Nuclear interaction of Arp2/3 complex and BRAFV600E promotes aggressive behavior and vemurafenib resistance of thyroid cancer.

The presence of mutant BRAF V600E correlates with the risk of recurrence in papillary thyroid cancer (PTC) patients. However, not all PTC patients with BRAF V600E are associated with poor prognosis. Thus, understanding the mechanisms by which certain PTC patients with nuclear BRAF V600E become aggressive and develop resistance to a selective BRAF inhibitor, PLX-4032, is urgently needed. The effect of nuclear localization of BRAFV600E using in vitro studies, xenograft mouse-model and human tissues was evaluated. PTC cells harboring a nuclear localization signal (NLS) of BRAFV600E were established and examined in nude mice implanted with TPC1-NLS-BRAFV600E cells followed by PLX-4032 treatment. Immunohistochemical (IHC) analysis was performed on 100 PTC specimens previously confirmed that they have BRAFV600E mutations. Our results demonstrate that 21 of 100 (21%) PTC tissues stained with specific BRAFV600E antibody had nuclear staining with more aggressive features compared to their cytosolic counterparts. In vitro studies show that BRAFV600E is transported between the nucleus and the cytosol through CRM1 and importin (α/ß) system. Sequestration of BRAFV600E in the cytosol sensitized resistant cells to PLX-4032, whereas nuclear BRAFV600E was associated with aggressive phenotypes and developed drug resistance. Proteomic analysis revealed Arp2/3 complex members, actin-related protein 2 (ACTR2 aliases ARP2) and actin-related protein 3 (ACTR3 aliases ARP3), as the most enriched nuclear BRAFV600E partners. ACTR3 was highly correlated to lymph node stage and extrathyroidal extension and was validated with different functional assays. Our findings provide new insights into the clinical utility of the nuclear BRAFV600E as a prognostic marker for PTC aggressiveness and determine the efficacy of selective BRAFV600E inhibitor treatment which opens new avenues for future treatment options.

Prognostic Role of BRAFV600E Cellular Localization in Melanoma.

BACKGROUND: Approximately half of cutaneous melanoma tissues harbor BRAFV600E mutations, resulting in a constitutive activation of the mitogen-activated protein kinase (MAPK) pathway. Nuclear-cytoplasmic transport machinery is dysregulated in neoplastic cells and alters the key regulatory proteins that can lead to tumor progression and drug resistance. The significance of nuclear localization of BRAFV600E has not been fully understood. We examined the clinical significance of intracellular localization of BRAFV600E in cutaneous melanoma. STUDY DESIGN: Immunohistochemical analysis of BRAFV600E was performed on formalin-fixed, paraffin-embedded specimens of cutaneous melanoma (n = 91). Staining intensity was graded in a blinded manner. Correlations to clinical factors were analyzed by Fisher's exact test and 2-tailed t-test. Localization of BRAFV600E was determined in melanoma cells, and we investigated their resistance to BRAFV600E-specific inhibitor according to nuclear localization in both in vitro and in vivo models. RESULTS: We included 91 patients, of whom 32% (29 of 91) had cytoplasmic BRAFV600E. Nuclear BRAFV600E was observed in 30% (27 of 91). Overall, BRAFV600E expression correlated with TNM stage (p = 0.011), mitotic activity (p = 0.010), and ulceration (p = 0.045). Nuclear BRAFV600E expression correlated with overall clinical stage (p < 0.001), tumor size (p < 0.001), regional lymph node (p < 0.017), depth of invasion (p = 0.005), Clark level (p < 0.001), mitotic activity (p < 0.001), ulceration (p < 0.001), and margin status (p = 0.017). On a cellular level, BRAFV600E was identified in the nucleus, and its translocation was serum dependent. Our in vitro and in vivo data revealed sequestration of BRAFV600E in the cytosol-sensitized resistant cells to vemurafenib; nuclear retention of BRAFV600E was associated with aggressiveness and drug resistance. CONCLUSIONS: Nuclear localization of BRAFV600E is associated with melanoma aggressiveness. Further multi-institutional studies are warranted to confirm the clinical relevance of nuclear localization of BRAFV600E.

Bortezomib sensitizes thyroid cancer to BRAF inhibitor in vitro and in vivo.

