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User:Patricia at GMMB/Joseph DeRisi Career

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Career and research

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DeRisi has been a faculty member of the UCSF biochemistry and biophysics department since 1999. As of 2022 he is a professor of biochemistry and biophysics and is also the director of UCSF's Sandler Program for Breakthrough Biomedical Research.[1][2]

DeRisi is known for printing the first whole-genome expression array,[3] performing the first broad analysis of differential gene expression in cancer cells,[4] profiling gene expression throughout the lifecycle of the malaria-causing protozoan Plasmodium falciparum,[5] genomic characterization of the SARS-CoV-1 virus,[6] and pioneering virus discovery using gene hybridization arrays and DNA sequencing technologies.[7]

In his early career, DeRisi was a pioneer of microarrays, and designed and built both hardware and software for microarrays. He was a proponent of open access to microarray technology,[8] and maintained a website with software and protocols for microarray operations.[9] He is also a proponent of open access publishing.[10]

In 2002, DeRisi and his research collaborator David Wang developed the ViroChip, a DNA microarray that could be used to rapidly identify viruses in a sample of blood or tissue.[11] He used the tool to help identify the SARS-CoV-1 virus in 2003. In 2004, DeRisi was named a MacArthur fellow (the "Genius" award) for his work with ViroChip and genomic diagnostic techniques.[10][12]

DeRisi became a Howard Hughes Medical Institute (HHMI) investigator in 2005, and received financial support from HHMI for his research.[2][13] He remained an investigator until 2016.[14]

DeRisi and his colleagues employ metagenomic next-generation sequencing (mNGS) for applications including to identify the causal agents in cases of infectious encephalitis and meningitis and to discriminate between autoimmune and infectious causes, diagnosing cases that are difficult to decipher using traditional clinical laboratory techniques.[11][15] Using metagenomic sequencing, DeRisi has identified disease-causing viruses in humans, and in animals ranging from parrots and cockatiels to honeybees and boa constrictors.[11][16] He and a research partner, Don Ganem, have identified a parasite, Nosema ceranae, that appears to be responsible for colony collapse among honeybees.[17] He has also de-bunked the relation of viruses to certain subsets of human cancer.[18]

DeRisi and his colleague Dr. Michael Wilson used a phage display to screen antibody samples from patients with autoimmune symptoms against a library of human proteins, allowing them to identify a cancer-associated autoantigen that is the cause of the symptoms.[18][19]

DeRisi’s lab at UCSF also conducts research to understand the genetics of the malaria-causing pathogen Plasmodium falciparum, the causative agent of the most deadly form of human malaria.[10][20] DeRisi's group has developed candidate drugs to cure malaria.[21] In 2011, the group determined the function of the apicoplast, a unique organelle in apicomplexans, identifying the target of an anti-malarial drug that was a preclinical candidate.[22][23]

In 2016, DeRisi became the co-president of the newly established CZ Biohub, alongside Stephen Quake.[24] After joining CZ Biohub, DeRisi established a team of developers to create a cloud-based metagenomic diagnostic platform based on code from his lab at UCSF. The platform, then named IDSeq, was initially launched for testing by a small group in 2018.[25][15] The development and computing costs were backed by the Chan Zuckerberg Initiative and CZ Biohub.[15] The platform is used to rapidly identify pathogens from metagenomic sequencing data,[26] and as of 2022 is known as CZ-ID.[27]

In 2020, early in the COVID-19 pandemic, DeRisi led a team that turned an empty lab space adjacent to the CZ Biohub into a CLIA-certified COVID-19 testing facility in eight days.[28][29] CLIAhub became one of the nation's leading COVID-19 testing centers, processing thousands of tests per day and becoming a model for the nation.[30][31][32] DeRisi’s early warning of the pandemic and development of rapid testing technology was documented by Michael Lewis in his book The Premonition: A Pandemic Story.[33][34] At the same time, DeRisi became an active proponent of developing a national COVID-19 surveillance system to identify and monitor mutations in the COVID-19 virus.[35][36][31]

