Exploring Transcriptional Adaptation: Therapeutic Potential and Impact on Human Genetics

/ABSTRACT Mutations can lead to a wide-variety of genetic diseases. Recent sequencing studies, however, have identified loss-of-function mutations, including within disease-relevant genes, in apparently healthy individuals, reviving the interest in the concept of genetic robustness. In previous studies, we identified transcriptional adaptation (TA), a novel mechanism through which cells can compensate for nonsense mutations by increasing the expression levels of functionally related genes (e.g., paralogs, or the wild-type (WT) allele in case of heterozygous mutations), in a manner dependent on mutant mRNA decay. We proposed a model whereby following mutant mRNA degradation, mRNA decay intermediates are translocated back to the nucleus to induce the upregulation of genes exhibiting sequence similarity. In my postdoctoral work, I identified ILF3 as the key RNA binding protein modulating the transport of mRNA degradation intermediates from the cytoplasm to the nucleus to induce TA. Additionally, I developed a screening strategy that identified ILF3-associated RNA fragments, termed “trigger RNAs,” which can activate gene expression when transfected into cells. Trigger RNAs hold the potential to be a new class of gene-augmenting therapeutic RNAs. In this K99/R00 application, my first aim is to characterize the molecular characteristics of trigger RNAs, including their sequence and structural requirements. These studies will enable better design of trigger RNAs, which can be beneficial for both genetic and non-genetic diseases. My second aim is to explore the broader physiological role of TA by investigating how TA influences the landscape of genetic diseases. Using a combination of functional genomics, and population genetics data analysis, I aim to identify genes whose perturbation phenotype is influenced by TA. Such genes could represent a class of genetic diseases that can be therapeutically targeted through harnessing TA. In addition, the studies will allow for better understanding of how different variants influence disease outcomes. My third aim will be to investigate the prevalence of dosage compensation to heterozygous mutations, and understand how TA contributes to tolerance of heterozygous mutations in mammals. My background in RNA biology and gene expression regulation, and having been a lead author in the discovery of TA, puts me in a unique position to accomplish this proposal. During the K99 phase, I will be supported by an outstanding team of mentors and advisors (Drs. Jonathan Weissman, Mark Daly, Olivia Corradin, Konrad Karczewski and Harvey Lodish) with expertise in all aspects and methodologies required for the completion of the proposed research. I will acquire new skills in population genetics and big data analysis. I shall also promote my soft skills, including grant writing, leadership and management skills, through formal coursework and training and institutional support from the Whitehead institute. The combination of mentored support, training and data obtained in the K99 phase will act as a stepping stone towards achieving independence as an investigator in the R00 phase and beyond, and leading a successful lab. Project Number: 1K99HG014205-01 | Fiscal Year: 2025 | NIH Institute/Center: National Human Genome Research Institute (NHGRI) | Principal Investigator: Mohamed El-Brolosy | Institution: WHITEHEAD INSTITUTE FOR BIOMEDICAL RES, CAMBRIDGE, MA | Award Amount: $178,416 | Activity Code: K99 | Study Section: Genome Research Study Section[GNOM-G] View on NIH RePORTER: https://reporter.nih.gov/project-details/11110660