Although overall survival rate for patients with thyroid cancer (TC) is high, there is an alarming 10-year recurrence rate of up to 30% conferring a ~50% survival among these high-risk patients. The BRAFV600E mutation is estimated to be present in over 50% of papillary thyroid cancer (PTC) cases besides being associated with carcinogenesis and poor prognosis. We assessed the status of NF-κB, Ki-67, cyclin D1 and BRAFV600E in TC tissues and TC cell lines using immunohistochemistry and Western blot analysis. Concurrently, we evaluated the outcomes of combined targeting of the proteasome pathway in addition to selective BRAF inhibitors in cases of PTC. In this study, BRAFV600E-bearing TC cells were treated with BRAFV600E inhibitor, Vemurafenib alone or in combination with the proteasome inhibitor, Bortezomib. The combination of both drugs showed synergistic effects as evidenced by cell growth inhibition (P < 0.05), increased G2-phase cell cycle arrest and induced apoptosis (P < 0.05). In our TC xenograft model, the combination of Vemurafenib and Bortezomib significantly reduced tumor size (P < 0.05) and expression of the markers of cell growth and proliferation, Ki-67 and cyclin D1 (P < 0.001), when compared to monotherapy. Further analysis demonstrated that treatment with Bortezomib sensitized TC cells to Vemurafenib via mitochondrial dysregulation and apoptosis of TC cells, as evidenced by the increase in the expression of p53, Noxa protein, the loss of mitochondrial membrane potential, cytochrome c release and Poly (ADP-ribose) polymerase cleavage. Our results demonstrate a strong clinical potential for the combination of the Bortezomib and the BRAF inhibitor Vemurafenib as an efficient therapeutic approach for the treatment of TC.

Incomplete MyoD-induced transdifferentiation is associated with chromatin remodeling deficiencies.

Our current understanding of cellular transdifferentiation systems is limited. It is oftentimes unknown, at a genome-wide scale, how much transdifferentiated cells differ quantitatively from both the starting cells and the target cells. Focusing on transdifferentiation of primary human skin fibroblasts by forced expression of myogenic transcription factor MyoD, we performed quantitative analyses of gene expression and chromatin accessibility profiles of transdifferentiated cells compared to fibroblasts and myoblasts. In this system, we find that while many of the early muscle marker genes are reprogrammed, global gene expression and accessibility changes are still incomplete when compared to myoblasts. In addition, we find evidence of epigenetic memory in the transdifferentiated cells, with reminiscent features of fibroblasts being visible both in chromatin accessibility and gene expression. Quantitative analyses revealed a continuum of changes in chromatin accessibility induced by MyoD, and a strong correlation between chromatin-remodeling deficiencies and incomplete gene expression reprogramming. Classification analyses identified genetic and epigenetic features that distinguish reprogrammed from non-reprogrammed sites, and suggested ways to potentially improve transdifferentiation efficiency. Our approach for combining gene expression, DNA accessibility, and protein-DNA binding data to quantify and characterize the efficiency of cellular transdifferentiation on a genome-wide scale can be applied to any transdifferentiation system.

Immunohistochemistry as an accurate tool for evaluating BRAF-V600E mutation in 130 samples of papillary thyroid cancer.

BACKGROUND: BRAFV600E mutation has been investigated by immunohistochemistry and has shown high sensitivity and specificity. We aim to investigate the accuracy of immunohistochemistry versus molecular testing of BRAFV600E in papillary thyroid cancer using a large number of polymerase chain reaction-positive BRAFV600E papillary thyroid cancer tissues. METHODS: We stained 130 formalin-fixed papillary thyroid cancer specimens using the VE1 antibody: 100 BRAFV600E positive and 30 BRAFV600E negative confirmed by PCR. The sensitivity, specificity, and predictive values of the antibody were assessed. RESULTS: Immunohistochemistry of BRAFV600E showed 98.0% sensitivity, 93.3% specificity, and positive and negative predictive values of 98.0% and 93.3%, respectively. Of 100 patients with BRAFV600E PCR-positive samples, 97 (97.0%) had cytoplasmic weak (4.0%), moderate (17.0%), and strong (76.0%) immunostaining. In BRAFV600E PCR-negative samples, cytoplasmic staining was not detected in 93.3% (28/30) of papillary thyroid cancer tissues. The receiver operating characteristic curve demonstrated a high validity and comparable immunohistochemistry method (area under the curve = 98.8%) compared with PCR testing. CONCLUSION: The use of VE1 immunohistochemistry for the detection of BRAFV600E in papillary thyroid cancer tissues is a clinically applicable method with high specificity, sensitivity, and positive and negative predictive values. The reliable use of BRAFV600E immunohistochemistry should promulgate the routine use of this method for BRAFV600E detection in papillary thyroid cancer tissues.

