The C-Circle Biomarker Is Secreted by Alternative-Lengthening-of-Telomeres Positive Cancer Cells inside Exosomes and Provides a Blood-Based Diagnostic for ALT Activity

Simple Summary

A clinical test for alternative-lengthening-of-telomeres (ALT) could assist with cancer diagnosis and monitoring of disease progression. ALT-targeted anticancer treatments are being developed; however, there is no appropriate companion ALT diagnostic. The C-Circle biomarker is the only known ALT specific molecule and the C-Circle Assay the only quantitative ALT assay that is amenable to clinical use. We show here that C-Circles are secreted by ALT+ cancer cell lines inside the exosomes and are protected from nucleases. We also show that secreted C-Circles, like intracellular C-Circles, are an ALT-specific biomarker, and in high-risk neuroblastoma, the blood-based C-Circle Assay has the potential to be an accurate diagnostic for ALT cancer activity. Therefore, the secretion of C-Circles by ALT+ cancer cells in the exosomes provides a stable blood-based biomarker and, potentially, a clinical diagnostic for ALT activity, which is required for the development of ALT-targeted therapies as well as for the diagnosis and monitoring of ALT+ cancer.

Abstract

C-Circles, self-primed telomeric C-strand templates for rolling circle amplification, are the only known alternative-lengthening-of-telomeres (ALT)-specific molecule. However, little is known about the biology of C-Circles and if they may be clinically useful. Here we show that C-Circles are secreted by ALT+ cancer cells inside exosomes, and that a blood-based C-Circle Assay (CCA) can provide an accurate diagnostic for ALT activity. Extracellular vesicles were isolated by differential centrifugation from the growth media of lung adenocarcinoma, glioblastoma, neuroblastoma, osteosarcoma, and soft tissue sarcoma cell lines, and C-Circles were detected in the exosome fraction from all eleven ALT+ cancer cell lines and not in any extracellular fraction from the eight matching telomerase positive cancer cell lines or the normal fibroblast strain. The existence of C-Circles in ALT+ exosomes was confirmed with exosomes isolated by iodixanol gradient separation and CD81-immunoprecipitation, and C-Circles in the exosomes were protected from nucleases. On average, 0.4% of the total ALT+ intracellular C-Circles were secreted in the exosomes every 24 h. Comparing the serum-based and tumor-based CCAs in 35 high risk neuroblastoma patients divided randomly into ALT+ threshold derivation and validation groups, we found the serum-based CCA to have 100% sensitivity (6/6), 70% specificity (7/10), and 81% concordance (13/16). We conclude that the secretion of C-Circles by ALT+ cancer cells in the exosomes provides a stable blood-based biomarker and a potential clinical diagnostic for ALT activity.

Epithelial splicing regulatory protein 1 and 2 paralogues correlate with splice signatures and favorable outcome in human colorectal cancer

ESRPs are master splice regulators implicated in alternative mRNA splicing programs important for epithelial-mesenchymal transition (EMT) and tumor progression. ESRP1 was identified in some tumors as good or worse predictor of outcome, but in colorectal cancer (CRC) the prognostic value of ESRPs and relation with mesenchymal splice variants is not clear. Here, we studied 68 CRC cases, compared tissue expression of ESRPs with clinical data and with EMT gene splice patterns of conditional CRC cells with deficient ESRP1 expression.Around 72% of patients showed global decreased transcript expression of both ESRPs in tumor as compared to matched non-neoplastic colorectal epithelium. Reduction of ESRP1 in tumor cells was evaluated by immunohistochemistry, associated with microsatellite stability and switch to mesenchymal splice signatures of FGFRs, CD44, ENAH and CTNND1(p120-catenin). Expression of ESRPs was significantly associated with favorable overall survival (log-rank test, P=0.0186 and 0.0408), better than prognostic stratification by tumor staging; and for ESRP1 confirmed with second TCGA cohort (log-rank test, P=0.0435). Prognostic value is independent of the pathological stage and microsatellite instability (ESRP1: HR=0.36, 95%CI 0.15-0.91, P=0.032; ESRP2: HR=0.23, 95%CI 0.08-0.65, P=0.006).Our study supports the role of ESRP1 as tumor suppressor and strongly suggests that ESRPs are candidate markers for early detection, diagnosis, and prognosis of CRC.

