Alternative Lengthening Of Telomeres Research Articles

Maintenance of R-loop structures by phosphorylated hTERT preserves genome integrity.

As aberrant accumulation of RNA-DNA hybrids (R-loops) causes DNA damage and genome instability, cells express regulators of R-loop structures. Here we report that RNA-dependent RNA polymerase (RdRP) activity of human telomerase reverse transcriptase (hTERT) regulates R-loop formation. We found that the phosphorylated form of hTERT (p-hTERT) exhibits RdRP activity in nuclear speckles both in telomerase-positive cells and telomerase-negative cells with alternative lengthening of telomeres (ALT) activity. The p-hTERT did not associate with telomerase RNA component in nuclear speckles but, instead, with TERRA RNAs to resolve R-loops. Targeting of the TERT gene in ALT cells ablated RdRP activity and impaired tumour growth. Using a genome-scale CRISPR loss-of-function screen, we identified Fanconi anaemia/BRCA genes as synthetic lethal partners of hTERT RdRP. Inactivation of RdRP and Fanconi anaemia/BRCA genes caused accumulation of R-loop structures and DNA damage. These findings indicate that RdRP activity of p-hTERT guards against genome instability by removing R-loop structures.

Pan-cancer analysis of telomere maintenance mechanisms.

Telomeres, protective caps at chromosome ends, maintain genomic stability and control cell lifespan. Dysregulated telomere maintenance mechanisms (TMM) are cancer hallmarks, enabling unchecked cell proliferation. We conducted a pan-cancer evaluation of TMM using RNA sequencing data from The Cancer Genome Atlas (TCGA) for 33 different cancer types and analyzed the activities of telomerase-dependent (TEL) and alternative lengthening of telomeres (ALT) TMM pathways in detail. To further characterize the TMM profiles, we categorized the tumors based on their ALT and TEL TMM pathway activities into five major phenotypes: ALT high TEL low, ALT low TEL low, ALT middle TEL middle, ALT high TEL high, and ALT low TEL high. These phenotypes refer to variations in telomere maintenance strategies, shedding light on the heterogeneous nature of telomere regulation in cancer. Moreover, we investigated the clinical implications of TMM phenotypes by examining their associations with clinical characteristics and patient outcomes. Specific TMM profiles were linked to specific survival patterns, emphasizing the potential of TMM profiling as a prognostic indicator and aiding in personalized cancer treatment strategies. Gene ontology analysis of the TMM phenotypes unveiled enriched biological processes associated with cell cycle regulation (both TEL and ALT), DNA replication (TEL), and chromosome dynamics (ALT) showing that telomere maintenance is tightly intertwined with cellular processes governing proliferation and genomic stability. Overall, our study provides an overview of the complexity of transcriptional regulation of telomere maintenance mechanisms in cancer.

Orphan nuclear receptors-induced ALT-associated PML bodies are targets for ALT inhibition.

Orphan nuclear receptors (NRs), such as COUP-TF1, COUP-TF2, EAR2, TR2and TR4, are implicated in telomerase-negative cancers that maintain their telomeres through the alternative lengthening of telomeres (ALT) mechanism. However, how telomere association of orphan NRs is involved in ALT activation remains unclear. Here, we demonstrate that telomeric tethering of orphan NRs in human fibroblasts initiates formation of ALT-associated PML bodies (APBs) and features of ALT activity, including ALT telomere DNA synthesis, telomere sister chromatid exchange, and telomeric C-circle generation, suggesting de novo ALT induction. Overexpression of orphan NRs exacerbates ALT phenotypes in ALT cells, while their depletion limits ALT. Orphan NRs initiate ALT via the zinc finger protein 827, suggesting the involvement of chromatin structure alterations for ALT activation. Furthermore, we found that orphan NRs and deficiency of the ALT suppressor ATRX-DAXX complex operate in concert to promote ALT activation. Moreover, PML depletion by gene knockout or arsenic trioxide treatment inhibited ALT induction in fibroblasts and ALT cancer cells, suggesting that APB formation underlies the orphan NR-induced ALT activation. Importantly, arsenic trioxide administration abolished APB formation and features of ALT activity in ALT cancer cell line-derived mouse xenografts, suggesting its potential for further therapeutic development to treat ALT cancers.

