DNA methylation-based subtype prediction for pediatric acute lymphoblastic leukemia

Jessica Nordlund; Christofer L Bäcklin; Vasilios Zachariadis; Lucia Cavelier; Johan Dahlberg; Ingegerd Öfverholm; Gisela Barbany; Ann Nordgren; Elin Övernäs; Jonas Abrahamsson; Trond Flaegstad; Mats M Heyman; Ólafur G Jónsson; Jukka Kanerva; Rolf Larsson; Josefine Palle; K. Schmiegelow; Mats G Gustafsson; Gudmar Lönnerholm; Erik Forestier; Ann-Christine Syvänen

doi:10.1186/s13148-014-0039-z

DNA methylation-based subtype prediction for pediatric acute lymphoblastic leukemia

Jessica Nordlund, Christofer L Bäcklin, Vasilios Zachariadis, Lucia Cavelier, Johan Dahlberg, Ingegerd Öfverholm, Gisela Barbany, Ann Nordgren, Elin Övernäs, Jonas Abrahamsson, Trond Flaegstad, Mats M Heyman, Ólafur G Jónsson, Jukka Kanerva, Rolf Larsson, Josefine Palle, K. Schmiegelow, Mats G Gustafsson, Gudmar Lönnerholm, Erik ForestierAnn-Christine Syvänen

Department of Clinical Medicine

28 Citations (Scopus)

Abstract

BACKGROUND: We present a method that utilizes DNA methylation profiling for prediction of the cytogenetic subtypes of acute lymphoblastic leukemia (ALL) cells from pediatric ALL patients. The primary aim of our study was to improve risk stratification of ALL patients into treatment groups using DNA methylation as a complement to current diagnostic methods. A secondary aim was to gain insight into the functional role of DNA methylation in ALL.

RESULTS: We used the methylation status of ~450,000 CpG sites in 546 well-characterized patients with T-ALL or seven recurrent B-cell precursor ALL subtypes to design and validate sensitive and accurate DNA methylation classifiers. After repeated cross-validation, a final classifier was derived that consisted of only 246 CpG sites. The mean sensitivity and specificity of the classifier across the known subtypes was 0.90 and 0.99, respectively. We then used DNA methylation classification to screen for subtype membership of 210 patients with undefined karyotype (normal or no result) or non-recurrent cytogenetic aberrations ('other' subtype). Nearly half (n = 106) of the patients lacking cytogenetic subgrouping displayed highly similar methylation profiles as the patients in the known recurrent groups. We verified the subtype of 20% of the newly classified patients by examination of diagnostic karyotypes, array-based copy number analysis, and detection of fusion genes by quantitative polymerase chain reaction (PCR) and RNA-sequencing (RNA-seq). Using RNA-seq data from ALL patients where cytogenetic subtype and DNA methylation classification did not agree, we discovered several novel fusion genes involving ETV6, RUNX1, and PAX5.

CONCLUSIONS: Our findings indicate that DNA methylation profiling contributes to the clarification of the heterogeneity in cytogenetically undefined ALL patient groups and could be implemented as a complementary method for diagnosis of ALL. The results of our study provide clues to the origin and development of leukemic transformation. The methylation status of the CpG sites constituting the classifiers also highlight relevant biological characteristics in otherwise unclassified ALL patients.

Original language	English
Journal	Clinical Epigenetics
Volume	7
Issue number	11
Pages (from-to)	1-12
Number of pages	12
ISSN	1868-7075
DOIs	https://doi.org/10.1186/s13148-014-0039-z
Publication status	Published - 17 Feb 2015

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Nordlund, J., Bäcklin, C. L., Zachariadis, V., Cavelier, L., Dahlberg, J., Öfverholm, I., Barbany, G., Nordgren, A., Övernäs, E., Abrahamsson, J., Flaegstad, T., Heyman, M. M., Jónsson, Ó. G., Kanerva, J., Larsson, R., Palle, J., Schmiegelow, K., Gustafsson, M. G., Lönnerholm, G., ... Syvänen, A-C. (2015). DNA methylation-based subtype prediction for pediatric acute lymphoblastic leukemia. Clinical Epigenetics, 7(11), 1-12. https://doi.org/10.1186/s13148-014-0039-z