LINE-1 induces hTERT and ensures telomere maintenance in tumour cell lines

A hallmark of cancer cells is an activated telomere maintenance mechanism, which allows prolonged survival of the malignant cells. In more than 80% of tumours, telomeres are elongated by the enzyme telomerase, which adds de novo telomere repeats to the ends of chromosomes. Cancer cells are also characterized by expression of active LINE-1 elements (L1s, long interspersed nuclear elements-1). L1 elements are abundant retrotransposons in the eukaryotic genome that are primarily known for facilitating aberrant recombination. Using L1-knockdown (KD), we show for the first time that L1 is critical for telomere maintenance in telomerase-positive tumour cells. The reduced length of telomeres in the L1-KD-treated cells correlated with an increased rate of telomere dysfunction foci, a reduced expression of shelterin proteins and an increased rate of anaphase bridges. The decreased telomere length was associated with a decreased telomerase activity and decreased telomerase mRNA level; the latter was increased upon L1 overexpression. L1-KD also led to a decrease in mRNA and protein expression of cMyc and KLF-4, two main transcription factors of telomerase and altered mRNA levels of other stem-cell-associated proteins such as CD44 and hMyb, as well as a corresponding reduced growth of spheroids. The KD of KLF-4 or cMyc decreased the level of L1-ORF1 mRNA, suggesting a specific reciprocal regulation with L1. Thus, our findings contribute to the understanding of L1 as a pathogenicity factor in cancer cells. As L1 is only expressed in pathophysiological conditions, L1 now appears to be target in the rational treatment of telomerase-positive cancer.

Abstract 2743: Telomere transcripts improve synthetic inhibitors of telomerase

Most tumors express telomerase for infinite cell growth capacity. Telomerase was recognized recently as central regulator of all of the hallmarks of cancer and synthetic inhibitors of telomerase, such as Imetelstat blocking the RNA subunit of telomerase TERC, are in clinical trials. RNA transcripts from telomeres called TERRA were identified to block telomerase activity (TA) potentially via direct binding to TERC. We established recombinant expression systems to modulate TERRA transcripts in cell culture cells and study in vitro cell growth and viability directly and in combination with telomerase inhibitors.

Adeno- and lentivirus constructs (AV and LV) were established for transient and stable recombinant TERRA expression in TA tumor cell lines (N=3) and mortal fibroblast cells as control. AV and LV express TERRA under control of hH1 promoter with around 120 units of UUAGGG repeats in sense (S) or anti-sense (AS) orientation. Similarly, AV and LV express polyadenylated form of TERRA under control of CMV promoter and polyadenylation signaling sites. Telomere length (TL), endogenous and recombinant TERRA expression was analyzed by qPCR, TA by TRAP assay. Population doubling (PD) times were calculated from cell growth numbers of LV clones. Small molecule telomerase inhibitors and AVs expressing dominant-negative telomerase and shRNA against hTERT were used in MTT cell viability and clonogenicity assays.

TERRA expression was modulated transiently and stably by recombinant AVs and LVs as compared to virus controls expressing eGFP. Moderate 1.5-1.7 fold elevation of recombinant TERRA-S transcripts caused reduction of TA to 23-38%. In contrast, AS expression reduced TERRA 3-8 fold without reduction of TA. TL, PD time, cell viability and clonogenicity were not affected by TERRA-S and -AS expression up to 3 weeks in culture. Single cell clones were isolated from cells infected by LVs. Significant improve of telomerase targeting approaches was identified as IC-50 values decreased 2.0-2.6 fold in LV cell clones expressing moderate recombinant TERRA-S compared to TERRA-AS and eGFP. Similarly, clone formation capacity decreased 1.3-1.7 fold. Human fibroblasts showed 15 fold increased TERRA expression compared to tumor cells and were not affected by treatments applied. Preliminary data with modified RNA oligonucleotides containing TERRA sequences indicate that up-take by cells was efficient. Furthermore, IC-50 values of TA inhibitor MST-312 in combination with 3 nM TERRA oligonucleotides decreased 1.9-3.9 fold compared to mismatch controls. Effective concentrations were 1000 fold lower compared to DNA oligonucleotide telomerase inhibitors currently in clinical trials.

