Alternative Lengthening Of Telomeres Cell Lines Research Articles

SUMO promotes DNA repair protein collaboration to support alternative telomere lengthening in the absence of PML.

The alternative lengthening of telomeres (ALT) pathway maintains telomere length in a significant fraction of cancers that are associated with poor clinical outcomes. A better understanding of ALT mechanisms is therefore necessary for developing new treatment strategies for ALT cancers. SUMO modification of telomere proteins contributes to the formation of ALT telomere-associated PML bodies (APBs), in which telomeres are clustered and DNA repair proteins are enriched to promote homology-directed telomere DNA synthesis in ALT. However, it is still unknown whether-and if so, how-SUMO supports ALT beyond APB formation. Here, we show that SUMO condensates that contain DNA repair proteins enable telomere maintenance in the absence of APBs. In PML knockout ALT cell lines that lack APBs, we found that SUMOylation is required for manifesting ALT features independent of PML and APBs. Chemically induced telomere targeting of SUMO produces condensate formation and ALT features in PML-null cells. This effect requires both SUMOylation and interactions between SUMO and SUMO interaction motifs (SIMs). Mechanistically, SUMO-induced effects are associated with the accumulation of DNA repair proteins, including Rad52, Rad51AP1, RPA, and BLM, at telomeres. Furthermore, Rad52 can undergo phase separation, enrich SUMO at telomeres, and promote telomere DNA synthesis in collaboration with the BLM helicase in a SUMO-dependent manner. Collectively, our findings suggest that SUMO condensate formation promotes collaboration among DNA repair factors to support ALT telomere maintenance without PML. Given the promising effects of SUMOylation inhibitors in cancer treatment, our findings suggest their potential use in perturbing telomere maintenance in ALT cancer cells.

Inhibition of p53 and ATRX increases telomeric recombination in primary fibroblasts.

Telomere length can be maintained either by the telomerase enzyme or by alternative lengthening of telomeres (ALT), which is based on telomeric recombination. However, both mechanisms are inactive in most human somatic cells. ATRX has been previously identified as an ALT repressor gene. Nonetheless, TP53 is also deficient in most ALT cell lines, and previous works showed that it is an inhibitor of homologous recombination (HR). Despite this, the role of p53 as an ALT repressor has not been previously examined. Therefore, we investigated the effects of p53 and ATRX inhibition on normal human fibroblasts (devoid of any mutation), in the presence or absence of X-ray-induced telomeric damage. Performing immunofluorescence with antibodies for RAD51, H2AX, and TRF1 (for studying HR-mediated DNA damage repair) and CO-FISH (for telomeric sister chromatid exchanges), we observed that HR is a normal mechanism for the repair of telomeric damage, present also in noncancer cells. Moreover, we discovered that telomeric HR, as for HR in general, is significantly inhibited by p53. Indeed, we observed that inhibition of p53 drastically increases telomeric sister chromatid exchanges. We also confirmed that ATRX inhibition increases telomeric recombination. In particular, we observed an increase in crossover products, but a much higher increase in noncrossover products.

Distinct characteristics of two types of alternative lengthening of telomeres in mouse embryonic stem cells.

Telomere length must be maintained in actively dividing cells to avoid cellular arrest or death. In the absence of telomerase activity, activation of alternative lengthening of telomeres (ALT) allows the maintenance of telomeric length and prolongs the cellular lifespan. Our previous studies have established two types of ALT survivors from mouse embryonic stem cells. The key differences between these ALT survivors are telomere-constituting sequences: non-telomeric sequences and canonical telomeric repeats, with each type of ALT survivors being referred to as type I and type II, respectively. We explored how the characteristics of the two types of ALT lines reflect their fates using multi-omics approaches. The most notable gene expression signatures of type I and type II ALT cell lines were chromatin remodelling and DNA repair, respectively. Compared with type II cells, type I ALT cells accumulated more mutations and demonstrated persistent telomere instability. These findings indicate that cells of the same origin have separate routes for survival, thus providing insights into the plasticity of crisis-suffering cells and cancers.

