ATRX Protein Research Articles

The ATRX cDNA is prone to bacterial IS10 element insertions that alter its structure

The SWI/SNF-like chromatin-remodeling protein ATRX has emerged as a key factor in the regulation of α-globin gene expression, incorporation of histone variants into the chromatin template and, more recently, as a frequently mutated gene across a wide spectrum of cancers. Therefore, the availability of a functional ATRX cDNA for expression studies is a valuable tool for the scientific community. We have identified two independent transposon insertions of a bacterial IS10 element into exon 8 of ATRX isoform 2 coding sequence in two different plasmids derived from a single source. We demonstrate that these insertion events are common and there is an insertion hotspot within the ATRX cDNA. Such IS10 insertions produce a truncated form of ATRX, which significantly compromises its nuclear localization. In turn, we describe ways to prevent IS10 insertion during propagation and cloning of ATRX-containing vectors, including optimal growth conditions, bacterial strains, and suggested sequencing strategies. Finally, we have generated an insertion-free plasmid that is available to the community for expression studies of ATRX.Electronic supplementary materialThe online version of this article (doi:10.1186/2193-1801-3-222) contains supplementary material, which is available to authorized users.

ATRX Dysfunction Induces Replication Defects in Primary Mouse Cells

The chromatin remodeling protein ATRX, which targets tandem repetitive DNA, has been shown to be required for expression of the alpha globin genes, for proliferation of a variety of cellular progenitors, for chromosome congression and for the maintenance of telomeres. Mutations in ATRX have recently been identified in tumours which maintain their telomeres by a telomerase independent pathway involving homologous recombination thought to be triggered by DNA damage. It is as yet unknown whether there is a central underlying mechanism associated with ATRX dysfunction which can explain the numerous cellular phenomena observed. There is, however, growing evidence for its role in the replication of various repetitive DNA templates which are thought to have a propensity to form secondary structures. Using a mouse knockout model we demonstrate that ATRX plays a direct role in facilitating DNA replication. Ablation of ATRX alone, although leading to a DNA damage response at telomeres, is not sufficient to trigger the alternative lengthening of telomere pathway in mouse embryonic stem cells.

Sp100 Isoform-Specific Regulation of Human Adenovirus 5 Gene Expression

Promyelocytic leukemia nuclear bodies (PML-NBs) are nuclear structures that accumulate intrinsic host factors to restrict viral infections. To ensure viral replication, these must be limited by expression of viral early regulatory proteins that functionally inhibit PML-NB-associated antiviral effects. To benefit from the activating capabilities of Sp100A and simultaneously limit repression by Sp100B, -C, and -HMG, adenoviruses (Ads) employ several features to selectively and individually target these isoforms. Ads induce relocalization of Sp100B, -C, and -HMG from PML-NBs prior to association with viral replication centers. In contrast, Sp100A is kept at the PML tracks that surround the newly formed viral replication centers as designated sites of active transcription. We concluded that the host restriction factors Sp100B, -C, and -HMG are potentially inactivated by active displacement from these sites, whereas Sp100A is retained to amplify Ad gene expression. Ad-dependent loss of Sp100 SUMOylation is another crucial part of the virus repertoire to counteract intrinsic immunity by circumventing Sp100 association with HP1, therefore limiting chromatin condensation. We provide evidence that Ad selectively counteracts antiviral responses and, at the same time, benefits from PML-NB-associated components which support viral gene expression by actively recruiting them to PML track-like structures. Our findings provide insights into novel strategies for manipulating transcriptional regulation to either inactivate or amplify viral gene expression. We describe an adenoviral evasion strategy that involves isoform-specific and active manipulation of the PML-associated restriction factor Sp100. Recently, we reported that the adenoviral transactivator E1A targets PML-II to efficiently activate viral transcription. In contrast, the PML-associated proteins Daxx and ATRX are inhibited by early viral factors. We show that this concept is more intricate and significant than originally believed, since adenoviruses apparently take advantage of specific PML-NB-associated proteins and simultaneously inhibit antiviral measures to maintain the viral infectious program. Specifically, we observed Ad-induced relocalization of the Sp100 isoforms B, C, and HMG from PML-NBs juxtaposed with viral replication centers. In contrast, Sp100A is retained at Ad-induced PML tracks that surround the newly formed viral replication centers, acting as designated sites of active transcription. The host restriction factors Sp100B, -C, and -HMG are potentially inactivated by active displacement from these sites, whereas Sp100A is retained to amplify Ad gene expression.

