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Expanding single-cell transcriptomics to chart the role of noncoding RNAs in normal hematopoiesis

Award Number: F30HL178248
ORGANIZATION: NATIONAL HEART, LUNG, & BLOOD INSTITUTE
OPDIV: NIH
AWARD CLASS: DISCRETIONARY
AWARD ACTIVITY TYPE: FELLOWSHIP/SCHOLARSHIP/STUDENT LOANS
PERIOD OF PERFORMANCE START DATE: 09/15/2025
PERIOD OF PERFORMANCE END DATE: 09/14/2029

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Expanding single-cell transcriptomics to chart the role of noncoding RNAs in normal hematopoiesis - PROJECT ABSTRACT Hematopoietic stem and progenitor cells (HSPCs) carry the important responsibility of producing an enormous number of myeloid and lymphoid cells. Defects in HSPC function can lead to benign and malignant neoplasms as well as bone marrow failure, often driven by somatic mutations in key regulators. Noncoding (nc)RNAs are emerging regulators of hematopoietic self-renewal and lineage specification. Long (l)ncRNAs specifically contribute by modulating genome topology, chromatin compaction, gene transcription, post-transcriptional processing, translation, and cellular signaling. In addition, transfer (t)RNAs, which shuttle amino acids to the ribosome, shape the cellular proteome by enhancing the translation of messenger RNAs enriched for cognate codons. When dysregulated, these ncRNAs contribute to the pathogenesis of hematologic neoplasms. Despite these advances, ncRNAs are not profiled in standard single-cell RNA sequencing (scRNAseq): ncRNAs are mostly not endogenously polyadenylated (EPA), preventing their capture by oligo-deoxythymidine primers. This limitation of scRNAseq critically prevents the study of how ncRNAs bias and commit cells toward hematopoietic lineages. We hypothesize that ncRNAs, particularly lncRNAs and tRNAs, bias HSPCs toward specific cellular fates. To test this hypothesis, we developed a method, single-cell total RNA sequencing (scTRS), that incorporates RNA de-modification and exogenous polyadenylation to extend RNA capture to modified and non- EPA ncRNAs, which are not captured by other methods. Here, first, I aim to develop a computational pipeline to enable the processing and analysis of scTRS data. Second, I will apply scTRS in primary HSPCs to identify candidate ncRNA drivers of normal hematopoiesis. Then, I propose a series of in vitro perturbation experiments to validate and examine the roles of these candidate drivers of normal differentiation. Finally, because the scTRS workflow is compatible with commercially available droplet-based platforms and the computational pipeline will be broadly shared, scTRS will be available to research groups across fields for broad impact. Collectively, this work will deliver novel and actionable insights into how ncRNAs help orchestrate human hematopoiesis.


Issue Date FY	Funding FY	Legal Entity Name	Legal Entity Address	Legal Entity City	Legal Entity State	Legal Entity Zip Code	Legal Entity COUNTY	Legal Entity COUNTRY	Assistance Listing	Award Code	Budget Year	Action Date	Action Type	Action Amount

Issue Date FY: 2026 ( Subtotal = $55,114 )
2026	2026	WEILL MEDICAL COLLEGE OF CORNELL UNIVERSITY	575 LEXINGTON AVE FL 9	NEW YORK	NY	10022	NEW YORK	USA	Blood Diseases and Resources Research	002	2	7/31/2026	NON-COMPETING CONTINUATION	$55,114
2026	2025	WEILL MEDICAL COLLEGE OF CORNELL UNIVERSITY	575 LEXINGTON AVE FL 9	NEW YORK	NY	10022	NEW YORK	USA	Blood Diseases and Resources Research	001	1	3/24/2026	NEW	$0
2026	2025	WEILL MEDICAL COLLEGE OF CORNELL UNIVERSITY	575 LEXINGTON AVE FL 9	NEW YORK	NY	10022	NEW YORK	USA	Blood Diseases and Resources Research	000	1	3/24/2026	NEW	$0
														Subtotal = $55,114

Issue Date FY: 2025 ( Subtotal = $54,538 )
2025	2025	WEILL MEDICAL COLLEGE OF CORNELL UNIVERSITY	575 LEXINGTON AVE FL 9	NEW YORK	NY	10022	NEW YORK	USA	Blood Diseases and Resources Research	000	1	9/3/2025	NEW	$54,538
														Subtotal = $54,538

Grand Total All Awards = $109,652

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Expanding single-cell transcriptomics to chart the role of noncoding RNAs in normal hematopoiesis

Award Number: F30HL178248

ORGANIZATION: NATIONAL HEART, LUNG, & BLOOD INSTITUTE

OPDIV: NIH

AWARD CLASS: DISCRETIONARY

AWARD ACTIVITY TYPE: FELLOWSHIP/SCHOLARSHIP/STUDENT LOANS

PERIOD OF PERFORMANCE START DATE: 09/15/2025

PERIOD OF PERFORMANCE END DATE: 09/14/2029

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