TOP3A amplification and ATRX inactivation are mutually exclusive events in pediatric osteosarcomas using ALT.

In some types of cancer, telomere length is maintained by the alternative lengthening of telomeres (ALT) mechanism. In many ALT cancers, the α‐thalassemia/mental retardation syndrome X‐linked (ATRX) gene is mutated leading to the conclusion that the ATRX complex represses ALT. Here, we report that most high‐grade pediatric osteosarcomas maintain their telomeres by ALT, and that the majority of these ALT tumors are ATRX wild‐type (wt) and instead carry an amplified 17p11.2 chromosomal region containing TOP3A. We found that TOP3A was overexpressed in the ALT‐positive ATRX‐wt tumors consistent with its amplification. We demonstrated the functional significance of these results by showing that TOP3A overexpression in ALT cancer cells countered ATRX‐mediated ALT inhibition and that TOP3A knockdown disrupted the ALT phenotype in ATRX‐wt cells. Moreover, we report that TOP3A is required for proper BLM localization and promotes ALT DNA synthesis in ALT cell lines. Collectively, our results identify TOP3A as a major ALT player and potential therapeutic target.

TERRA transcription destabilizes telomere integrity to initiate break-induced replication in human ALT cells

Alternative Lengthening of Telomeres (ALT) is a Break-Induced Replication (BIR)-based mechanism elongating telomeres in a subset of human cancer cells. While the notion that spontaneous DNA damage at telomeres is required to initiate ALT, the molecular triggers of this physiological telomere instability are largely unknown. We previously proposed that the telomeric long noncoding RNA TERRA may represent one such trigger; however, given the lack of tools to suppress TERRA transcription in cells, our hypothesis remained speculative. We have developed Transcription Activator-Like Effectors able to rapidly inhibit TERRA transcription from multiple chromosome ends in an ALT cell line. TERRA transcription inhibition decreases marks of DNA replication stress and DNA damage at telomeres and impairs ALT activity and telomere length maintenance. We conclude that TERRA transcription actively destabilizes telomere integrity in ALT cells, thereby triggering BIR and promoting telomere elongation. Our data point to TERRA transcription manipulation as a potentially useful target for therapy.

RAD54 promotes alternative lengthening of telomeres by mediating branch migration.

Cancer cells can activate the alternative lengthening of telomeres (ALT) pathway to promote replicative immortality. The ALT pathway promotes telomere elongation through a homologous recombination pathway known as break‐induced replication (BIR), which is often engaged to repair single‐ended double‐stranded breaks (DSBs). Single‐ended DSBs are resected to promote strand invasion and facilitate the formation of a local displacement loop (D‐loop), which can trigger DNA synthesis, and ultimately promote telomere elongation. However, the exact proteins involved in the maturation, migration, and resolution of D‐loops at ALT telomeres are unclear. In vitro, the DNA translocase RAD54 both binds D‐loops and promotes branch migration suggesting that RAD54 may function to promote ALT activity. Here, we demonstrate that RAD54 is enriched at ALT telomeres and promotes telomeric DNA synthesis through its ATPase‐dependent branch migration activity. Loss of RAD54 leads to the formation of unresolved recombination intermediates at telomeres that form ultra‐fine anaphase bridges in mitosis. These data demonstrate an important role for RAD54 in promoting ALT‐mediated telomere synthesis.

ALT: A Multi-Faceted Phenomenon.

One of the hallmarks of cancer cells is their indefinite replicative potential, made possible by the activation of a telomere maintenance mechanism (TMM). The majority of cancers reactivate the reverse transcriptase, telomerase, to maintain their telomere length but a minority (10% to 15%) utilize an alternative lengthening of telomeres (ALT) pathway. Here, we review the phenotypes and molecular markers specific to ALT, and investigate the significance of telomere mutations and sequence variation in ALT cell lines. We also look at the recent advancements in understanding the different mechanisms behind ALT telomere elongation and finally, the progress made in identifying potential ALT-targeted therapies, including those already in use for the treatment of both hematological and solid tumors.