Clinical Neuropathology practice news 2-2014: ATRX, a new candidate biomarker in gliomas

Genome-wide molecular approaches have substantially elucidated molecular alterations and pathways involved in the oncogenesis of brain tumors. In gliomas, several molecular biomarkers including IDH mutation, 1p/19q co-deletion, and MGMT promotor methylation status have been introduced into neuropathological practice. Recently, mutations of the ATRX gene have been found in various subtypes and grades of gliomas and were shown to refine the prognosis of malignant gliomas in combination with IDH and 1p/19q status. Mutations of ATRX are associated with loss of nuclear ATRX protein expression, detectable by a commercially available antibody, thus turning ATRX into a promising prognostic candidate biomarker in the routine neuropathological setting.

Neuroendocrine Tumors of the Pancreas: Current Concepts and Controversies

In the past decade, the clinico-pathologic characteristics of neuroendocrine tumors (NETs) in the pancreas have been further elucidated. Previously termed "islet cell tumors/carcinomas" or "endocrine neoplasms", they are now called pancreatic NETs (PanNETs). They occur in relatively younger patients and may arise anywhere in the pancreas. Some are associated with von Hippel-Lindau, MEN1, and other syndromes. It is now widely recognized that, with the exception of tumorlets (minute incipient neoplasms) that occur in some syndromes like MEN1, all PanNETs are malignant, albeit low-grade, and although they have a protracted clinical course and overall 10-year survival of 60-70 %, even low-stage and low-grade examples may recur and/or metastasize on long-term follow-up. Per recent consensus guidelines adopted by both European and North American NET Societies (ENETS and NANETs) and WHO-2010, PanNETs are now graded and staged separately, unlike previous classification schemes that used a combination of grade, stage, and adjunct prognosticators in an attempt to define "benign behavior" or "malignant" categories. For staging, the ENETs proposal may be more applicable than CAP/AJCC, which is based on the staging of exocrine tumors. Current grading of PanNETs is based on mitotic activity and ki-67 index. Other promising prognosticators such as necrosis, CK19, c-kit, and others are still under investigation. It has also been recognized that PanNETs have a rather wide morphologic repertoire including oncocytic, pleomorphic, ductulo-insular, sclerosing, and lipid-rich variants. Most PanNETs are diagnosed by fine needle aspiration biopsy, in which single, monotonous plasmacytoid cells with fair amounts of cytoplasm and distinctive neuroendocrine chromatin are diagnostic. Molecular alterations of PanNETs are also very different than that of ductal or acinar tumors. Loss of expression of DAXX and ATRX proteins has been recently identified in 45 %. Along with these improvements, several controversies remain, including grading, value of current cutoff ranges, and the best methods for counting ki-67 index (manual count by computer-captured image may be the most practical for the time being). More important is the controversial use of the term "carcinoma", which was previously employed in WHO-2004 only for invasive and metastatic cases but has now been made synonymous with grade 3 group of tumors. It is becoming clear that grade 3 group comprises two distinct categories: (1) differentiated but proliferatively more active tumors which typically have ki-67 indices in the 20-50 % range and (2) true poorly differentiated NE carcinomas as defined in the lung, with ki-67 typically >50 %. Further studies are needed to address these controversial aspects of PanNETs.