Extrachromosomal telomere DNA derived from excessive strand displacements

Alternative lengthening of telomeres (ALT) is a telomere maintenance mechanism mediated by break-induced replication, evident in approximately 15% of human cancers. A characteristic feature of ALT cancers is the presence of C-circles, circular single-stranded telomeric DNAs composed of C-rich sequences. Despite the fact that extrachromosomal C-rich single-stranded DNAs (ssDNAs), including C-circles, are unique to ALT cells, their generation process remains undefined. Here, we introduce a method to detect single-stranded telomeric DNA, called 4SET (Strand-Specific Southern-blot for Single-stranded Extrachromosomal Telomeres) assay. Utilizing 4SET, we are able to capture C-rich single-stranded DNAs that are near 200 to 1500 nucleotides in size. Both linear C-rich ssDNAs and C-circles are abundant in the fractions of cytoplasm and nucleoplasm, which supports the idea that linear and circular C-rich ssDNAs are generated concurrently. We also found that C-rich ssDNAs originate during Okazaki fragment processing during lagging strand DNA synthesis. The generation of C-rich ssDNA requires CST-PP (CTC1/STN1/TEN1-PRIMASE-Polymerase alpha) complex-mediated priming of the C-strand DNA synthesis and subsequent excessive strand displacement of the C-rich strand mediated by the DNA Polymerase delta and the BLM helicase. Our work proposes a model for the generation of C-rich ssDNAs and C-circles during ALT-mediated telomere elongation.

Abstract LT07: Signalling Inhibition by Ponatinib Disrupts Productive Alternative Lengthening of Telomeres (ALT)

Abstract Enabling replicative immortality is one prominent feature of cancer cells. To that end, cancer cells activate means to elongate their telomeres. While 85% of cancers re-express telomerase, around 15% of all cancers rely on the ALT (Alternative Lengthening of Telomeres) mechanism. Despite its frequency, no clinically approved ALT-targeted therapy exists to date. By performing anti-cancer compound library screen on isogenic cell lines and using extrachromosomal telomeric C-circles, as a bona fide marker of ALT activity, we identified a receptor tyrosine kinase inhibitor, ponatinib, that deregulates ALT mechanisms, induces telomeric dysfunction, reduced ALT- associated telomere synthesis, and targets, in vivo, ALT-positive cells. By scrutinizing the mode of action of ponatinib on ALT, we identified an ABL1-JNK-JUN signalling circuit to be inhibited by ponatinib and to have a role in suppressing extrachromosomal telomeric C-circle formation. Furthermore, transcriptome and interactome analyses of JUN suggested a role of JUN in DNA damage repair pathways, independently of its capacity as a transcription factor. These results were corroborated by new synergistic drug interactions between ponatinib and either DNA synthesis or repair inhibitors such as triciribine and KU-60019, respectively. Overall, we identified a novel signalling pathway impacting ALT which can be targeted by a clinically approved kinase inhibitor. Citation Format: Frances Kusuma, Aishvaryaa Prabhu, Galen Tieo, Syed Moiz Ahmad, Pushkar Dakle, Wai Khang Yong, Elina Pathak, Vikas Madan, Yan Yi Jiang, Wai Leong Tam, Dennis Kappei, Peter Dröge, H. Phillip Koeffler, Maya Jeitany. Signalling Inhibition by Ponatinib Disrupts Productive Alternative Lengthening of Telomeres (ALT) [abstract]. In: Proceedings of Frontiers in Cancer Science; 2023 Nov 6-8; Singapore. Philadelphia (PA): AACR; Cancer Res 2024;84(8_Suppl):Abstract nr LT07.

BLM helicase unwinds lagging strand substrates to assemble the ALT telomere damage response

The Bloom syndrome (BLM) helicase is critical for alternative lengthening of telomeres (ALT), a homology-directed repair (HDR)-mediated telomere maintenance mechanism that is prevalent in cancers of mesenchymal origin. The DNA substrates that BLM engages to direct telomere recombination during ALT remain unknown. Here, we determine that BLM helicase acts on lagging strand telomere intermediates that occur specifically in ALT-positive cells to assemble a replication-associated DNA damage response. Loss of ATRX was permissive for BLM localization to ALT telomeres in S and G2, commensurate with the appearance of telomere C-strand-specific single-stranded DNA (ssDNA). DNA2 nuclease deficiency increased 5'-flap formation in a BLM-dependent manner, while telomere C-strand, but not G-strand, nicks promoted ALT. These findings define the seminal events in the ALT DNA damage response, linking aberrant telomeric lagging strand DNA replication with a BLM-directed HDR mechanism that sustains telomere length in a subset of human cancers.

