Novel Rho-GTPase regulatory protein gene family variants are frequent and associate with poor survival in patients (pts) with acute myeloid leukemia (AML)

Introduction: AML is a molecularly heterogeneous disease that is classified by recurrent cytogenetic abnormalities and gene mutations. Recent studies have shown divergent frequencies of several genetic aberrations depending on genetic ancestry and self-reported race/ethnicity, highlighting the need to broaden sequencing efforts to include more diverse pts. Methods: We performed paired tumor/normal whole exome sequencing (WES) and transcriptome sequencing on 271 ancestry and/or ethnically diverse pts [including 100 African American (AA) and 71 self-identified Hispanic pts; CALGB/Alliance], and a validation cohort of 45 AA pts (University of Pennsylvania). Results: We identified >20 genes to be mutated in 3-8% of pts that were not seen in previous sequencing efforts of predominantly non-Hispanic White/European ancestry (EA) pts. Notably, variants in genes encoding Rho-GTPase regulatory proteins ( ARHG family, belonging to the RAS gene superfamily) were identified in 12% of pts, placing these genes in the top 5 of recurrently mutated genes in this pt cohort. This frequency was confirmed in the second cohort of AA pts (n=7/45, 15%). In contrast, analysis of 805 EA adults with WES data (BeatAML 2022) and 877 pediatric AML pts (TARGET) found ARHG gene family variants in 26/805 (3%) and 17/877 (1.9%) of EA AML pts, respectively. With a median age of 41y, ARHG -mutated(m) pts tended to be younger (P=.16) and more often diagnosed with core-binding factor AML (39% vs 19%, P=.02). ARHG mutations frequently co-occurred with NRAS and FLT3 mut (each found in 35% of ARHG m pts). Notably, survival of ARHG m pts was poor, with a median overall survival (OS) of <12 months, thereby mirroring OS of the 2022 European LeukemiaNet (ELN) Adverse risk group. Within the 2022 ELN Favorable risk group in the ancestry diverse cohort, ARHG m pts had shorter OS than ARHG wt pts (P=.02). The clinical outcome was especially poor in young adolescents and adults (AYA, 18-39y) (mut vs wt; 3y disease-free survival, 10% vs 50%, P<.001; 3y OS, 20% vs 55%, P=.008). RNAseq of 17 ARHG m pts showed transcriptomic RAS pathway activation, with 52% displaying a RAS-associated signature, also in the absence of other RAS mutations. Furthermore, bulk transcriptomic analyses of 1250 AML pts identified 120 predicted RAS signature genes, with the upregulated genes being enriched in metallopeptidases, MAP kinase phosphatases, and ARHG genes. Conclusion: We identified mutations in ARHG family genes as frequent yet thus far unrecognized RAS pathway activators in AML associated with poor survival that are not yet included in clinical testing panels. Their lack of recognition is likely due to the heterogeneity of mutationally affected ARHG family genes, enrichment in AYA pts and the high frequency in pts of non-European ancestry, both of which are pt populations that were underrepresented in previous sequencing efforts.