Loss of ATRX Does Not Confer Susceptibility to Osteoarthritis

The chromatin remodelling protein ATRX is associated with the rare genetic disorder ATR-X syndrome. This syndrome includes developmental delay, cognitive impairment, and a variety of skeletal deformities. ATRX plays a role in several basic chromatin-mediated cellular events including DNA replication, telomere stability, gene transcription, and chromosome congression and cohesion during cell division. We have used a loss-of-function approach to directly investigate the role of Atrx in the adult skeleton in three different models of selective Atrx loss. We specifically targeted deletion of Atrx to the forelimb mesenchyme, to cartilage and to bone-forming osteoblasts. We previously demonstrated that loss of ATRX in forelimb mesenchyme causes brachydactyly while deletion in chondrocytes had minimal effects during development. We now show that targeted deletion of Atrx in osteoblasts causes minor dwarfism but does not recapitulate most of the skeletal phenotypes seen in ATR-X syndrome patients. In adult mice from all three models, we find that joints lacking Atrx are not more susceptible to osteoarthritis, as determined by OARSI scoring and immunohistochemistry. These results indicate that while ATRX plays limited roles during early stages of skeletal development, deficiency of the protein in adult tissues does not confer susceptibility to osteoarthritis.

Loss of DAXX and ATRX Are Associated With Chromosome Instability and Reduced Survival of Patients With Pancreatic Neuroendocrine Tumors

Sporadic pancreatic neuroendocrine tumors (pNETs) are rare and genetically heterogeneous. Chromosome instability (CIN) has been detected in pNETs from patients with poor outcomes, but no specific genetic factors have been associated with CIN. Mutations in death domain-associated protein gene (DAXX) or ATR-X gene (ATRX) (which both encode proteins involved in chromatin remodeling) have been detected in 40% of pNETs, in association with activation of alternative lengthening of telomeres. We investigated whether loss of DAXX or ATRX, and consequent alternative lengthening of telomeres, are related to CIN in pNETs. We also assessed whether loss of DAXX orATRX is associated with specific phenotypes of pNETs. We collected well-differentiated primary pNET samples from 142 patients at the University Hospital Zurich and from 101 patients at the University Hospital Bern (both located in Switzerland). Clinical follow-up data were obtained for 149 patients from general practitioners and tumor registries. The tumors were reclassified into 3 groups according to the 2010 World Health Organization classification. Samples were analyzed by immunohistochemistry and telomeric fluorescence in situ hybridization. We correlated loss of DAXX, or ATRX, expression, and activation of alternative lengthening of telomeres with data from comparative genomic hybridization array studies, as well as with clinical and pathological features of the tumors and relapse and survival data. Loss of DAXX or ATRX protein and alternative lengthening of telomeres were associated with CIN in pNETs. Furthermore, loss of DAXX or ATRX correlated with tumor stage and metastasis, reduced time of relapse-free survival, and decreased time of tumor-associated survival. Loss of DAXX or ATRX is associated with CIN in pNETs and shorter survival times of patients. These results support the hypothesis that DAXX- and ATRX-negative tumors are a more aggressive subtype of pNET, and could lead to identification of strategies to target CIN in pancreatic tumors.

Clinicopathologic significance of immunostaining of α-thalassemia/mental retardation syndrome X-linked protein and death domain–associated protein in neuroendocrine tumors

α-Thalassemia/mental retardation syndrome X-linked protein (ATRX) and death domain-associated protein (DAXX) genes are tumor suppressors whose mutations have been identified in sporadic pancreatic neuroendocrine tumors as well as in patients with MEN1. However, it is unknown whether ATRX and DAXX alterations are specific for pancreatic neuroendocrine tumor. In addition, the association of ATRX/DAXX protein loss with tumor cell proliferation has not been examined. We, therefore, immunostained ATRX and DAXX in 10 gastric, 15 duodenal, 20 rectal, 70 pancreatic, and 22 pulmonary neuroendocrine tumors with 15 nonneoplastic pancreases and 27 pancreatic adenocarcinomas to elucidate the site-specific roles of ATRX/DAXX abnormalities. At least 1 loss of ATRX and DAXX immunoreactivity was detected in all neuroendocrine tumor cases but not in any of nonneoplastic pancreatic tissues or pancreatic adenocarcinomas. The loss of DAXX protein was correlated with the Ki-67 index (ATRX, P = .904; DAXX, P = .044). The status of DAXX immunoreactivity correlated positively with World Health Organization histologic grade (P = .026). These results suggest that the status of ATRX or DAXX protein loss in neuroendocrine tumor differed among the organs in which these tumors arose, and these proteins may play site-specific roles in the development of these tumors.

