Gene Expression Profiling Signatures Allow the Identification of Unclassifiable Leukemic B-Cell Lymphoid Neoplasms

Abstract

Leukemic B-cell chronic lymphoproliferative disorders (B-CLPD) encompass a heterogeneous group of defined disease entities. However, around 10% of the cases cannot be reliably classified based on the current criteria and are considered B-CLPD not otherwise specified (B-CLPD NOS). Few recurrent mutations and genetic alterations have been reported in some entities, but none is specific.We performed gene expression profiling (GEP) to develop a robust GEP-molecular classifier for leukemic B-CLPD. We analyzed purified blood of 189 B-CLPD, including 54 chronic lymphocytic leukemia (CLL), 54 mantle cell lymphoma (MCL), 12 follicular lymphoma (FL), 23 splenic marginal zone lymphoma (SMZL), 4 splenic diffuse red pulp lymphoma (SDRPL), 4 hairy cell leukemia (HCL), 4 HCL-variant (HCL-v), 6 lymphoplasmacytic lymphoma (LPL) and 28 B-CLPD NOS. We used a multiple step approach to build a GEP-array classifier and then analyzed an additional series as a validation cohort by quantitative PCR (qPCR). Mutational analysis of BRAF, MAP2K1, MYD88, NOTCH1, NOTCH2, SF3B1 and TP53 and copy number alterations were studied.In the training set, a supervised analysis clustering revealed that each B-CLPD entity has a specific expression profile. By a multi-step GEP classifier using 43 genes (Table 1) we could classify CLL, SOX11-positive MCL (MCLc), HCL, FL, SOX11-negative MCL (MCLi) and HCL-v cases in six successive stages. However, we were not able to clearly identify distinct signatures for LPL, SMZL and SDRPL. Furthermore, we could classify 36% of B-CLPD NOS cases. Interestingly, the 43-gene signature identified in leukemic samples could also classify the 28 tumor splenic biopsies. Finally, we built a simple 8-gene predictive model using qPCR data (including: FMOD, KSR2, SOX11, MYOF, MME, CCND1, CXCR4, and CAMSAP2) that was used in an independent validation cohort and classified 14% B-CLPD NOS cases. The classification yield increased to 61% and 50%, for GEP-array and qPCR, respectively, when additional morphological, molecular and genetic features were considered.Our findings support the use in a routine base of a simple test as a diagnostic tool that can be applied to help multiparameter interpretation in the classification of leukemic B-CLPD and specially B-CLPD NOS.Table 1Gene signatures (43 genes) and steps used for the GEP-array model.Step modelB-CLPDSpecific signatures1CLLFMOD, KSR2, ADTRP, CLNK, LEF1, FILIP1L, CTLA4, IGSF3, EBF12MCLcSOX11, PLEKHG4B, HDGFRP3, CNN3, PON2, SH3BP4, FCGBP, STMN1, FARP1, DBN1, NREP, NINL, MARCKSL1, MEX3D, CRIM1, KAZN3HCLHPGDS, IL1R2, TJP1, PLOD2, EMP1, NOVA14FLMME, SLC2A5, SMAD1, PRDM155MCLiCCND16HCL-vTUSC1, LRP1B, KCNJ3, NRCAM, MS4A14, FAM129C,CXCR47MiscellaneousLPL-SDRPL-SMZLNo specific genes CLLchronic lymphocytic leukemia; FL: follicular lymphoma, HCL: hairy cell leukemia;HCL-v: hairy cell leukemia variant; LPL, lymphoplasmacytic lymphoma; MCLc: conventionalSOX11-positive mantle cell lymphoma; MCLi: indolent SOX11-negative mantle cell lymphoma;SDRPL, splenic diffuse red pulp lymphoma; SMZL, splenic marginal zone lymphoma.Bold letters indicate some of the genes included in the simple qPCR model. DisclosuresLopez-Guillermo:Roche, Celgene, Mundipharma, Gilead, Novartis: Membership on an entity's Board of Directors or advisory committees, Research Funding.