Linking 3D genome folding to gene activity in single cells
Bridging the gap: joint modeling of single-cell 1D and 3D genomics
['FUNDING_OTHER'] · UNIVERSITY OF TX MD ANDERSON CAN CTR · NIH-11181253
Researchers are building tools that read how DNA folds in individual cells and connect that folding to gene activity to help people with cancers such as acute lymphoblastic leukemia and patients receiving CAR‑T therapy.
Quick facts
| Phase | ['FUNDING_OTHER'] |
|---|---|
| Study type | Nih_funding |
| Sex | All |
| Sponsor | UNIVERSITY OF TX MD ANDERSON CAN CTR (nih funded) |
| Locations | 1 site (HOUSTON, UNITED STATES) |
| Trial ID | NIH-11181253 on ClinicalTrials.gov |
What this research studies
This project makes new computer tools to score how genes sit inside 3D genome structures measured in single cells. The team will use machine learning to fill in missing information about histone marks and chromatin contacts so each cell has a richer epigenomic and 3D profile. They will combine those signals into an epigenomic regulatory score to pinpoint promoter‑enhancer interactions at single‑cell and single‑gene resolution. The methods will then be applied to samples from CAR‑T immunotherapy patients to learn how differences in distant gene regulation relate to treatment response.
Who could benefit from this research
Good fit: Ideal candidates would be people with cancers such as acute lymphoblastic leukemia or patients receiving CAR‑T therapy who can provide blood or tumor samples for genomic profiling.
Not a fit: People without cancers tied to gene‑regulation changes or those who cannot provide biological samples are unlikely to benefit directly from this project.
Why it matters
Potential benefit: If successful, these tools could help identify molecular signs that predict who will respond to therapies like CAR‑T and reveal new targets for more precise treatments.
How similar studies have performed: There are emerging single‑cell 3D genome and multimodal studies, but combining scHi‑C gene‑level scoring with epigenomic imputation and direct application to CAR‑T patient responses is largely new.
Where this research is happening
HOUSTON, UNITED STATES
- UNIVERSITY OF TX MD ANDERSON CAN CTR — HOUSTON, UNITED STATES (ACTIVE)
Researchers
- Principal investigator: ZHENG, YE — UNIVERSITY OF TX MD ANDERSON CAN CTR
- Study coordinator: ZHENG, YE
About this research
- This is an active NIH-funded research project — typically early-stage science, not a clinical trial accepting patient enrollment.
- Some NIH-funded labs run parallel clinical studies or seek volunteers for related work. To check, contact the principal investigator or institution listed above.
- For full project details, budget, and progress reports, visit the official NIH RePORTER page below.