Immune Profiling Suggests an IGH Signaling-Dependent Subtype of Aggressive B-ALL
Authors: Carlson Christopher S , Pulsipher Michael A. , Langholz Bryan , Sherwood Anna , Desmarais Cindy , Robins Harlan , Kalos Michael , Grupp Stephan A. 
Published: October 2019

Abstract
Abstract 1428
The majority of B-cell acute lymphocytic leukemias (ALL) in childhood are derived from precursor B cells. In order to more precisely define the stage in cellular differentiation of the B-cell that gave rise to the tumor, we applied high-throughput sequencing techniques to profile the IGH repertoire in marrow at the time of diagnosis in a set of nine B-ALL patients who ultimately received a bone marrow transplant. These pediatric patients were enrolled on the Children's Oncology Group ASCT0431 trial, a phase 3, randomized trial stem cell transplantation for high risk ALL. In eight of these patients we identified a dominant IGH VDJ clone accounting for 45%-99% of all sequences, consistent with the oncogenic transformation event occurring in a cell no longer capable of further IGH rearrangement. In the ninth patient, no single VDJ clone dominated, but we observed a highly recurrent rearrangement of a specific pair of IGH diversity-joining segments (D7–27 and J4) which also conserved a four base pair non-templated sequence at the N2 junction between D and J. We observed at least 143 rearrangements sharing this D-N2-J sequence, accounting for 22% of total sequences from the patient. These sequences recombined a variety of V-N1 sequences with the common D-N2-J sequence, consistent with a primary tumor that had initially rearranged the D-J segments but continued to express the RAG recombinases, allowing for full for V-DJ recombination. Of note, 140 out of 143 of these sequences were in frame, significantly more frequently than the one in three expected. This suggests that in this specific patient, the primary tumor bearing the common D-J rearrangement was relatively indolent, and signaling through a subsequently, successfully rearranged and expressed IGH protein was an important event contributing to to the malignancy. The rearranged IGH sequences show little evidence of somatic hypermutation, so the expansion signal being received through the IGH protein appears to be coinsistent with normal positive selection during pro-B cell development, rather than an antigen-specific signal. This is consistent with the signal delivered by the pre-B receptor at the pro to pre-B stage of B cell development. We are investigating additional samples to assess the frequency of this subtype of B-ALL (a single clonal rearrangement of D-J, followed by many subclones expressing different, in frame full V-DJ rearrangements), by sequencing patients at diagnosis, relapse pre-transplant, and relapse post-transplant. Our ongoing analysis of patients enrolled on this trial at various stages of relapse will allow us to determine the prevalence of this subtype among high-risk cases, and whether differential outcomes are observed in similar cases.

Disclosures:
Carlson: Adaptive Biotechnologies: Consultancy, Equity Ownership. Sherwood:Adaptive Biotechnologies: Employment. Robins:Adaptive Biotechnologies: Consultancy, Equity Ownership. Kalos:University of Pennsylvania: Employment, Patents & Royalties.