Abstract 3949: SMARCAL1 is a novel synthetic lethal target in ALT+ osteosarcoma and neuroblastoma

Abstract Osteosarcoma (OS) is an aggressive pediatric solid tumor that is difficult to treat with established therapies. We performed CRISPR/Cas9 screening in 13 OS cell lines as part of the Dependency Map project. Mining this data to identify genes whose knockout (KO) leads to selective anti-viability in OS, we observed the helicase SMARCAL1 as a selective dependency in OS (p<0.0001; effect size = -0.275). Given the genomic instability of OS and SMARCAL1’s related, established role in replication stress, we first validated our screens by CRISPR KO in OS lines in vitro. This demonstrated selective antiviability of SMARCAL1 KO in dependent OS lines. To orthogonally validate SMARCAL1 dependency, we deployed a dTAG system, utilizing a hetero-bifunctional small molecule targeting the tagged protein for degradation by an E3 ubiquitin ligase. We observed antiviability of dependent lines after SMARCAL1 degradation. In parallel, in order to ascertain importance of this gene in vivo, we performed a barcoded CRISPR pooled screen against pre-selected OS dependencies in an OS cell line xenograft in NSG mice. After sequencing of tumor gDNA, we identified SMARCAL1 as a top hit, suggesting relevance in vivo.We next investigated biomarkers of SMARCAL1 dependency. A role for SMARCAL1 has been described in alternative lengthening of telomeres (ALT). We asked whether ALT+ OS cell lines are enriched for SMARCAL1 dependency. We found a correlation between ALT+ OS and SMARCAL1 dependence in our CRISPR screens. We then asked if this extends to other ALT+ tumors. Neuroblastoma (NB), the most common extracranial pediatric solid tumor, is enriched for ALT. When we looked specifically at NB models, we observed that SMARCAL1 was the most enriched dependency in ALT+ NB compared with other NB lines (p<0.0001; effect size = -0.785). We then performed SMARCAL1 KO in 2 ALT+ ATRX-altered NB lines and one ALT+ ATRX-WT NB line. We found that SMARCAL1 KO led to antiviability in the ATRX-altered ALT+ cell lines, while the ALT+ ATRX-WT cell line was unaffected. This suggests that dependency on SMARCAL1 is specific to ATRX alteration, rather than ALT alone.In order to confirm synthetic lethality between ATRX and SMARCAL1, we next utilized a human OS line not included in the DepMap screen, which has biallelic inactivation of SMARCAL1. We infected this line with our SMARCAL1 dTAG, leading to constitutive overexpression of SMARCAL1, and then performed ATRX KO. We observed that SMARCAL1 overexpression rescued the antiviability effect of ATRX KO. This could be reversed by degradation of exogenous SMARCAL1, suggesting that ATRX and SMARCAL1 can compensate for one another. Taken together, these findings demonstrate that SMARCAL1 is a selective dependency engendered by the loss of WT ATRX in OS and NB and that SMARCAL1 is playing a critical role in mediating ALT. Studies are ongoing to determine the mechanism of SMARCAL1’s activity and potential for targeting this enzyme for therapeutic benefit. Citation Format: Monika Wierdl, Jerrel L. Catlett, Nicole Ocasio-Martinez, Jon D. Johnson, Amy Herman, Neekesh V. Dharia, Gabriela Alexe, E. Alejandro Sweet-Cordero, Emily Bernstein, Kimberly Stegmaier, Lillian M. Guenther. SMARCAL1 is a novel synthetic lethal target in ALT+ osteosarcoma and neuroblastoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3949.

Abstract 418: BLM helicase unwinds lagging strand substrates to assemble the ALT telomere damage response