Nordlund, J, Bäcklin, CL, Zachariadis, V, Cavelier, L, Dahlberg, J, Öfverholm, I, Barbany, G, Nordgren, A, Övernäs, E, Abrahamsson, J, Flaegstad, T, Heyman, MM, Jónsson, ÓG, Kanerva, J, Larsson, R, Palle, J, Schmiegelow, K, Gustafsson, MG, Lönnerholm, G, Forestier, E & Syvänen, A-C 2015, 'DNA methylation-based subtype prediction for pediatric acute lymphoblastic leukemia', Clinical Epigenetics, vol. 7, no. 11, pp. 1-12. https://doi.org/10.1186/s13148-014-0039-z

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title = "DNA methylation-based subtype prediction for pediatric acute lymphoblastic leukemia",

abstract = "BACKGROUND: We present a method that utilizes DNA methylation profiling for prediction of the cytogenetic subtypes of acute lymphoblastic leukemia (ALL) cells from pediatric ALL patients. The primary aim of our study was to improve risk stratification of ALL patients into treatment groups using DNA methylation as a complement to current diagnostic methods. A secondary aim was to gain insight into the functional role of DNA methylation in ALL.RESULTS: We used the methylation status of ~450,000 CpG sites in 546 well-characterized patients with T-ALL or seven recurrent B-cell precursor ALL subtypes to design and validate sensitive and accurate DNA methylation classifiers. After repeated cross-validation, a final classifier was derived that consisted of only 246 CpG sites. The mean sensitivity and specificity of the classifier across the known subtypes was 0.90 and 0.99, respectively. We then used DNA methylation classification to screen for subtype membership of 210 patients with undefined karyotype (normal or no result) or non-recurrent cytogenetic aberrations ('other' subtype). Nearly half (n = 106) of the patients lacking cytogenetic subgrouping displayed highly similar methylation profiles as the patients in the known recurrent groups. We verified the subtype of 20% of the newly classified patients by examination of diagnostic karyotypes, array-based copy number analysis, and detection of fusion genes by quantitative polymerase chain reaction (PCR) and RNA-sequencing (RNA-seq). Using RNA-seq data from ALL patients where cytogenetic subtype and DNA methylation classification did not agree, we discovered several novel fusion genes involving ETV6, RUNX1, and PAX5.CONCLUSIONS: Our findings indicate that DNA methylation profiling contributes to the clarification of the heterogeneity in cytogenetically undefined ALL patient groups and could be implemented as a complementary method for diagnosis of ALL. The results of our study provide clues to the origin and development of leukemic transformation. The methylation status of the CpG sites constituting the classifiers also highlight relevant biological characteristics in otherwise unclassified ALL patients.",

author = "Jessica Nordlund and B{\"a}cklin, {Christofer L} and Vasilios Zachariadis and Lucia Cavelier and Johan Dahlberg and Ingegerd {\"O}fverholm and Gisela Barbany and Ann Nordgren and Elin {\"O}vern{\"a}s and Jonas Abrahamsson and Trond Flaegstad and Heyman, {Mats M} and J{\'o}nsson, {{\'O}lafur G} and Jukka Kanerva and Rolf Larsson and Josefine Palle and K. Schmiegelow and Gustafsson, {Mats G} and Gudmar L{\"o}nnerholm and Erik Forestier and Ann-Christine Syv{\"a}nen",

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doi = "10.1186/s13148-014-0039-z",

language = "English",

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T1 - DNA methylation-based subtype prediction for pediatric acute lymphoblastic leukemia

AU - Nordlund, Jessica

AU - Bäcklin, Christofer L

AU - Zachariadis, Vasilios

AU - Cavelier, Lucia

AU - Dahlberg, Johan

AU - Öfverholm, Ingegerd

AU - Barbany, Gisela

AU - Nordgren, Ann

AU - Övernäs, Elin

AU - Abrahamsson, Jonas

AU - Flaegstad, Trond

AU - Heyman, Mats M

AU - Jónsson, Ólafur G

AU - Kanerva, Jukka

AU - Larsson, Rolf

AU - Palle, Josefine

AU - Schmiegelow, K.

