Charles Kim, PhD

Assistant Professor

RESEARCH INTERESTS

Despite over a century of research since the discovery of Plasmodium parasites, malaria continues to be one of the top causes of infectious mortality in the world. An effective vaccine could significantly reduce malaria prevalence, but our lack of understanding of immune control mechanisms hinders the rational design of such a tool. To advance us toward this goal, we wish to understand how malaria infection is recognized by the host immune system, and how these recognition events subsequently promote activation of immune responses responsible for parasite elimination.

We are employing a combination of immunology and systems biology approaches to understand these processes in the Plasmodium chabaudi mouse model of malaria infection. Our current interests are focused on the discovery of novel signaling pathways and regulatory network architecture in leukocytes of the innate immune system, combinatorial interactions between these pathways, identifying innate-adaptive interactions, and determining how these intracellular and intercellular interactions combine into a cohesive effector response capable of clearance of malaria parasites.


EDUCATION AND TRAINING

University of Illinois, Urbana-Champaign, BS, 1997
Stanford University, PhD, 2004
University of California, San Francisco, Postdoctoral Fellow, 2005-2011
Education
Postdoctoral Studies, - Graduate Division, University of California, San Francisco
Publications

  1. Allen ML, Kim CC, Braat S, Jones K, Winter N, Hucker TR, Chia A, Lang C, Brooks SL, Williams DL. Post-discharge opioid use and handling in surgical patients: A multicentre prospective cohort study. Anaesthesia and intensive care 2020. PMID: 32050781


  2. Allen ML, Leslie K, Parker AV, Kim CC, Brooks SL, Braat S, Schug SA, Story DA. Post-surgical opioid stewardship programs across Australia and New Zealand: Current situation and future directions. Anaesthesia and intensive care 2019. PMID: 31766854


  3. Kim CC, Baccarella AM, Bayat A, Pepper M, Fontana MF. FCRL5+ Memory B Cells Exhibit Robust Recall Responses. Cell reports 2019. PMID: 31042472


  4. Baccarella A, Williams CR, Parrish JZ, Kim CC. Empirical assessment of the impact of sample number and read depth on RNA-Seq analysis workflow performance. BMC bioinformatics 2018. PMID: 30428853


  5. Hoyer N, Zielke P, Hu C, Petersen M, Sauter K, Scharrenberg R, Peng Y, Kim CC, Han C, Parrish JZ, Soba P. Ret and Substrate-Derived TGF-ß Maverick Regulate Space-Filling Dendrite Growth in Drosophila Sensory Neurons. Cell reports 2018. PMID: 30157422


  6. Chitre AS, Kattah MG, Rosli YY, Pao M, Deswal M, Deeks SG, Hunt PW, Abdel-Mohsen M, Montaner LJ, Kim CC, Ma A, Somsouk M, McCune JM. A20 upregulation during treated HIV disease is associated with intestinal epithelial cell recovery and function. PLoS pathogens 2018. PMID: 29505600


  7. Boiko N, Medrano G, Montano E, Jiang N, Williams CR, Madungwe NB, Bopassa JC, Kim CC, Parrish JZ, Hargreaves KM, Stockand JD, Eaton BA. TrpA1 activation in peripheral sensory neurons underlies the ionic basis of pain hypersensitivity in response to vinca alkaloids. PloS one 2017. PMID: 29084244


  8. Lindow JC, Wunder EA, Popper SJ, Min JN, Mannam P, Srivastava A, Yao Y, Hacker KP, Raddassi K, Lee PJ, Montgomery RR, Shaw AC, Hagan JE, Araújo GC, Nery N, Relman DA, Kim CC, Reis MG, Ko AI. Correction: Cathelicidin Insufficiency in Patients with Fatal Leptospirosis. PLoS pathogens 2017. PMID: 28950012


  9. Fontana MF, de Melo GL, Anidi C, Hamburger R, Kim CY, Lee SY, Pham J, Kim CC. Correction: Macrophage Colony Stimulating Factor Derived from CD4+ T Cells Contributes to Control of a Blood-Borne Infection. PLoS pathogens 2017. PMID: 28146583


  10. Williams CR, Baccarella A, Parrish JZ, Kim CC. Empirical assessment of analysis workflows for differential expression analysis of human samples using RNA-Seq. BMC bioinformatics 2017. PMID: 28095772