Abstract The Bloom Syndrome helicase (BLM) is critical for Alternative Lengthening of Telomeres (ALT), a homology directed repair mediated telomere maintenance mechanism that is prevalent in cancers of mesenchymal origin. The DNA substrates that BLM engages to direct telomere recombination during ALT remain unknown. Here, we determine that BLM helicase acts on lagging strand telomere intermediates that occur specifically in ALT positive cells to assemble a replication stress associated DNA damage response. Loss of ATRX was permissive for BLM localization to ALT telomeres in S and G2 commensurate with the appearance of telomere C-strand specific single-stranded DNA. Moreover, DNA2 nuclease deficiency increased 5’-lagging strand flap formation and ALT in a BLM dependent manner, and BLM promoted ALT in response to telomere C-strand, but not G-strand, single-stranded nicks. These findings define the seminal events in the ALT DNA damage response, linking aberrant lagging strand DNA replication with a BLM directed HDR mechanism that sustains telomere length in a subset of human cancers. Citation Format: Aravind M. Krishnan, Haoyang Jiang, Tianpeng Zhang, Hardeep Kaur, Tao Shi, Youngho Kwon, Patrick Sung, Roger A. Greenberg. BLM helicase unwinds lagging strand substrates to assemble the ALT telomere damage response [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 418.

Abstract 2995: The ectopic expression of miR-380-5p interferes with the aggressive traits of diffuse malignant peritoneal mesothelima cells

Abstract Telomerase activity (TA) and the alternative lengthening of telomere (ALT) pathway are two telomere maintenance mechanisms (TMM) yet identified in human cancers. Although the activation of either TMM seems to be equivalent in supporting tumor cell immortalization (a hallmark of cancer), the contribution of TA and ALT to tumor progression and aggressiveness may be different. Mounting evidence suggests that cancer cell aggressiveness could be associated with a TA↔ALT shift that would allow the acquisition of distinct aggressive traits. We previously showed that an ALT-like phenotype emerged in diffuse malignant peritoneal mesothelioma (DMPM) cells upon miR-380-5p-dependent inhibition of TA (Cimino-Reale G, et al. J Hematol Oncol. 2017). To analyze the transcriptomic changes associated with the emergence of such a phenotype, gene expression profiling was carried out. Results showed that 3331 genes were differentially expressed (FDR<0.05, adjusted for multiple hypothesis testing) in miR-380-5p- vs. preNeg-transfected DMPM cells, out of which 1673 genes were up-regulated and 1658 genes down-regulated. To get biological meaning about the molecular events occurring upon miR-380-5p reconstitution, Gene Set Enrichment Analysis was performed. Results showed a positive enrichment of 188 gene sets, restricted for an FDR < 0.05, out of which signatures related to DNA replication, DNA recombination and telomere maintenance via recombination were present. Conversely, only 1 gene set (GO: positive regulation of blood vessel endothelial cell migration) was negatively enriched at significant level. Notably, among the leading edge genes, PTGS2, which encodes for cyclooxygenase-2 (COX-2) and represents a predicted target of miR-380-5p (miRWalk), was the most significantly down-regulated gene (FDR< 0.000001; log(fold-change): -2.15). Notably, a complete abrogation of PTGS2 expression levels and COX-2 protein amounts was observed in miR-380-5p- compared to preNeg-transfected cells upon validation by qRT-PCR and western blotting, respectively. This evidence was paralleled by reduced amounts of phospho-FAK (focal adhesion kinase) and impaired migrating/invading capabilities of cells ectopically expressing miR-380-5p. Moreover, a reduction of Vimentin and a slight increase in P-Cadherin protein levels were also observed in cells ectopically expressing miR-380-5p, likely indicating the occurrence of a reverse-EMT program. Finally, a pronounced increase in the sensitivity to Cisplatin and Doxorubicin was also appreciable in miR-380-5p- vs. preNeg-transfected cells, suggesting that miRNA-mediated induction of a reverse-EMT may, at least in part, contribute to improve the response of DMPM cells to chemotherapeutic drugs. Citation Format: Stefano Percio, Lorenzo Di Pietro, Eisa Naghshineh, Marcello Deraco, Nadia Zaffaroni, Marco Folini. The ectopic expression of miR-380-5p interferes with the aggressive traits of diffuse malignant peritoneal mesothelima cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 2995.