Immunohistochemistry as a reliable method for detection of BRAF-V600E mutation in melanoma: a systematic review and meta-analysis of current published literature.

BACKGROUND: The BRAF-V600E mutation is associated with tumor aggressiveness and poor prognosis in melanoma patients. Identification of this mutation is clinically important as we now have Food and Drug Administration-approved targeted therapies, such as BRAF and MEK inhibitors, which have been shown to retard disease progression in these patients. Detection of BRAF-V600E by genetic analysis using polymerase chain reaction is the gold standard method for melanoma cases. However, immunohistochemistry (IHC) using a VE1 antibody is rapidly emerging as a trustworthy method for the determination of mutation status in patients' specimens. Our objective in this study was to assess the reliability of IHC compared with genetic methods for successful identification of BRAF-V600E mutation in melanoma tissue specimens. METHODS: A literature search of PubMed, Web of Science, and Embase was performed for studies comparing IHC with genetic analysis for the detection of BRAF in melanoma patients published through May 28, 2015. Pooled sensitivity, specificity, diagnostic odds ratio, positive, and negative likelihood ratios were calculated using a bivariate model. Logit estimates of sensitivity and specificity with their respective variances were used to plot a hierarchical receiver operating characteristic curve and area under the curve. Heterogeneity was assessed using the Q- and I-squared statistics. RESULTS: An initial literature search resulted in 287 articles. After two independent reviews and consensus-based discussion to resolve disparities, 21 studies involving a total of 1687 cases met the eligibility criteria and were included in the analysis. The pooled sensitivity of IHC for BRAF-V600E detection was 0.96; 95% confidence interval (CI, 0.94-0.98), specificity 1.00; 95% CI (0.97-1.00), positive likelihood ratio 194.2; 95% CI (37.6-1003.3), negative likelihood ratio 0.04; 95% CI (0.02-0.07), and diagnostic odds ratio 5503 (1199-25,263), as compared with genetic analysis. A high heterogeneity was observed between these studies (Q value of 40.17 & I(2) = 95%; 95% CI (91-99, P < 0.001) which may be explained by studies using different cutoff values for labeling IHC as positive. High accuracy of IHC was depicted by area under the curve in the receiver operating characteristic curve which was 0.99; 95 % CI (0.98-1.00). CONCLUSIONS: Meta-analysis demonstrates that IHC is highly sensitive and specific for the detection of BRAF-V600E in melanoma cases. IHC is likely to be useful in BRAF mutation detection because it is highly comparable with the genetic methods. Any negative or low staining cases may be selected to undergo genetic analysis based on other clinical and histopathologic features.

Metadherin Expression is Associated with Extrathyroidal Extension in Papillary Thyroid Cancer Patients.

BACKGROUND: Metadherin (MTDH) is widely recognized as a promising molecular marker for tumor recurrence and poor survival in many cancers. By multiple pathways, MTDH promotes oncogenesis, metastasis, and chemoresistance. This study investigated the role of MTDH in papillary thyroid carcinoma (PTC) to determine its potential association with aggressive clinical and pathologic features, including its relation in tumors harboring a BRAF (V600E) mutation. METHODS: Expression of MTDH was assessed by immunohistochemistry in 96 cases of PTC, including primary thyroid malignancies and lymph node metastases. The status of BRAF (V600E) mutation was determined by real-time polymerase chain reaction. RESULTS: Overexpression of MTDH was observed in 26 % (23/88) of primary PTC cases. High-intensity staining was observed in 75 % (6/8) of lymph nodes with metastatic PTC and moderate staining in 25 % (2/8) of cases. Normal adjacent thyroid tissue and benign thyroid controls were found to have significantly lower MTDH expression than cancer tissue (p < 0.05). Apical staining of MTDH was observed in 19 % of thyroid tumors and not observed in normal thyroid tissue. Interestingly, MTDH expression was associated with extrathyroidal extension (p < 0.05) and not associated with age, gender, overall tumor stage, or BRAF (V600E) mutation status. CONCLUSION: In a subset of PTC patients, MTDH was overexpressed and associated with extrathyroidal extension. Further studies are warranted to explore the utility of MTDH to improve risk stratification of current molecular panels for PTC.

