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Epigenetic dysregulation and poorer prognosis in DAXX-deficient pancreatic neuroendocrine tumours.

Pipinikas CP, Dibra H, Karpathakis A, Feber A, Novelli M, Oukrif D, Fusai G, Valente R, Caplin M, Meyer T, Teschendorff A, Bell C, Morris TJ, Salomoni P, Luong TV, Davidson B, Beck S, Thirlwell C - Endocr. Relat. Cancer (2015)

View Article: PubMed Central - PubMed

Affiliation: Medical Genomics Laboratory, University College London Cancer Institute, University College London72 Huntley Street, London, WC1E 6BT, UK.

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Exome sequencing of sporadic pancreatic neuroendocrine tumours (PNETs) has identified mutually exclusive mutations in the chromatin regulators α-thalassaemia/mental retardation X-linked (ATRX) and death-associated protein 6 (DAXX) genes in 43% of cases (18 and 23% of cases respectively in 68 cases studied)... Although it was initially reported that ATRX/DAXX mutant tumours had superior 10-year survival and outcome, a recent larger study on 243 tumours demonstrated that ATRX and DAXX loss and associated ALT in PNETs correlates with CIN, advanced tumour stage, the development of metastases and poorer progression-free survival (PFS) and overall survival (OS)... Mutually exclusive mutations in ATRX and DAXX are also found in neurological tumours, including neuroblastomas, paediatric glioblastomas, oligodendrogliomas and medulloblastomas... Notably, H3.3 is mutated in paediatric glioblastoma and bone tumours, and H3.3 mutations are often associated with changes in global DNA methylation... Because of the known interaction between ATRX and DNMT3A/3L and the interplay between ATRX and DAXX, it is likely that PNETs with a loss of these tumour suppressor genes would have different genome-wide DNA methylation patterns as compared to those tumours that retain this function... Independent comparisons of either DAXX-negative (n=18) or ATRX-negative (n=7) with ATRX/DAXX-positive tumours (n=23) revealed 4352 MVPs and 34 differentially methylated regions (DMRs) and 258 MVPs and one DMR respectively... When ATRX-negative and DAXX-negative tumours were compared, we identified 196 195 MVPs and 6708 DMRs... A Benjamini–Hochberg (BH) adjusted P value of <0.05 that corrected for multiple testing (false discovery rate) was used throughout the various comparisons in order to identify significantly methylated variable positions... When ATRX-negative and DAXX-negative tumours were compared as one group to normal pancreatic samples, we identified 133 938 MVPs (BH adjusted P value <0.05) and 4664 DMRs... Copy number variation (CNV) was determined in ATRX/DAXX-negative and ATRX/DAXX-positive tumours using DNA methylation data as previously described... ATRX-negative and DAXX-negative tumours demonstrated increased CNV as compared to positive tumours (Fig. 1F)... Previous studies have analysed PNETs with ATRX and DAXX loss in a single cohort, because mutations in these genes are predominantly mutually exclusive... These findings are also relevant to other neurological tumours which are driven by ATRX and DAXX loss... C P Pipinikas, A Karpathakis, A Feber, M Novelli, M Caplin, T Meyer, A Teschendorff, C Bell, P Salomoni, S Beck and C Thirlwell critically revised the manuscript... C P Pipinikas, A Karpathakis, D Oukrif, T J Morris and T-V Luong provided technical support.