Pericentric Heterochromatin Generated by HP1 Protein Interaction-defective Histone Methyltransferase Suv39h1

Pericentric regions form epigenetically organized silent heterochromatin structures that accumulate histone H3 lysine 9 trimethylation (H3K9me3) and HP1. At pericentric regions, Suv39h is the major enzyme that generates H3K9me3. Suv39h also interacts directly with HP1, a methylated H3K9-binding protein. However, it is not well characterized how HP1 interaction is important for Suv39h accumulation and Suv39h-mediated H3K9me3 formation at the pericentromere. To address this, we introduced the HP1 binding-defective N-terminally truncated mouse Suv39h1 (ΔN) into Suv39h-deficient embryonic stem cells. Interestingly, pericentric accumulation of ΔN and ΔN-mediated H3K9me3 was observed to recover, but HP1 accumulation was only marginally restored. ΔN also rescued DNA methyltransferase Dnmt3a and -3b accumulation and DNA methylation of the pericentromere. In contrast, other pericentric heterochromatin features, such as ATRX protein association and H4K20me3, were not recovered. Finally, derepressed major satellite repeats were partially silenced by ΔN expression. These findings clearly showed that the Suv39h-HP1 binding is dispensable for pericentric H3K9me3 and DNA methylation, but this interaction and HP1 recruitment/accumulation seem to be crucial for complete formation of heterochromatin.

Abstract A06: A novel cell line model of the alternative lengthening of telomeres (ALT) telomere maintenance mechanism

Abstract Unlimited replicative capacity is a key hallmark of cancer that requires the abrogation of telomere attrition due to the end-replication problem. The vast majority of tumors maintain telomere lengths by expressing the enzyme telomerase; however, a subset utilizes a cancer-specific, telomerase-independent telomere maintenance mechanism, termed Alternative Lengthening of Telomeres (ALT). We recently uncovered a strong correlation between ALT and recurrent cancer-associated somatic inactivating mutations in the ATRX and DAXX genes. The ATRX and DAXX proteins form a chromatin remodeling complex with histone chaperone activity, targeting incorporation of the histone variant H3.3 to G-rich repetitive regions of the genome, including the telomeres, which are known to normally be maintained in a repressed heterochromatic state. Here, we have developed an isogenic cell line pair derived from first generation telomerase knock-out (KO) mouse embryonic fibroblasts. Compared to early-passage telomerase KO cells and late passage WT control cells, late-passage telomerase KO cells spontaneously developed the ALT phenotype. These ALT(+) cells display increased DNA damage, as observed by dramatically increased accumulation of γH2AX foci. We plan to use this unique cell line to identify drugs exhibiting selective toxicity for ALT(+) cells. Preliminary results indicate that ALT(+) late-passage telomerase KO cells exhibit an increased sensitivity to the DNA-PK inhibitor NU7441 compared to the isogenic early-passage ALT(-) telomerase KO cells. The identification of bona fide ALT-specific drugs will pave the way for the development of new targeted treatments for the significant number of cancers that harbor this unique molecular phenotype. Citation Format: Christopher M. Heaphy, Michael C. Haffner, Alan K. Meeker. A novel cell line model of the alternative lengthening of telomeres (ALT) telomere maintenance mechanism. [abstract]. In: Proceedings of the AACR Special Conference on Chromatin and Epigenetics in Cancer; Jun 19-22, 2013; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2013;73(13 Suppl):Abstract nr A06.

