# Decoding the Molecular Basis of Dysregulated Cleavage and Polyadenylation in Myeloid Malignancies - Resubmission - 1

> **NIH NIH F30** · NEW YORK UNIVERSITY SCHOOL OF MEDICINE · 2024 · $41,614

## Abstract

PROJECT SUMMARY
This proposal aims to investigate dysregulation of alternative polyadenylation (APA) in acute myeloid leukemia
(AML). Dysregulation of APA has been identified in hematopoietic stem and progenitor cells in AML, but
previous studies have compared bulk populations of HSPCs from AML patients to healthy donors. Therefore,
the extent of dysregulation in malignant hematopoietic stem cells (HSCs) and the molecular regulators driving
this phenomenon remain poorly understood. To address these questions, this proposal outlines two specific
aims that leverage a previously developed computational platform for identifying shifts in polyA site usage at
single-cell resolution. The first aim will use single-cell RNA sequencing data from AML patients to characterize
changes in polyA site usage between malignant and healthy HSPCs at matched differentiation stages within
the same donor. This will identify if changes in APA originate in leukemic stem cells or are restricted to more
committed progenitors. PolyA site usage is heterogenous between patients and even healthy donors, so
comparisons within the same donor will improve accuracy on identifying true changes in polyA site usage. The
second aim extends a sequence-based deep learning framework to model polyA site usage in human HSPCs
with over/under expression of different CPA regulators. This model will elucidate the extent to which CPSF6, a
subunit of cleavage-factor I complex that is downregulated at the transcriptional level in AML patients, drives
aberrant polyA site usage in AML. If CPSF6 downregulation is not sufficient to explain dysregulated polyA site
usage, additional factors that contribute will be identified. Finally, CRISPR perturbation studies will be used to
assess if modulating the expression of CPSF6 expression (and other implicated regulators) affects
differentiation state in AML cell lines, providing functional evidence that APA is involved in maintaining a
leukemic state. The completion of these aims will provide a new understanding of APA in myeloid
malignancies and may lead to the identification of novel therapeutic targets.

## Key facts

- **NIH application ID:** 10995444
- **Project number:** 1F30CA287962-01A1
- **Recipient organization:** NEW YORK UNIVERSITY SCHOOL OF MEDICINE
- **Principal Investigator:** Madeline Heidi Kowalski
- **Activity code:** F30 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2024
- **Award amount:** $41,614
- **Award type:** 1
- **Project period:** 2024-07-01 → 2028-06-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10995444

## Citation

> US National Institutes of Health, RePORTER application 10995444, Decoding the Molecular Basis of Dysregulated Cleavage and Polyadenylation in Myeloid Malignancies - Resubmission - 1 (1F30CA287962-01A1). Retrieved via AI Analytics 2026-05-25 from https://api.ai-analytics.org/grant/nih/10995444. Licensed CC0.

---

*[NIH grants dataset](/datasets/nih-grants) · CC0 1.0*