Joe Derisi, PhD

Department of Biochemistry and Biophysics
+1 415 418-3647
Research Description: 

Our lab exploits whole genome approaches to tackle problems in yeast molecular biology and human infectious disease. These projects can be classified into three separate areas:

Functional genomics of Plasmodium falciparum, the causative agent of human malaria.
Malaria is one of the most deadly and profound human health problems in existence and results in approximately 1.5 to 2.7 million deaths annually. The most fatal and prevalent form of malaria is caused by the blood-borne pathogen Plasmodium falciparum. Beyond the lives this parasite claims every year, hundreds of millions of people will become clinically ill. The socioeconomic impact of this disease to developing countries, especially those on the African continent, is beyond measure. There exist no vaccines with an operational impact and resistance of the parasite to current anti-malarial drugs has spread worldwide. Because the vast majority of malaria occurs in poor nations, there is little profit incentive for large western and European drug companies to pursue new anti-malarial therapies, yet novel approaches are in desperate need

The paucity of new anti-malarial medications is partly attributable to the lack of validated drug targets. Indeed, all currently approved drugs and those in development are directed against only a handful of gene products and processes. Unlike many bacterial pathogens, both genetic and molecular biological approaches have been difficult in Plasmodia. Fortunately, the completion of the Plasmodium falciparum sequencing project will inherently broaden the range of potential drug targets by identifying all possible open reading frames. Although a great deal of functional annotation may be accomplished by sequence based homology comparisons, this information will not be sufficient to determine whether a gene product actually participates in a function or process at any given time during the development of the parasite. In addition, the majority of gene products discovered through the sequencing of the genome will not reveal significant sequence homology and therefore will remain hypothetical and uncharacterized. We are utilizing the full potential of the completed sequence by implementing a functional genomics approach to the elucidation of metabolic and stage specific gene expression. This is being accomplished by systematic perturbation of P. falciparum cultures in conjunction with genome wide gene expression profiling, exhaustive homology based sequence comparison, pathway analysis, and functional characterization.

Whole genome approaches to the molecular biology of Saccharomyces cerevisiae
We are using DNA microarrays to investigate several different aspects of yeast biology. These include chromatin immunoprecipitation techniques to reconstruct the protein-DNA topology of the genome, gene expression profiles to investigate the action of small molecule drugs, and immunoprecipitation of RNA binding proteins to screen for novel regulatory mechanisms. Other yeast-based projects in the lab seek to elucidate the mechanisms responsible for the various steps of meiotic recombination through genetics and biochemistry.

Searching for a link between asthma and viral infection.
The notion that acute asthma attacks are frequently precipitated by respiratory infection is part of the training of every physician and is well supported in general terms by numerous clinical investigations. However, the prevalence of respiratory infection in acute asthma and the identities of the responsible pathogen(s) have been more controversial. Studies based upon culture and/or viral antigen detection in respiratory secretions of asthmatics have generally recorded rates of infection between 20-40%; these studies typically identify rhinoviruses, coronaviruses, adenoviruses, influenza and parainfluenza viruses. This is likely to be an underestimate and likely define a minimal estimate of the contribution of viral infection to acute asthma attacks.

We are constructing and using a viral DNA microarray based system customized for the goal of detecting and differentiating between pathogens commonly found in the respiratory tract. This technology will allow us to investigate whether there is a positive correlation between viral infection and asthma attacks, if so, which viral types are so associated. To accomplish this goal, we are actively collaborating with an on-going clinical research study of asthma here at UCSF.

Primary Thematic Area: 
Human Genetics
Secondary Thematic Area: 
Research Summary: 
Genomic approaches to yeast molecular biology and infectious disease



Validation of a murine proteome-wide phage display library for the identification of autoantibody specificities.

bioRxiv : the preprint server for biology

Rackaityte E, Proekt I, Miller HS, Ramesh A, Brooks JF, Kung AF, Mandel-Brehm C, Yu D, Zamecnik C, Bair R, Vazquez SE, Sunshine S, Abram CL, Lowell CA, Rizzuto G, Wilson MR, Zikherman J, Anderson MS, DeRisi JL

Integrated host/microbe metagenomics enables accurate lower respiratory tract infection diagnosis in critically ill children.

The Journal of clinical investigation

Mick E, Tsitsiklis A, Kamm J, Kalantar KL, Caldera S, Lyden A, Tan M, Detweiler AM, Neff N, Osborne CM, Williamson KM, Soesanto V, Leroue M, Maddux AB, Sim?es EA, Carpenter TC, Wagner BD, DeRisi JL, Ambroggio L, Mourani PM, Langelier CR

Field assessment of BinaxNOW antigen tests as COVID-19 treatment entry point at a community testing site in San Francisco during evolving omicron surges.

PloS one

Schrom J, Marquez C, Wang CY, Saxena A, Mitchell AM, Ribeiro S, Pilarowski G, Nakamura R, Rojas S, Black D, Contreras Oseguera MG, Diaz EC, Payan J, Rojas S, Jones D, Tulier-Laiwa V, Zavaleta A, Martinez J, Chamie G, Glaser C, Jacobson K, Petersen M, DeRisi J, Havlir DV

Genomic analysis, immunomodulation and deep phenotyping of patients with nodding syndrome.

Brain : a journal of neurology

Soldatos A, Nutman TB, Johnson T, Dowell SF, Sejvar JJ, Wilson MR, DeRisi JL, Inati SK, Groden C, Evans C, O'Connell EM, Toliva BO, Aceng JR, Aryek-Kwe J, Toro C, Stratakis CA, Buckler AG, Cantilena C, Palmore TN, Thurm A, Baker EH, Chang R, Fauni H, Adams D, Macnamara EF, Lau CC, Malicdan MCV, Pusey-Swerdzewski B, Downing R, Bunga S, Thomas JD, Gahl WA, Nath A

Broad sensitivity of Candida auris strains to quinolones and mechanisms of resistance.

bioRxiv : the preprint server for biology

Lohse MB, Laurie MT, Levan S, Ziv N, Ennis CL, Nobile CJ, DeRisi J, Johnson AD