Simultaneous suppression of the MAP kinase and NF-κB pathways provides a robust therapeutic potential for thyroid cancer.

The MAP kinase and NF-κB signaling pathways play an important role in thyroid cancer tumorigenesis. We aimed to examine the therapeutic potential of dually targeting the two pathways using AZD6244 and Bortezomib in combination. We evaluated their effects on cell proliferation, cell-cycle progression, apoptosis, cell migration assay, and the activation of the MAPK pathway in vitro and the in vivo using tumor size and immunohistochemical changes of Ki67 and ppRB. We found inhibition of cell growth rate by 10%, 20%, and 56% (p <0.05), migration to 55%, 61%, and 29% (p <0.05), and induction of apoptosis to 10%, 15%, and 38% (p <0.05) with AZD6244, Bortezomib, or combination, respectively. Induction of cell cycle arrest occurred only with drug combination. Dual drug treatment in the xenograft model caused a 94% reduction in tumor size (p <0.05) versus 15% with AZD6244 and 34% with Bortezomib (p < 0.05) and also reduced proliferative marker Ki67, and increased pRb dephosphorylation. Our results demonstrate a robust therapeutic potential of combining AZD6244 and Bortezomib as an effective strategy to overcome drug resistance encountered in monotherapy in the treatment of thyroid cancer, strongly supporting clinical trials to further test this strategy.

Stem cell biology in thyroid cancer: Insights for novel therapies.

Currently, thyroid cancer is one of the most common endocrine cancer in the United States. A recent involvement of sub-population of stem cells, cancer stem cells, has been proposed in different histological types of thyroid cancer. Because of their ability of self-renewal and differentiation into various specialized cells in the body, these putative cells drive tumor genesis, metastatic activity and are responsible to provide chemo- and radioresistant nature to the cancer cells in the thyroid gland. Our Review was conducted from previously published literature to provide latest apprises to investigate the role of embryonic, somatic and cancer stem cells, and discusses the hypothesis of epithelial-mesenchymal transition. Different methods for their identification and isolation through stemness markers using various in vivo and in vitro methods such as flow cytometry, thyrosphere formation assay, aldehyde dehydrogenase activity and ATP-binding cassette sub-family G member 2 efflux-pump mediated Hoechst 33342 dye exclusion have been discussed. The review also outlines various setbacks that still remain to target these tumor initiating cells. Future perspectives of therapeutic strategies and their potential to treat advanced stages of thyroid cancer are also disclosed in this review.

A novel mouse model of metastatic thyroid carcinoma using human adipose tissue-derived stromal/stem cells.

BACKGROUND/AIM: Scientists have been in quest for the best in vivo model to evaluate chemotherapies for radioiodine-resistant metastatic thyroid carcinomas. Human adipose tissue-derived stromal/stem cells (ASCs) have been found to promote in vitro growth and in vivo tumorigenesis. In the present study, we describe a novel model of metastatic human thyroid carcinoma by combining ASCs with the papillary thyroid cancer, K1 cell line. MATERIALS AND METHODS: Three groups of severe combined immunodefecient mice were investigated. The first group was injected subcutaneously with K1 cells plus ASCs, the second group with K1 cell only, and the last group with ASCs only. Mean tumor volumes and standard deviations were calculated and compared. RESULTS: Concomitant injection of ASCs with the K1 cell line led to the development of significantly larger tumors compared to the other groups (p<0.05). In addition, the lungs of this group demonstrated gross tumor metastasis and pathological features of high-grade neoplasms. CONCLUSION: In the present study we describe a novel mouse model using ASCs with the potential to be used for assessment of new treatments for the management of metastatic thyroid carcinomas.