Abstract A14: Understanding the role of ATRX in the development and progression of glioma

Abstract Gliomas are tumors that arise from glial cells within the brain and spinal cord and account for approximately 30% of all central nervous system neoplasms. Emerging evidence indicates that unique molecular and genetic footprints define glioma subtypes. The Atrx gene is commonly mutated in a subset of gliomas across all tumor grades and within both the pediatric and adult populations. ATRX is a chromatin remodeling protein that is necessary for proper neural development. Loss of ATRX conditionally in the forebrain of the mouse starting at embryonic day 8.5 leads to an increase in replication stress and p53-mediated cortical cell death. Microarray analysis of control and Atrx-null neonatal forebrains indicates a significant increase in the expression of many cancer-related genes. Many of these overexpressed genes are involved in cellular migration, invasion, and epithelial-mesenchymal transition — important cellular phenotypes known to contribute to glioma development. Our data highlight oncogenic signaling pathways that become activated in the absence of the ATRX protein in the brain that may promote tumorigenesis when combined with additional genetic mutations, such as p53 mutations. Citation Format: Hannah E. Goldberg, Kristin D. Kernohan, Nathalie G. Berube. Understanding the role of ATRX in the development and progression of glioma. [abstract]. In: Proceedings of the AACR Special Conference on Chromatin and Epigenetics in Cancer; Jun 19-22, 2013; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2013;73(13 Suppl):Abstract nr A14.

Oocyte heterogeneity with respect to the meiotic silencing of unsynapsed X chromosomes in the XY female mouse

In the XY pachytene spermatocyte, the sex chromosomes do not synapse except for the pseudoautosomal region and become transcriptionally silenced. It has been suggested that the meiotic silencing of unsynapsed chromatin (MSUC) also occurs in oocytes. In the XY sex-reversed female mouse, the sex chromosomes fail to pair in the majority of oocytes and a greater number of oocytes are eliminated during the meiotic prophase compared to the XX female. Yet, many XY oocytes survive to reach the second meiotic metaphase. The goal of our current study was to determine whether the single X chromosome shows the characteristics of asynapsis and meiotic silencing in a proportion of XY oocytes, which can explain the survival of the remaining oocytes. We first examined the accumulation of markers associated with asynapsis or transcriptional silencing, i.e., BRCA1, γH2AX, H3K9me3, and H3K27me3, at the single X chromosome in the XY oocyte. We found that γH2AX and BRCA1 were enriched on the single X chromosome whereas H3K9me3 was not, and H3K27me3 was enriched at all chromosomes in the majority of XY oocytes. We next examined the meiotic silencing of the single X chromosome using enrichment of the X-encoded ATRX protein. On average, ATRX enrichment was lower in XY oocytes than in XX oocytes as expected from its half gene dosage. However, the intensity of ATRX staining in XY oocytes harboring γH2AX domains showed a remarkable heterogeneity. We conclude that MSUC occurs with varying consequences, resulting in a heterogeneous population of oocytes with respect to protein enrichment in the XY female mouse.

Neuroradiologic Features in X-linked α-Thalassemia/Mental Retardation Syndrome

X-linked α-thalassemia/mental retardation syndrome (Mendelian Inheritance in Man, 301040) is one of the X-linked intellectual disability syndromes caused by mutations of the ATRX gene and characterized by male predominance, central hypotonic facies, severe cognitive dysfunction, hemoglobin H disease (α-thalassemia), genital and skeletal abnormalities, and autistic and peculiar behavior. More than 200 patients in the world, including >70 Japanese patients, have been diagnosed with ATR-X syndrome. We reviewed the brain MRI and/or CT findings of 27 Japanese patients with ATR-X with ATRX mutations retrospectively. The findings were categorized into 5 types: 1) nonspecific brain atrophy (17/27); 2) white matter abnormalities, especially around the trigones (11/27); 3) widespread and scattered white matter abnormalities (1/27); 4) delayed myelination (4/27); and 5) severe and rapidly progressive cortical brain atrophy (1/27). This is the first report on a comprehensive study of brain MRI/CT findings of ATR-X syndrome. Our findings suggest that the ATRX protein seems to be involved in normal myelination. The classification will require revisions in the near future, but it will be helpful in establishing the relationship between ATRX mutation and brain development and understanding the ATRX protein function in the brain.

