Integrative Study of EZH2 Mutational Status, Copy Number, Protein Expression and H3K27 Trimethylation in AML/MDS Patients

Introduction Enhancer of Zeste Homolog 2 (EZH2), the catalytic domain of Polycomb Repressive Complex 2 (PRC2), mediates the repressive mark of trimethylation of histone H3 lysine 27 (H3K27me3). The EZH2 gene is located on chromosome (chr.) 7q36.1 (frequently deleted in AML/MDS). Its role in tumorigenesis appears to be context-dependent since both EZH2 overexpression and loss of function are associated with different types of cancer. In patients (pts) with MDS or MDS/MPN, loss-of-function EZH2 mutations (mut) are recurrently found, associated with a poor prognosis, and EZH2 is considered a tumor suppressor gene (TSG). In AML, the incidence of EZH2-mut is lower and less well-studied. We wished to determine the effects of EZH2-mut and copy number (CN) on EZH2 expression, and the consequences for H3K27me3 levels in vivo. Methods Fifty-eight pts (51 AML, 3 MDS, 4 MDS/MPN), median age 63.5 years (yr, range 20-86, almost all diagnosed between 2015 and 2017), with available sequencing data, EZH2 CN status and EZH2 expression data were studied. Mutation status was determined by next-generation sequencing (NGS) including a panel of 54 genes (Illumina Myeloid NGS panel). Metaphase cytogenetics and/or fluorescence in situ hybridization and single nucleotide polymorphism arrays (selected pts) were conducted to determine EZH2 CN status. Protein expression of EZH2 and H3K27me3 was assessed semi-quantitatively by immunohistochemistry (IHC) on formalin-fixed EDTA-decalcified paraffin-embedded bone marrow (BM) core biopsies. The Kruskal-Wallis test and Dunn's multiple comparison test were used to address whether EZH2 protein expression was associated with EZH2-mut and CN. Results The EZH2 gene showed mutations (mostly missense or nonsense, median variant allele frequency (VAF) 45%, range 7-63%) in 13/58 pts and was unmutated in 45/58 pts. EZH2-mut pts had a median of 4 mutations. Additional mutations were most frequently found in ASXL1 (10/13; median VAF 35%, range 19-48%), less frequently in TET2, RUNX1, STAG2 (3/13 each), NRAS (2/13), and DNMT3A (1/13). In contrast, EZH2-wt pts had a median of 2 mutations, most frequently in DNMT3A (12/45), followed by NRAS (10/45), IDH1 (9/45), FLT3 (8/45), and NPM1 (7/45). Regarding chr. 7, 43 pts had no detectable deletion, 15 had 7q-/-7. Notably, the incidence of EZH2-mut was similar in pts with 7q-/-7 lesions (3/15, i.e. 20%) and pts with normal chr. 7 (10/43, 23%). EZH2 expression in neoplastic BM cells ranked from no (score 0) to strong expression (score 3). While the hematopoietic BM cells of healthy donors usually showed a moderate EZH2 expression (score 2), in our cohort the score was 0 in 3, 1 in 13, 2 in 23, and 3 in 19 pts, respectively. We next asked whether EZH2 protein expression differed between pts depending on EZH2-mut and chr. 7 status. In Figure 1, 4 subgroups are depicted, showing highest expression in pts with EZH2-wt and either no chr. 7 abnormalities (group A, n=33) or 7q-/-7 (group C, n=12). In comparison, expression was significantly reduced in pts with EZH2-mut and no chr. 7 abnormalities (group B, n=10), and lowest in pts with EZH2-mut and chr. 7 abnormalities (group D, n=3), p<0.05 (indicated by asterisks). Since functional EZH2 protein is necessary for the trimethylation of H3K27, the presence of this histone mark was also determined semi-quantitatively by IHC in 40 pts. H3K27me3 levels were variable, and a test for a possible association between EZH2 and H3K27me3 levels by linear regression analysis did not show an association (R²=0.13). Sixty-two % of EZH2-mut (median age 71 yr) and 51% of EZH2-wt pts (median age 61 yr) received allografting. Median overall survival in EZH2-mut pts was 16.1 months compared to 23.5 in EZH2-wt pts (p=0.16). Conclusions Inactivating EZH2 mutations are infrequent events in AML. In our study, they were strongly associated with mutations of ASXL1 (also involved in PRC2 function). We did not observe overrepresentation of EZH2-mut in 7q-/-7 pts, in line with Bejar et al. (N Engl J Med 2011); this is in contrast to the frequent cooperative events between TSG mutations and deletions, e.g. of TP53. Functionally, EZH2 mutations appeared to have a stronger effect on decreased EZH2 expression than hemizygosity. Global H3K27me3 levels were not altered by EZH2 reduction, which could be due to compensatory upregulation of EZH1, supporting the clinical development of EZH1/2 inhibition. Disclosures No relevant conflicts of interest to declare.