DNA methylation and differentiation: HOX genes in muscle cells.

BACKGROUND: Tight regulation of homeobox genes is essential for vertebrate development. In a study of genome-wide differential methylation, we recently found that homeobox genes, including those in the HOX gene clusters, were highly overrepresented among the genes with hypermethylation in the skeletal muscle lineage. Methylation was analyzed by reduced representation bisulfite sequencing (RRBS) of postnatal myoblasts, myotubes and adult skeletal muscle tissue and 30 types of non-muscle-cell cultures or tissues. RESULTS: In this study, we found that myogenic hypermethylation was present in specific subregions of all four HOX gene clusters and was associated with various chromatin epigenetic features. Although the 3' half of the HOXD cluster was silenced and enriched in polycomb repression-associated H3 lysine 27 trimethylation in most examined cell types, including myoblasts and myotubes, myogenic samples were unusual in also displaying much DNA methylation in this region. In contrast, both HOXA and HOXC clusters displayed myogenic hypermethylation bordering a central region containing many genes preferentially expressed in myogenic progenitor cells and consisting largely of chromatin with modifications typical of promoters and enhancers in these cells. A particularly interesting example of myogenic hypermethylation was HOTAIR, a HOXC noncoding RNA gene, which can silence HOXD genes in trans via recruitment of polycomb proteins. In myogenic progenitor cells, the preferential expression of HOTAIR was associated with hypermethylation immediately downstream of the gene. Other HOX gene regions also displayed myogenic DNA hypermethylation despite being moderately expressed in myogenic cells. Analysis of representative myogenic hypermethylated sites for 5-hydroxymethylcytosine revealed little or none of this base, except for an intragenic site in HOXB5 which was specifically enriched in this base in skeletal muscle tissue, whereas myoblasts had predominantly 5-methylcytosine at the same CpG site. CONCLUSIONS: Our results suggest that myogenic hypermethylation of HOX genes helps fine-tune HOX sense and antisense gene expression through effects on 5' promoters, intragenic and intergenic enhancers and internal promoters. Myogenic hypermethylation might also affect the relative abundance of different RNA isoforms, facilitate transcription termination, help stop the spread of activation-associated chromatin domains and stabilize repressive chromatin structures.

Synergistic inhibition of thyroid cancer by suppressing MAPK/PI3K/AKT pathways.

BACKGROUND: Although a wide spectrum of inhibitors of the MEK/ERK and PI3K/AKT pathways have been discovered and entered clinical trials, the effects of their individual use in thyroid cancer were often disappointing. We hypothesized that dual targeting of these two pathways would be a safe and effective strategy against aggressive thyroid cancers. METHODS: We examined the antiproliferative effects of the MEK/ERK inhibitor AZD6244 and the PI3K/AKT inhibitor GDC0941, individually or in combination, on thyroid cancer cells harboring both the BRAF(V600E) and PIK3CA mutations. The effects of drug exposure on both total and phosphorylated (p-) forms of AKT and ERK were monitored by Western blotting analysis. Effects of these inhibitors on cell-cycle progression and apoptosis were measured by flow cytometry and DNA-fragmentation analyses, respectively. RESULTS: We observed significant toxicities to viability of cells with low concentrations of AZD6244 or GDC0941, which were synergistic when the two inhibitors were used in combination (P < 0.01). AZD6244 abrogated p-ERK and GDC0941 abrogated p-AKT levels, confirming their expected target effects. Unexpectedly, monotherapy with AZD6244 resulted in activation of the PI3K signaling pathway in some cancer cell lines and co-exposure to AZD6244 and GDC0941 was necessary to suppress both pathways. Flow cytometry showed G1 arrest. DNA fragmentation analysis showed an increased apoptosis of cells dually treated with the two inhibitors. CONCLUSION: Concomitant suppression of MEK/ERK and PI3K/AKT pathways by AZD6244 and GDC0941 abrogates compensatory mechanisms of tumor survival and causes synergistic cytotoxicity in thyroid cancer cells.

Early de novo DNA methylation and prolonged demethylation in the muscle lineage.