References

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  1. ^ "Sandler Program for Breakthrough Biomedical Research: Our Leadership". UCSF Sandler Program for Breakthrough Biomedical Research. Retrieved 2022-10-28.
  2. ^ a b Hopkin, Karen (2005-11-20). "SARS, Malaria, and the Microarray". The Scientist Magazine. Retrieved 2022-10-17.
  3. ^ DeRisi, JL; Iyer, VR; Brown, PO (1997). "Exploring the metabolic and genetic control of gene expression on a genomic scale". Science. 278 (5338): 680–6. Bibcode:1997Sci...278..680D. CiteSeerX 10.1.1.335.7937. doi:10.1126/science.278.5338.680. PMID 9381177.
  4. ^ DeRisi, J; Penland, L; Brown, PO; Bittner, ML; Meltzer, PS; Ray, M; Chen, Y; Su, YA; Trent, JM (1996). "Use of a cDNA microarray to analyse gene expression patterns in human cancer". Nat Genet. 14 (4): 457–60. doi:10.1038/ng1296-457. PMID 8944026. S2CID 23091561.
  5. ^ Llinas, Manuel; Bozdech, Zbynek; Wong, Edith D.; Adai, Alex T.; Derisi, Joseph L. (2006), "Comparative whole genome transcriptome analysis of three Plasmodium falciparum strains", Nucleic Acids Research, 34 (4): 1166–73, doi:10.1093/nar/gkj517, PMC 1380255, PMID 16493140
  6. ^ Rota, Paul A.; Oberste, M. Steven; Monroe, Stephan S.; Nix, W. Allan; Campagnoli, Ray; Icenogle, Joseph P.; Penaranda, Silvia; Bankamp, Bettina; Maher, Kaija; Bellini, William J. (2003), "Characterization of a Novel Coronavirus Associated with Severe Acute Respiratory Syndrome", Science, 300 (5624): 1394–9, Bibcode:2003Sci...300.1394R, doi:10.1126/science.1085952, PMID 12730500
  7. ^ Wang, D; Coscoy, L; Zylberberg, M; Avila, PC; Boushey, HA; Ganem, D; DeRisi, JL (2002). "Microarray-based detection and genotyping of viral pathogens". Proc Natl Acad Sci U S A. 99 (24): 15687–92. Bibcode:2002PNAS...9915687W. doi:10.1073/pnas.242579699. PMC 137777. PMID 12429852.
  8. ^ Adams, Amy. "PhD alum Joe DeRisi brings innovation to the masses". Stanford Medicine Magazine. Vol. Summer 2002. Retrieved 2022-10-18.
  9. ^ Kahn, Jennifer (2006-12-02). "New Chips on the Block" (PDF). The Economist Technology Quarterly. Retrieved 2022-10-12.
  10. ^ a b c Russell, Sabin (2004-09-28). "THE MACARTHUR GRANTS: BAY AREA PROFILES / His quick work on SARS gave crucial answers". SF Gate. Retrieved 2022-10-28.
  11. ^ a b c Kahn, Jennifer (2021-06-03). "The Disease Detective". The New York Times. ISSN 0362-4331. Retrieved 2022-10-12.
  12. ^ "Joseph DeRisi". Macarthur Foundation. Retrieved 2022-11-01.
  13. ^ O'Brien, Jennifer (2005-03-22). "Two UCSF Scientists Named Howard Hughes Medical Institute Investigators | UC San Francisco". UCSF. Retrieved 2022-10-31.
  14. ^ "Joseph L. DeRisi" (Text). HHMI. Retrieved 2022-10-31.
  15. ^ a b c Yong, Ed (2018-10-16). "A Simpler Way to Get to the Bottom of Mysterious Illnesses in Poor Countries". The Atlantic. Retrieved 2022-11-01.
  16. ^ Dubey, Divyanshu; Mandel-Brehm, Caleigh (July 4, 2019). "Kelch-like Protein 11 Antibodies in Seminoma-Associated Paraneoplastic Encephalitis". The New England Journal of Medicine. 381 (1): 47–54. doi:10.1056/NEJMoa1816721. PMC 6800027. PMID 31269365.
  17. ^ "UCSF Sleuths Identify Suspects in Mystery of Vanishing Honeybees". UCSF.com. Retrieved October 28, 2022.
  18. ^ a b Allday, Erin (July 15, 2019). "Rare disease discovery: Antibodies fighting cancer go on to attack brain". sfchronicle.com. Retrieved May 1, 2021.
  19. ^ Mandel-Brehm, Caleigh; Dubey, Divyanshu; Kryzer, Thomas J.; O’Donovan, Brian D.; Tran, Baouyen; Vazquez, Sara E.; Sample, Hannah A.; Zorn, Kelsey C.; Khan, Lillian M.; Bledsoe, Ian O.; McKeon, Andrew; Pleasure, Samuel J.; Lennon, Vanda A.; DeRisi, Joseph L.; Wilson, Michael R.; Pittock, Sean J. (2019-07-04). "Kelch-like Protein 11 Antibodies in Seminoma-Associated Paraneoplastic Encephalitis". New England Journal of Medicine. 381 (1): 47–54. doi:10.1056/NEJMoa1816721. ISSN 0028-4793. PMID 31269365. Retrieved 2022-11-01.