We demonstrated that recombinant expression of TERRA significantly improved telomerase targeting approaches in tumor cells but not in mortal fibroblasts. TERRA oligonucleotides are candidates for in vivo application in combination with telomerase targeting approaches or other tumor therapies.

Citation Format: Sandra Sampl, Doris Mejri, Christian Stern, Hui Wang, Klaus Holzmann. Telomere transcripts improve synthetic inhibitors of telomerase. [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 2743. doi:10.1158/1538-7445.AM2014-2743

Canine and human sarcomas exhibit predominant FGFR1 expression and impaired viability after inhibition of signaling

Fibroblast growth factor receptors (FGFRs) are important in malignant progression of several human epithelial tumors. However, little is known about FGFRs in canine or human soft tissue sarcomas. Thus, our aim was to investigate expression of FGFRs and their involvement in cell survival in sarcomas of both species. FGFR1-4 and FGFRL1 transcripts as well as IIIb/IIIc splice variants of FGFR1-3 were evaluated in 3 canine- and 6 human sarcoma cell lines and 19 spontaneous canine sarcomas by SYBRqPCR. FGFR1 protein expression was assessed by immunohistochemistry. Growth inhibitory effects of FGFR1 inhibitor PD166866 and dominant negative recombinant FGFR adenoviral expression constructs (dnFGFR) on tumor cell lines were analyzed. Profiling of multiple FGFR transcripts detected comparable co-expression in most of human and canine sarcoma cell lines and canine tumor specimens. This indicates existence of closely related regulation mechanisms for FGFR expression in sarcomas of both species. FGFR1 with splice variant IIIc was consistently expressed with highest transcript levels. In 88% of the spontaneous tumor samples a heterogeneous FGFR1 protein expression was observed. Significant growth inhibition and cell death was seen after infection with dnFGFR1 in canine and human sarcoma cells, but not with dnFGFR3 and 4. PD166866 showed selective cytotoxicity with IC50 values between 12.1 and 26.4 μM. FGFR1 inhibition blocked ligand-induced tyrosine phosphorylation of ERK1/2 mitogen-activated protein kinase isoforms. This study emphasizes the important role FGFR1, especially splice variant IIIc, likely plays in sarcomas. Inhibitory small molecules could be of potential use for targeted therapy in aggressive sarcomas of both species.

Abstract 4597: Telomere maintenance mechanism and expression in colorectal cancer

Tumors can overcome cellular senescence, one of the main barriers to tumor development and immortality by telomere maintenance mechanism (TMM). 90% of colorectal carcinomas (CRC) use telomerase activity (TA) as TMM. Mechanisms of remaining CRC tumors are not well analyzed yet and may utilize alternative lengthening of telomeres (ALT) or a not defined telomere maintenance mechanism (NDTMM). Both TA and expression of telomeric repeat containing RNA (TERRA) were recently identified to correlate with tumor grade. This led us to evaluate possible correlations of TMM and TERRA levels to clinical data. Tissues from 49 CRC patients (35 grade II, 14 grade III, 2 polyps) and cell lines (N = 7) were assessed. Tumor tissues were compared to matched adjacent non-tumor tissues. Mean telomere length (TL) was measured by real-time PCR and telomere restriction fragment (TRF) length analyses. TMM were evaluated by measuring TA with telomere amplification protocol (TRAP) and by detection of ALT with c-circles. Real-time RT-PCR assays for relative quantity (RQ) of transcript levels for TERRA, telomerase genes hTERT and hTERC were determined in relation to levels of house-keeping genes and normal tissues. RQ values were analyzed for significant differences between groups by Mann-Whitney test and were assessed after log-transformation with the Pearson's correlation calculation. TL of grade II and grade III tumors were in the range of 5.5 ± 1.3kbp and 5.3 ± 0.5kbp, respectively (mean ± SD), and were comparable with TL of normal tissue and cell lines. TA was detected with mean of 27 TPG units in 90% (34 of 38) and with mean of 4 units in 24% (9 of 38) of tumor and normal tissues, respectively. All cell lines analyzed demonstrate TA with mean of 51 units. A restricted set of tumors consisting of 2 with and 4 without TA was analyzed for ALT. One of the analyzed tumors without detectable TA showed significantly elevated levels of c-circles, but did not reach levels of sarcomas and cell models with ALT, indicating the existence of NDTMM in CRC. Within the transcripts analyzed, TERRA levels showed a moderate negative correlation with TA (Pearson r=−0.45, p<0.0001), supporting the inhibitory function of TERRA on TA as recently described in vitro. TERRA levels of grade II and III tumors decreased compared to normal tissues, but did not differ between grades. However, TA and TERRA levels of tumors increased and decreased, respectively, in stage II compared to stage I tumors, indicating a role in tumor progression. Correlation with patient survival will be performed and presented. In conclusion, we identified TA and NDTMM, but not ALT in our patient series of CRC. Our preliminary data suggest that TERRA expression together with TA correlates with diagnoses and thus can be considered promising candidates as clinical markers for CRC.