In silico analysis of detrimental mutations in ADD domain of chromatin remodeling protein ATRX that cause ATR-X syndrome: X-linked disorder

Many biological functions involve specific interactions of proteins. Mutations in ATRX gene can change the sequence and structure of a protein thereby impairing its function. Thus, the dysfunction of chromatin remodeling protein ATRX as a result of amino acid substitution in ADD domain often underlies the human disease, ATR-X syndrome. In general, it is mainly caused by amino acid substitution that interfered with the interactions of interest at the interface level. Hence, the study of protein–protein interactions and the interface that mediate the interactions stand important for understanding of biological function. In this work, we address the loss of function in chromatin remodeling protein ATRX due to loss of structural stability that affect the functional activity in mutant ADD domain by 17 missense mutations viz., G175E, N179S, P190A, P190L, P190S, L192F, V194I, C200S, Q219P, C220R, C220Y, W222S, C243F, R246C, R246L, G249C, and G249D. Furthermore, the loss of binding affinity of ADD domain with their interacting partner namely histone H3-peptide were investigated by (1) computing the RMSD (root mean square deviation) for the ADD domain of native with all the 17 mutants, (2) computing intra-molecular interactions in ADD domain of native with all the mutants, (3) computing binding affinity of native and mutant structures of ADD domain with histone H3-peptide through docking studies, and (4) cross validating the loss of function on binding affinity through inter-molecular interactions and normal mode analysis. Finally, as from our computational result, we concluded that all the parameters mentioned above used for studying ADD domain of mutant structures showed the decreased potential values compared to native structure that underlie ATR-X syndrome.

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

Molecular and Morphologic Correlates of the Alternative Lengthening of Telomeres Phenotype in High‐Grade Astrocytomas

Recent studies suggest that the telomere maintenance mechanism known as alternative lengthening of telomeres (ALT) is relatively more common in specific glioma subsets and strongly associated with ATRX mutations. We retrospectively examined 116 high-grade astrocytomas (32 pediatric glioblastomas, 65 adult glioblastomas, 19 anaplastic astrocytomas) with known ALT status using tissue microarrays to identify associations with molecular and phenotypic features. Immunohistochemistry was performed using antibodies against ATRX, DAXX, p53 and IDH1(R132H) mutant protein. EGFR amplification was evaluated by fluorescence in situ hybridization (FISH). Almost half of fibrillary and gemistocytic astrocytomas (44%) demonstrated ALT. Conversely all gliosarcomas (n = 4), epithelioid (n = 2), giant cell (n = 2) and adult small cell astrocytomas (n = 7) were ALT negative. The ALT phenotype was positively correlated with the presence of round cells (P = 0.002), microcysts (P < 0.0002), IDH1 mutant protein (P < 0.0001), ATRX protein loss (P < 0.0001), strong P53 immunostaining (P < 0.0001) and absence of EGFR amplification (P = 0.004). There was no significant correlation with DAXX expression. We conclude that ALT represents a specific phenotype in high-grade astrocytomas with distinctive pathologic and molecular features. Future studies are required to clarify the clinical and biological significance of ALT in high-grade astrocytomas.

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.

Association of Age at Diagnosis and Genetic Mutations in Patients With Neuroblastoma

