New Insights to the MLL Recombinome Including 8 Novel Partner Genes ACTN4, C2CD3, DCP1A, FLNA, LAMC3, LOC100128568, NRIP3, and TNRC18.
Authors: Meyer Claus , Kowarz Eric , Hofmann Julia , Fischer Thomas , Ashkar Sara El , Teigler-Schlegel Andrea , Balgobind Brian , Burmeister Thomas , De Braekeleer Etienne , Delabesse Eric , Renneville Aline , Dingermann Theo , Klingebiel Thomas , Marschalek Rolf 
Published: April 2020

Abstract
Rearrangements of the MLL (mixed lineage leukemia) gene are associated with pediatric, adult and therapy-related acute leukemias of both the myeloid and lymphoid lineage. Today, about 60 MLL fusion partner genes have been characterized at the molecular level involving almost all chromosomes. Nearly one-third of these partner genes have been identified at the DCAL (Diagnostic Center of Acute Leukemia) where more than 700 MLL rearrangements, including 36 different partner genes, have been analyzed so far. 85% of the analyzed MLL rearrangements account for the 6 most frequent partner genes, and 15% for less frequent partner genes including the 8 novel partner genes ACTN4, C2CD3, DCP1A, FLNA, LAMC3, LOC100128568, NRIP3, and TNRC18. Here, we present an overview of all current known translocation partner genes. This overview indicates all the specific introns of the TPGs found to be involved in MLL translocations, their chromosomal locations and the type of genetic abnormality that is leading to the MLL fusion. Additionally, the current breakpoint cluster region (bcr) is also presented for the 10 most frequent partner genes, namely AFF1 (AF4), MLLT3 (AF9), MLLT1 (ENL), MLLT10, MLLT4 (AF6), ELL, EPS15, MLLT6 (AF17), MLLT11 (AF1Q) and partial tandem duplications (PTDs). These bcrs have been used as basis for the development of an long range multiplex PCR. This is an additional tool for the identification of genomic MLL breakpoints to enhance the diagnostic efficiency. Approximately 20% of all MLL rearrangements are complex ones. In this study, we have identified 109 (15%) complex rearrangements. Within these complex rearrangements, the 5’ part of the MLL gene is generally fused in frame to one of the most frequent partner genes. But the 3’ part of the MLL gene is fused in 45 cases (41%) to a novel so-called “reciprocal MLL partner gene” like ADSS or ATG16L2. This heterogeneous group of novel translocation partner genes had not been identified as fusion partners to the 5’ part of the MLL gene before. Whether the pathobiology of complex rearrangements is different in comparison to their not complex counterparts has still to be proven. Also a novel “spliced MLL fusion” involving the AFF1 gene has been identified at the DCAL. In this case, the breakpoint is 90 kb up-stream of the AFF1 gene. Unfortunately, no cDNA/RNA was left to identify the chimeric fusion transcript. Nevertheless, the disease phenotype of a biphenotypic AL strengthens the involvement of the AFF1 gene. With these results, the number of genes involved in „ spliced MLL fusions“ has increased from seven to eight. For five patients, no partner gene could be identified at the molecular level. Also the “spliced MLL fusions” which is a mechanism to generate functional chimeric fusion transcripts with neighbouring genes described already for 8 partner genes of the MLL gene, could not be identified for these patients by RACE and RT-PCR. Furthermore, the determined patient-specific fusion sequences are succesfully used worldwide for minimal residual disease (MRD) monitoring to improve the treatment and outcome of acute leukemia patients.