Download Full-text

Integrative study of EZH2 mutational status, copy number, protein expression and H3K27 trimethylation in AML/MDS patients

Clinical Epigenetics ◽

10.1186/s13148-021-01052-2 ◽

2021 ◽

Vol 13 (1) ◽

Author(s):

Julia Stomper ◽

Ruth Meier ◽

Tobias Ma ◽

Dietmar Pfeifer ◽

Gabriele Ihorst ◽

...

Keyword(s):

Acute Myeloid Leukemia ◽

Protein Expression ◽

Copy Number ◽

Myeloid Leukemia ◽

Myeloproliferative Neoplasms ◽

H3k27 Trimethylation ◽

Myeloid Neoplasms ◽

Mutational Status ◽

Ezh2 Expression ◽

Acute Myeloid

Abstract Background Mutations in the EZH2 gene are recurrently found in patients with myeloid neoplasms and are associated with a poor prognosis. We aimed to characterize genetic and epigenetic alterations of EZH2 in 58 patients (51 with acute myeloid leukemia and 7 with myelodysplastic or myeloproliferative neoplasms) by integrating data on EZH2 mutational status, co-occurring mutations, and EZH2 copy number status with EZH2 protein expression, histone H3K27 trimethylation, and EZH2 promoter methylation. Results EZH2 was mutated in 6/51 acute myeloid leukemia patients (12%) and 7/7 patients with other myeloid neoplasms. EZH2 mutations were not overrepresented in patients with chromosome 7q deletions or losses. In acute myeloid leukemia patients, EZH2 mutations frequently co-occurred with CEBPA (67%), ASXL1 (50%), TET2 and RAD21 mutations (33% each). In EZH2-mutated patients with myelodysplastic or myeloproliferative neoplasms, the most common co-mutations were in ASXL1 (100%), NRAS, RUNX1, and STAG2 (29% each). EZH2 mutations were associated with a significant decrease in EZH2 expression (p = 0.0002), which was similar in patients with chromosome 7 aberrations and patients with intact chromosome 7. An association between EZH2 protein expression and H3K27 trimethylation was observed in EZH2-unmutated patients (R2 = 0.2, p = 0.01). The monoallelic state of EZH2 was not associated with EZH2 promoter hypermethylation. In multivariable analyses, EZH2 mutations were associated with a trend towards an increased risk of death (hazard ratio 2.51 [95% confidence interval 0.87–7.25], p = 0.09); similarly, low EZH2 expression was associated with elevated risk (hazard ratio 2.54 [95% confidence interval 1.07–6.04], p = 0.04). Conclusions Perturbations of EZH2 activity in AML/MDS occur on different, genetic and non-genetic levels. Both low EZH2 protein expression and, by trend, EZH2 gene mutations predicted inferior overall survival of AML patients receiving standard chemotherapy.

Download Full-text

Alterations of insulin-like growth factor-1 receptor gene copy number and protein expression are common in non-small cell lung cancer

Journal of Clinical Pathology ◽

10.1136/jclinpath-2014-202347 ◽

2014 ◽

Vol 67 (11) ◽

pp. 985-991 ◽

Cited By ~ 10

Author(s):

T N Tran ◽

C I Selinger ◽

B Yu ◽

C C Ng ◽

M R J Kohonen-Corish ◽

...

Keyword(s):

