-infected HM showed progressive aberrant methylation of seven genes (RASSF1A, HPP1, DcR1, TMS1, CRBP1, HIC-1, and RRAD) during serial passage. Our results demonstrate a relationship between SV40 and methylation of multiple genes in MM, indicating that the virus plays a role in the pathogenesis of MM.

Differential methylation of genes that regulate cytokine signaling in lymphoid and hematopoietic tumors

The perturbations of the cytokine signaling pathway play an important role in lymphoid/hematopoietic tumors. Aberrant promoter methylation is the major mechanism of gene silencing in tumors. We examined 150 lymphoid/hematopoietic tumors or potential premalignant specimens, 55 control specimens and 12 EBV-transformed B lymphoblastoid cultures and 10 lymphoma/leukemia (L/L) or multiple myeloma (MM) cell lines for the methylation (and, in cell lines, of the expression status) of three genes involved in the cytokine signaling pathway. The genes were: SHP1, a protein tyrosine phosphatase; SYK, a protein kinase; and SOCS1, a suppressor of cytokine signaling. Our major findings were: (1) one or more of the three genes was frequently methylated in L/L and MM cell lines and there was good concordance (90-100%) between methylation and loss of gene expression; (2) treatment of L/L cell lines with a demethylating agent resulted in re-expression of SHP1 protein and downregulation of phosphorylated STAT3 in L/L cell lines; (3) all 55 control specimens and the lymphoblastoid cultures were negative for methylation of the three genes; (4) non-Hodgkin's lymphomas (100%), and leukemias (94%) had almost universal methylation of SHP1 and relatively less frequent (<30%) methylation of SOCS1 and SYK; (5) MM and monoclonal gammopathy of unknown significance (MGUS) had infrequent methylation of SHP1 (<20%), and occasional methylation of SOCS1 and SYK; and (6) comparable methylation frequencies for SOCS1 were observed in MM and MGUS, suggesting that SOCS1 methylation is an early event in MM pathogenesis. At least one gene was methylated in 119 of 130 (93%) of the malignant and 12 of 20 (60%) of the MGUS samples. Our findings demonstrate that the perturbations of cytokine signaling via silencing of these three genes are almost universal in lymphoid/hematopoietic tumors but the patterns of gene methylated for L/L and plasma cell dyscrasias are different.

Presence of Simian Virus 40 DNA Sequences in Human Lymphoid and Hematopoietic Malignancies and Their Relationship to Aberrant Promoter Methylation of Multiple Genes

The simian polyoma virus SV40 has been detected in specific human tumors including non-Hodgkin's lymphomas, although a causative role for the virus has not been convincingly demonstrated. Aberrant methylation of CpG islands in promoter regions is a frequent method of silencing tumor suppressor genes (TSGs) in cancers and may be induced by oncogenic viruses. We investigated the relationship between the presence of SV40 or EBV DNA sequences and the methylation profiles for 10 TSGs in 90 cases of non-Hodgkin's lymphomas/leukemias and 56 control tissues. SV40 sequences were present in 33/90 (37%) non-Hodgkin's lymphomas/leukemias, and EBV was present in 11/42 (26%) of non-Hodgkin's lymphomas. We found a highly significant correlation between the presence of SV40 and methylation of seven genes (P values, 0.006 to <0.0001). In lymphomas, there was no relationship between EBV and methylation. Oncogenic viruses and methylation were rarely present in control tissues. We investigated methylation of the same 10 TSGs in peripheral blood mononuclear cells (PBMC) from a healthy volunteer infected with EBV or EBV and SV40. Promoter methylation of CDH1 and CDH13 were noted in dual SV40- and EBV-infected PBMC, and these two genes were also highly significantly correlated to the presence of SV40 sequences in tumors. SV40 infection also resulted in appearance of the lymphoma/leukemia-specific marker, methylated SHP1. Methylation was completely absent in uninfected and EBV-infected PBMC. Our results demonstrate that the presence of SV40 in hematological malignancies is associated with promoter methylation of TSGs and that in all probability, the virus plays a role in tumor pathogenesis.

TP53 mutation and haplotype analysis of two large African American families

Two large apparently unrelated African American families with a high incidence of breast cancer and other tumors characteristic of Li-Fraumeni breast sarcoma cancer family syndrome were studied. Mutation screening revealed that in both families the affected members carried a germline mutation of the TP53 gene at codon 133 (ATG--> ACG, M133T). In order to determine whether an ancestral haplotype was shared by these two families, polymorphic markers within and flanking the TP53 gene were studied. Haplotype analysis using five markers revealed an identical haplotype shared by the two families. Loss of heterozygosity at the TP53 locus in the probands' tumor tissues from each family was observed; in each case, the retained allele carried the common haplotype. The frequency of this haplotype in the general African American population is <0.003. This unique haplotype, combined with the rare TP53 mutation, suggests that these African American families share a common ancestry. This finding suggests that other African Americans may be carriers of this mutation and thus may be at risk of early-onset breast cancer or other cancers characteristic of the Li-Fraumeni breast sarcoma cancer family syndrome. The finding of recurring mutations in African Americans may facilitate carrier screening and identification in this population.

Deletion of the c-kit protooncogene in the human developmental defect piebald trait

The protooncogene c-kit is critical for development of hematopoietic stem cells, germ cells, and melanoblasts in the mouse. Homozygous mutations of this gene in the mouse cause anemia, infertility, and albinism, whereas heterozygous mutant mice usually exhibit only a white forehead blaze and depigmentation of the ventral body, tail, and feet. The heterozygous mouse phenotype is very similar to human piebald trait, which is characterized by a congenital white hair forelock and ventral and extremity depigmentation. To investigate the possibility that alterations in the human c-kit gene may be a cause of piebald trait, DNA from seven unrelated affected individuals was examined by Southern blot analysis. One subject, although cytogenetically normal, has a heterozygous deletion of the c-kit protooncogene. This deletion encompasses the entire coding region for c-kit and also involves the closely linked gene for platelet-derived growth factor receptor alpha. Fluorescence in situ hybridization of genomic c-kit probes to metaphase chromosomes independently confirmed the deletion in this case. These findings provide molecular evidence mapping piebald trait to the c-kit locus on chromosome 4. Although we cannot exclude the involvement of other closely linked genes, the demonstration of a genomic c-kit deletion in one subject with piebald trait and the marked concordance of the human and mouse phenotypes provide strong evidence for the role of c-kit in the development of human melanocytes and in the pathogenesis of piebald trait.