Verification of prognostic expression biomarkers is improved by examining enriched leukemic blasts rather than mononuclear cells from acute myeloid leukemia patients

Era L Pogosova-Agadjanyan; Xing Hua; Megan Othus; Frederick R Appelbaum; Thomas R Chauncey; Harry P Erba; Matthew P Fitzgibbon; Isaac C Jenkins; Min Fang; Stanley C Lee; Anna Moseley; Jasmine Naru; Jerald P Radich; Jenny L Smith; Brooke E Willborg; Cheryl L Willman; Feinan Wu; Soheil Meshinchi; Derek L Stirewalt

doi:10.1186/s40364-023-00461-0

Verification of prognostic expression biomarkers is improved by examining enriched leukemic blasts rather than mononuclear cells from acute myeloid leukemia patients

Biomark Res. 2023 Mar 16;11(1):31. doi: 10.1186/s40364-023-00461-0.

Authors

Era L Pogosova-Agadjanyan¹, Xing Hua², Megan Othus², Frederick R Appelbaum^{1

3}, Thomas R Chauncey^{3

4}, Harry P Erba⁵, Matthew P Fitzgibbon⁶, Isaac C Jenkins^{1

7}, Min Fang¹, Stanley C Lee¹, Anna Moseley², Jasmine Naru¹, Jerald P Radich^{1

3}, Jenny L Smith^{1

8}, Brooke E Willborg¹, Cheryl L Willman⁹, Feinan Wu⁶, Soheil Meshinchi^{1

8}, Derek L Stirewalt^{10

11}

Affiliations

¹ Clinical Research Division, Fred Hutchinson Cancer Center, 1100 Fairview Ave N, D5-112, Seattle, WA, 98109, USA.
² SWOG Statistical Center, Fred Hutchinson Cancer Center, Seattle, WA, USA.
³ Departments of Oncology and Hematology, University of Washington, Seattle, WA, USA.
⁴ VA Puget Sound Health Care System, Seattle, WA, USA.
⁵ Duke Cancer Institute, Durham, NC, USA.
⁶ Bioinformatics Shared Resource, Fred Hutchinson Cancer Center, Seattle, WA, USA.
⁷ Clinical Biostatistics, Fred Hutchinson Cancer Center, Seattle, WA, USA.
⁸ Department of Pediatrics, University of Washington, Seattle, WA, USA.
⁹ Department of Laboratory Medicine and Pathology, Mayo Clinic Comprehensive Cancer Center, Rochester, MN, USA.
¹⁰ Clinical Research Division, Fred Hutchinson Cancer Center, 1100 Fairview Ave N, D5-112, Seattle, WA, 98109, USA. dstirewa@fredhutch.org.
¹¹ Departments of Oncology and Hematology, University of Washington, Seattle, WA, USA. dstirewa@fredhutch.org.

Abstract

Background: Studies have not systematically compared the ability to verify performance of prognostic transcripts in paired bulk mononuclear cells versus viable CD34-expressing leukemic blasts from patients with acute myeloid leukemia. We hypothesized that examining the homogenous leukemic blasts will yield different biological information and may improve prognostic performance of expression biomarkers.

Methods: To assess the impact of cellular heterogeneity on expression biomarkers in acute myeloid leukemia, we systematically examined paired mononuclear cells and viable CD34-expressing leukemic blasts from SWOG diagnostic specimens. After enrichment, patients were assigned into discovery and validation cohorts based on availability of extracted RNA. Analyses of RNA sequencing data examined how enrichment impacted differentially expressed genes associated with pre-analytic variables, patient characteristics, and clinical outcomes.

Results: Blast enrichment yielded significantly different expression profiles and biological pathways associated with clinical characteristics (e.g., cytogenetics). Although numerous differentially expressed genes were associated with clinical outcomes, most lost their prognostic significance in the mononuclear cells and blasts after adjusting for age and ELN risk, with only 11 genes remaining significant for overall survival in both cell populations (CEP70, COMMD7, DNMT3B, ECE1, LNX2, NEGR1, PIK3C2B, SEMA4D, SMAD2, TAF8, ZNF444). To examine the impact of enrichment on biomarker verification, these 11 candidate biomarkers were examined by quantitative RT/PCR in the validation cohort. After adjusting for ELN risk and age, expression of 4 genes (CEP70, DNMT3B, ECE1, and PIK3CB) remained significantly associated with overall survival in the blasts, while none met statistical significance in mononuclear cells.

Conclusions: This study provides insights into biological information gained/lost by examining viable CD34-expressing leukemic blasts versus mononuclear cells from the same patient and shows an improved verification rate for expression biomarkers in blasts.

Keywords: Acute myeloid leukemia; Biomarkers; Genetic biomarkers; Hematological cancers; Leukemias; Prognostic biomarkers; Transcriptome; Translational research.

Abstract

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