Myogenic cell cultures derived from muscle biopsies are excellent models for human cell differentiation. We report the first comprehensive analysis of myogenesis-specific DNA hyper- and hypo-methylation throughout the genome for human muscle progenitor cells (both myoblasts and myotubes) and skeletal muscle tissue vs. 30 non-muscle samples using reduced representation bisulfite sequencing. We also focused on four genes with extensive hyper- or hypo-methylation in the muscle lineage (PAX3, TBX1, MYH7B/MIR499 and OBSCN) to compare DNA methylation, DNaseI hypersensitivity, histone modification, and CTCF binding profiles. We found that myogenic hypermethylation was strongly associated with homeobox or T-box genes and muscle hypomethylation with contractile fiber genes. Nonetheless, there was no simple relationship between differential gene expression and myogenic differential methylation, rather only for subsets of these genes, such as contractile fiber genes. Skeletal muscle retained ~30% of the hypomethylated sites but only ~3% of hypermethylated sites seen in myogenic progenitor cells. By enzymatic assays, skeletal muscle was 2-fold enriched globally in genomic 5-hydroxymethylcytosine (5-hmC) vs. myoblasts or myotubes and was the only sample type enriched in 5-hmC at tested myogenic hypermethylated sites in PAX3/CCDC140 andTBX1. TET1 and TET2 RNAs, which are involved in generation of 5-hmC and DNA demethylation, were strongly upregulated in myoblasts and myotubes. Our findings implicate de novo methylation predominantly before the myoblast stage and demethylation before and after the myotube stage in control of transcription and co-transcriptional RNA processing. They also suggest that, in muscle, TET1 or TET2 are involved in active demethylation and in formation of stable 5-hmC residues.

DNA replication timing is maintained genome-wide in primary human myoblasts independent of D4Z4 contraction in FSH muscular dystrophy.

Facioscapulohumeral muscular dystrophy (FSHD) is linked to contraction of an array of tandem 3.3-kb repeats (D4Z4) at 4q35.2 from 11-100 copies to 1-10 copies. The extent to which D4Z4 contraction at 4q35.2 affects overall 4q35.2 chromatin organization remains unclear. Because DNA replication timing is highly predictive of long-range chromatin interactions, we generated genome-wide replication-timing profiles for FSHD and control myogenic precursor cells. We compared non-immortalized myoblasts from four FSHD patients and three control individuals to each other and to a variety of other human cell types. This study also represents the first genome-wide comparison of replication timing profiles in non-immortalized human cell cultures. Myoblasts from both control and FSHD individuals all shared a myoblast-specific replication profile. In contrast, male and female individuals were readily distinguished by monoallelic differences in replication timing at DXZ4 and other regions across the X chromosome affected by X inactivation. We conclude that replication timing is a robust cell-type specific feature that is unaffected by FSHD-related D4Z4 contraction.

Gene expression during normal and FSHD myogenesis.

BACKGROUND: Facioscapulohumeral muscular dystrophy (FSHD) is a dominant disease linked to contraction of an array of tandem 3.3-kb repeats (D4Z4) at 4q35. Within each repeat unit is a gene, DUX4, that can encode a protein containing two homeodomains. A DUX4 transcript derived from the last repeat unit in a contracted array is associated with pathogenesis but it is unclear how. METHODS: Using exon-based microarrays, the expression profiles of myogenic precursor cells were determined. Both undifferentiated myoblasts and myoblasts differentiated to myotubes derived from FSHD patients and controls were studied after immunocytochemical verification of the quality of the cultures. To further our understanding of FSHD and normal myogenesis, the expression profiles obtained were compared to those of 19 non-muscle cell types analyzed by identical methods. RESULTS: Many of the ~17,000 examined genes were differentially expressed (>2-fold, p<0.01) in control myoblasts or myotubes vs. non-muscle cells (2185 and 3006, respectively) or in FSHD vs. control myoblasts or myotubes (295 and 797, respectively). Surprisingly, despite the morphologically normal differentiation of FSHD myoblasts to myotubes, most of the disease-related dysregulation was seen as dampening of normal myogenesis-specific expression changes, including in genes for muscle structure, mitochondrial function, stress responses, and signal transduction. Other classes of genes, including those encoding extracellular matrix or pro-inflammatory proteins, were upregulated in FSHD myogenic cells independent of an inverse myogenesis association. Importantly, the disease-linked DUX4 RNA isoform was detected by RT-PCR in FSHD myoblast and myotube preparations only at extremely low levels. Unique insights into myogenesis-specific gene expression were also obtained. For example, all four Argonaute genes involved in RNA-silencing were significantly upregulated during normal (but not FSHD) myogenesis relative to non-muscle cell types. CONCLUSIONS: DUX4's pathogenic effect in FSHD may occur transiently at or before the stage of myoblast formation to establish a cascade of gene dysregulation. This contrasts with the current emphasis on toxic effects of experimentally upregulated DUX4 expression at the myoblast or myotube stages. Our model could explain why DUX4's inappropriate expression was barely detectable in myoblasts and myotubes but nonetheless linked to FSHD.