Differential requirements for DNA repair proteins in immortalized cell lines using alternative lengthening of telomere mechanisms.

Cancer cells require telomere maintenance to enable uncontrolled growth. Most often telomerase is activated, although a subset of human cancers are telomerase-negative and depend on recombination-based mechanisms known as ALT (Alternative Lengthening of Telomeres). ALT depends on proteins that are essential for homologous recombination, including BLM and the MRN complex, to extend telomeres. This study surveyed the requirement for requisite homologous recombination proteins, yet to be studied in human ALT cell lines, by protein depletion using RNA interference. Effects on ALT were evaluated by measuring C-circle abundance, a marker of ALT. Surprisingly, several proteins essential for homologous recombination, BARD1, BRCA2, and WRN, were dispensable for C-circle production, while PALB2 had varying effects on C-circles among ALT cell lines. Depletion of homologous recombination proteins BRCA1 and BLM, which have been previously studied in ALT, decreased C-circles in all ALT cell lines. Depletion of the non-homologous end joining proteins 53BP1 and LIG4 had no effect on C-circles in any ALT cell line. Proteins such as chromatin modifiers that recruit double-strand break proteins, RNF8 and RNF168, and other proteins loosely grouped into excision DNA repair processes, XPA, MSH2, and MPG, reduced C-circles in some ALT cell lines. MSH2 depletion also reduced recombination at telomeres as measured by intertelomeric exchanges. Collectively, the requirement for DNA repair proteins varied between the ALT cell lines compared. In sum, our study suggests that ALT proceeds by multiple mechanisms that differ between cell lines and that some of these depend on DNA repair proteins not associated with homologous recombination pathways.

Suppression of alternative telomere lengthening in cancer cells with reverse transcriptase inhibitors

Telomerase is a ribonucleoprotein enzyme that elongates telomeres and therefore maintains chromosomal stability in germline, and in the majority of cancer cells, during cell doubling. However, up to 30 % of human tumors of different types do not express telomerase, but instead use an alternative lengthening of telomeres (ALT). Here authors show that human tumor-derived ALT cell lines express a LINE-1 (L1) retrotransposon, which suggests its participation in telomere maintenance, possibly by a «slippage» mechanism of telomeric DNA synthesis. Moreover, suppression of the L1 encoded reverse transcriptase activity using an antisense strategy, or treatment of the ALT cells with the reverse transcriptase inhibitor 3'-azido-2',3'-dideoxythymidine (AZT), induces progressive telomere loss, arrest in G2-phase of the cell cycle, and, eventually, in cancer cell death. This finding suggests an exciting opportunity for the cure of up to 30 % of cancer cases.

Telomere Transcripts Target Telomerase in Human Cancer Cells

Long non-coding transcripts from telomeres, called telomeric repeat-containing RNA (TERRA), were identified as blocking telomerase activity (TA), a telomere maintenance mechanism (TMM), in tumors. We expressed recombinant TERRA transcripts in tumor cell lines with TA and with alternative lengthening of telomeres (ALT) to study effects on TMM and cell growth. Adeno- and lentivirus constructs (AV and LV) were established for transient and stable expression of approximately 130 units of telomere hexanucleotide repeats under control of cytomegalovirus (CMV) and human RNase P RNA H1 (hH1) promoters with and without polyadenylation, respectively. Six human tumor cell lines either using telomerase or ALT were infected and analyzed for TA levels. Pre-infection cells using telomerase had 1%–3% of the TERRA expression levels of ALT cells. AV and LV expression of recombinant TERRA in telomerase positive cells showed a 1.3–2.6 fold increase in TERRA levels, and a decrease in TA of 25%–58%. Dominant-negative or small hairpin RNA (shRNA) viral expression against human telomerase reverse transcriptase (hTERT) results in senescence, not induced by TERRA expression. Population doubling time, cell viability and TL (telomere length) were not impacted by ectopic TERRA expression. Clonal growth was reduced by TERRA expression in TA but not ALT cell lines. ALT cells were not affected by treatments applied. Established cell models and tools may be used to better understand the role of TERRA in the cell, especially for targeting telomerase.