  11. Fontana MF, de Melo GL, Anidi C, Hamburger R, Kim CY, Lee SY, Pham J, Kim CC. Macrophage Colony Stimulating Factor Derived from CD4+ T Cells Contributes to Control of a Blood-Borne Infection. PLoS pathogens 2016. PMID: 27923070


  12. Lindow JC, Wunder EA, Popper SJ, Min JN, Mannam P, Srivastava A, Yao Y, Hacker KP, Raddassi K, Lee PJ, Montgomery RR, Shaw AC, Hagan JE, Araújo GC, Nery N, Relman DA, Kim CC, Reis MG, Ko AI. Cathelicidin Insufficiency in Patients with Fatal Leptospirosis. PLoS pathogens 2016. PMID: 27812211


  13. Fontana MF, Baccarella A, Craft JF, Boyle MJ, McIntyre TI, Wood MD, Thorn KS, Anidi C, Bayat A, Chung MR, Hamburger R, Kim CY, Pearman E, Pham J, Tang JJ, Boon L, Kamya MR, Dorsey G, Feeney ME, Kim CC. A Novel Model of Asymptomatic Plasmodium Parasitemia That Recapitulates Elements of the Human Immune Response to Chronic Infection. Volume 11 of Issue 9. PloS one 2016. PMID: 27583554


  14. Kim CC, Nakamura MC, Hsieh CL. Brain trauma elicits non-canonical macrophage activation states. Journal of neuroinflammation 2016. PMID: 27220367


  15. Lui H, Zhang J, Makinson SR, Cahill MK, Kelley KW, Huang HY, Shang Y, Oldham MC, Martens LH, Gao F, Coppola G, Sloan SA, Hsieh CL, Kim CC, Bigio EH, Weintraub S, Mesulam MM, Rademakers R, Mackenzie IR, Seeley WW, Karydas A, Miller BL, Borroni B, Ghidoni R, Farese RV, Paz JT, Barres BA, Huang EJ. Progranulin Deficiency Promotes Circuit-Specific Synaptic Pruning by Microglia via Complement Activation. Cell 2016. PMID: 27114033


  16. Robblee MM, Kim CC, Porter Abate J, Valdearcos M, Sandlund KL, Shenoy MK, Volmer R, Iwawaki T, Koliwad SK. Saturated Fatty Acids Engage an IRE1a-Dependent Pathway to Activate the NLRP3 Inflammasome in Myeloid Cells. Cell reports 2016. PMID: 26971994


  17. Williams CR, Baccarella A, Parrish JZ, Kim CC. Trimming of sequence reads alters RNA-Seq gene expression estimates. BMC bioinformatics 2016. PMID: 26911985


  18. Fontana MF, Baccarella A, Kellar D, Oniskey TK, Terinate P, Rosenberg SD, Huang EJ, Herbert DR, Kim CC. Myeloid expression of the AP-1 transcription factor JUNB modulates outcomes of type 1 and type 2 parasitic infections. Parasite immunology 2015. PMID: 26178310


  19. Huang X, He Y, Dubuc AM, Hashizume R, Zhang W, Reimand J, Yang H, Wang TA, Stehbens SJ, Younger S, Barshow S, Zhu S, Cooper MK, Peacock J, Ramaswamy V, Garzia L, Wu X, Remke M, Forester CM, Kim CC, Weiss WA, James CD, Shuman MA, Bader GD, Mueller S, Taylor MD, Jan YN, Jan LY. EAG2 potassium channel with evolutionarily conserved function as a brain tumor target. Nature neuroscience 2015. PMID: 26258683


  20. Huang BW, Pearman E, Kim CC. Mouse Models of Uncomplicated and Fatal Malaria. Bio-protocol 2015. PMID: 26236758


  21. Lin WY, Williams C, Yan C, Koledachkina T, Luedke K, Dalton J, Bloomsburg S, Morrison N, Duncan KE, Kim CC, Parrish JZ. The SLC36 transporter Pathetic is required for extreme dendrite growth in Drosophila sensory neurons. Genes & development 2015. PMID: 26063572


  22. Sullivan RT, Kim CC, Fontana MF, Feeney ME, Jagannathan P, Boyle MJ, Drakeley CJ, Ssewanyana I, Nankya F, Mayanja-Kizza H, Dorsey G, Greenhouse B. FCRL5 Delineates Functionally Impaired Memory B Cells Associated with Plasmodium falciparum Exposure. Volume 11 of Issue 5. PLoS pathogens 2015. PMID: 25993340