DNaseI hypersensitivity at gene-poor, FSH dystrophy-linked 4q35.2.

A subtelomeric region, 4q35.2, is implicated in facioscapulohumeral muscular dystrophy (FSHD), a dominant disease thought to involve local pathogenic changes in chromatin. FSHD patients have too few copies of a tandem 3.3-kb repeat (D4Z4) at 4q35.2. No phenotype is associated with having few copies of an almost identical repeat at 10q26.3. Standard expression analyses have not given definitive answers as to the genes involved. To investigate the pathogenic effects of short D4Z4 arrays on gene expression in the very gene-poor 4q35.2 and to find chromatin landmarks there for transcription control, unannotated genes and chromatin structure, we mapped DNaseI-hypersensitive (DH) sites in FSHD and control myoblasts. Using custom tiling arrays (DNase-chip), we found unexpectedly many DH sites in the two large gene deserts in this 4-Mb region. One site was seen preferentially in FSHD myoblasts. Several others were mapped >0.7 Mb from genes known to be active in the muscle lineage and were also observed in cultured fibroblasts, but not in lymphoid, myeloid or hepatic cells. Their selective occurrence in cells derived from mesoderm suggests functionality. Our findings indicate that the gene desert regions of 4q35.2 may have functional significance, possibly also to FSHD, despite their paucity of known genes.

Epigenetics of a tandem DNA repeat: chromatin DNaseI sensitivity and opposite methylation changes in cancers.

DNA methylation and chromatin DNaseI sensitivity were analyzed in and adjacent to D4Z4 repeat arrays, which consist of 1 to approximately 100 tandem 3.3-kb units at subtelomeric 4q and 10q. D4Z4 displayed hypomethylation in some cancers and hypermethylation in others relative to normal tissues. Surprisingly, in cancers with extensive D4Z4 methylation there was a barrier to hypermethylation spreading to the beginning of this disease-associated array (facioscapulohumeral muscular dystrophy, FSHD) despite sequence conservation in repeat units throughout the array. We infer a different chromatin structure at the proximal end of the array than at interior repeats, consistent with results from chromatin DNaseI sensitivity assays indicating a boundary element near the beginning of the array. The relative chromatin DNaseI sensitivity in FSHD and control myoblasts and lymphoblasts was as follows: a non-genic D4Z4-adjacent sequence (p13E-11, array-proximal)> untranscribed gene standards > D4Z4 arrays> constitutive heterochromatin (satellite 2; P < 10(-4) for all comparisons). Cancers displaying D4Z4 hypermethylation also exhibited a hypermethylation-resistant subregion within the 3.3-kb D4Z4 repeat units. This subregion contains runs of G that form G-quadruplexes in vitro. Unusual DNA structures might contribute to topological constraints that link short 4q D4Z4 arrays to FSHD and make long ones phenotypically neutral.

Hybridization analysis of D4Z4 repeat arrays linked to FSHD.