Abstract LB-084: A role of long interspersed nuclear element-1 (LINE-1) for telomere maintenance in cells with alternative lengthening of telomeres

Abstract LINE-1 elements (L1s, long interspersed nuclear elements-1) are abundant retrotransposons in the eukaryotic genome that are primarily known for facilitating aberrant recombination. Here we show the involvement of L1 in telomere maintenance in cells using the less characterized alternative lengthening of telomeres (ALT) mechanism. Interestingly, ALT cells show significantly higher expression levels of L1 when compared to TA cells. Knock-down (KD) of L1 in ALT cell lines was associated with reduced length of telomeres, an increase in telomere dysfunction foci, a reduced expression of ALT characteristics such as c-circles and ALT associated PML bodies, and a decreased growth. On the other hand, overexpression of L1 in ALT cell lines lead to a higher rate of c-circles and increased length of telomeres. LINE-1 not only bound to the C-strand of telomeric DNA but also to telomere-repeat-containing RNA (TERRA), a multifunctional component of human telomeres that is highly expressed in ALT cells and has been described to be involved in telomere stabilization. Whereas L1-KD decreased overall TERRA, L1 overexpression increased this RNA. Moreover, L1 KD abrogated the nuclear retention of TERRA. Moreover, the L1-ribonucleoprotein can use the polyadenylated form of TERRA as a template to generate telomere-specific DNA. Thus, L1 appears to contribute to telomere maintenance by a mechanism involving TERRA, either by ensuring its nuclear localization or by using this RNA as a template for the generation of telomere-specific DNA. Our findings now render L1 proteins a promising target in cancer therapy by interfering with telomere lengthening in ALT cells. Citation Format: Thomas Aschacher, Brigitte Wolf, Philip Kienzl, Florian Enzmann, Barbara Messner, Klaus Holzmann, Michael M. Bergmann. A role of long interspersed nuclear element-1 (LINE-1) for telomere maintenance in cells with alternative lengthening of telomeres. [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 LB-084. doi:10.1158/1538-7445.AM2015-LB-084

PML induces compaction, TRF2 depletion and DNA damage signaling at telomeres and promotes their alternative lengthening.

The alternative lengthening of telomeres (ALT) mechanism allows cancer cells to escape senescence and apoptosis in the absence of active telomerase. A characteristic feature of this pathway is the assembly of ALT-associated promyelocytic leukemia (PML) nuclear bodies (APBs) at telomeres. Here, we dissected the role of APBs in a human ALT cell line by performing an RNA interference screen using an automated 3D fluorescence microscopy platform and advanced 3D image analysis. We identified 29 proteins that affected APB formation, which included proteins involved in telomere and chromatin organization, protein sumoylation and DNA repair. By integrating and extending these findings, we found that APB formation induced clustering of telomere repeats, telomere compaction and concomitant depletion of the shelterin protein TRF2 (also known as TERF2). These APB-dependent changes correlated with the induction of a DNA damage response at telomeres in APBs as evident by a strong enrichment of the phosphorylated form of the ataxia telangiectasia mutated (ATM) kinase. Accordingly, we propose that APBs promote telomere maintenance by inducing a DNA damage response in ALT-positive tumor cells through changing the telomeric chromatin state to trigger ATM phosphorylation.

Alternative lengthening of telomeres in neuroblastoma cell lines is associated with a lack of MYCN genomic amplification and with p53 pathway aberrations.

