# The role for phase separation in oncogenesis and aberrant chromatin looping formation

> **NIH NIH R01** · UNIV OF NORTH CAROLINA CHAPEL HILL · 2022 · $577,786

## Abstract

PROJECT SUMMARY/ABSTRACT
Rearrangement of NUP98 gene (NUP98-r) is recurrent in leukemias such as acute myeloid leukemia (AML).
Patients with NUP98-r show poor prognosis and therapy failure. Most NUP98-r partners (>30 identified from
patients) are a DNA-binding domain of transcription factor (TF; e.g. HOXA9) or a histone-binding motif such as
Plant Homeodomain (PHD), suggesting chromatin deregulation as an oncogenic mechanism. NUP98-r fusions
invariably retain Phenylalanine-Glycine (FG) repeats, termed intrinsically disordered region (IDR), from NUP98.
How unstructured IDR contributes to oncogenesis remains elusive. Our studies of NUP98-HOXA9, an AML
NUP98-TF chimera, unveil an essential requirement of NUP98’s IDR for liquid-liquid phase separation (LLPS).
We also show that IDR and LLPS are critical for the much-enhanced genome binding by NUP98-HOXA9 and
for long-distance chromatin looping between oncogene promoters and enhancers, leading to development of
aggressive AML in mice. Our unpublished preliminary studies of other recurrent leukemic fusions (namely,
NUP98-PHD fusions and MSI2-HOXA9, a leukemia-related chimera formed by fusing a less-studied IDR of an
RNA-binding protein with HOXA9’s DNA-binding domain) all point to involvements of IDR and LLPS for
oncogenesis. Thus, we hypothesize that, due to aberrant genic fusions, a number of leukemia-related onco-
TFs and chromatin factors acquire a phase-separation-inducing IDR to establish LLPS, which confers chimera
a much more enhanced ability in genomic targeting; consequently, an oncogenic gene-expression program is
over-activated while aberrant chromatin loops are formed between oncogene promoters and enhancers, which
drives formation of aggressive leukemias. Dissection of the mechanisms underlying the IDR- and phase-
separation-mediated aberrant genome organization and oncogene activation in cancer cells shall provide new
and paradigm-shifting views as for how aggressive cancer develops, implicative of potentially new treatments
in future. Towards this goal, we will further characterize the role for the un-studied IDR (that of MSI2) in
establishing LLPS in vitro and in cells (Aim 1A) and will use primary human hematopoietic stem/progenitor
cells (HSPCs) and derived cells to define roles of IDR and LLPS in regulating genomic targeting (1B), the
target gene expression (1C), and leukemic transformation in vitro/vivo (1D) by various fusions (NUP98-PHD
and MSI2/NUP98-HOXA9). LLPS-indued chromatin looping is CTCF-independent and represents a previously
unstudied mechanism underlying 3D chromatin organization. We will further define the 3D chromatin structure
alterations caused by various NUP98-r and MSI2-HOXA9 fusions in disease-relevant cells (Aim 2A), define the
molecular mechanisms driving formation/maintenance of LLPS-dependent loops (2B), and determine the
impact of LLPS DNA loops on the sustained activation of oncogenes by using a novel CRISPR/dCas9-IDR
fusion strategy (2C). As phase-separati...

## Key facts

- **NIH application ID:** 10539807
- **Project number:** 1R01CA271603-01A1
- **Recipient organization:** UNIV OF NORTH CAROLINA CHAPEL HILL
- **Principal Investigator:** Douglas H. Phanstiel
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2022
- **Award amount:** $577,786
- **Award type:** 1
- **Project period:** 2022-07-01 → 2027-06-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10539807

## Citation

> US National Institutes of Health, RePORTER application 10539807, The role for phase separation in oncogenesis and aberrant chromatin looping formation (1R01CA271603-01A1). Retrieved via AI Analytics 2026-05-24 from https://api.ai-analytics.org/grant/nih/10539807. Licensed CC0.

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