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Editorials
nized by RNA-sequencing indicates a weakness of this novel technique. Some fusion genes can be missed by RNA-sequencing if only low or uneven coverage is achieved. Thus, a high read depth of samples is essential for RNA-sequencing in order to detect all fusion genes. Furthermore, some affected genes might be more easily missed if they are not highly expressed (i.e., RNA- sequencing is highly dependent on gene expression). However, RNA-sequencing allowed the authors to detect 26 cases with known recurrent fusion events that failed to be detected by routine diagnostics. Furthermore, Kerbs and colleagues also detected two novel recurrent fusion genes by RNA-sequencing. The fusion gene NRIP1- MIR99AHG was found in 1.1% of patients, and the fusion gene LTN1-MX1 in 0.25% of patients. These are just exam- ples that demonstrate that many more recurrent fusion genes will be detected if RNA-sequencing becomes employed more widely in AML. It is therefore very likely that we currently still underestimate the occurrence of fusion genes in AML with conventional diagnostics.
The encouraging results with RNA-sequencing also raise the questions of whether the technique should be applied to all AML patients at the time of diagnosis and whether it could replace conventional diagnostics. Currently, there are still a few obstacles to routine use of RNA-sequencing in all AML patients. Besides costs and labor-consuming aspects of this technique, analysis of results and data interpretation are very challenging. In particular, the high rate of false positive calls for fusion genes raises concerns and requires awareness. So far, interpretation of RNA-sequencing data has not been standardized and over 20 algorithms for fusion gene detection by RNA-sequencing have been described.9 However, standardization is a critical require- ment for using this technique more widely and in routine clinical practice. In this sense, it is encouraging as well as important that Kerbs and colleagues have developed and report a workflow with integrated filtering strategies for the identification of robust fusion gene candidates by RNA-sequencing. Similar steps need to be undertaken in the future in order to implement RNA-sequencing in rou- tine diagnostics. The wider use of RNA-sequencing in AML is likely to have positive impacts on diagnostic clas- sification as well as prognostic stratification.
RNA-sequencing can also open the door to novel thera- peutic strategies in individual AML patients. Gene fusions involving the NTRK gene constitute an encouraging exam- ple. NTRK fusions rarely occur in AML and are easily missed with routine diagnostics.10 Larotrectinib is a target- ed therapy that has shown efficacy in a broad spectrum of NTRK fusion-positive cancers. Many fusion genes occur- ring through chromosomal translocations encode tyrosine kinases that are involved in signal transduction. The devel- opment of tyrosine kinase inhibitors represents an attrac-
tive therapeutic strategy for patients with such fusions and RNA-sequencing will be essential for identifying these patients. It is therefore very likely that the increase in detection of recurrent gene fusions will also expand oppor- tunities for targeted therapies in AML. RNA-sequencing may also have further implications for monitoring measur- able residual disease in AML. Fusion genes are ideally suit- ed for molecular measurable residual disease assessment as they can be detected by RT-PCR as well as next-generation sequencing very sensitively.11 Of note, RNA-sequencing is evolving as an upcoming standard in solid cancers as well.
In summary, the study by Kerbs and colleagues is an important step towards implementing RNA-sequencing in routine AML diagnostics. Further work is undoubtedly required (especially regarding standardizing data analysis), but the manuscript already gives an encouraging outlook of how RNA-sequencing can translate into clinical applica- tions.
Disclosures
No conflicts of interest to disclose.
References
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2. Mitelman DatabaseChromosome Aberrations and Gene Fusions in Cancer. https://mitelmandatabase.isb-cgcorg/. 2021. Last accessed June 30, 2021.
3. Wiemels JL, Cazzaniga G, Daniotti M, et al. Prenatal origin of acute lymphoblastic leukaemia in children. Lancet. 1999;354(9189):1499- 1503.
4. Drilon A, Laetsch TW, Kummar S, et al. Efficacy of larotrectinib in TRK fusion-positive cancers in adults and children. N Engl J Med. 2018;378(8):731-739.
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8. Dohner H, Estey E, Grimwade D, et al. Diagnosis and management of AML in adults: 2017 ELN recommendations from an international expert panel. Blood. 2017;129(4):424-447.
9. Haas BJ, Dobin A, Li B, Stransky N, Pochet N, Regev A. Accuracy assessment of fusion transcript detection via read-mapping and de novo fusion transcript assembly-based methods. Genome Biol. 2019;20(1):213.
10. Joshi SK, Qian K, Bisson WH, et al. Discovery and characterization of targetable NTRK point mutations in hematologic neoplasms. Blood. 2020;135(24):2159-2170.
11. Thol F, Gabdoulline R, Liebich A, et al. Measurable residual disease monitoring by NGS before allogeneic hematopoietic cell transplan- tation in AML. Blood. 2018;132(16):1703-1713.
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