Alternative lengthening of telomeres (ALT) is a telomerase-independent telomere length maintenance mechanism that enables the unlimited proliferation of a subset of cancer cells. Some neuroblastoma (NB) tumors appear to maintain telomere length by activating ALT. Of 40 NB cell lines, we identified four potential ALT cell lines (CHLA-90, SK-N-FI, LA-N-6, and COG-N-291) that were telomerase-negative and had long telomeres (a feature of ALT cells). All four cell lines lacked MYCN amplification and were p53 non-functional upon irradiation. Two of these cell lines (CHLA-90 and SK-N-FI) were positive for C-circles (telomeric DNA circles) and ALT-associated promyelocytic leukemia nuclear bodies, both of which are phenotypic characteristics of ALT. Mutation of ATRX (associated with ALT in tumors) was only found in CHLA-90. Thus, the ALT phenotype in NB may not be limited to tumors with ATRX mutations but is associated with a lack of MYCN amplification and alterations in the p53 pathway.

WRN Loss Induces Switching of Telomerase-Independent Mechanisms of Telomere Elongation

Telomere maintenance can occur in the presence of telomerase or in its absence, termed alternative lengthening of telomeres (ALT). ALT adds telomere repeats using recombination-based processes and DNA repair proteins that function in homologous recombination. Our previous work reported that the RecQ-like BLM helicase is required for ALT and that it unwinds telomeric substrates in vitro. WRN is also a RecQ-like helicase that shares many biochemical functions with BLM. WRN interacts with BLM, unwinds telomeric substrates, and co-localizes to ALT-associated PML bodies (APBs), suggesting that it may also be required for ALT processes. Using long-term siRNA knockdown of WRN in three ALT cell lines, we show that some, but not all, cell lines require WRN for telomere maintenance. VA-13 cells require WRN to prevent telomere loss and for the formation of APBs; Saos-2 cells do not. A third ALT cell line, U-2 OS, requires WRN for APB formation, however WRN loss results in p53-mediated apoptosis. In the absence of WRN and p53, U-2 OS cells undergo telomere loss for an intermediate number of population doublings (50–70), at which point they maintain telomere length even with the continued loss of WRN. WRN and the tumor suppressor BRCA1 co-localize to APBs in VA-13 and U-2 OS, but not in Saos-2 cells. WRN loss in U-2 OS is associated with a loss of BRCA1 from APBs. While the loss of WRN significantly increases telomere sister chromatid exchanges (T-SCE) in these three ALT cell lines, loss of both BRCA1 and WRN does not significantly alter T-SCE. This work demonstrates that ALT cell lines use different telomerase-independent maintenance mechanisms that variably require the WRN helicase and that some cells can switch from one mechanism to another that permits telomere elongation in the absence of WRN. Our data suggest that BRCA1 localization may define these mechanisms.

Telomerase Suppresses Formation of ALT-Associated Single-Stranded Telomeric C-Circles

Telomere maintenance is an essential characteristic of cancer cells, most commonly achieved by activation of telomerase. Telomeres can also be maintained by a recombination-based mechanism, alternative lengthening of telomeres (ALT). Cells using ALT are characterized by the presence of ALT-associated promyelocytic leukemia (PML) bodies (APB), long, heterogeneously sized telomeres, extrachromosomal telomeric circular DNA, and elevated telomeric recombination. Consistent with other reports, we found that liposarcomas containing APBs, but lacking telomerase expression, always contained C-rich circles (C-circles), and these C-circles were never present in the absence of APBs, indicating a tight link between these features in ALT cells. However, a rare subgroup of tumors showing evidence of telomere maintenance by both telomerase and ALT did not contain C-circles. To test the hypothesis that telomerase expression disrupts the tight link between APBs and C-circles, we used ALT cell lines that were engineered to express telomerase. Introduction of telomerase activity in these ALT cells resulted in, on average, shorter telomeres with retention of APBs. However, at high passage, the level of C-circles was significantly reduced, which was paralleled by a switch from C-strand overhangs to G-strand overhangs. We propose that by extending critically short telomeres in these cells, telomerase is disrupting a key step in the ALT pathway necessary for production and/or maintenance of C-circles.

