Philip C. Hanawalt

Curriculum Vitae

Last updated: December 2015

I. Education

II. Appointments - Stanford University, California

III. Government Service and Advisory Committees (Partial List)

IV. Editorial Service

V. Professional Recognition and Awards

VI. Professional Societies

VII. Scientific Conferences Organized

VIII. Teaching

Twenty-nine graduate students have completed their Ph.D. in Hanawalt's laboratory; over 60 postdoctoral research
associates, fellows and visiting senior scientists have participated in Hanawalt's research program at Stanford since
1962. The laboratory has maintained an international flavor with participants from 36 different countries over the years.

Courses taught at Stanford University: (Current courses underlined)

• Maintenance of the Genome, freshman seminar (BioSci 026)
• DNA Replication and Genome Maintenance, graduate and upper division (BioSci 210)
• Molecular Biophysics, graduate level
• DNA Repair and Mutagenesis, graduate & upper division lecture course (BioSci 205)
• DNA Replication, upper division undergraduate seminar course (BioSci 134)
• Highlights in Photobiology, graduate & upper division lecture course
• Molecular Biology, undergraduate "core" lecture course
• Cell Physiology, undergraduate "core" lecture course
• Research Seminar on DNA Repair and Genetic Toxicology (BioSci 305) Course on DNA replication and genomic maintenance, visiting professor at Deep Springs College, 2009
  

VIX. Principal Research Accomplishments

Hanawalt has been a productive researcher in the field of DNA repair since his pioneering discovery of repair replication in E. coli in 1963. He also first demonstrated repair replication in mycoplasmata and in a eukaryote (Tetrahymena) and he has developed a number of important experimental approaches for studying repair, beginning with the BrdUrd density labeling method for resolving semiconservatively replicated DNA from parental DNA containing repair patches. Hanawalt's approach was used by James Cleaver in 1968 to document a DNA repair defect in xeroderma pigmentosum (the first example of a human disease with DNA repair defect). The method was also used to validate the widely-used phenomenon of unscheduled DNA synthesis as a measure of DNA repair. Other significant research contributions from Hanawalt's laboratory have included: the demonstration of preferential mutagenesis by N-methyl nitrosoguanidine at DNA replication forks and its application to mapping genes; early evidence for membrane association of DNA replication complexes in E. coli and in mammalian cells; discovery of long-patch excision-repair in E. coli and the demonstration that it is an inducible component of the RecA-LexA regulatory circuit; discovery of a gene controlling nucleoside uptake in E. coli; development of permeabilized bacterial and mammalian cell systems to study excision-repair pathways; demonstration of enhanced survival of UV irradiated Simian Virus 40 upon treating the host cells with low doses of UV or chemical carcinogens; discovery that the repair enzyme, T4 endonuclease V, operates processively on damaged DNA; discovery that certain types of damage in transfecting plasmid DNA markedly enhances the efficiency of stable transformation in human cells; and the discovery that UV irradiation of short sequences of nucleotides can result in their ligation through pyrimidine dimerization, providing a plausible mechanism for prebiotic assembly of high molecular weight duplex DNA.

In 1982 Hanawalt and his colleagues reported the first example of intragenomic DNA repair heterogeneity: chemical adducts in centromeric alpha DNA sequences in African green monkey kidney cells were not as efficiently repaired as in the genome overall. In 1983 Mansbridge and Hanawalt discovered that cells from xeroderma pigmentosum (group C) only repair limited genomic domains, now known to include expressed genes. Hanawalt and his colleagues discovered that repair of some types of damage is selective; active genes are preferentially repaired, and in fact a special repair pathway, termed transcription-coupled repair (TCR), operates on the transcribed strands of expressed genes. TCR was documented in mammalian cells, in E. coli, and in yeast chromosomal and plasmid borne genes.The discovery of TCR in Hanawalt's laboratory has had profound implications for the fields of mutagenesis, environmental carcinogenesis, and risk assessment.

The prototype recQ gene was discovered in E. coli in Hanawalt's laboratory, and we now know of five homologues in humans including the genes mutated in the cancer prone hereditary diseases: Bloom's syndrome, Werner's syndrome, and Rothman Thompson syndrome. In E. coli the RecQ helicase was shown to play an important role in the accurate recovery of arrested replication forks.

More recent studies have focused upon the regulation of TCR and the global genomic nucleotide excision repair (GGR) pathway. Features of the TCR pathway (that is defective in Cockayne syndrome) include the possibility of "gratuitous TCR" at transcription pause sites in undamaged DNA. The GGR pathway was shown to be controlled through the SOS stress response in E. coli and through the activated product of the p53 tumor suppressor gene in human cells. These regulatory systems particularly affect the efficiency of repair of the predominant UV-induced photoproduct, the cyclobutane pyrimidine dimer, as well as that of chemical carcinogen DNA adducts, such as benzo(a)pyrene diol-epoxide. Rodent cells (typically lacking the p53-controlled GGR pathway) and tumor virus infected human cells (in which p53 function is abrogated) are unable to carry out efficient GGR of some lesions. Therefore, caution should be exercised in the interpretation of results from such systems for risk assessment in genetic toxicology.

Thierry Nouspikel in Hanawalt's laboratory discovered that the attenuated GGR in terminally differentiated human cells, is in fact a consequence of reduced activity of the E1 ubiquitin activating enzyme. Thus, E1 levels control excision repair! This has profound implications for our understanding of DNA repair regulation, and the possibility of modulating the repair response in tumors of patients undergoing chemotherapy.

Current research efforts focus upon naturally occurring non-canonical DNA structures as encumbrances to transcription, and the likelihood of gratuitous TCR. These studies, led by Silvia Tornaletti and Boris Belotserkovskii, have demonstrated that structures such as Z-DNA, H-DNA, G-quartets and PNA-DNA complexes can arrest transcription. A novel method for cancer chemotherapy employing peptide nucleic acid (PNA) for generating a stable R-loop (RNA-DNA hybrid) in a uniquely expressed gene in selected tumor cells is being developed to render the very act of transcription toxic in these cells.

Another area of current research interest is the molecular basis of the DNA repair defects in patients with Cockayne syndrome (CS) and UV-sensitive syndrome (UVSS). Unlike XP, sun-sensitive patients with CS or UVSS do not develop cancers of any type. Graciela Spivak in Hanawalt's group has shown that although both CS and UVSS cells are deficient in TCR of UV-induced DNA damage, only CS cells appear to be hypersensitive to oxidative DNA damage. We hypothesized that the severe developmental and neurological problems in CS may be a consequence of defective processing of endogenous oxidative DNA lesions. An ultrasensitive assay termed comet-FISH with single-stranded fluorescent DNA probes was used to examine repair of the prominent oxidative base lesion, 8oxoGuanine (at physiological levels ~100-fold lower than typically studied) by a postdoc, Jia Guo, who along with Spivak and Hanawalt have shown that CS and UVSS cells are equally deficient in TCR of this important lesion. Moreover, hOGG1 and XPA are required for this process, suggesting a crossover between the base excision and nucleotide excision repair pathways.