By Emily Cerf
October 17, 2024
The UC Santa Cruz Genomics Institute has awarded grants of up to $50,000 to six multidisciplinary research projects in the inaugural year of its seed funding program. These projects address human disease, species conservation, tool development, and more.
The new program aims to help high-risk ideas get off the ground with an initial round of funding. These funds can help researchers establish proof of concept for their projects, providing a potential pathway to growing their projects through fundraising activities the GI will assist with to help them acquire additional grants, donor gifts, and/or nonprofit or corporate collaboration.
“We sought and are supporting highly ambitious projects that take risks in envisioning bold solutions to pressing real-world problems,” said Lauren Linton, Executive Director of the Genomics Institute. “All six projects are being led by co-investigators from at least two different academic departments, spanning divisions, and showcase the nimble, long-range problem- solving mindset that UC Santa Cruz specializes in. I believe each one has the potential for transformative impact.”
The seed funding program called for projects that aligned with the Genomics Institute’s themes, which include diversity, equity and inclusion; science literacy; global and community health; understanding disease; conservation and environment biology; and tool and platform development. The call was distributed broadly across the entire university and ended up funding projects equally across the science and engineering divisions, in some cases bringing researchers together for the first time.
“By developing and applying rigorous engineering and computational methods to highly relevant biological challenges, we have the opportunity for profound impact in health, medicine, conservation, and more,” said Alexander Wolf, Dean of the Baskin School of Engineering. “I’m proud of our researchers who are taking risks and applying their expertise to these important projects, and am particularly impressed with the multidisciplinarity of the projects that have been funded.”
A major goal of the seed funding program is to encourage collaboration across departmental and even divisional lines, bringing together partners with very different insights to work on the same complex problem.
“The Genomics Institute continues to be one of UC Santa Cruz’s crown jewels,” said Bryan Gaensler, Dean of the UCSC Science Division. “Its membership spans divisions and is truly a university effort. I’m excited to see the new and innovative ways in which the Institute’s seed funding program has incentivized both scientists and engineers across divisions to work together.”
While the grants provide funding for up to one year, the researchers were asked to break their timelines into “go-no-go” points, with the funding broken out into these increments. They will be asked to report on the progress of their work. If their project is no longer viable, a “no-go,” the grant funding will end at that point.
“Through my research and development background in drug discovery, I know that failing early is considered valuable, in that it conserves resources, it allows us to see which big ideas should continue to be funded, and which may need to shift their approaches,” Linton said. “I look forward to seeing how these timelines evolve as we sharpen the focus on results – to balance the risks we have taken.
The funding for this seed program comes from the Genomics Institute’s Healthier World Fund, which is supported by a generous 10-year gift from an anonymous donor.
The program will fund the following projects:
Development of tools for the study of the epigenome and its response to environmental cues
Principal investigators: Assistant Professor of Microbiology and Environmental Toxicology Raquel Chamorro-Garcia, Associate Research Professor of Microbiology & Environmental Toxicology Carlos Diaz-Castillo, and Assistant Professor of Molecular, Cell, and Developmental (MCD) Biology Upasna Sharma
Previous research has shown that predisposition to disease might be passed down from our ancestors, and that our own exposures to disease could be passed down to our descendants — but further understanding of these dynamics requires investigating a myriad of data from genomes, cells, and individuals. This project aims to study which elements of the somatic and germ cells may be relevant to the genomic and phenotypic elements of inheritance. The team aims to use the methods developed in this project to inform future efforts for accumulating, long-term storing, browsing, and further analyzing epigenomic data.
Identifying structural variants associated with high temperature tolerance for giants of the coast
Principal investigators: Associate Professor of Ecology and Evolutionary Biology Malin Pinsky, Associate Professor of Biomolecular Engineering Karen Miga and Professor of Biomolecular Engineering Benedict Paten
As climate change increases ocean temperatures, key species such as giant kelp, which support highly productive ecosystems in California, are under increasing stress. This project will use long-read genome sequencing approaches developed at UCSC to uncover genomic variants associated with climate tolerance. The research team will build partnerships for integrating evolutionary resilience into kelp management and restoration in California and beyond, and use this project to demonstrate the potential of this evolutionary resilience approach for conservation of other regions and species.
The druggable RNA atlas
Principal investigators: Professor of MCD Biology Jeremy Sanford and Professor of Chemistry and Biochemistry Michael Stone
This project’s long-term vision aims to investigate RNA metabolism, specifically splicing — the process in which non-coding RNA is removed from coding RNA — and its role in rare genetic diseases. The team will compile what they call the Druggable RNA Atlas, a comprehensive guide to the genetic variants that negatively affect RNA splicing in people with rare genetic diseases. This atlas is aimed to transform and accelerate research around rare genetic disorders by shining light on possible pathways for targeting harmful variants through pharmaceutical treatment.
How introns change the function of the human genome
Principal Investigator: Assistant Professor of Biomolecular Engineering Ali Shariati, Associate Professor of Biomolecular Engineering Russell Corbett-Detig, and Distinguished Professor of MCD Biology Manuel Ares
This project builds on research by professors Corbett-Detig and Ares into the origin and function of introns, mysterious elements of the genome that are spliced out in the process of translating DNA to RNA. While their previous work has found that introns may be a major contributor to genomic diversity, this project will further investigate how the addition of new introns to the human genome affect humans on a molecular and fitness level. The scientists believe that basic science research in this area could lead to a great deal of applications in synthetic biology and the mitigation of human disease.
Using single-cell transcriptomics to elucidate the role of post-viral lung disease in promoting metastasis
Principal investigators: Assistant Professor MCD Biology Shaheen Sikandar, Assistant Professor of MCD Biology David Boyd, GI Xena Browser researchers Jing Zhu and Mary Goldman
Metastasis is the process in which cancer spreads from its original location to other parts of the body, and evidence has shown that metastasis occurs more often in tissue that has been damaged by past infections. This project will study the impact of severe respiratory viral infections due to influenza and SARS-CoV-2 on cancer metastasis in the lungs, using RNA sequencing data to better understand the mechanisms that may influence this. These results may help the design of treatments to keep cancerous tumors dormant and prevent metastasis.
Molecular classification of Osteosarcoma using artificial intelligence
Principal investigator: Assistant Professor of Computer Science and Engineering Yuyin Zhou
Co-investigator: Associate Professor of MCD Biology Olena Vaske
Osteosarcoma is a type of rare, aggressive cancer that starts in the cells that form bones and mostly affects children and young adults. Osteosarcoma has three subtypes, which are typically identified through a highly labor-intensive careful examination by a specialist, but this research aims to introduce AI methods to aid in the classification of these subtypes. The researchers will develop and apply innovative AI techniques that make up for the lack of well-annotated datasets and the rarity of the disease, two factors which currently hinder the use of AI methods for this problem. They hope this research will provide a foundation for applying similar AI approaches for other diseases and to further the clinical diagnostics of pediatric and young adult cancers.