  23. Kim CC, Thai B, Yamaoka N, Aboutalib O. Hemispherical reflectance model for passive images in an outdoor environment. Journal of the Optical Society of America. A, Optics, image science, and vision 2015. PMID: 26366926


  24. Fontana MF, Baccarella A, Pancholi N, Pufall MA, Herbert DR, Kim CC. JUNB is a key transcriptional modulator of macrophage activation. Journal of immunology (Baltimore, Md. : 1950) 2014. PMID: 25472994


  25. Jiménez-Díaz MB, Ebert D, Salinas Y, Pradhan A, Lehane AM, Myrand-Lapierre ME, O'Loughlin KG, Shackleford DM, Justino de Almeida M, Carrillo AK, Clark JA, Dennis AS, Diep J, Deng X, Duffy S, Endsley AN, Fedewa G, Guiguemde WA, Gómez MG, Holbrook G, Horst J, Kim CC, Liu J, Lee MC, Matheny A, Martínez MS, Miller G, Rodríguez-Alejandre A, Sanz L, Sigal M, Spillman NJ, Stein PD, Wang Z, Zhu F, Waterson D, Knapp S, Shelat A, Avery VM, Fidock DA, Gamo FJ, Charman SA, Mirsalis JC, Ma H, Ferrer S, Kirk K, Angulo-Barturen I, Kyle DE, DeRisi JL, Floyd DM, Guy RK. (+)-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 2014. PMID: 25453091


  26. Baccarella A, Huang BW, Fontana MF, Kim CC. Loss of Toll-like receptor 7 alters cytokine production and protects against experimental cerebral malaria. Malaria journal 2014. PMID: 25192715


  27. Chen F, Wu W, Millman A, Craft JF, Chen E, Patel N, Boucher JL, Urban JF, Kim CC, Gause WC. Neutrophils prime a long-lived effector macrophage phenotype that mediates accelerated helminth expulsion. Nature immunology 2014. PMID: 25173346


  28. Jagannathan P, Kim CC, Greenhouse B, Nankya F, Bowen K, Eccles-James I, Muhindo MK, Arinaitwe E, Tappero JW, Kamya MR, Dorsey G, Feeney ME. Loss and dysfunction of Vd2? ?d T cells are associated with clinical tolerance to malaria. Volume 6 of Issue 251. Science translational medicine 2014. PMID: 25163477


  29. Jiang N, Soba P, Parker E, Kim CC, Parrish JZ. The microRNA bantam regulates a developmental transition in epithelial cells that restricts sensory dendrite growth. Development (Cambridge, England) 2014. PMID: 24924190


  30. Parrish JZ, Kim CC, Tang L, Bergquist S, Wang T, Derisi JL, Jan LY, Jan YN, Davis GW. Krüppel mediates the selective rebalancing of ion channel expression. Neuron 2014. PMID: 24811378


  31. Krow-Lucal ER, Kim CC, Burt TD, McCune JM. Distinct functional programming of human fetal and adult monocytes. Blood 2014. PMID: 24518760


  32. Kim CC, Lanier LL. Beyond the transcriptome: completion of act one of the Immunological Genome Project. Current opinion in immunology 2013. PMID: 24168965


  33. Baccarella A, Fontana MF, Chen EC, Kim CC. Toll-like receptor 7 mediates early innate immune responses to malaria. Infection and Immunity 2013. PMID: 24042114


  34. Hsieh CL, Kim CC, Ryba BE, Niemi EC, Bando JK, Locksley RM, Liu J, Nakamura MC, Seaman WE. Traumatic brain injury induces macrophage subsets in the brain. European journal of immunology 2013. PMID: 23630120


  35. Broadhurst MJ, Ardeshir A, Kanwar B, Mirpuri J, Gundra UM, Leung JM, Wiens KE, Vujkovic-Cvijin I, Kim CC, Yarovinsky F, Lerche NW, McCune JM, Loke P. Therapeutic helminth infection of macaques with idiopathic chronic diarrhea alters the inflammatory signature and mucosal microbiota of the colon. PLoS pathogens 2012. PMID: 23166490


  36. Kim CC, Nelson CS, Wilson EB, Hou B, DeFranco AL, DeRisi JL. Splenic red pulp macrophages produce type I interferons as early sentinels of malaria infection but are dispensable for control. PloS one 2012. PMID: 23144737