  20. ^ Wade, Nicholas (2003-08-12). "New Chink in the Armor Of the Malaria Parasite". The New York Times. ISSN 0362-4331. Retrieved 2022-11-01.
  21. ^ Jiménez-Díaz, María; Ebert, Daniel (December 1, 2014). "(+)-SJ733, a clinical candidate for malaria that acts through ATP4 to induce rapid host-mediated clearance of Plasmodium". Proceedings of the National Academy of Sciences of the United States of America. 111 (50): E5455-62. Bibcode:2014PNAS..111E5455J. doi:10.1073/pnas.1414221111. PMC 4273362. PMID 25453091.
  22. ^ Palca, Joe (2011-08-30). "A Remnant From Algae In Malaria Parasite May Prove Its Weakness". NPR. Retrieved 2022-11-01.
  23. ^ Yeh, Ellen; DeRisi, Joseph L. (2011-08-30). "Chemical Rescue of Malaria Parasites Lacking an Apicoplast Defines Organelle Function in Blood-Stage Plasmodium falciparum". PLOS Biology. 9 (8): –1001138. doi:10.1371/journal.pbio.1001138. ISSN 1545-7885. Retrieved 2022-11-01.{{cite journal}}: CS1 maint: unflagged free DOI (link)
  24. ^ DeFrancesco, Laura (2020-09-11). "The making of the Biohub". Nature Biotechnology. 38 (10): 1116ñ1120. doi:10.1038/s41587-020-0685-y. ISSN 1546-1696. Retrieved 2022-05-13.
  25. ^ Molteni, Megan (2020-03-10). "A Disease Tracker Backed by Gates and Zuckerberg Tackles Covid-19". Wired. ISSN 1059-1028. Retrieved 2022-11-01.
  26. ^ Kalantar, Katrina L; Carvalho, Tiago; de Bourcy, Charles F A; Dimitrov, Boris; Dingle, Greg; Egger, Rebecca; Han, Julie; Holmes, Olivia B; Juan, Yun-Fang; King, Ryan; Kislyuk, Andrey (October 2020). "IDseq—An open source cloud-based pipeline and analysis service for metagenomic pathogen detection and monitoring". GigaScience. 9 (10). doi:10.1093/gigascience/giaa111. ISSN 2047-217X. PMC 7566497. PMID 33057676.
  27. ^ Mick, Eran; Tsitsiklis, Alexandra; Spottiswoode, Natasha; Caldera, Saharai; Serpa, Paula Hayakawa; Detweiler, Angela M.; Neff, Norma; Pisco, Angela Oliveira; Li, Lucy M.; Retallack, Hanna; Ratnasiri, Kalani; Williamson, Kayla M.; Soesanto, Victoria; Simões, Eric A. F.; Smith, Christiana; Abuogi, Lisa; Kistler, Amy; Wagner, Brandie D.; DeRisi, Joseph L.; Ambroggio, Lilliam; Mourani, Peter M.; Langelier, Charles R. (2022-07-08). "Upper airway gene expression shows a more robust adaptive immune response to SARS-CoV-2 in children". Nature Communications. 13 (1): 3937. doi:10.1038/s41467-022-31600-0. ISSN 2041-1723. Retrieved 2022-11-30.
  28. ^ "A Model for the Nation: Building a COVID-19 Testing Lab in Only Eight Days". chanzuckerberg.com. October 21, 2020. Retrieved May 1, 2021.
  29. ^ Lewis, Michael (April 16, 2020). "The Covid Test Lab That Could Save America". bloomberg.com. Retrieved May 1, 2021.
  30. ^ Lewis, Michael (May 8, 2020). "Armed With Swabs, Covid Hunters Stalk Their Prey". bloomberg.com. Retrieved May 1, 2021.
  31. ^ a b Lewis, Michael (June 21, 2020). "The New Weapon in the Covid-19 War". bloomberg.com. Retrieved May 1, 2021.
  32. ^ Lewis, Michael (April 7, 2020). "In Berkeley, Hunting Toilet Paper and Dodging Hikers". bloomberg.com. Retrieved May 1, 2021.
  33. ^ Confessore, Nicholas (2021-05-06). "Michael Lewis Chronicles the Story of Covid's Cassandras". The New York Times. ISSN 0362-4331. Retrieved 2022-11-01.
  34. ^ O’Connell, Mark (2021-05-05). "The Premonition by Michael Lewis review – a pandemic story". The Guardian. ISSN 0261-3077. Retrieved 2022-11-01.
  35. ^ Dunn, Lauren (January 8, 2021). "As U.K. variant spreads in U.S., scientists warn that country isn't doing enough to track Covid strains". NBCNews.com. Retrieved May 1, 2021.
  36. ^ Allday, Erin (January 23, 2021). "The inside story of how the Bay Area coronavirus variant was discovered". sfchronicle.com. Retrieved May 1, 2021.
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