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(A) Details of the study cohort. (B and C) Kaplan–Meier survival curves for ATRX- and DAXX-negative cases (n=17) as compared to ATRX/DAXX-positive cases (n=17) and ATRX-negative (n=8) and DAXX-negative (n=9) cases analysed independently and compared to ATRX/DAXX-positives cases respectively. The 5-year PFS was 85% for positive cases, 52% for ATRX-negative cases and 16% for DAXX-negative cases. (D) Unsupervised cluster analysis using the top 1000 MVPs that showed segregation of ATRX-negative (in green) and DAXX-negative (in orange) tumours as compared to normal pancreatic tissue. Of the six ATRX/DAXX-negative tumour samples (from six cases) that clustered with the normal control pancreatic samples, only one case (G1, DAXX-negative) progressed (PFS 51 months), and two cases had no follow-up data. Of the six metastatic samples included in this study, two of them (both DAXX-negative) had a matched G1 tumour sample. One of them grouped tightly with the G1 primary tumour. DNA methylation values (β-value 0–1) are represented using a colour scale, where yellow=low methylation and blue=high methylation. Samples are shown on the x-axis, and probes are shown on the y-axis. (E) Confirmation of tumour segregation primarily by grade and then by ATRX or DAXX status using the top 1000 MVPs. (F) Copy number variation (CNV) profiles associated with low and intermediate PNETs. The top panel demonstrates increasing CNV across the genome for low-grade (G1, ki-67 <2%) tumours, with the least CNV occurring in the ATRX/DAXX-positive primary (left). Increasing CNV alterations are seen in the ATRX/DAXX-negative tumour (middle) and most CNV alterations occur in the ATRX/DAXX-negative G1 liver metastasis (right). The same is observed in intermediate grade (G2, ki-67 3–20%) tumours in the bottom panel. Segmented copy numbers are shown as a red line, and sequential chromosomes are shown in green and black (chr. 1–22).
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fig1: (A) Details of the study cohort. (B and C) Kaplan–Meier survival curves for ATRX- and DAXX-negative cases (n=17) as compared to ATRX/DAXX-positive cases (n=17) and ATRX-negative (n=8) and DAXX-negative (n=9) cases analysed independently and compared to ATRX/DAXX-positives cases respectively. The 5-year PFS was 85% for positive cases, 52% for ATRX-negative cases and 16% for DAXX-negative cases. (D) Unsupervised cluster analysis using the top 1000 MVPs that showed segregation of ATRX-negative (in green) and DAXX-negative (in orange) tumours as compared to normal pancreatic tissue. Of the six ATRX/DAXX-negative tumour samples (from six cases) that clustered with the normal control pancreatic samples, only one case (G1, DAXX-negative) progressed (PFS 51 months), and two cases had no follow-up data. Of the six metastatic samples included in this study, two of them (both DAXX-negative) had a matched G1 tumour sample. One of them grouped tightly with the G1 primary tumour. DNA methylation values (β-value 0–1) are represented using a colour scale, where yellow=low methylation and blue=high methylation. Samples are shown on the x-axis, and probes are shown on the y-axis. (E) Confirmation of tumour segregation primarily by grade and then by ATRX or DAXX status using the top 1000 MVPs. (F) Copy number variation (CNV) profiles associated with low and intermediate PNETs. The top panel demonstrates increasing CNV across the genome for low-grade (G1, ki-67 <2%) tumours, with the least CNV occurring in the ATRX/DAXX-positive primary (left). Increasing CNV alterations are seen in the ATRX/DAXX-negative tumour (middle) and most CNV alterations occur in the ATRX/DAXX-negative G1 liver metastasis (right). The same is observed in intermediate grade (G2, ki-67 3–20%) tumours in the bottom panel. Segmented copy numbers are shown as a red line, and sequential chromosomes are shown in green and black (chr. 1–22).

Mentions: In total, 53 formalin-fixed paraffin-embedded tumour specimens (46 primaries and seven liver metastases from 39 cases) were included in this study (Fig. 1A). Of these, 27 specimens (51%) had lost either ATRX (n=9; 33%) or DAXX (n=18; 67%) protein expression, as determined by immunohistochemistry (Anti-ATRX (SAB4502258) and Anti-DAXX (HPA008736) antibodies (both rabbit polyclonal) were provided by Sigma–Aldrich). Endothelial cells that stained positive for ATRX and DAXX served as the internal control in each immunochemistry section from cases that lacked expression of the corresponding protein. Seven of 26 (27%) low-grade primary tumours (G1, ki-67 of <2%) exhibited ATRX/DAXX loss as compared to 13 of 19 (68%) intermediate-grade tumours (G2, ki-67 2–20%) (P=0.008, Fisher's exact test). One G3 and six of seven metastatic specimens also exhibited ATRX/DAXX loss.


Epigenetic dysregulation and poorer prognosis in DAXX-deficient pancreatic neuroendocrine tumours.