Lung Cancer ◽

Protein Expression ◽

Copy Number ◽

Gene Copy Number ◽

Small Cell ◽

Clinicopathological Features ◽

Gene Copy ◽

Small Cell Lung ◽

Mutational Status ◽

Node Metastases

AimsInsulin-like growth factor-1 receptor (IGF1R) is a tyrosine kinase membrane receptor involved in tumourigenesis that may be a potential therapeutic target. We aimed to investigate the incidence and prognostic significance of alterations in IGF1R copy number, and IGF1R protein expression in resected primary non-small cell lung cancer (NSCLC), and lymph node metastases.MethodsIGF1R gene copy number status was evaluated by chromogenic silver in situ hybridisation and IGF1R protein expression was evaluated by immunohistochemistry in tissue microarray sections from a retrospective cohort of 309 surgically resected NSCLCs and results were compared with clinicopathological features, including EGFR and KRAS mutational status and patient survival.ResultsIGF1R gene copy number status was positive (high polysomy or amplification) in 29.2% of NSCLC, and 12.1% exhibited IGF1R gene amplification. High IGF1R expression was found in 28.3%. There was a modest correlation between IGF1R gene copy number and protein expression (r=0.2, p<0.05). Alterations of IGF1R gene copy number and protein expression in primary tumours were significantly associated with alterations in lymph node metastases (p<0.01). High IGF1R gene copy number and protein expression was significantly higher in squamous cell carcinomas (SCC) compared with other subtypes of NSCLC (p<0.05). There were no other associations between IGF1R status and other clinicopathological features including patient age, gender, smoking status, tumour size, stage, grade, EGFR or KRAS mutational status or overall survival.ConclusionsHigh IGF1R gene copy number and protein overexpression are frequent in NSCLC, particularly in SCCs, but they are not prognostically relevant.

Download Full-text

Tracking Subclonal Mutations in IGHV-Mutated CLL with Progressive Disease

Blood ◽

10.1182/blood.v124.21.1962.1962 ◽

2014 ◽

Vol 124 (21) ◽

pp. 1962-1962

Author(s):

Matthew JJ Rose-Zerilli ◽

Gibson Jane ◽

Jun Wang ◽

William J Tapper ◽

Helen Parker ◽

...

Keyword(s):

Clinical Features ◽

Deep Sequencing ◽

Copy Number ◽

Progressive Disease ◽

Conflicts Of Interest ◽

Early Stage ◽

Temporal Shift ◽

Dna Mutation ◽

Mutational Status ◽

Good Risk

Abstract Most CLL is diagnosed with a low tumor burden with no indication for therapy. Biomarkers, such as unmutated IGHV genes, TP53 loss/mutation and raised β2M predict short time to first treatment and overall survival; however there remain patients with good risk biomarkers who nevertheless develop progressive disease. Advances in genomics and immunogenetics have lead to the discovery of new biomarkers and their integration with cytogenetic data refines outcome prediction. However these novel markers are predominantly found in IGHV unmutated cases (U-CLL). To identify novel genetic mechanisms that may contribute to progression, we have studied 13 patients (pts) presenting with cMBL (n=3) or Stage Binet A/Rai 0 disease and good risk markers: IGHV-mutated, excluding poor risk stereotypes (n=13), no 17p or 11q deletion by FISH, (n=13), sole del13q14 (n=8), low CD38 expression (n=13) who all developed lymphocytosis (n=13), between two untreated timepoints (TP1 & TP2), 10 of whom subsequently required treatment. Copy number analysis (SNP6), whole exome sequencing (WES; Agilent SureSelect & Illumina sequencing) of tumour-germline pairs and targeted deep sequencing (TDS; Haloplex, Agilent) of the the WES-identified variants and the 22 most frequently mutated genes in CLL, to a mean depth of 3681 fold, were performed at TP1 and TP2. TP1 was close to diagnosis (median of 1 yr, range 0.11-7.33) with a median time to TP2 of 4.5 yrs (0.2-8.9). In addition, TDS was undertaken at later time points in one patient described in point 4), who relapsed and ultimately transformed. Our analysis shows the following potential mechanisms: 1. Our germline WES data revealed 5 heterozygous missense/frameshift variants in 5 genes in 5 pts, also known to be targeted by somatic mutation in CLL (eg: FBXW7, POT1, SAMHD1. Fig1). 2. We then established the somatically-acquired mutation profile of each patient. We validated 72% (224/312) of the mutations discovered by WES using TDS and identified clinically relevant mutations earlier on in disease, supporting the hypothesis that sub-clonal mutations in genes in addition to TP53 may drive a progressive clinical course. At diagnosis (TP1) by WES/TDS, 5/13 pts had mutations in CLL driver genes (ATM, NOTCH1, SF3B1, TP53) and 2/13 pts had mutations in genes of undetermined clinical significance (CHD2, NFKBIE, ZMYM3). One patient was MYD88 mutated at TP1 and remains untreated after follow up of 12 yrs. In total, the following 9 genes (ATM, CHD2, DDX3X, MYD88, NOTCH1, NFKBIE, SF3B1, TP53 & ZMYM3) were mutated in 62% (8/13) pts at TP1. 3. Of the remaining 5/13 pts lacking a detectable mutation in any of the established CLL genes, we observed on average 7 mutations/patient in genes involved in cancer and each patient harboured one or more mutated genes with a role in haematological malignancy (eg. ITGA6, KLHL6, LTF, TNFAIP3). 4. One patient exhibited a remarkable temporal shift in copy number changes and mutations. At TP2, SNP6 analysis could not detect the del13q observed at TP1, and a clonal trisomy 12 had emerged, along with several mutations associated with progressive disease (BIRC3, IRF4, NOTCH1), that predominate in U-CLL. As a consequence we re-analysed the IGHV mutational status at TP2, and showed that rather than the IGHV3-48 with 92% germline identity identified at diagnosis, our patient exhibited an additional and dominant IGHV5-10-1*01 (100% identity) clone at TP2, 8 yrs after TP1. Additional analysis of intermediate samples detected the unmutated clone as far back as 4 yrs post diagnosis, and TDS analysis showed the NOTCH1 mutation was a minor subclone at diagnosis (0.06% VAF). Ultimately, this patient developed Richters syndrome with expansion of the NOTCH1 mutation (27% VAF). Retrospective sequential immunogenetic analysis of the other 12 cases yielded no other example of this phenomenon. In summary, IGHV-mutated cMBL/early stage CLL with a progressive outcome can be associated with, the presence of germline or subclonal gene mutations of known or putative importance in CLL, or the emergence of a IGHV-unmutated clone. Our data supports deep sequencing in the clinical setting for earlier detection of pathogenetic mutations and emerging immunogenetically distinct subclones in patients with early stage 'good risk' disease. Figure 1: Heatmap representation of the cohorts clinical features and DNA mutation. Patient 287 haboured the IGHV-unmutated clone at TP2-5. Figure 1:. Heatmap representation of the cohorts clinical features and DNA mutation. Patient 287 haboured the IGHV-unmutated clone at TP2-5. Disclosures No relevant conflicts of interest to declare.

