Pathogenic Genes

Variants of unknown significance are becoming a growing area of research within personal genomics, which generally falls within individualized medicine, a growing field that offers to pinpoint difficult-to-diagnosis patients with rare or untreatable diseases. Additionally, understanding the proteins' 3D change of structure (variant versus wild type versus polymorphism) will allow us to extrapolate possible functional relationships that arise from structure, and then specific cases of protein dysfunction may be documented through our platform and further probed with computational tools to keep up with the thousands of new variants identified every year with Mayo Clinic and external collaborators. After establishing this platform, our lab would seek to further the project for hypothesis generation, but more importantly, to obtain data to inform and aid physicians, leading to future studies on druggability mechanisms with our peer institutions to create a central protein diagnostics depot for individualized medicine clinicians and academic and pharmaceutical researchers.

Personalized medicine theorizes that a patient's genomic information can be used to identify custom therapies that will be more effective and less toxic than the current standard of care. Unfortunately, realization of personalized medicine is hampered by our incomplete knowledge of the impact of the majority of genomic variations also known as variants of uncertain significance (VUS). To move personalized medicine away from the theoretical and into the practical application in everyday patient care, we need to identify rapid and robust ways to determine VUS pathogenicity.

Regrettably, current tools or approaches are either too time-consuming or rely on known pathogenic or benign variants, limiting their utility in a clinical setting. The goal of rapid and robust methods to determine VUS pathogenicity will require new experimental tactics that increase current predictive capabilities and provide functional validation. Ideally, we envision a disease agnostic and easily accessible platform to evaluate the likely pathogenicity of an identified VUS. Before we can achieve this ideal, we need to understand how VUSs affect the:

1. Function of the genetic product
2. Interaction with known enzymatic partners
3. Cellular and organismal fitness

Here, we will build this knowledge through a combination of modeling tools and functional assays allowing for integration of experimental results identifying likely trends, patterns and idiosyncrasies that result from genetic variations.

To remain within the realm of clinical application, tested VUSs will be sourced from Mayo Clinic's Center for Individualized Medicine. Given the wide array of expertise required for the proposed approach, this project will be a partnership between three premier laboratories, each with the knowledge and tools required to fulfill one of the three needed arms of research to:

• Develop a novel molecular modeling platform for identifying VUSs' impact on protein structure, dynamics and interaction via statistical mechanics models
• Assess VUSs functional impact on cell physiology via combination of organ-on-a-chip systems for screening the pathogenicity of identified VUSs
• Evaluate the VUSs pathological impact in high-throughput humanized in vivo models by providing in vivo functional assessment of identified VUSs

Information from all three are used to develop a working prototype for rapid discovery of pathogenic behavior in patient-observed VUSs.

Dr. Caulfield's research team includes principal investigators and researchers, such as Y. Shrike Zhang, Ph.D., (Harvard Medical School) and Christopher E. Hopkins, Ph.D., M.B.A., (InVivo Biosystems), who have expertise with organ-on-a-chip and genetic animal variant high-throughput screening.

Related publications

Dr. Caulfield's research publications on defining and dissecting pathogenicity with VUSs include:

• Norris GA, Tsai AC, Schneider KW, Wu YH, Caulfield T, Green AL. A novel, germline, deactivating CBL variant p.L493F alters domain orientation and is associated with multiple childhood cancers. Cancer Genetics. 2021; doi:10.1016/j.cancergen.2021.01.008.
• Richter JE Jr, Hines S, Selvam P, Atwal H, Farres H, Caulfield TR, Atwal PS. Clinical description & molecular modeling of novel MAX pathogenic variant causing pheochromocytoma in family, supports paternal parent-of-origin effect. Cancer Genetics. 2021; doi:10.1016/j.cancergen.2021.01.004.
• Ahuja AS, Selvam P, Vadlamudi C, Chopra H, Richter JE Jr, Macklin SK, Samreen A, Helmi H, Mohammaad AN, Hines S, Davila MC, Atwal PS, Caulfield TR. Genomics combined with a protein informatics platform to assess a novel pathogenic variant c.1024 A>G (p.K342E) in OPA1 in a patient with autosomal dominant optic atrophy. Ophthalmic Genetics. 2020; doi:10.1080/13816810.2020.1814344.
• Coban MA, Blackburn PR, Whitelaw ML, Haelst MMV, Atwal PS, Caulfield TR. Structural models for the dynamic effects of loss-of-function variants in the human SIM1 protein transcriptional activation domain. Biomolecules. 2020; doi:10.3390/biom10091314.
• Macklin SK, Bruno KA, Vadlamudi C, Helmi H, Samreen A, Mohammad AN, Hines S, Atwal PS, Caulfield TR. Examination of molecular effects of MYLK deletion in a patient with extensive aortic, carotid, and abdominal dissections that underlie the genetic dysfunction. Case Reports in Medicine. 2020; doi:10.1155/2020/5108052.
• Coban M, Fraga S, Caulfield T. Structural and computational perspectives of selectively targeting mutant proteins. Current Drug Discovery Technologies. 2020; doi:10.2174/1570163817666200311114819.
• Richter JE Jr, Vadlamudi C, Macklin SK, Samreen A, Helmi H, Broderick D, Mohammad AN, Hines SL, VanGerpen JA, Atwal PS, Caulfield TR. Characterization of a pathogenic variant in the ABCD1 gene through protein molecular modeling. Case Reports in Genetics. 2020; doi:10.1155/2020/3256539.
• Blackburn PR, Sullivan AE, Gerassimou AG, Kleinendorst L, Bersten DC, Cooiman M, Harris KG, Wierenga KJ, Klee EW, van Gerpen JA, Ross OA, van Haelst MM, Whitelaw ML, Caulfield TR, Atwal PS. Functional analysis of the SIM1 variant p.G715V in 2 patients with obesity. The Journal of Clinical Endocrinology and Metabolism. 2020; doi:10.1210/clinem/dgz192. PMID: 31872862.
• Richter JE Jr, Samreen A, Vadlamudi C, Helmi H, Mohammad AN, Wierenga K, Hines S, Atwal PS, Caulfield TR. Genomic observations of a rare/pathogenic SMAD3 variant in Loeys-Dietz syndrome 3 confirmed by protein informatics and structural investigations. Medicina (Kaunas). 2019; doi:10.3390/medicina55050137.
• Hines SL, Mohammad AN, Jackson J, Macklin S, Caulfield TR. Integrative data fusion for comprehensive assessment of a novel CHEK2 variant using combined genomics, imaging, and functional-structural assessments via protein informatics. Molecular Omics. 2019; doi:10.1039/c8mo00137e.
• Richter JE, Robles HG, Mauricio E, Mohammad A, Atwal PS, Caulfield TR. Protein molecular modeling shows residue T599 is critical to wild-type function of POLG and description of a novel variant associated with the SANDO phenotype. Human Genome Variation. 2018; doi:10.1038/hgv.2018.16.