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 4597. doi:1538-7445.AM2012-4597

Abstract 832: Evaluation of relevance of genes expressed in cancer stem cells and under hypoxia in astrocytic brain tumors

The dismal prognosis of patients suffering from astrocytomas, especially glioblastoma multiforme (GBM) emphasizes the need for more precise expressional characterization of these tumors in order to identify potential prognostic factors and therapeutic targets. Tumor growth leads to formation of low oxygenated regions that are considered as stem cell niches. GBM are described with high cancer stem cell content and with hypoxic and necrotic areas. This study investigates in astrocytomas WHO grade II to IV the transcript levels of genes expressed in cancer stem cells (NANOG, ALDH1A1, ALDH3A1, CD133, NOTCH1, ABCB1, ABCG2) and hypoxia regulators and regulated genes (HIF1α, HIF2α, CA9, VEGF). A relationship between some of these factors and patient survival or tumor grade has been reported in previous studies.

Tissue samples (ts) from 46 patients were histologically graded as: 12 diffuse astrocytomas (DA) gr II, 6 anaplastic astrocytomas (AA) gr III and 28 GBM gr IV. RNA was isolated from ts. Gene expression levels measured by real-time qRT-PCR in the separate tumor samples were compared to levels found in 6 non-tumor ts from patients suffering epileptic lesions and to beta actin. Relative quantities were compared between ts groups by Mann-Whitney test and log-transformed for Pearson correlation calculation.

Increase of HIF2α (200-fold), CA9 (2.7-fold) and VEGF (3.4-fold) mRNA was observed in GBM compared to non-tumor or DA (p<0.05). HIF1α and NANOG mRNA levels did not change (p>0.05). In contrast, a decrease of expression in GBM compared to DA of ABCB1 (10-fold), ABCG2 (10-fold), NOTCH1 (4.2-fold) and ALDH1A1 (6.8-fold) mRNA was observed (p<0.05). ALDH3A1 mRNA was increased 29-fold in GBM compared to DA, but decreased 270-fold compared to non-tumor (p<0.05). Weak and interesting significant correlations of mRNA levels were observed between NOTCH1, NANOG, ABCG2 and ALDH1A1 (Pearson's coefficient P=0.43 to 0.60), between NANOG and CA9 (P=0.67) and between VEGF and ALDH1A1 (P=-0.43). Primary analysis of expression and survival data indicates a significant connection of overall survival and expression of ALDH1A1. Low ALDH1A1 mRNA correlates with a poor prognosis. Part of our findings could be confirmed by comparison with mRNA levels from public database Rembrandt (Repository of Molecular Brain Neoplasia Data) containing results from experiments with gene expression and copy number arrays.

Conclusion: Transcript levels of analyzed genes are significantly related to tumor grade, except are HIF1α and NANOG. Decreased transcript levels of genes expressed in cancer stem cells are in contrast to a high content of cancer stem cells described for GBM. Expression levels of most of the investigated genes can be considered promising candidates as prognostic and diagnostic markers in astrocytomas.

This project was supported in part by a grant from the Herzfelder-Familien-Stiftung, Austria.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 832.