Download Full-text

Identifying Possible Candidate Factors Influencing the Penetrance of Heterozygous NFKB1 Loss of Function Mutations By Whole Exome Sequencing

Blood ◽

10.1182/blood.v128.22.3706.3706 ◽

2016 ◽

Vol 128 (22) ◽

pp. 3706-3706

Author(s):

Cyrill Schipp ◽

Arndt Borkhardt ◽

Polina Stepensky ◽

Ute Fischer

Keyword(s):

Exome Sequencing ◽

Whole Exome Sequencing ◽

Inflammatory Responses ◽

Conflicts Of Interest ◽

Incomplete Penetrance ◽

Loss Of Function ◽

Sequencing Data ◽

Bioinformatics Analyses ◽

Factors Influencing ◽

Whole Exome

Abstract Introduction The NFκB signaling pathway is a master regulator of immune and inflammatory responses. Recently we and other groups reported heterozygous NFKB1 loss-of-function mutations in patients with combined variable immunodeficiency (CVID) characterized by recurrent infections, autoimmunity and immunoglobulin deficiency. Pedigree analysis revealed incomplete penetrance of the disease causing mutation in 5 of the 6 analyzed families. While patients showed a severe phenotype including hypogammaglobulinemia, chronic infections and cytopenias, other carriers of the same mutation were unaffected except for slightly perturbed immunoglobulin levels indicating the existence of other factors influencing the penetrance of these mutations. Methods To identify genetic factors associated with complete penetrance of dominant NFKB1 mutations, whole exome sequencing was carried out using DNA extracted from blood samples derived from two patients and their families. Sequencing data of two patients and X unaffected carriers of the same NFKB1 mutations (p.R157X and p.I47fsX2) were then screened in silico for single nucleotide variations, small insertions and deletions present in modulators of immune responses in general and the NFκB pathway in particular, employing lists generated based on publicly available data on gene interactions (including e.g. data of the KEGG, and STRING databases). Results We detected no deleterious mutations in known modifier genes such as IL10, IL1B, IL6, CCR5, CCL5, RANTES, TGFB1 and others. But strikingly both patients harbored two polymorphisms (g.797C>A, Gly54Asp, Gly57Glu) in the Mannose Binding Lectin 2 (MBL2) gene that were previously reported as disease causing mutations in patients with primary immunodeficiency. These polymorphisms lead to reduced MBL2 expression and are linked with high susceptibility to infections. We hypothesize that low MBL2 expression in an NFKB1 haploinsufficient background may promote disease penetrance or increase the predisposition to infections. Conclusion Our combined next-generation sequencing and bioinformatics analyses approach identified MBL2 as an interesting candidate factor whose deficient expression may influence the penetrance of NFKB1 loss-of-function mutations. Further analysis of greater cohorts is needed to reinforce the role of MBL2 in the pathogenesis of NFKB1 haploinsufficiency. Disclosures No relevant conflicts of interest to declare.