Abstract 580: Increased DNA repair capacities and p53/MDM2 pathway aberrations hallmark neuroblastoma cell lines with the alternative lengthening of telomeres (ALT) phenotype.

Abstract Introduction: Neuroblastoma (NB) is a malignant pediatric tumor of the sympathetic nervous system. Approximately 10-20% of neuroblastoma tumors maintain telomere length by activating a telomerase-independent alternative lengthening of telomeres (ALT) mechanism, and that these tumors are associated with high-stage disease, and a poor prognosis. Methods: mRNA expression of TERT (the catalytic component of telomerase) and TERC (RNA template), determination of MYCN copy number, and telomerase activity (TA) was measured by RT-PCR. Telomere content (TC) and C-Circle (CC) content was assayed by quantitative PCR, p53 function was assessed by quantifying induction of p21 protein by flow cytometry after irradiation. Expression profiling was carried out with custom-designed Taq-Man Low Density Arrays (TLDAs) (ABI) that quantified expression of 61 DNA-repair genes in a panel of 12 NB cell lines, 4 ALT and 8 telomerase-positive. Of the telomerase-positive lines, 2 were drug-sensitive, 6 multi-drug resistant. Cell line identities were confirmed using short tandem repeat (STR) genotyping. Response to cytotoxic drugs was assessed using the DIMSCAN fluorescence imaging system. ATRX protein expression was measured with immunoblots. Results: From a panel of 40 human NB cell lines we identified 4 ALT NB lines, LA-N-6, SK-N-FI, CHLA-90, and COG-N-291, that had elevated TC > 2-fold that of TA+ NB cell lines (p<.005), two of which demonstrated telomere repeat C-circles, and all lacked MYCN genomic amplification. All 4 ALT+ NB cell lines maintain telomere length with significantly low levels of telomerase activity (p<.005) and mRNA expression of TERT relative to telomerase-positive NB cell lines; 3 of the 4 ALT lines lacked p53 function and LA-N-6, the sole p53-functional ALT line carries a homozygous deletion of p14(ARF). ALT lines had a significant increase (p<.05) in the expression of 28 of the 61 DNA-repair genes analyzed by TLDA relative to telomerase-positive lines (including those that manifest multidrug resistance); 10 of these genes are involved in the nucleotide excision repair pathway. All 4 ALT cell lines showed a high degree of multi-drug resistance, with the mean concentration cytotoxic to 90% of the ALT cells (IC90) being higher than clinically achievable plasma levels for melphalan (2-fold), etoposide (4-fold), topotecan (5-fold), and carboplatin (4-fold). CHLA-90 had undetectable ATRX protein levels, whereas the other three ALT+ NB cell lines expressed ATRX. Conclusions: ALT-based telomere maintenance in NB cell lines was associated with loss of p53 function, increased expression of DNA-repair genes, and resistance to DNA-damaging chemotherapy. Loss of ATRX expression is not essential for ALT to develop in NB. Novel, p53-independent therapies should be considered to treat neuroblastomas harboring the ALT phenotype. Citation Format: Ahsan Farooqi, Ashly Hindle, Balakrishna Koneru, Jerry Shay, Patrick Reynolds. Increased DNA repair capacities and p53/MDM2 pathway aberrations hallmark neuroblastoma cell lines with the alternative lengthening of telomeres (ALT) phenotype. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 580. doi:10.1158/1538-7445.AM2013-580

Loss of Wild-Type ATRX Expression in Somatic Cell Hybrids Segregates with Activation of Alternative Lengthening of Telomeres

