Loss of KDM6A/UTX Function Is a Common Event in a Mouse Model of Multiple Myeloma, Human Cell Lines and Patients.
Authors: Keats Jonathan J , Chesi Marta , Braggio Esteban , Palmer Stephan , Baker Angela , Barrett Michael , Carpten John , Fonseca Rafael , Bergsagel P. Leif 
Published: October 2019

Abstract 606

Multiple myeloma is a complex malignancy with multiple underlying genetic events. Our group has spent considerable effort over the last 15 years to elucidate the genetic underpinnings of myeloma. Most recently, we used array-based comparative genomic hybridization (aCGH) as a discovery tool in 62 myeloma patients and 46 myeloma cell lines. In that preliminary screen using the Agilent 44B aCGH platform (∼70kb resolution) we identified a diverse array of abnormalities, which resulted in constitutive activation of the NF-kB pathways. That initial analysis concentrated on the 43 genes we identified as potential targets of the 13 homozygous deletion events detected in the patient samples. A pathway analysis of these genes revealed a single pathway involving TRAF3, TRAF2, BIRC2, BIRC3, and CYLD. This first analysis focused exclusively on abnormalities present in the patient samples as we worried some abnormalities identified exclusively in the cell lines might not be relevant to the pathogenesis of myeloma in patients. However, several abnormalities were equally or more frequent overall but occurred exclusively in cell lines including CDKN2C (14 samples), CDKN1B (4 samples), KDM6A/UTX (4 samples), RB1 (3 samples), TP53 (3 samples). Given the fact that KDM6A/UTX deletions were as frequent as many of the best-described tumor suppressors it seemed like a good candidate but in the absence of patient events or a known function at the time it was not prioritized for further study.

Recently, as part of the Multiple Myeloma Research Consortium (MMRC) Genomics Initiative, we have completed the analysis of a cohort of 250 myeloma patient samples by aCGH using the Agilent 244A aCGH platform (∼15kb resolution) and gene expression profiling using the Affymetrix U133Plus2.0 genechip. In this cohort with a significantly improved aCGH platform we identified 17 genes that are recurrently inactivated by homozygous deletions including DIAPH2 (15 samples), CDKN2C (14 samples), TRAF3 (11 samples), CYLD (8 samples), BIRC2/3 (7 samples), KDM6A/UTX (6 samples), and RB1 (5 samples). Based on the significant improvement in resolution and data quality achieved with the Agilent 244A aCGH platform we rescreen all of the cell lines on this improved platform. This significantly changed the frequency of several homozygous deletions in this population with the most frequently targeted genes now being CDKN2C (20 samples), KDM6A/UTX (13 samples), DIAPH2 (7 samples), RB1 (4 samples), TP53 (4 samples), CDKN1B (4 samples), and TRAF3 (4 samples). Moreover, as part of the genomic characterization of a spontaneous myeloma mouse model that we have developed, Vk*-Myc, we have identified recurrent (∼50%) homozygous deletions of Kdm6a/Utx. Therefore, one of the genes most commonly targeted by a homozygous deletion in human and mouse myeloma is KDM6A/UTX.

In late 2007 after we had identified the first patients with KDM6A/UTX deletions it was shown that UTX is a functional histone demethylase that removes methyl groups from histone H3 lysine 27 (H3K27me). Given the high incidence of deletions and the fact that MMSET, the overexpressed target gene of t(4;14) in myeloma, is predicted to methylate H3K27, H3K36, and/or H4K20 by evolutionary conservation we developed the hypothesis that myeloma is characterized by abnormalities that result in excessive H3K27me (typically a repressive chromatin mark). Given the extensive whole genome sequencing occurring in the MMRC genomics initiative we elected to focus our resequencing efforts on the cell lines exclusively. These studies identified an additional 4 samples with LOH and an inactivating mutation bringing the total percentage of inactivated cell lines to 33%. Clearly, in the expanded patient and cell line cohorts the inactivation of KDM6A/UTX is not independent of MMSET overexpression suggesting they may act independently or synergistically. We are currently attempting to identify the genes controlled by KDM6A/UTX inactivation to better understand the functional consequences of this highly recurrent event. However, in the mouse model unlike the patient or cell lines, the gene expression profiling has identified a gene expression signature that differentiates UTX inactivated and functional samples suggesting an oncogenic function of inactivation.

Disclosures:

No relevant conflicts of interest to declare.