Download Full-text

Mutations in PLCG1 Is a Frequent Event in Cutaneous T-Cell Lymphomas

Blood ◽

10.1182/blood.v120.21.300.300 ◽

2012 ◽

Vol 120 (21) ◽

pp. 300-300

Author(s):

Pablo L Ortiz-Romero ◽

Gonzalo Gomez-Lopez ◽

Sagrario Gómez de Benito ◽

Veronica Monsalvez ◽

Jose P Vaque ◽

...

Keyword(s):

T Cell ◽

Molecular Mechanisms ◽

Somatic Mutations ◽

Catalytic Domain ◽

Conflicts Of Interest ◽

Immunohistochemical Analysis ◽

Sequencing Data ◽

Coding Region ◽

Regulatory Pathways ◽

Frequent Event

Abstract Abstract 300 Background: Cutaneous T-cell lymphoma (CTCL) is a heterogeneous group of diseases characterized by clonal expansion of malignant T-cells in the skin. The two predominant clinical forms of CTCL are mycosis fungoides (MF) and Sezary syndrome (SS). Tumor-stage MF has an unfavorable prognosis with a 10-year survival of approximately 40%. The molecular pathogenesis of CTCL is still basically unknown, although some data suggest that signalling from T-cell receptor (TCR) is a driving force. However, the molecular mechanisms responsible for this activation have not been fully clarified. Methods: Based on the hypothesis that TCR activation may depend, at least in part, on somatic mutations, we have investigated this in a selection of genes belonging to TCR, or related pathways, such as NFkB, JAK/STAT, by means of deep sequencing. A Target Enrichment method using SureSelect system (Agilent) has been used to enrich in exons and regulatory regions of 524 genes belonging to these pathways. DNA from 2 tumoral-MF, 5 erythrodermic-MF and 4 SS patients, both normal and tumoral, were processed and sequenced with Genome Analyzer GA2 (Illumina) (PE-42bp). Sequencing data were first checked by FastQC and aligned to the human reference genome (GRCh37) using BWA and BFAST alignments. Somatic variants were identified using GATK. Thus, SNPs available at dbSNP 135 (hg19) and 1000 Genomes Project were filtered out from VCF output files. The GATK-QUAL field was employed for ranking selected somatic variants. Biological impact predictions for detected variants were obtained from Ensembl Variant Effect Predictor. Putative variants were manually reviewed and validated by capillary sequencing. Immunohistochemical analysis for NFAT, p50, p52 and STAT·p was also performed. qPCR-genotyping for specific variants was performed in a new cohort of 60 CTCL patients including SS and tumoral MFs. Results: Several mutations were found in essential genes belonging to pathways implicated in the Treg and Th17 regulatory pathways, NFkB and JAK/STAT, among others. PLCG1 was found mutated in three samples, two of them sharing the same mutation affecting one of the PLCG1 protein catalytic domains. This mutation was further analyzed by qPCR-genotyping in the new series of patients, being detected in 20% of samples. PLCG mutated cases showed a strong paraffin immunostaining for nuclear NFAT, p50 and p52. Additionally, immunological studies performed by flow cytometry in CTCL cell lines show aberrant coexpression of TH17 and Treg phenotypes. Conclusions: Activation of the TCR in CTCL might be partially dependent on the acquisition of somatic mutations in the coding region of genes known to play an essential role in T-cell differentiation processes and acquisition of TH17 and Treg phenotypes. Especially relevant is the finding that the catalytic domain of PLCG1 is frequently mutated in tumoral MF samples. Disclosures: No relevant conflicts of interest to declare.

Download Full-text

Risk of Central Nervous System (CNS) Involvement in Patients with Mantle Cell Lymphoma (MCL): Analysis of Clinico-Biological Factors in a Series of 283 Cases

Blood ◽

10.1182/blood.v124.21.1677.1677 ◽

2014 ◽

Vol 124 (21) ◽

pp. 1677-1677

Author(s):

Eva Giné ◽

Sílvia Beà ◽

Alba Navarro ◽

Nuria Martínez-Cibrián ◽

Itziar Salaverría ◽

...

