Personalized Single-Cell Proteogenomics to Distinguish Acute Myeloid Leukemia from Nonmalignant Clonal Hematopoiesis

Abstract

Genetic mutations associated with acute myeloid leukemia (AML) also occur in agerelated clonal hematopoiesis, often in the same individual. This makes confident assignment of detected variants to malignancy challenging. The issue is particularly crucial for AML posttreatment measurable residual disease monitoring, where results can be discordant between genetic sequencing and flow cytometry. We show here that it is possible to distinguish AML from clonal hematopoiesis and to resolve the immunophenotypic identity of clonal architecture. To achieve this, we first design patient-specific DNA probes based on patient's whole-genome sequencing and then use them for patient-personalized single-cell DNA sequencing with simultaneous single-cell antibodyoligonucleotide sequencing. Examples illustrate AML arising from DNMT3A-and TET2-mutated clones as well as independently. The ability to personalize single-cell proteogenomic assessment for individual patients based on leukemia-specific genomic features has implications for ongoing AML precision medicine efforts.SigNifiCANCe: This study offers a proof of principle of patient-personalized customized single-cell proteogenomics in AML including whole-genome sequencing-defined structural variants, currently unmeasurable by commercial "off-the-shelf" panels. This approach allows for the definition of genetic and immunophenotype features for an individual patient that would be best suited for measurable residual disease tracking.

Pembrolizumab and decitabine for refractory or relapsed acute myeloid leukemia

“…These patients have been reported previously. 37 76 (C) Kaplan-Meier survival curve with 95% CI. (D) Summary of grades 3 and 4 adverse events and irAEs that occurred during treatment.…”

“…We have previously reported the use of patient-personalized scDNA-seq on baseline samples for these two patients to resolve leukemic clonal landscape. 37 We therefore also acquired scDNA-seq with oligonucleotide-conjugated antibodies against myeloid markers on these relapse samples ( figure 6C, D ). We confirmed that the relapsing AML had the same genomic mutational features and cell-surface immunophenotype as baseline and that the HLA class I and class II of the leukemic clone remained stable at relapse compared with initial diagnosis.…”

“…All experimental acquisition, library generation, sequencing, data processing, and analyses were performed exactly as previously described. 37 …”

Natural Barcodes for Longitudinal Single Cell Tracking of Leukemic and Immune Cell Dynamics

“…However, this approach is unable to target personal mutations and less frequent variants ( 98 , 99 ) that would otherwise substantially increase the resolution of leukemic evolution ( 100 , 101 ). This shortcoming can be addressed either through screening of personal mutations with WES and subsequent targeted single-cell sequencing ( 102 , 103 ), or with unbiased scWGS-seq. Similar to the analysis of CNV, a critical step in the identification of somatic nuclear mutations from scWGS-seq involves stringent filtering of false positive results ( 104 ).…”

Molecular Minimal Residual Disease Detection in Acute Myeloid Leukemia

“…Miles et al observed that CD11b expression co-occurred with sub-clones harboring a RAS mutation [ 91 ]. Another recent study explored the utility of proteogenomics in three AML patients, and concluded that it can potentially improve precision medicine in AML [ 92 ].…”