Congratulations to Our 2025 Multi-Omics Grant Winners

Multi-omics research projects help investigators understand biological systems through the integration of any combination of genomics, transcriptomic, epigenomic, proteomic, and metabolomic data. These tools, among others, can help bridge the gap between genotype and phenotype to help the researchers not only understand what is happening to a cell or cells but also why. Understanding the 3D organization of the genome is yet another tool in the multi-omics toolbox, which can help researchers gain a more complete understanding of the relationship between genotype and phenotype, across a range of biochemical processes and disease states.

We received an overwhelming amount of outstanding submissions for our 2025 Multi-Omics Grant Program. Although it was difficult to select just three winners, we are excited to to see how they will enable 3D genomics into their research projects:

Grant Recipient: Terry Furey, PhD

Terry Furey, PhD and his lab will analyze intestinal tissue samples from IBD patients using functional genomics and 3D chromatin mapping to investigate gene regulation changes and chromatin alterations associated with disease phenotypes.

Institution: University of North Carolina at Chapel Hill

Project Title: The 3D Chromatin Landscape in IBD

Project Overview: Impact: Understanding the genetic and molecular underpinnings of the inflammatory bowel diseases (IBD), namely Crohn’s disease and ulcerative colitis, is a major challenge. IBD is highly heterogeneous in presentation, progression, and response to treatment. Current treatments focus on addressing symptoms of disease, but there is no cure.

Feasibility: We have collected intestinal tissue samples from the large and small intestines of IBD patients, along with detailed clinical information. Using these samples, we have performed hundreds of functional genomics experiments to explore gene expression and regulation changes in disease, including in regions where genetic variation has been associated with increased disease risk through genome-wide association studies (GWAS).

Alignment: Hi-C data generated using our IBD patient tissue samples will provide important complementary information on the 3D chromatin landscape. These data will enhance our current omic annotations to not only help us better understand altered regulatory programs in IBD, but also to determine whether larger-scale chromatin changes are present in IBD patients that contribute to disease phenotypes.

Grant Recipient: Jonathan Rennhack, PhD

Jonathan Rennhack, PhD will use genome-wide Hi-C profiling to map 3D chromatin interactions in metastatic colorectal cancer, integrating these data with multi-omic analyses to identify key regulatory DNA loops and structural changes that drive metastasis and reveal new therapeutic vulnerabilities.

Institution: University Loyola Chicago

Project Title: Mapping the Metastatic Transcriptome of Colorectal Cancer

Project Overview: Colorectal cancer (CRC), a leading cause of cancer-related deaths, is alarmingly increasing in young patients. Metastasis, primarily to the lung or liver, is the main cause of death, yet the underlying mechanisms remain poorly understood. Recent research suggests that epigenetic modifications, rather than genetic mutations, drive the altered gene expression (transcriptome) observed in metastatic CRC cells. We hypothesize that these transcriptional shifts are orchestrated by dynamic changes in 3D genome organization, such as altered enhancer-promoter loops and TAD boundaries.

To investigate this, we will utilize Arima’s genome-wide HiC profiling to pinpoint critical regulatory DNA interactions driving the observed transcriptional changes. We will integrate this HiC data with our existing multi-omic data to gain comprehensive understanding of metastatic CRC to identify potential therapeutic vulnerabilities for this devastating stage of CRC.

Grant Recipient: Abdalla Ahmed

Abdalla Ahmed and his team will use 3D genomics to uncover how age-related changes in histone PTMs reshape the three-dimensional genome organization in human cardiac cells, revealing how these structural alterations drive cellular aging and cardiovascular disease risk.

Institution: Stanford University

Project Title: Identifying Epigenetic Drivers of Cardiac Disease Risk in the Aging Human Heart at Single-Cell Resolution

Project Overview: Aging is the top risk factor for heart disease, but the molecular details behind this process are still unclear. Our team is using advanced imaging to map over 40 histone modifications—chemical changes that regulate DNA—in every cell type of the human heart. By combining this with cutting-edge single-cell and 3D genomics technologies, we can see how these modifications and the 3D structure of the genome change as we age.

Our goal is to discover how shifts in histone modifications and genome architecture drive aging in heart cells. Understanding these changes could reveal new ways to prevent or treat age-related heart disease, keeping hearts healthier for longer.

Congratulations to these scientists and thank you to all who applied! Learn more about Arima technology and how 3D genomics can serve a critical role in your multi-omics research. Be on the look out for the next grant program opening in the coming months.