Pipinikas CP, Dibra H, Karpathakis A, Feber A, Novelli M, Oukrif D, Fusai G, Valente R, Caplin M, Meyer T, Teschendorff A, Bell C, Morris TJ, Salomoni P, Luong TV, Davidson B, Beck S, Thirlwell C - Endocr. Relat. Cancer (2015)

(A) Details of the study cohort. (B and C) Kaplan–Meier survival curves for ATRX- and DAXX-negative cases (n=17) as compared to ATRX/DAXX-positive cases (n=17) and ATRX-negative (n=8) and DAXX-negative (n=9) cases analysed independently and compared to ATRX/DAXX-positives cases respectively. The 5-year PFS was 85% for positive cases, 52% for ATRX-negative cases and 16% for DAXX-negative cases. (D) Unsupervised cluster analysis using the top 1000 MVPs that showed segregation of ATRX-negative (in green) and DAXX-negative (in orange) tumours as compared to normal pancreatic tissue. Of the six ATRX/DAXX-negative tumour samples (from six cases) that clustered with the normal control pancreatic samples, only one case (G1, DAXX-negative) progressed (PFS 51 months), and two cases had no follow-up data. Of the six metastatic samples included in this study, two of them (both DAXX-negative) had a matched G1 tumour sample. One of them grouped tightly with the G1 primary tumour. DNA methylation values (β-value 0–1) are represented using a colour scale, where yellow=low methylation and blue=high methylation. Samples are shown on the x-axis, and probes are shown on the y-axis. (E) Confirmation of tumour segregation primarily by grade and then by ATRX or DAXX status using the top 1000 MVPs. (F) Copy number variation (CNV) profiles associated with low and intermediate PNETs. The top panel demonstrates increasing CNV across the genome for low-grade (G1, ki-67 <2%) tumours, with the least CNV occurring in the ATRX/DAXX-positive primary (left). Increasing CNV alterations are seen in the ATRX/DAXX-negative tumour (middle) and most CNV alterations occur in the ATRX/DAXX-negative G1 liver metastasis (right). The same is observed in intermediate grade (G2, ki-67 3–20%) tumours in the bottom panel. Segmented copy numbers are shown as a red line, and sequential chromosomes are shown in green and black (chr. 1–22).
© Copyright Policy - open-access
Related In: Results  -  Collection

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fig1: (A) Details of the study cohort. (B and C) Kaplan–Meier survival curves for ATRX- and DAXX-negative cases (n=17) as compared to ATRX/DAXX-positive cases (n=17) and ATRX-negative (n=8) and DAXX-negative (n=9) cases analysed independently and compared to ATRX/DAXX-positives cases respectively. The 5-year PFS was 85% for positive cases, 52% for ATRX-negative cases and 16% for DAXX-negative cases. (D) Unsupervised cluster analysis using the top 1000 MVPs that showed segregation of ATRX-negative (in green) and DAXX-negative (in orange) tumours as compared to normal pancreatic tissue. Of the six ATRX/DAXX-negative tumour samples (from six cases) that clustered with the normal control pancreatic samples, only one case (G1, DAXX-negative) progressed (PFS 51 months), and two cases had no follow-up data. Of the six metastatic samples included in this study, two of them (both DAXX-negative) had a matched G1 tumour sample. One of them grouped tightly with the G1 primary tumour. DNA methylation values (β-value 0–1) are represented using a colour scale, where yellow=low methylation and blue=high methylation. Samples are shown on the x-axis, and probes are shown on the y-axis. (E) Confirmation of tumour segregation primarily by grade and then by ATRX or DAXX status using the top 1000 MVPs. (F) Copy number variation (CNV) profiles associated with low and intermediate PNETs. The top panel demonstrates increasing CNV across the genome for low-grade (G1, ki-67 <2%) tumours, with the least CNV occurring in the ATRX/DAXX-positive primary (left). Increasing CNV alterations are seen in the ATRX/DAXX-negative tumour (middle) and most CNV alterations occur in the ATRX/DAXX-negative G1 liver metastasis (right). The same is observed in intermediate grade (G2, ki-67 3–20%) tumours in the bottom panel. Segmented copy numbers are shown as a red line, and sequential chromosomes are shown in green and black (chr. 1–22).
Mentions: In total, 53 formalin-fixed paraffin-embedded tumour specimens (46 primaries and seven liver metastases from 39 cases) were included in this study (Fig. 1A). Of these, 27 specimens (51%) had lost either ATRX (n=9; 33%) or DAXX (n=18; 67%) protein expression, as determined by immunohistochemistry (Anti-ATRX (SAB4502258) and Anti-DAXX (HPA008736) antibodies (both rabbit polyclonal) were provided by Sigma–Aldrich). Endothelial cells that stained positive for ATRX and DAXX served as the internal control in each immunochemistry section from cases that lacked expression of the corresponding protein. Seven of 26 (27%) low-grade primary tumours (G1, ki-67 of <2%) exhibited ATRX/DAXX loss as compared to 13 of 19 (68%) intermediate-grade tumours (G2, ki-67 2–20%) (P=0.008, Fisher's exact test). One G3 and six of seven metastatic specimens also exhibited ATRX/DAXX loss.

