Abstract 2498: Prognostically significant molecular pathways in infants diagnosed with acute lymphoblastic leukemia with KMT2A gene rearrangement
Authors: Ramesh Sidharth , Pushel Irina , Yoo Byunggil , Farooqi Midhat S. , Pastinen Tomi , Brown Patrick , Guest Erin 
Published: June 2022

Two-thirds of infants diagnosed with acute lymphoblastic leukemia (ALL) with KMT2A gene rearrangement (KMT2A-r) relapse; however, the biological mechanisms underlying this relapse are unknown. Relapsed infant ALL carries a particularly poor prognosis and is often resistant to further attempts at re-induction. Here, we use single-cell RNA sequencing (scRNAseq) data on samples collected at diagnosis from KMT2A-r infant ALL patients to identify genes differentially expressed between cases known to later relapse versus those known to stay in remission. We subsequently describe potential molecular pathways that may explain the predisposition for the majority of these patients to relapse.

We performed 10x Genomics Chromium single-cell sequencing (Multiome v1 chemistry) to obtain gene expression data on blood or bone marrow samples collected at diagnosis from a total of 25 infants with KMT2A-r ALL; 19 of these cases later went on to relapse (the Rel group) while 6 did not (non-Rel). Differential expression analysis (DEA) was performed using the Seurat package (v4.0.2) in R 4.0.3, selecting positive (upregulated) genes only with a log fold change cutoff of 0.25. QIAGEN Ingenuity Pathway Analysis (IPA) software (v1.20.04) was then used to generate a list of molecular pathways described by these differentially upregulated genes (p&lt;.05), one for each group: Rel as compared to non-Rel and vice versa. We then compared the two lists to identify potentially biologically significant markers with possible prognostic value.

We sequenced an average of 1191 cells total per patient over six captures. Following DEA, we found a total of 1168 genes that were enriched in the Rel group relative to the non-Rel group. Conversely, a total of 1240 genes were enriched in the non-Rel group relative to the Rel group. These genes were cross referenced to the KEGG database’s “Pathways in Cancer” list (hsa05200). The top 3 genes in the Rel group were ZBTB16, IL6ST, BCL2L11. The top 3 genes in the non-Rel group were MSH6, LEF1, and CDK6. Following IPA analysis, a total of 160 canonical pathways were described in the Rel group, and a total of 70 canonical pathways were described in the non-Rel group. Three intracellular signal transduction pathways present in the KEGG list above that were disproportionately present in the Rel group at diagnosis with statistical significance and potential prognostic value were PI3K, AKT, and mTOR signaling.

Since increased activation of the PI3K/AKT/mTOR pathway is specifically associated with chemoresistance in ALL, our findings suggest that this pathway could potentially be used as an indicator of potential relapse in infant ALL patients. Future studies, currently in progress, will compare the above data to scRNAseq data from infant KMT2A-r ALL samples collected at relapse to further investigate signaling pathway activation and clonal evolution in infant ALL.

Citation Format: Sidharth Ramesh, Irina Pushel, Byunggil Yoo, Midhat S. Farooqi, Tomi Pastinen, Patrick Brown, Erin Guest. Prognostically significant molecular pathways in infants diagnosed with acute lymphoblastic leukemia with KMT2A gene rearrangement [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2498.