Abstract 3009: ATRX loss blocks the differentiation of mesenchymal stem cells and promotes undifferentiated sarcoma development

Abstract Soft tissue sarcomas (STSs) are a collection of rare tumor types originated from the mesenchymal tissues. Among the over 70 histological subtypes of STS, undifferentiated sarcoma (US), which lacks any discernible morphological features of differentiated tissues, accounts for over 20% of all STSs and is correlated with high tumor grade and poor prognosis. Recent genomic profiling in US has identified p53 and ATRX among the most frequently mutated or deleted genes. ATRX is a SWI/SNF2 type of chromatin remodeling factor which functions in a histone variant H3.3-specific chaperone complex to orchestrates replication-independent nucleosome assembly at repetitive heterochromatic DNA regions including telomeres. Loss-of-function mutations occur frequently in many tumor types and is associated with the development of alternative lengthening of telomere (ALT). However, how loss of ATRX function may contribute to tumorigenesis is largely unknown. Here, we demonstrated that ATRX is required for the terminal differentiation of mouse mesenchymal stem cells (MSCs) into multiple lineages, such as adipocytes and osteocytes. Targeted deletion of Atrx in mouse MSCs, but not terminally differentiated mesenchymal lineage cells, accelerated sarcoma initiation induced by loss of p53 and significantly shortened the overall survival. Atrx-deficient tumors express high level of MSC markers such as CD44 and CD29 and exhibit pathological features highly reminiscent of human high-grade US. Transcriptomic analysis indicates that Atrx deficiency is associated with enhanced proliferation. Together, our data indicates that ATRX deficiency contributes to undifferentiated sarcoma development by inhibiting mesenchymal stem cell differentiation. Citation Format: Yiming Cai, Jun Yao, Dean N. Pan, Yanqiang Jin, James M. You, Wantong Yao, Haoqiang Ying. ATRX loss blocks the differentiation of mesenchymal stem cells and promotes undifferentiated sarcoma development [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3009.

KU70 and CAF-1 in Arabidopsis: Divergent roles in rDNA stability and telomere homeostasis.

Deficiency in chromatin assembly factor-1 (CAF-1) in plants through dysfunction of its components, FASCIATA1 and 2 (FAS1, FAS2), leads to the specific and progressive loss of rDNA and telomere repeats in plants. This loss is attributed to defective repair mechanisms for the increased DNA breaks encountered during replication, a consequence of impaired replication-dependent chromatin assembly. In this study, we explore the role of KU70 in these processes. Our findings reveal that, although the rDNA copy number is reduced in ku70 mutants when compared with wild-type plants, it is not markedly affected by diverse KU70 status in fas1 mutants. This is consistent with our previous characterisation of rDNA loss in fas mutants as a consequence part of the single-strand annealing pathway of homology-dependent repair. In stark contrast to rDNA, KU70 dysfunction fully suppresses the loss of telomeres in fas1 plants and converts telomeres to their elongated and heterogeneous state typical for ku70 plants. We conclude that the alternative telomere lengthening pathway, known to be activated in the absence of KU70, overrides progressive telomere loss due to CAF-1 dysfunction.

Telomere maintenance mechanisms in neuroblastoma: New insights and translational implications

The clinical behaviour of neuroblastoma ranges from spontaneous tumour regression or maturation into benign ganglioneuroma to fatal progression despite intensive treatment [1,2]. The mechanisms underlying the distinct phenotypes have remained uncertain yet. A number of recent studies noticed that activation of telomere maintenance mechanisms (TMM) in the malignant neuroblasts is strongly associated with high-risk disease and poor outcome, whereas TMM are absent in spontaneously regressing low-risk tumours, suggesting that telomere maintenance is essential to drive neuroblasts into the fully malignant state. Stabilization of the telomeres above a critical threshold is essential for cancer cells to gain replicative immortality and has thus been considered a hallmark of cancer [3]. In most high-risk neuroblastomas, TMM is conferred by induction of telomerase, either through genomic rearrangements of the TERT locus, encoding for the catalytic subunit of telomerase, or amplification of the MYCN proto-oncogene, whereas the alternative lengthening of telomeres (ALT) pathway is activated in approximately one-quarter of high-risk tumours [4–8]. We here review recent advances on our understanding of the mechanistic role of telomere maintenance in neuroblastoma pathogenesis, and discuss potential implications on neuroblastoma risk assessment and on the development of novel therapies directed against TMM.

ATR limits Rad18-mediated PCNA monoubiquitination to preserve replication fork and telomerase-independent telomere stability.