AU - Gustafsson, Mats G

AU - Lönnerholm, Gudmar

AU - Forestier, Erik

AU - Syvänen, Ann-Christine

PY - 2015/2/17

Y1 - 2015/2/17

N2 - BACKGROUND: We present a method that utilizes DNA methylation profiling for prediction of the cytogenetic subtypes of acute lymphoblastic leukemia (ALL) cells from pediatric ALL patients. The primary aim of our study was to improve risk stratification of ALL patients into treatment groups using DNA methylation as a complement to current diagnostic methods. A secondary aim was to gain insight into the functional role of DNA methylation in ALL.RESULTS: We used the methylation status of ~450,000 CpG sites in 546 well-characterized patients with T-ALL or seven recurrent B-cell precursor ALL subtypes to design and validate sensitive and accurate DNA methylation classifiers. After repeated cross-validation, a final classifier was derived that consisted of only 246 CpG sites. The mean sensitivity and specificity of the classifier across the known subtypes was 0.90 and 0.99, respectively. We then used DNA methylation classification to screen for subtype membership of 210 patients with undefined karyotype (normal or no result) or non-recurrent cytogenetic aberrations ('other' subtype). Nearly half (n = 106) of the patients lacking cytogenetic subgrouping displayed highly similar methylation profiles as the patients in the known recurrent groups. We verified the subtype of 20% of the newly classified patients by examination of diagnostic karyotypes, array-based copy number analysis, and detection of fusion genes by quantitative polymerase chain reaction (PCR) and RNA-sequencing (RNA-seq). Using RNA-seq data from ALL patients where cytogenetic subtype and DNA methylation classification did not agree, we discovered several novel fusion genes involving ETV6, RUNX1, and PAX5.CONCLUSIONS: Our findings indicate that DNA methylation profiling contributes to the clarification of the heterogeneity in cytogenetically undefined ALL patient groups and could be implemented as a complementary method for diagnosis of ALL. The results of our study provide clues to the origin and development of leukemic transformation. The methylation status of the CpG sites constituting the classifiers also highlight relevant biological characteristics in otherwise unclassified ALL patients.

AB - BACKGROUND: We present a method that utilizes DNA methylation profiling for prediction of the cytogenetic subtypes of acute lymphoblastic leukemia (ALL) cells from pediatric ALL patients. The primary aim of our study was to improve risk stratification of ALL patients into treatment groups using DNA methylation as a complement to current diagnostic methods. A secondary aim was to gain insight into the functional role of DNA methylation in ALL.RESULTS: We used the methylation status of ~450,000 CpG sites in 546 well-characterized patients with T-ALL or seven recurrent B-cell precursor ALL subtypes to design and validate sensitive and accurate DNA methylation classifiers. After repeated cross-validation, a final classifier was derived that consisted of only 246 CpG sites. The mean sensitivity and specificity of the classifier across the known subtypes was 0.90 and 0.99, respectively. We then used DNA methylation classification to screen for subtype membership of 210 patients with undefined karyotype (normal or no result) or non-recurrent cytogenetic aberrations ('other' subtype). Nearly half (n = 106) of the patients lacking cytogenetic subgrouping displayed highly similar methylation profiles as the patients in the known recurrent groups. We verified the subtype of 20% of the newly classified patients by examination of diagnostic karyotypes, array-based copy number analysis, and detection of fusion genes by quantitative polymerase chain reaction (PCR) and RNA-sequencing (RNA-seq). Using RNA-seq data from ALL patients where cytogenetic subtype and DNA methylation classification did not agree, we discovered several novel fusion genes involving ETV6, RUNX1, and PAX5.CONCLUSIONS: Our findings indicate that DNA methylation profiling contributes to the clarification of the heterogeneity in cytogenetically undefined ALL patient groups and could be implemented as a complementary method for diagnosis of ALL. The results of our study provide clues to the origin and development of leukemic transformation. The methylation status of the CpG sites constituting the classifiers also highlight relevant biological characteristics in otherwise unclassified ALL patients.

U2 - 10.1186/s13148-014-0039-z

DO - 10.1186/s13148-014-0039-z

M3 - Journal article

C2 - 25729447

SN - 1868-7075

VL - 7

SP - 1

EP - 12

JO - Clinical Epigenetics (Print)

JF - Clinical Epigenetics (Print)

IS - 11

ER -

DNA methylation-based subtype prediction for pediatric acute lymphoblastic leukemia

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