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Expression data for diagnosis acute lymphoblastic leukemia samples

ABSTRACT: We studied a cohort of 221 high-risk pediatric B-progenitor ALL patients that excluded known high risk ALL subtypes (BCR-ABL1 and infant ALL), using Affymetrix single nucleotide polymorphism microarrays, gene expression profiling and candidate gene resequencing. A CNA poor outcome predictor was identified using a semi-supervised principal components approach, and tested in an independent validation cohort of 258 pediatric B-progenitor ALL cases. Over 50 regions of recurring somatically acquired CNA, with the most frequently targeted genes encoding regulators of B-lymphoid development (66.8% of cases; with PAX5 targeted in 31.7% and IKZF1 in 28.6%). A CNA classifier identified a very poor outcome subgroup in the high-risk cohort (P=4.2x10-5) and was strongly associated with the presence of deletions involving IKZF1, which encodes the early lymphoid transcription factor IKAROS. This classifier, and IKZF1 deletions, also predicted poor outcome and elevated minimal residual disease at the end of induction therapy in the validation cohort. The gene expression signature of the poor outcome group was characterized by reduced expression of B lineage specific genes, and was highly related to the expressing signature of BCR-ABL1 ALL, a known high-risk ALL subtype also characterized by a high frequency of IKZF1 deletion.Somatically acquired deletions involving IKZF1 identify a very poor outcome subgroup of pediatric ALL patients. Incorporation of molecular tests to identify IKZF1 deletion in diagnostic leukemic blasts should improve the ability to accurately risk stratify patients for appropriate therapy. Affymetrix U133A arrays were performed according to the maufacturers directions on RNA extracted from cryopreserved diagnostic bone marrow or peripheral blood samples. Samples with less than 80% blasts were flow sorted prior to RNA extraction

ORGANISM(S): Homo sapiens

PROVIDER: GSE12995 | GEO | 2008/10/02

SECONDARY ACCESSION(S): PRJNA112609

REPOSITORIES: GEO

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Project description:We studied a cohort of 221 high-risk pediatric B-progenitor ALL patients that excluded known high risk ALL subtypes (BCR-ABL1 and infant ALL), using Affymetrix single nucleotide polymorphism microarrays, gene expression profiling and candidate gene resequencing. A CNA poor outcome predictor was identified using a semi-supervised principal components approach, and tested in an independent validation cohort of 258 pediatric B-progenitor ALL cases. Over 50 regions of recurring somatically acquired CNA, with the most frequently targeted genes encoding regulators of B-lymphoid development (66.8% of cases; with PAX5 targeted in 31.7% and IKZF1 in 28.6%). A CNA classifier identified a very poor outcome subgroup in the high-risk cohort (P=4.2x10-5) and was strongly associated with the presence of deletions involving IKZF1, which encodes the early lymphoid transcription factor IKAROS. This classifier, and IKZF1 deletions, also predicted poor outcome and elevated minimal residual disease at the end of induction therapy in the validation cohort. The gene expression signature of the poor outcome group was characterized by reduced expression of B lineage specific genes, and was highly related to the expressing signature of BCR-ABL1 ALL, a known high-risk ALL subtype also characterized by a high frequency of IKZF1 deletion.Somatically acquired deletions involving IKZF1 identify a very poor outcome subgroup of pediatric ALL patients. Incorporation of molecular tests to identify IKZF1 deletion in diagnostic leukemic blasts should improve the ability to accurately risk stratify patients for appropriate therapy. Affymetrix U133A arrays were performed according to the maufacturers directions on RNA extracted from cryopreserved diagnostic bone marrow or peripheral blood samples. Samples with less than 80% blasts were flow sorted prior to RNA extraction Experiment Overall Design: One hundred seventy five pediatric B-progenitor ALL samples were studied using either Affymetrix U133A

Project description:Background Children with Down Syndrome have an augmented risk for B-cell acute lymphoblastic leukaemia (DS-ALL), which is associated with a survival lower than in non-DS ALL, due to increased chemotherapy-related toxicity and a higher relapse rate, thus demanding new tailored therapeutic strategies. Cytogenetic abnormalities common in childhood ALL are less frequent in DS-ALL, while alterations in CRLF2 and IKZF1 genes are increased. Aim of the study was to evaluate in DS-ALL children the incidence and prognostic value of the Philadelphia Chromosome-Like (Ph-like) status and the “IKZF1plus” profile, both associated with poor outcome in non-DS ALL and therefore introduced in current therapeutic protocols for BCP-ALL. Method Seventy DS-ALL patients at diagnosis treated in Italian centres from 2000 to 2014 were evaluated for their cytogenetic status, including the Ph-like ALL profile, while the IKZF1plus feature was investigated in a larger cohort of 134 patients treated in Italian and German centres from 2000 to 2011. Findings Forty-six out of 70 (65•7%) AIEOP DS-ALL patients displayed the Ph-like ALL gene expression signature, mostly characterized by CRLF2 (n=33) and IKZF1 (n=16) alterations (13 had both alterations); only one case was positive for an ABL-class and one for a PAX5 fusion gene. In the Italian and German joint cohort, we observed 35•6% patients positive for P2RY8::CRLF2 fusion, 24•8% for IKZF1 deletion and 18% for IKZF1plus feature. Unexpectedly, a higher IKZF1 expression and activity were observed in IKZF1plus than IKZF1 wt DS-ALL patients. Ph-like signature and IKZF1 deletion were associated with poor outcome, which further worsens when IKZF1 deletion was co-occurring with P2RY8::CRLF2, qualifying for the IKZF1plus definition. Interpretation These subgroups, which for the most part are not associated with other high risk features, need new and tailored therapeutic strategies, not only focussed on the use of drugs that restore IKZF1 function.

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Expression data for diagnosis acute lymphoblastic leukemia samples

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