  37. Bezman NA, Kim CC, Sun JC, Min-Oo G, Hendricks DW, Kamimura Y, Best JA, Goldrath AW, Lanier LL. Molecular definition of the identity and activation of natural killer cells. Nature immunology 2012. PMID: 22902830


  38. Sun JC, Lopez-Verges S, Kim CC, DeRisi JL, Lanier LL. NK cells and immune "memory". Journal of immunology (Baltimore, Md. : 1950) 2011. PMID: 21289313


  39. Loke P, Hammond SN, Leung JM, Kim CC, Batra S, Rocha C, Balmaseda A, Harris E. Gene expression patterns of dengue virus-infected children from nicaragua reveal a distinct signature of increased metabolism. PLoS neglected tropical diseases 2010. PMID: 20559541


  40. Zhang S, Kim CC, Batra S, McKerrow JH, Loke P. Delineation of diverse macrophage activation programs in response to intracellular parasites and cytokines. PLoS neglected tropical diseases 2010. PMID: 20361029


  41. Kim CC, Wilson EB, DeRisi JL. Improved methods for magnetic purification of malaria parasites and haemozoin. Malaria journal 2010. PMID: 20074366


  42. Kim CC, Derisi JL. VersaCount: customizable manual tally software for cell counting. Source code for biology and medicine 2010. PMID: 20180957


  44. Kim CC, Parikh S, Sun JC, Myrick A, Lanier LL, Rosenthal PJ, DeRisi JL. Experimental malaria infection triggers early expansion of natural killer cells. 2008. PMID: 18824529


  45. Brotcke A, Weiss DS, Kim CC, Chain P, Malfatti S, Garcia E, Monack DM. Identification of MglA-regulated genes reveals novel virulence factors in Francisella tularensis. Infection and Immunity 2006. PMID: 17000729


  46. Lawley TD, Chan K, Thompson LJ, Kim CC, Govoni GR, Monack DM. Genome-wide screen for Salmonella genes required for long-term systemic infection of the mouse. PLoS pathogens 2006. PMID: 16518469


  49. Goguet de la Salmonière YO, Kim CC, Tsolaki AG, Pym AS, Siegrist MS, Small PM. High-throughput method for detecting genomic-deletion polymorphisms. Journal of clinical microbiology 2004. PMID: 15243038


  50. Joyce EA, Kawale A, Censini S, Kim CC, Covacci A, Falkow S. LuxS is required for persistent pneumococcal carriage and expression of virulence and biosynthesis genes. Infection and Immunity 2004. PMID: 15102809


  51. Merrell DS, Thompson LJ, Kim CC, Mitchell H, Tompkins LS, Lee A, Falkow S. Growth phase-dependent response of Helicobacter pylori to iron starvation. Infection and Immunity 2003. PMID: 14573673


  52. Mueller A, O'Rourke J, Chu P, Kim CC, Sutton P, Lee A, Falkow S. Protective immunity against Helicobacter is characterized by a unique transcriptional signature. Proceedings of the National Academy of Sciences of the United States of America 2003. PMID: 14528007


  53. Kim CC, Monack D, Falkow S. Modulation of virulence by two acidified nitrite-responsive loci of Salmonella enterica serovar Typhimurium. Infection and Immunity 2003. PMID: 12761099


  54. Kim CC, Falkow S. Significance analysis of lexical bias in microarray data. BMC bioinformatics 2003. PMID: 12697067


  55. Chan K, Baker S, Kim CC, Detweiler CS, Dougan G, Falkow S. Genomic comparison of Salmonella enterica serovars and Salmonella bongori by use of an S. enterica serovar typhimurium DNA microarray. Journal of bacteriology 2003. PMID: 12511502


  56. Kim CC, Joyce EA, Chan K, Falkow S. Improved analytical methods for microarray-based genome-composition analysis. Genome biology 2002. PMID: 12429064


  57. Ghim SY, Kim CC, Bonner ER, D'Elia JN, Grabner GK, Switzer RL. The Enterococcus faecalis pyr operon is regulated by autogenous transcriptional attenuation at a single site in the 5' leader. Journal of bacteriology 1999. PMID: 9973361


  58. Combadière B, Reis e Sousa C, Trageser C, Zheng LX, Kim CR, Lenardo MJ. Differential TCR signaling regulates apoptosis and immunopathology during antigen responses in vivo. Immunity 1998. PMID: 9768750