Our research uses cell and molecular, clinical and computational approaches, and has been supported over the past decade by the NCI, NHLBI, Gates/FNIH, Department of Defense and Butterfly Guild.
Genetic instability syndromes / human genetic variation
We work on two of the human RECQ helicase deficiency syndromes Werner and Bloom syndrome, and the bone marrow failure syndrome Fanconi anemia. All are recessive genomic instability syndromes and cancer predispositions, with other associated developmental or acquired features.
We use experimental approaches to determine physiologic functions of the RECQ and FANC genes, and bioinformatics and computational approaches to identify and analyze genetic variation members of both gene families. These analyses, in turn, provide the foundation for high-throughput functional phenotyping of DNA basepair-level genetic variation. Our initial efforts have focused on frequently altered members of the Fanconi anemia gene family, where we make use of bar-coded genetic variant libraries to quatitatively track specific variants in disease-relevant primary and secondary cellular and biochemical assays.
We are also directly involved with clinical and translational aspects of the RECQ helicase deficiency syndromes and Fanconi anemia. We organized and sponsored the 3rd International Meeting on 'RECQ Helicases in Biology and Medicine' on 28-30 May 2016 at the Fred Hutchinson Cancer Center in Seattle WA. This was the largest ever gathering of patients, clinicians and scientists from around the world focused on understanding and treating RECQ helicase disorders. We also helped organize and host the 28th Annual Fanconi Anemia Research Symposium in Bellevue, WA in Sept. 2016, and in organizing the ‘International Meeting on RECQ Helicases and Related Diseases 2018’ with Japanese colleagues that was held in February 2018 in Chiba, Japan.
We have had a longstanding interest in identifying and exploiting cancer-specific therapeutic vulnerabilities linked to defects in DNA damage repair pathways or to aberrant replication behavior. This work is part of a highly interdisciplinary NCI-funded Program Project that includes basic scientists, clinicians, bioengineers and cancer bioinformatics specialists. We work with patient samples, genetic and genomic information and stem cell models of two different types of cancer, adult acute myeloid leukemia (AML) and glioblastoma multiforme (GBM). Results from this work have already begun to guide therapeutic choice, e.g., in newly diagnosed AML patients. Our larger goal is to improve therapy and treated outcomes for patients with both of these lethal diseases.
With cancer bioinformatics colleagues we have also participated in the TCGA Pan-Cancer Atlas Project, and recently published our systematic analysis of DNA damage repair pathway alterations in 33 different cancer types that included genomic data from 9,125 patients. Our Cell Reports manuscript of this project is included in our 2018 Publications listing.
DNA Replication Dynamics
We developed and popularized microfluidic-assisted replication track analysis (or maRTA) technology to analyze DNA replication dynamics in human cells. Our maRTA protocols allow replicating DNA molecules - visualized as 'tracks' – to be labeled in vivo under physiologic conditions, then easily visualized and measured to reveal replication dynamics and the repair of DNA breaks in vivo at the single molecule level. This powerful technology is being used by ever-larger numbers of investigators interested in high resolution analyses to probe mechanistic details of DNA replication, fork protection and repair, and how genetic, environmental and pharmacologic perturbations alter these processes in human normal and cancer cells.
See colleague Julia Sidorova's detailed guides to the use of maRTA to analyze DNA replication (Nature Protocols 2009) and DNA repair (Methods 2016). This technology now forms the core platform for work in Julia’s new position and lab.
We developed homing endonucleases ('meganucleases') as genome engineering tools, and use these and derivatives of the TALENs and CRISPR/Cas9 nucleases for genome engineering on a daily basis. Projects have focused on site-specific DNA double strand break repair dynamics; targeted correction of heritable mutations; functional characterization of new human chromosomal 'safe harbor' sites; and germline genome engineering of Anopheles gambiae mosquitoes to interrupt malaria transmission as part of the Target Malaria Project.
Human Somatic Mutation
We maintain an active interest in human somatic mutation and genomic instability. In prior research we used the X-linked HPRT and ch.4-linked glycophorin-A (GPA) loci as targets to quantify mutation frequencies, rates and the molecular spectrum of somatic and germline mutations in human cells. The most useful of our HPRT protocols, publications and data can be found on our Publications and Links and Downloads page tabs.
Collaborative, open science is a powerful way to advance basic and disease-oriented research, and there is no better day job than to work with and learn from bright colleagues across a range of disciplines. Our interdisciplinary collaborative science efforts include our NCI-funded Program grant on cancer therapeutic response mechanisms; the research and education programs of the Fanconi Anemia Research Fund (FARF); The Cancer Genome Atlas Analysis Working Group on DNA Damage Response and Repair Pathways (TCGA-DDR); and Target Malaria, an international consortium developing gene drive approaches in Anopheles gambiae to suppress malaria transmission in Africa.