Acute Leukemia Classification Using Transcriptional Profiles From Low-Cost Nanopore mRNA Sequencing.

Purpose: Most cases of pediatric acute leukemia occur in low- and middle-income countries, where health centers lack the tools required for accurate diagnosis and disease classification. Recent research shows the robustness of using unbiased short-read RNA sequencing to classify genomic subtypes of acute leukemia. Compared with short-read sequencing, nanopore sequencing has low capital and consumable costs, making it suitable for use in locations with limited health infrastructure.
Materials and Methods: We show the feasibility of nanopore mRNA sequencing on 134 cryopreserved acute leukemia specimens (26 acute myeloid leukemia [AML], 73 B-lineage acute lymphoblastic leukemia [B-ALL], 34 T-lineage acute lymphoblastic leukemia, and one acute undifferentiated leukemia). Using multiple library preparation approaches, we generated long-read transcripts for each sample. We developed a novel composite classification approach to predict acute leukemia lineage and major B-ALL and AML molecular subtypes directly from gene expression profiles.
Results: We demonstrate accurate classification of acute leukemia samples into AML, B-ALL, or T-lineage acute lymphoblastic leukemia (96.2% of cases are classifiable with a probability of > 0.8, with 100% accuracy) and further classification into clinically actionable genomic subtypes using shallow RNA nanopore sequencing, with 96.2% accuracy for major AML subtypes and 94.1% accuracy for major B-lineage acute lymphoblastic leukemia subtypes.
Conclusion: Transcriptional profiling of acute leukemia samples using nanopore technology for diagnostic classification is feasible and accurate, which has the potential to improve the accuracy of cancer diagnosis in low-resource settings.
Competing Interests: Mahler RevsineEmployment: Epic SystemsTravel, Accommodations, Expenses: Epic Systems Mark R. LitzowConsulting or Advisory Role: Omeros, Jazz PharmaceuticalsResearch Funding: Amgen, Astellas Pharma, Actinium Pharmaceuticals, Pluristem Therapeutics, AbbVie/Genentech, Tolero Pharmaceuticals, AbbVieOther Relationship: BioSight Yuri FedoriwHonoraria: Alexion Pharmaceuticals Kathryn G. RobertsStock and Other Ownership Interests: Amgen Charles G. MullighanStock and Other Ownership Interests: AmgenHonoraria: Amgen, IlluminaConsulting or Advisory Role: IlluminaSpeakers' Bureau: Amgen, PfizerResearch Funding: Loxo, Pfizer, AbbViePatents, Royalties, Other Intellectual Property: Inventor on a pending patent application related to gene expression signatures for detection of underlying Philadelphia chromosome–like events and therapeutic targeting in leukemia (PCT/US2012/069228), WO 2021/022076 A1. This Patent Highlight shows representative PROTAC compounds bound to JAK2, where ruxolitinib and baricitinib bind to the human JAK2 JH1. Furthermore, representative data illustrate protein degradation, cytotoxicity, and effect of the JAKSTAT signaling pathway of the PROTAC compounds in MHHCALL-4 cellsTravel, Accommodations, Expenses: Amgen, IlluminaNo other potential conflicts of interest were reported.