Upon replication fork stalling, the RPA-coated single-stranded DNA (ssDNA) formed behind the fork activates the ataxia telangiectasia-mutated and Rad3-related (ATR) kinase, concomitantly initiating Rad18-dependent monoubiquitination of PCNA. However, whether crosstalk exists between these two events and the underlying physiological implications of this interplay remain elusive. In this study, we demonstrate that during replication stress, ATR phosphorylates human Rad18 at Ser403, an adjacent residue to a previously unidentified PIP motif (PCNA-interacting peptide) within Rad18. This phosphorylation event disrupts the interaction between Rad18 and PCNA, thereby restricting the extent of Rad18-mediated PCNA monoubiquitination. Consequently, excessive accumulation of the tumor suppressor protein SLX4, now characterized as a novel reader of ubiquitinated PCNA, at stalled forks is prevented, contributing to the prevention of stalled fork collapse. We further establish that ATR preserves telomere stability in alternative lengthening of telomere (ALT) cells by restricting Rad18-mediated PCNA monoubiquitination and excessive SLX4 accumulation at telomeres. These findings shed light on the complex interplay between ATR activation, Rad18-dependent PCNA monoubiquitination, and SLX4-associated stalled fork processing, emphasizing the critical role of ATR in preserving replication fork stability and facilitating telomerase-independent telomere maintenance.

TERRA-LSD1 phase separation promotes R-loop formation for telomere maintenance in ALT cancer cells

The telomere repeat-containing RNA (TERRA) forms R-loops to promote homology-directed DNA synthesis in the alternative lengthening of telomere (ALT) pathway. Here we report that TERRA contributes to ALT via interacting with the lysine-specific demethylase 1A (LSD1 or KDM1A). We show that LSD1 localizes to ALT telomeres in a TERRA dependent manner and LSD1 function in ALT is largely independent of its demethylase activity. Instead, LSD1 promotes TERRA recruitment to ALT telomeres via RNA binding. In addition, LSD1 and TERRA undergo phase separation, driven by interactions between the RNA binding properties of LSD1 and the G-quadruplex structure of TERRA. Importantly, the formation of TERRA-LSD1 condensates enriches the R-loop stimulating protein Rad51AP1 and increases TERRA-containing R-loops at telomeres. Our findings suggest that LSD1-TERRA phase separation enhances the function of R-loop regulatory molecules for ALT telomere maintenance, providing a mechanism for how the biophysical properties of histone modification enzyme-RNA interactions impact chromatin function.

TERRA and the alternative lengthening of telomeres: a dangerous affair.

Eukaryotic telomeres are transcribed into the long noncoding RNA TERRA. A fraction of TERRA remains associated with telomeres by forming RNA:DNA hybrids dubbed telR-loops. TERRA and telR-loops are essential to promote telomere elongation in human cancer cells that maintain telomeres through a homology-directed repair pathway known as alternative lengthening of telomeres or ALT. However, TERRA and telR-loops compromise telomere integrity and cell viability if their levels are not finely tuned. The study of telomere transcription in ALT cells will enormously expand our understanding of the ALT mechanism and of how genome integrity is maintained. Moreover, telomere transcription, TERRA and telR-loops are likely to become exceptionally suited targets for the development of novel anti-cancer therapies.

The C250T Mutation of TERTp Might Grant a Better Prognosis to Glioblastoma by Exerting Less Biological Effect on Telomeres and Chromosomes Than the C228T Mutation.

TERTp mutations were assessed in a retrospective cohort of 258 uniformly treated glioblastoma patients. RNA-sequencing and whole exome sequencing results were available in a subset of patients. Overall, there were no differences in outcomes between patients with mutated TERTp-wt or TERTp. However, we found significant differences according to the type of TERTp mutation. Progression-free survival (mPFS) was 9.1 months for those with the C250T mutation and 7 months for those with either the C228T mutation or TERTp-wt (p = 0.016). Overall survival (mOS) was 21.9 and 15 months, respectively (p = 0.026). This differential effect was more pronounced in patients with MGMTp methylation (mPFS: p = 0.008; mOS: p = 0.021). Multivariate analysis identified the C250T mutation as an independent prognostic factor for longer mOS (HR 0.69; p = 0.044). We found no differences according to TERTp mutation status in molecular alterations common in glioblastoma, nor in copy number variants in genes related to alternative lengthening of telomeres. Nevertheless, in the gene enrichment analysis adjusted for MGMTp methylation status, some Reactome gene sets were differentially enriched, suggesting that the C250T mutation may exert a lesser effect on telomeres or chromosomes. In our series, patients exhibiting the C250T mutation had a more favorable prognosis compared to those with either TERPp-wt or TERTp C228T mutations. Additionally, our findings suggest a reduced involvement of the C250T mutation in the underlying biological mechanisms related to telomeres.