Keyword(s):

Risk Factors ◽

Copy Number ◽

Mutational Analysis ◽

Conflicts Of Interest ◽

Genetic Alterations ◽

High Dose ◽

Biological Parameters ◽

Cns Involvement ◽

Biological Variables ◽

Mutational Status

Abstract Introduction: MCL is a mature B-cell neoplasm characterized by t(11;14) (q13;q32) and cyclin D1 (CCND1) overexpression. Molecular studies have revealed other alterations in cell-cycle regulation, DNA damage response and cell survival pathways, with a landscape of somatic mutations being recently identified. CNS involvement is a well known complication, occurring in 4-26% of MCL at five years, with an ominous significance. Although different clinical variables have been identified as risk factors for CNS infiltration, the biological parameters related to this complication have not been extensively studied. The aim of the study was to explore the biological parameters associated with CNS involvement in a multicentre and retrospective series of MCL patients. Patients and Methods: 285 patients (M:74%; 64 yr) diagnosed of MCL between 1990-2014 (median survival of 4 years) were analysed. In addition to standard clinico-biological variables, IGHV mutational analysis, chromosomal alteration studies and Sanger sequencing of NOTCH1, NOTCH2, TP53, BIRC3, WHSC1, MEF2B, MLL2, TLR2 and PRDM1 were performed. Results: CNS involvement was observed in 15/285 MCL patients (5.2%), with a 5-yr risk of 9.1% (95%CI: 4.6-13.6), one patient at diagnosis, and at first or second/ulterior progressions in 7 cases each. The clinical, pathological and molecular risk factors identified are detailed in the Table. In addition to what has been already described, CNS involvement was usually observed in MCL cases with a clinical nodal presentation (p=0.05). In fact, no indolent MCL with a non-nodal presentation developed this complication during the follow-up period. No differences were observed in the risk of CNS involvement between patients treated in first-line with conventional or high-dose intense treatment (5-yr risk: 6.1%+/-6% vs. 10.7%+/-10.6%, p=ns). Regarding the biological features, no differences in terms of the IGHV mutational status were observed in cases developing CNS involvement compared to the others (75% vs. 68.7%, using 97% identity cut-off). Similarly, the IGHV gene usage of CNS involved cases corresponded to the more frequent IGHV genes observed in MCL (usually IGHV1-18, IGHV3-23, IGHV4-34, IGHV4-59). Although not significant, a predominance of high number copy number alterations (CNA) (>4) could be observed in the genetic study of MCL cases with CNS involvement as could be expected for the enrichment in blastoid variants (up to 50% of these cases). In fact, we did not observe any case with CNS involvement among those cases with 3 or less CNA. CNS involvement was not related to common poor prognosis genetic alterations such as 9p, 11p and 17p losses, but the presence of 8q gains was associated with a higher risk of CNS involvement (p=0.05). We did not find any significant association between CNS involvement and the large number of oncogenic mutations studied. Conclusions: CNS involvement in MCL is associated with initial aggressive clinico-biological characteristics. Non-nodal MCL cases with a low number of genetic alterations did not present CNS involvement. Finally, the presence of 8q gains was associated with a higher risk of CNS infiltration. Table Initial Clinical Features Category N 5 yr-CNS involvement (%, 95%CI) HR p Performance status (ECOG) > 1 8/51 41.5 (+/-28) 4.2 .003 ≤ 1 7/128 9.4 (+/-5.5) Nodal disease Yes 14/185 13.3 (+/-7.6) 6.1 .05 No 1/77 1.4 (+/-2.7) Hemoglobin (g/L) < 105 12/93 24.7 (+/-14.7) 3.2 .05 ≥ 105 3/78 5.3 (+/-6.3) LDH > ULN 4/89 27.1(+/-19.4) 6.7 <.001 < ULN 11/137 5.6 (+/-6.3) B2microglobulin > ULN 11/114 21.6 (+/-14.9) 3.5 .04 < ULN 3/66 8.7(+/-10) Molecular & Pathological data Histological variant Blastoid 6/58 17.3 (+/-13.7) 3.5 .02 Others 8/156 1.3 (+/-7.2) Ki-67 > 30% 5/44 17.5 (+/-14.9) 3.6 .06 ≤ 30% 3/61 6.7 (+/-9.4) SOX11 Positive 8/153 2.9 (+/- 5.7) 2.6 ns Negative 1/42 2.1 (+/-2.4) IGHV ≥97% 6/109 9.5 (+/-9.6) 1.9 ns <97% 2/49 6 (+/-8.2) CNA > 4 2/87 3.9 (+/-5.7) 1.1 ns ≤ 4 1/44 2.3 (+/-4.3) Chromotripsis Yes 1/17 12.5 (+/-22) 3.2 ns No 2/106 1.9 (+/-2.7) 8q gain Yes 2/30 13.1(+/-19) 7.5 .05 No 2/97 1 (+/-1.96) CNA: copy number alteration; IGHV: immunoglobulin heavy chain; LDH: Lactate dehydrogenase Disclosures No relevant conflicts of interest to declare.