Neuroblastoma is diagnosed over a wide age range from birth through young adulthood, and older age at diagnosis is associated with a decline in survivability. To identify genetic mutations that are associated with age at diagnosis in patients with metastatic neuroblastoma. Whole genome sequencing was performed on DNA from diagnostic tumors and their matched germlines from 40 patients with metastatic neuroblastoma obtained between 1987 and 2009. Age groups at diagnosis included infants (0-<18 months), children (18 months-<12 years), and adolescents and young adults (≥12 years). To confirm the findings from this discovery cohort, validation testing using tumors from an additional 64 patients obtained between 1985 and 2009 also was performed. Formalin-fixed, paraffin-embedded tumor tissue was used for immunohistochemistry and fluorescence in situ hybridization. Telomere lengths were analyzed using whole genome sequencing data, quantitative polymerase chain reaction, and fluorescent in situ hybridization. Somatic recurrent mutations in tumors from patients with neuroblastoma correlated with the age at diagnosis and telomere length. In the discovery cohort (n = 40), mutations in the ATRX gene were identified in 100% (95% CI, 50%-100%) of tumors from patients in the adolescent and young adult group (5 of 5), in 17% (95% CI, 7%-36%) of tumors from children (5 of 29), and 0% (95% CI, 0%-40%) of tumors from infants (0 of 6). In the validation cohort (n = 64), mutations in the ATRX gene were identified in 33% (95% CI, 17%-54%) of tumors from patients in the adolescent and young adult group (9 of 27), in 16% (95% CI, 6%-35%) of tumors from children (4 of 25), and in 0% (95% CI, 0%-24%) of tumors from infants (0 of 12). In both cohorts (N = 104), mutations in the ATRX gene were identified in 44% (95% CI, 28%-62%) of tumors from patients in the adolescent and young adult group (14 of 32), in 17% (95% CI, 9%-29%) of tumors from children (9 of 54), and in 0% (95% CI, 0%-17%) of tumors from infants (0 of 18). ATRX mutations were associated with an absence of the ATRX protein in the nucleus and with long telomeres. ATRX mutations were associated with age at diagnosis in children and young adults with stage 4 neuroblastoma. clinicaltrials.gov Identifier: NCT00588068.

Herpesvirus saimiri antagonizes nuclear domain 10-instituted intrinsic immunity via an ORF3-mediated selective degradation of cellular protein Sp100.

In recent studies, the nuclear domain 10 (ND10) components PML, Sp100, human Daxx (hDaxx), and ATRX were identified to be cellular restriction factors that are able to inhibit the replication of several herpesviruses. The antiviral function of ND10, however, is antagonized by viral effector proteins by a variety of strategies, including degradation of PML or relocalization of ND10 proteins. In this study, we analyzed the interplay between infection with herpesvirus saimiri (HVS), the prototypic rhadinovirus, and cellular defense by ND10. In contrast to other herpesviruses, we found that HVS specifically degraded the cellular ND10 component Sp100, whereas other factors like PML or hDaxx remained intact. We could further identify the ORF3 tegument protein of HVS, which shares homology with the cellular formylglycinamide ribotide amidotransferase (FGARAT) enzyme, to be the viral factor that induces the proteasomal degradation of Sp100. Interestingly, recent studies showed that the ORF3-homologous proteins ORF75c of murine gammaherpesvirus 68 and BNRF-1 of Epstein-Barr virus modulate the ND10 proteins PML and ATRX, respectively, suggesting that the ND10 targets of viral FGARAT-homologous proteins diversified during evolution. Furthermore, a virus with the ORF3 deletion was efficiently complemented in Sp100-depleted cells, indicating that Sp100 is able to inhibit HVS in the absence of antagonistic mechanisms. In contrast, we observed that PML, which was neither degraded nor redistributed after HVS infection, strongly restricted both wild-type HVS and virus with the ORF3 deletion. Thus, HVS may lack a factor that efficiently counteracts the repressive function of PML, which may foster latency as the outcome of infection.

ATRX in chromatin assembly and genome architecture during development and disease

The regulation of genome architecture is essential for a variety of fundamental cellular phenomena that underlie the complex orchestration of mammalian development. The ATP-dependent chromatin remodeling protein ATRX is emerging as a key regulatory component of nucleosomal dynamics and higher order chromatin conformation. Here we provide an overview of the role of ATRX at chromatin and during development, and discuss recent studies exposing a repertoire of ATRX functions at heterochromatin, in gene regulation, and during mitosis and meiosis. Exciting new progress on several fronts suggest that ATRX operates in histone variant deposition and in the modulation of higher order chromatin structure. Not surprisingly, dysfunction or absence of ATRX protein has devastating consequences on embryonic development and leads to human disease.