Alternative Lengthening of Telomeres (ALT) is a non-telomerase mechanism of telomere lengthening that occurs in about 10% of cancers overall and is particularly common in astrocytic brain tumors and specific types of sarcomas. Somatic cell hybridization analyses have previously shown that normal telomerase-negative fibroblasts and telomerase-positive immortalized cell lines contain repressors of ALT activity, indicating that activation of ALT results from loss of one or more unidentified repressors. More recently, ATRX or DAXX was shown to be mutated both in tumors with telomere lengths suggestive of ALT activity and in ALT cell lines. Here, an ALT cell line was separately fused to each of four telomerase-positive cell lines, and four or five independent hybrid lines from each fusion were examined for expression of ATRX and DAXX and for telomere lengthening mechanism. The hybrid lines expressed either telomerase or ALT, with the other mechanism being repressed. DAXX was expressed normally in all parental cell lines and in all of the hybrids. ATRX was expressed normally in each of the four telomerase-positive parental cell lines and in every telomerase-positive hybrid line, and was abnormal in the ALT parental cells and in all but one of the ALT hybrids. This correlation between ALT activity and loss of ATRX expression is consistent with ATRX being a repressor of ALT.

Loss of ATRX, Genome Instability, and an Altered DNA Damage Response Are Hallmarks of the Alternative Lengthening of Telomeres Pathway

The Alternative Lengthening of Telomeres (ALT) pathway is a telomerase-independent pathway for telomere maintenance that is active in a significant subset of human cancers and in vitro immortalized cell lines. ALT is thought to involve templated extension of telomeres through homologous recombination, but the genetic or epigenetic changes that unleash ALT are not known. Recently, mutations in the ATRX/DAXX chromatin remodeling complex and histone H3.3 were found to correlate with features of ALT in pancreatic neuroendocrine cancers, pediatric glioblastomas, and other tumors of the central nervous system, suggesting that these mutations might contribute to the activation of the ALT pathway in these cancers. We have taken a comprehensive approach to deciphering ALT by applying genomic, molecular biological, and cell biological approaches to a panel of 22 ALT cell lines, including cell lines derived in vitro. Here we show that loss of ATRX protein and mutations in the ATRX gene are hallmarks of ALT–immortalized cell lines. In addition, ALT is associated with extensive genome rearrangements, marked micronucleation, defects in the G2/M checkpoint, and altered double-strand break (DSB) repair. These attributes will facilitate the diagnosis and treatment of ALT positive human cancers.

Modulation of Telomeres in Alternative Lengthening of Telomeres Type I Like Human Cells by the Expression of Werner Protein and Telomerase

The alternative lengthening of telomeres (ALT) is a recombination-based mechanism of telomere maintenance activated in 5–20% of human cancers. In Saccharomyces cerevisiae, survivors that arise after inactivation of telomerase can be classified as type I or type II ALT. In type I, telomeres have a tandem array structure, with each subunit consisting of a subtelomeric Y′ element and short telomere sequence. Telomeres in type II have only long telomere repeats and require Sgs1, the S. cerevisiae RecQ family helicase. We previously described the first human ALT cell line, AG11395, that has a telomere structure similar to type I ALT yeast cells. This cell line lacks the activity of the Werner syndrome protein, a human RecQ helicase. The telomeres in this cell line consist of tandem repeats containing SV40 DNA, including the origin of replication, and telomere sequence. We investigated the role of the SV40 origin of replication and the effects of Werner protein and telomerase on telomere structure and maintenance in AG11395 cells. We report that the expression of Werner protein facilitates the transition in human cells of ALT type I like telomeres to type II like telomeres in some aspects. These findings have implications for the diagnosis and treatment of cancer.