Download Full-text

Usefulness of tissue microarrays for assessment of protein expression, gene copy number and mutational status of EGFR in lung adenocarcinoma

Virchows Archiv ◽

10.1007/s00428-010-0963-z ◽

2010 ◽

Vol 457 (4) ◽

pp. 483-495 ◽

Cited By ~ 32

Author(s):

Marius I. Ilie ◽

Véronique Hofman ◽

Christelle Bonnetaud ◽

Katia Havet ◽

Virginie Lespinet-Fabre ◽

...

Keyword(s):

Protein Expression ◽

Lung Adenocarcinoma ◽

Copy Number ◽

Gene Copy Number ◽

Tissue Microarrays ◽

Gene Copy ◽

Mutational Status

Download Full-text

Title: SNP Microarray Reveals Predicted Outcomes of a Novel High Risk AML Subgroup with ERG Amplification

Blood ◽

10.1182/blood-2019-121408 ◽

2019 ◽

Vol 134 (Supplement_1) ◽

pp. 2737-2737

Author(s):

Sandra Mazzoni ◽

Brian T. Hess ◽

Cynthia Schandl ◽

Iya Znoyko ◽

Georges Nahhas ◽

...

Keyword(s):

High Risk ◽

Copy Number ◽

Tp53 Mutation ◽

Validation Cohort ◽

Loss Of Function ◽

Discovery Cohort ◽

Mutational Status ◽

Molecular Sequencing ◽

And Control ◽

Very High

Increased expression of ERG (ETS-related gene), a proto-oncogene within the ETS (erythroblast transformation specific) family, is associated with an unfavorable clinical outcome in AML patients. A mechanism for ERG over-expression is ERG amplification. ERG amplification is present in 4-6% of adult AML. This study investigates the genetic profile of ERG-amplified AML by assessment of genomic copy number changes and mutational status of AML-related genes and how this correlates to treatment response and overall outcome. Currently copy number analysis is not recommended by ELN or WHO as a diagnostic standard in AML. An institutional retrospective review of 205 adult AML cases from 2015 to 2018 provided two cohorts: a discovery cohort and control cohort. The discovery cohort includes 11 cases (4%) with ERG amplification. All cases in the discovery cohort include either TP53 mutation and/or loss/LOH of 17p. Thus, we developed a control cohort of 39 cases with TP53 abnormalities without ERG amplifications to determine the role TP53 plays in the observed outcomes. The 179 adult AML cases from the TCGA public database comprises the validation cohort, which incorporates both copy number and molecular sequencing data. Approximately 4% of AML cases in the TCGA dataset show ERG amplification. For our discovery and control cohorts, genomic DNA was extracted (Maxwell, Promega, Madison, WI) from fresh bone marrow aspirates. Copy number/LOH analysis was performed using the CytoSNP microarray (Illumina, San Diego, CA). Sequence variants were evaluated in hotspot regions of 49 genes using the ThunderBolts Myeloid Panel library preparation (RainDance Technologies, Billerica, MA) and paired-end sequencing (MiSeq, Illumina, San Diego, CA). Alignment and variant calling was performed with MiSeq Reporter (Illumina) and NextGene (Soft Genetics, State College, PA) and sequences were annotated using VarSeq (Golden Helix, Bozman, MT). SNP microarray analysis of the discovery cohort revealed a distinct pattern of complex cytogenetics including chromothripsis, TP53 loss/LOH and loss of 5q. Molecular sequencing was available for 10 of 11 patients. All specimens analyzed for mutational status demonstrated TP53 loss of function mutations. The majority of cases (9/11) demonstrated complete loss of function of TP53 by mutation in conjunction with a "second hit" in the form of loss due to deletion or LOH of 17p. These nine patients failed to achieve any response with chemotherapy with a median survival time of 3.8 months. The two surviving patients had a single TP53 mutation with an intact second allele. Both of these patients are post-allogeneic stem cell transplant with no evidence of relapse. There is an association of ERG amplification with MDS as 8 of the 11 patients transformed from very-high risk MDS. The interaction between ERG and TP53 allows one to predict treatment response and outcomes based on the presence or absence of an intact TP53 allele. Within the control group, there were no significant differences in survival or response to treatment based on number of intact TP53 alleles. The validation cohort of TCGA patients confirmed the strong positive correlation between ERG amplification and TP53 mutations. There were 8 cases with ERG amplification. Of these, 6 cases had a similar genetic pattern found in the discovery cohort including TP53 mutations, loss of 5q and complex cytogenetics. The median overall survival (OS) of this cohort of ERG amplified + TP53 mutation was 2.5 months. ERG amplification classifies a high-risk population of AML detected by copy number/LOH analysis with a distinct genetic signature including loss of 5q, complex cytogenetics including chromothripsis and loss of function TP53 mutation. The successive loss of the second TP53 allele in the setting of ERG amplification identifies a subset of patients with resistance to cytarabine and a very poor prognosis. These patients are unlikely to benefit from cytotoxic chemotherapy and may have improved outcomes with alternative regimens and/or clinical trial. ERG amplification is associated with AML that transforms from very-high risk MDS. Recognizing these patients before transforming to AML could allow for early transplant. This high-risk subgroup is currently un-recognized by standard cytogenetics and genetic mutation profiling; therefore, we recommend that copy number/LOH analysis become part of the standard diagnostic testing for MDS and AML. Disclosures No relevant conflicts of interest to declare.

