PS928 “3C‐UP” A NEW ADULT PHILADELPHIA NEGATIVE ACUTE LYMPHOBLASTIC LEUKEMIA SUBGROUP: NOVEL MOLECULAR MARKERS
Authors: Ferrari A. , Vitali S. , Robustelli V. , Luserna di Rorà A. Ghelli , Baldazzi C. , Righi S. , Fonzi E. , De Matteis S. , Ghetti M. , Napolitano R. , Tebaldi M. , Salvi S. , Papayannidis C. , Marconi G. , Paolini S. , Ferrari G. , Fontana M. , Imbrogno E. , Padella A. , Simonetti G. , Pasquini G. , Santoro A. , Hernández‐Rivas J. , Calistri D. , Castellani G. , Sabattini E. , Testoni N. , Remondini D. , Martinelli G. 
Published: June 2019

Background:

The adult “triple negative” [Ph‐/‐/‐; neg for t(9;22); t(1;19); t(4;11); 61% of adult B‐ALL (Roberts KG et al., JCO. 2017)] B‐ALL group is characterized by an high genetic heterogeneity and poor survival. Many very low freq subgroups have been recently distinguished in a very large international cohort of pts (Gu Z, NatGenet. 2019); identified them (also Ph‐like) is challenging cause to genetic complexity, to not unique worldwide guidelines and to expensive algorithms that require multi‐NGS approaches. CRLF2 is frequently altered in adult B‐ALL, especially in Ph‐like (50–75% of cases) and Ph‐ pts. Alterations that lead, in the majority of cases, to a CRLF2 overexpr.. Adult pts with CRLF2 upreg have poor outcome and novel strategies are needed to improve it.

Aims:

We focused to CRLF2 overexpr. event to understand the genomic background of all Ph‐/‐/‐ ALL and subsequently clustering the Ph‐/‐/‐, in order to assess biomarkers in these subgroups to test new drugs and to quickly/economically identify them.

Methods:

GEP were performed on 55 Ph‐/‐/‐, 29 Ph+ B‐ALL and on 7 donors. We cluster Ph‐/‐/‐ GEP data with our validated pipeline, based on CRLF2 upreg and in a top ten‐gene list. Ph‐/‐/‐ samples were then characterized for the presence of gene fusions, Copy Number Alterations (CNAs) and mutations using different approaches (1385 RNA Panel and/or RNASeq; dMLPA; SNP Array; Target Seq, PCR and 44 WES).

Results:

Ph‐/‐/‐ WES analysis identified some recurrent mutated genes (NRAS, PAX5, JAK2, TP53, PTPN11, CREBBP) previously reported to be involved in B‐ALL, confirming the pivotal roles of these gene in ALL. For the first time we described PKHD1L1 as highly mutated (7.2%; Fig 1A). TP53 was the most mutated gene and that between these genes is the only one associated to a worst OS (p = 0.004). The Ph‐/‐/‐ fusions rate is of 43% (23/52), denoting that Ph‐/‐/‐ are not usually widely characterized. Combining our new Ph‐/‐/‐ GEP clustering to SNVs, Fusion and CNA results we identify a defined 2‐clusters‐subdivision (Gr1 and Gr2). The Gr2 is characterized by CTGF, CRLF2 and CD200 (Gr2 = 3C‐up; Fig 1B) co‐overexpression and it represents 14.1% of all B‐ALL. The Gr2 GEP is similar to Ph+ one (Fig 1C), similarly to Ph‐like. Fusion, CNAs and mutational screening done, detected that “3C‐Up” group has a higher frequency of Ph‐like associated lesions (primarily CRLF2, JAK2, IL7R mutation or deletion), that mainly affect JAK‐STAT pathway. Also IKZF1 and EBF1 del are significantly associated to Gr2 (p = 0.003; p = 0.016). Gr1 represents 46.9% of all B‐ALL and RAS pathway genes are highly affected in this group. Notably p53 pathway is enriched in both groups but with different deregulated genes: CHEK2 is upregulated in the group1 and CDK6 in the Gr2. Preliminary data seems to confirm an higher effect on cell viability of Bosutinib on Gr2 primary cell pt (vs Gr1 pt). Lastly, we develop a cytofluorimetric (IF) a B‐ALL panel to quickly detect 3C‐Up at diagnosis/relapse. With this test, we confirm that 3C marker co‐overexpr. is confirmed at protein level in pt MNCs.

Summary/Conclusion:

we identified a new signature, related to CRLF2 high expression, to classify Ph‐/‐/‐ B‐ in 2 subgroups. 3C‐Up has Ph‐like related alterations and high co‐expression of CRLF2, CTGF and CD200 that we could easily identify with IF. This new Ph‐/‐/‐ subclassification identify new potential therapeutic targets with available drugs (i.e. α‐CTGF, α‐CD200, CHK2 and CDK6 inhibitors; TKIs already effective on Ph+ and Ph‐like) to test. Supported by: AIL, FP7 NGS‐PTL project, Harmony.

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