Validating a gene expression signature proposed to differentiate liposarcomas that use different telomere maintenance mechanisms

A gene expression signature meant to distinguish between telomerase and alternative lengthening of telomeres (ALT) utilization was recently described (Lafferty-Whyte et al., 2009). This was generated from the intersection of two independent signatures obtained from cell lines and liposarcoma tumors, respectively, which utilize different telomere maintenance mechanisms (TMMs). To assess the utility of this signature, we used U133plus2.0 arrays (Affymetrix, Santa Clara, CA, USA) to undertake a similar analysis of an independent collection of liposarcomas with defined TMMs (see GEO accession {type:entrez-geo,attrs:{text:GSE20559,term_id:20559}}GSE20559, which includes full details of the methods). For our data set, use of the 297 gene signature causes the liposarcomas to cluster not on the basis of TMM, but rather on the basis of tumor histological subtype (Figure 1a), consistent with the signatures reported by others (Matushansky et al., 2008). Figure 1 Heatmap visualizations of the 297 gene signature from Lafferty-Whyte et al. (2009) for all genes having a corresponding Affymetrix probeset. Where more than one probeset was available, the one with the highest median expression across the dataset was ... To control for the effect of histological subtypes, we then restricted our analysis to dedifferentiated liposarcomas. Despite this constraint, when using linear modeling for microarrays (Limma; (Smyth, 2004)) to assess differential expression, we obtained no genes that are significantly changed, unless the data are pre-filtered to remove low-expressing non-varying probesets (cv 2), with no genes in common with the 297-gene signature of Lafferty-Whyte et al. (2009). This is in agreement with the previous study, where a similar approach failed to identify any genes that are significantly correlated with TMM, an observation that motivated their use of Fisher's exact test to produce a list of >6700 differentially expressed genes. We also performed unsupervised clustering of the dedifferentiated tumor data corresponding to the 297-gene signature (Figure 1b) and found no strong correlation between gene expression and TMM. It is possible that the discrepancies between our data and those of Lafferty-Whyte et al. (2009) reflect differences in microarray platform or tumor samples used. However, as the authors noted, the cell lines used in their study differ not only in TMM, but also in tissue of origin, with 75% of the telomerase-positive cell lines being of epithelial origin and 75% of the ALT cell lines being of fibroblastic origin. The initial gene signature obtained from comparing these two groups would be expected to contain a strong signature reflective of cell type, in addition to any putative TMM signature. Likewise, although we note that the histological subtypes of liposarcomas used to generate the 297 gene signature were not specified in this publication, or in the information uploaded into the GEO database, it can be largely deduced from an earlier publication from the same group (Cairney et al., 2008). Based on Table 1 in that report, we note that the ALT tumors are predominantly dedifferentiated liposarcomas, whereas the telomerase tumors are predominantly myxoid/round cell liposarcomas. Thus, a comparison of ALT versus telomerase tumors using this data set suffers from the confounding effect of differing histological subtypes in the two groups. Given the large-scale gene expression changes seen between cells of different origin and tumors of different histologies, it is perhaps not surprising that the 297 gene signature contains a strong component related to differentiation state, as shown in Figure 1a. Dedifferentiated liposarcomas differ markedly from myxoid liposarcomas; different genetic mechanisms drive the formation of these two types of liposarcoma. Dedifferentiated liposarcomas harbor complex karyotypes commonly containing Chr.12q12–15 amplification, whereas 90% of myxoid/round cell liposarcomas are characterized by a t(12;16)(q13–14;p11) translocation. Indeed, translocation driven sarcomas are generally telomerase positive, whereas those with complex karyotypes utilize ALT at an appreciable frequency (Montgomery et al., 2004; Ulaner et al., 2004), underscoring the bias in the sample set analyzed. This likely introduces a major confounding effect in their data set, with the set of ALT tumors heavily biased for dedifferentiated liposarcomas. As the expression signature of dedifferentiated liposarcoma more closely resembles mesenchymal stem cells than does that of myxoid/round cell liposarcoma (Matushansky et al., 2008), this may provide an explanation for their finding that ALT tumors appear to cluster with the mesenchymal stem cell samples. Certainly, our observation that the 297 gene signature fails to distinguish tumors based upon TMM in our independent set of tumors comprising a single histological type of liposarcoma suggests that this signature is not a robust indicator of TMM. Instead, it is likely that this 297-gene signature reflects differentiation differences associated with varying histological subtypes of liposarcoma.