Download Full-text

ARID1A alterations and their clinical significance in cholangiocarcinoma

PeerJ ◽

10.7717/peerj.10464 ◽

2020 ◽

Vol 8 ◽

pp. e10464

Author(s):

Achira Namjan ◽

Anchalee Techasen ◽

Watcharin Loilome ◽

Prakasit Sa-ngaimwibool ◽

Apinya Jusakul

Keyword(s):

Protein Expression ◽

Clinical Significance ◽

Somatic Mutation ◽

Stage Iv ◽

Tumor Stage ◽

Sequencing Data ◽

Synthetic Lethal ◽

Ezh2 Expression ◽

Promising Therapeutic Target ◽

Wide Range

Background ARID1A is a member of the SWI/SNF chromatin remodeling complex. It functions as a tumor suppressor and several therapeutic targets in ARID1A-mutated cancers are currently under development, including EZH2. A synthetic lethal relationship between ARID1A and EZH2 has been revealed in several tumor entities. Although genomic alterations of ARID1A have been described in various cancers, no study has examined correlations between ARID1A gene mutation and protein expression with clinicopathologic parameters and prognosis, particularly in liver fluke-related cholangiocarcinoma (Ov-CCA). Here, we investigated the clinical significance of ARID1A mutations and protein expression in CCA tissues and determined whether there is a correlation with EZH2 protein expression. Methods We evaluated ARID1A and EZH2 immunoreactivity using immunohistochemistry in 98 Ov-CCA with a wide range of clinicopathological features. Somatic mutations of ARID1A were analyzed using the ICGC sequencing data in 489 of Ov and non Ov-CCA and assessed prognostic values. Results While detecting a loss or reduction of ARID1A expression in 54 cases (55%) in Ov-CCA, ARID1A expression was associated with ARID1A mutations (p < 0.001, adjusted p-value < 0.001). We observed that 12 of 13 tumors (92%) with loss of ARID1A expression had truncating mutations. There were nine of 13 tumors (69%) with loss of ARID1A expression and 25 of 41 tumors (61%) with low ARID1A expression exhibited distant metastasis (p = 0.028, adjusted p-value = 0.168). ARID1A was predominantly mutated in Ov-CCA compared to non Ov-CCA (24% and 14% in Ov-CCA and non Ov-CCA, respectively, p = 0.027). There were 36 of 72 (50%) and 52 of 79 (66%) tumors with ARID1A mutation showed tumor stage IV and T3/T4, respectively. The significant mutual exclusivity and co-occurrence between ARID1A and TP53/KRAS mutations were not found in ICGC cohort. In addition, high EZH2 expression, a potential synthetic lethal target in ARID1A-mutated tumors, was detected in 49 of 98 Ov-CCA (50%). Importantly, neither ARID1A expression nor ARID1A mutations correlated with EZH2 expression in this cohort. Conclusion We found that ARID1A inactivation, by somatic mutation or by loss of expression, frequently occurs in Ov-CCA. Reduction of ARID1A expression and/or somatic mutation was shown to be associated with CCA progression. These findings suggest that ARID1A may serve as a prognostic biomarker, and thus may be a promising therapeutic target for CCA.

Download Full-text