August 2026

NEUROSCIENCES

NOVEL SPATIAL TECHNOLOGY MAY IMPROVE THE UNDERSTANDING OF CANCER BIOLOGY

Northwestern Medicine scientists have developed a novel high-resolution spatial genomics platform to support research on how genome organization and genetic alterations contribute to the development of disease, including cancer, as detailed in a recent study published in Nature Methods. 

“What is particularly exciting is that we can simultaneously profile 3D genome organization and chromatin accessibility while preserving the native spatial context of cells and tissues, and we can also detect genomic alterations such as copy-number changes and structural variations in cancer,” says co-corresponding author Feng Yue, PhD.

Key Context

Recent advances in spatial “omics” techniques have enabled scientists to profile different molecular features while preserving their spatial context within tissues, but the techniques do not capture 3D genome folding.

Imaging-based approaches have also been used to study the genome organization and its relationship to biological processes, but they typically interrogate selected loci or regions in the genome, underscoring the need for complementary sequencing-based technologies that can map the entire genome.

Addressing the Gap

Dr. Yue’s team developed Spatial-ATAC-Hi-C, a microfluidic-based spatial platform that can profile both 3D genome organization and chromatin accessibility within native tissue samples.

To validate their approach, the scientists applied Spatial-ATAC-Hi-C to adult mouse brain tissue and adult human brain tissue samples, revealing unique chromatin architecture features and gene regulatory programs in both neuronal and non-neuronal cell populations.

What the Study Found

In glioblastoma and astrocytoma patient samples, Spatial-ATAC-Hi-C was also able to detect spatially resolved 3D genome alterations, in addition to genetic copy number variations and structure variations in certain regions of the tumors.

“We showed even within the same tumor, different regions can harbor distinct copy number alterations or structural variations,” says Dr. Yue. “Being able to detect these genomic differences while preserving their spatial context could help us better understand tumor heterogeneity.”

Overall, Spatial-ATAC-Hi-C provides a new technology for studying genome organization and gene regulation in cancer and developmental biology, according to Dr. Yue.

​This work was supported by NIH grants R35GM124820, 1R01HG009906, and R01HG011207, T32 CA009560 and T32 CA070085; a Neurosurgery Research and Education Foundation Fellowship; the U.S. (CA230856); American Brain Tumor Association Basic Research Fellowship (fully supported by Tap Cancer Out); and the Society of Neurological Surgeons.
Feng Yue, PhD, the Duane and Susan Burnham Professor of Molecular Medicine and a professor of Biochemistry and Molecular Genetics and of Pathology at Northwestern Medicine, was senior author of the study.
Amy Heimberger, MD, PhD, the Jean Malnati Miller Professor of Brain Tumor Research and vice chair for research in the Department of Neurological Surgery at Northwestern Medicine, was a co-author of the study.
​Adam Sonabend, MD, the Etka Frimerman Professor of Neurosurgery at Northwestern Medicine, was a co-author of the study.

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