View Article: PubMed Central - PubMed

Affiliation: Medical Genomics Laboratory, University College London Cancer Institute, University College London72 Huntley Street, London, WC1E 6BT, UK.

AUTOMATICALLY GENERATED EXCERPT
Please rate it.

Exome sequencing of sporadic pancreatic neuroendocrine tumours (PNETs) has identified mutually exclusive mutations in the chromatin regulators α-thalassaemia/mental retardation X-linked (ATRX) and death-associated protein 6 (DAXX) genes in 43% of cases (18 and 23% of cases respectively in 68 cases studied)... Although it was initially reported that ATRX/DAXX mutant tumours had superior 10-year survival and outcome, a recent larger study on 243 tumours demonstrated that ATRX and DAXX loss and associated ALT in PNETs correlates with CIN, advanced tumour stage, the development of metastases and poorer progression-free survival (PFS) and overall survival (OS)... Mutually exclusive mutations in ATRX and DAXX are also found in neurological tumours, including neuroblastomas, paediatric glioblastomas, oligodendrogliomas and medulloblastomas... Notably, H3.3 is mutated in paediatric glioblastoma and bone tumours, and H3.3 mutations are often associated with changes in global DNA methylation... Because of the known interaction between ATRX and DNMT3A/3L and the interplay between ATRX and DAXX, it is likely that PNETs with a loss of these tumour suppressor genes would have different genome-wide DNA methylation patterns as compared to those tumours that retain this function... Independent comparisons of either DAXX-negative (n=18) or ATRX-negative (n=7) with ATRX/DAXX-positive tumours (n=23) revealed 4352 MVPs and 34 differentially methylated regions (DMRs) and 258 MVPs and one DMR respectively... When ATRX-negative and DAXX-negative tumours were compared, we identified 196 195 MVPs and 6708 DMRs... A Benjamini–Hochberg (BH) adjusted P value of <0.05 that corrected for multiple testing (false discovery rate) was used throughout the various comparisons in order to identify significantly methylated variable positions... When ATRX-negative and DAXX-negative tumours were compared as one group to normal pancreatic samples, we identified 133 938 MVPs (BH adjusted P value <0.05) and 4664 DMRs... Copy number variation (CNV) was determined in ATRX/DAXX-negative and ATRX/DAXX-positive tumours using DNA methylation data as previously described... ATRX-negative and DAXX-negative tumours demonstrated increased CNV as compared to positive tumours (Fig. 1F)... Previous studies have analysed PNETs with ATRX and DAXX loss in a single cohort, because mutations in these genes are predominantly mutually exclusive... These findings are also relevant to other neurological tumours which are driven by ATRX and DAXX loss... C P Pipinikas, A Karpathakis, A Feber, M Novelli, M Caplin, T Meyer, A Teschendorff, C Bell, P Salomoni, S Beck and C Thirlwell critically revised the manuscript... C P Pipinikas, A Karpathakis, D Oukrif, T J Morris and T-V Luong provided technical support.

No MeSH data available.


Related in: MedlinePlus