Facioscapulohumeral muscular dystrophy (FSHD) is an autosomal dominant disease involving shortening of D4Z4, an array of tandem 3.3-kb repeat units on chromosome 4. These arrays are in subtelomeric regions of 4q and 10q and have 1-100 units. FSHD is associated with an array of 1-10 units at 4q35. Unambiguous clinical diagnosis of FSHD depends on determining the array length at 4q35, usually with the array-adjacent p13E-11 probe after pulsed-field or linear gel electrophoresis. Complicating factors for molecular diagnosis of FSHD are the phenotypically neutral 10q D4Z4 arrays, cross-hybridizing sequences elsewhere in the genome, deletions including the genomic p13E-11 sequence and part of D4Z4, translocations between 4q and 10q D4Z4 arrays, and the extremely high G + C content of D4Z4 arrays (73%). In this study, we optimized conditions for molecular diagnosis of FSHD with a 1-kb D4Z4 subfragment probe after hybridization with p13E-11. We demonstrate that these hybridization conditions allow the identification of FSHD alleles with deletions of the genomic p13E-11 sequence and aid in determination of the nonpathogenic D4Z4 arrays at 10q. Furthermore, we show that the D4Z4-like sequences present elsewhere in the genome are not tandemly arranged, like those at 4q35 and 10q26.

Postoperative prognosis of node-negative breast cancers predicted by gene-expression profiling on a cDNA microarray of 25,344 genes.

BACKGROUND: In Japan, postoperative relapse occurs within five years in 9.2 to 16% of patients whose breast cancers have not metastasized to lymph nodes at the time of initial surgery(node-negative, n0). Attempts to find molecular markers able to classify n0 breast cancers in terms of postoperative prognosis have not been successful. METHODS: To identify molecular indicators of prognosis for this type of cancer, we used a cDNA microarray consisting of 25,344 human genes to investigate expression profiles of 12 primary breast cancers from patients whose tumors recurred within five years after surgery(5Y-R) and 12 from patients who survived disease-free for more than five years (5Y-F). RESULTS: Sets of genes characterizing each group in terms of expression patterns in the tumors were selected by Mann-Whitney and random-permutation tests: these panels included 21 genes expressed highly in 5Y-R tumors than in 5Y-F tumors, and 37 with higher expression in the 5Y-F group than in the 5Y-R group. CONCLUSIONS: We established a scoring system to prediction of postoperative prognosis which was 100% accurate as to the actual clinical outcomes of the 24 cases and therefore might be useful for predicting prognosis of n0 breast cancers in a clinical setting. The prognostic score system clearly separated the two groups without any overlap, and accurately predicted prognosis in 6 additional cases. Moreover, the extensive list of tumor-related genes identified in these experiments provides valuable information about progression of breast cancer and suggests potential target molecules for therapy of n0 breast cancers.

A DNA repeat, NBL2, is hypermethylated in some cancers but hypomethylated in others.

Hypermethylation at certain CpG-rich promoters and hypomethylation at repeated DNA sequences are very frequently found in cancers. We provide the first report that a DNA sequence (NBL2) can be either extensively hypermethylated or hypomethylated in cancer. Previously, it was shown that NBL2, a complex tandem DNA repeat in the acrocentric chromosomes, is hypomethylated at NotI sites in >70% of neuroblastomas and hepatocellular carcinomas and in cells from ICF syndrome (DNMT3B-deficiency) patients. Unexpectedly, by Southern blot analysis of 18 ovarian carcinomas, 51 Wilms tumors, and various somatic control tissues, we found that >70% of the cancers exhibited large increases in methylation at HhaI sites in NBL2 compared with all the controls. In contrast, 17% of the carcinomas showed major decreases in methylation at HhaI and NotI sites. The intermediate levels of methylation at HhaI sites in somatic controls enabled this discovery of cancer-linked hypermethylation and hypomethylation in NBL2. In a comparison of ovarian epithelial carcinomas, low malignant potential tumors, and cystadenomas, NBL2 hypermethylation at HhaI sites was significantly related to the degree of malignancy, and hypomethylation was seen only in the carcinomas. By RT-PCR, we found NBL2 transcripts at low levels in a few cancers and undetectable in various normal tissues. In the tumors there was no association of NBL2 hypomethylation and transcription, but this may reflect NBL2's lack of identifiable promoter elements and our evidence for run-through transcription from adjacent sequences into NBL2. The propensity of NBL2 sequences to become either hypermethylated or hypomethylated in cancer suggests that these opposite epigenetic changes share an early step during carcinogenesis and that cancer-linked hypermethylation might be spontaneously reversible.