Unzipped genome assemblies of polyploid root-knot nematodes reveal unusual and clade-specific telomeric repeats

Using long-read sequencing, we assembled and unzipped the polyploid genomes of Meloidogyne incognita, M. javanica and M. arenaria, three of the most devastating plant-parasitic nematodes. We found the canonical nematode telomeric repeat to be missing in these and other Meloidogyne genomes. In addition, we find no evidence for the enzyme telomerase or for orthologs of C. elegans telomere-associated proteins, suggesting alternative lengthening of telomeres. Instead, analyzing our assembled genomes, we identify species-specific composite repeats enriched mostly at one extremity of contigs. These repeats are G-rich, oriented, and transcribed, similarly to canonical telomeric repeats. We confirm them as telomeric using fluorescent in situ hybridization. These repeats are mostly found at one single end of chromosomes in these species. The discovery of unusual and specific complex telomeric repeats opens a plethora of perspectives and highlights the evolutionary diversity of telomeres despite their central roles in senescence, aging, and chromosome integrity.

Mechanisms of telomere maintenance and associated therapeutic vulnerabilities in malignant gliomas.

A majority of cancers (~85%) activate the enzyme telomerase to maintain telomere length over multiple rounds of cellular division. Telomerase-negative cancers activate a distinct, telomerase-independent mechanism of telomere maintenance termed Alternative lengthening of telomeres (ALT). ALT uses homologous recombination to maintain telomere length and exhibits features of break-induced DNA replication. In malignant gliomas, the activation of either telomerase or ALT is nearly ubiquitous in pediatric and adult tumors, and the frequency with which these distinct telomere maintenance mechanisms is activated varies according to genetically-defined glioma subtypes. In this review, we summarize the current state of the field of telomere maintenance mechanisms (TMMs) and their relevance to glioma biology and therapy. We review the genetic alterations and molecular mechanisms leading to telomerase activation or ALT induction in pediatric and adult gliomas. With this background, we review emerging evidence on strategies for targeting TMMs for glioma therapy. Finally, we comment on critical gaps and issues for moving the field forward to translate our improved understanding of glioma telomere maintenance into better therapeutic strategies for patients.

Effects of p53 and ATRX inhibition on telomeric recombination in aging fibroblasts

In order to avoid replicative senescence, tumor cells must acquire a telomere maintenance mechanism. Beside telomerase activation, a minority of tumors employs a recombinational mechanism called Alternative Lengthening of Telomeres (ALT). Several studies have investigated the potential ALT stimulation by inactivation of ATRX in tumor cells, obtaining contrasting results. Differently, since ALT can be viewed as a mechanism to overcome telomere shortening-mediated replicative senescence, we have investigated the effects of the inhibition of ATRX and p53 in aging primary fibroblasts. We observed that senescence leads to a phenotype that seems permissive for ALT activity, i.e. high levels of ALT-associated PML bodies (APB), telomeric damage and telomeric cohesion. On the other hand, RAD51 is highly repressed and thus telomeric recombination, upon which the ALT machinery relies, is almost absent. Silencing of ATRX greatly increases telomeric recombination in young cells, but is not able to overcome senescence-induced repression of homologous recombination. Conversely, inhibition of both p53 and ATRX leads to a phenotype reminiscent of some aspects of ALT activity, with a further increase of APB, a decrease of telomere shortening (and increased proliferation) and, above all, an increase of telomeric recombination.

The Role of Glia Telomere Dysfunction in the Pathogenesis of Central Nervous System Diseases.

Maintaining the telomere length is decisive for the viability and homeostasis process of all the cells of an organism, including human glial cells. Telomere shortening of microglial cells has been widely associated with the onset and progression of neurodegenerative diseases such as Parkinson's and Alzheimer's disease. Additionally, traumatic brain injury appears to have a positive correlation with the telomere-shortening process of microglia, and telomere length can be used as a non-invasive biomarker for the clinical management of these patients. Moreover, telomere involvement through telomerase reactivation and homologous recombination also known as the alternative lengthening of telomeres (ALT) has been described in gliomagenesis pathways, and particular focus has been given in the translational significance of these mechanisms in gliomas diagnosis and prognostic classification. Finally, glia telomere shortening is implicated in some psychiatric diseases. Given that telomere dysfunction of glial cells is involved in the central nervous system (CNS) disease pathogenesis, it represents a promising drug target that could lead to the incorporation of new tools in the medicinal arsenal for the management of so far incurable conditions.