Karin Pelka, PhD

Title(s)Assistant Investigator, Gladstone Institutes
SchoolSchool of Medicine
ORCID ORCID Icon0000-0003-2856-8602 Additional info
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    Other Positions
    Title(s)Assistant Professor, Department of Microbiology and Immunology


    Collapse Biography 
    Collapse Education and Training
    Broad Institute of MIT and Harvard, Cambridge, MA, USAPostdoc2021Tumor Immunology and Systems Biology
    University of Bonn, GermanyPhD2016Innate Immunity
    University of Bonn, GermanyDiploma2010Molecular Biomedicine
    Leibniz Kolleg, Tübingen, Germany2005Interdisciplinary Studies
    UCSF School of Medicine, San Francisco, CA, USA2022Diversity, Equity, and Inclusion Champion Training (DEI)
    Collapse Awards and Honors
    National Cancer Institute2021  - 2024NIH Pathway to Independence Award K99/R00
    Stand Up To Cancer2020  - 2022Phillip A. Sharp Innovation in Collaboration Award
    Stand Up To Cancer2019  - 2021Peggy Prescott Early Career Scientist Award in Colorectal Cancer Research
    Broad Institute of MIT and Harvard2019  - 2021BroadIgnite Award supporting bold ideas of early-career scientists
    German Research Foundation2018  - 2020Research Fellowship
    University of Bonn2016  - 2016PhD ‘summa cum laude’
    German Academic Scholarship Foundation2005  - 2010Scholar

    Collapse Overview 
    Collapse Overview
    Karin Pelka’s lab studies the cellular interactions that shape immune responses in human tumors, focusing on how these responses are regulated. Using a combination of large-scale genomic analyses and tissue imaging approaches, Pelka has identified hubs in tumor tissues where tumor cells come into close contact with immune cells. By characterizing the cells in these hubs, and the gene networks that are turned on in these cells, she aims to uncover novel ways to harness the immune system in the fight against cancer.

    Collapse Research 
    Collapse Research Activities and Funding
    Malignant Cell Engagement in Immune Circuits of Human Microsatellite-stable and Microsatellite-instable Colorectal Cancer
    NIH R00CA259511Apr 8, 2021 - Aug 31, 2024
    Role: Principal Investigator
    Malignant Cell Engagement in Immune Circuits of Human Microsatellite-stable and Microsatellite-instable Colorectal Cancer
    NIH K99CA259511Apr 1, 2021 - Aug 31, 2021
    Role: Principal Investigator
    Can scRNAseq-derived gene programs predict anti-PD-1 response in high TMB CRC and NSCLC patients?
    SU2C-AACR-PS-32Jul 1, 2020 - Jun 30, 2022
    Role: Principal Investigator
    Exploiting myeloid cells to gain immune control of human colorectal cancer
    SU2C Peggy Prescott Early Career Scientist Award PA-6146Jun 1, 2019 - Nov 30, 2021
    Role: Principal Investigator
    BroadIgnite Award Apr 1, 2019 - Mar 31, 2021
    Role: Principal Investigator
    Studying the co-evolution of malignant cells and anti-tumor immunity
    German Research Foundation (DFG) PE 2842/1-1Apr 1, 2018 - Mar 31, 2020
    Role: Principal Investigator

    Collapse ORNG Applications 
    Collapse Featured Publications

    Collapse Bibliographic 
    Collapse Publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help. to make corrections and additions.
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Quantized multi-task learning for context-specific representations of gene network dynamics. bioRxiv. 2024 Aug 19. Chen H, Venkatesh MS, Ortega JG, Mahesh SV, Nandi TN, Madduri RK, Pelka K, Theodoris CV. PMID: 39229018; PMCID: PMC11370383.
      View in: PubMed   Mentions:
    2. Single-cell transcriptomic analyses reveal distinct immune cell contributions to epithelial barrier dysfunction in checkpoint inhibitor colitis. Nat Med. 2024 May; 30(5):1349-1362. Thomas MF, Slowikowski K, Manakongtreecheep K, Sen P, Samanta N, Tantivit J, Nasrallah M, Zubiri L, Smith NP, Tirard A, Ramesh S, Arnold BY, Nieman LT, Chen JH, Eisenhaure T, Pelka K, Song Y, Xu KH, Jorgji V, Pinto CJ, Sharova T, Glasser R, Chan P, Sullivan RJ, Khalili H, Juric D, Boland GM, Dougan M, Hacohen N, Li B, Reynolds KL, Villani AC. PMID: 38724705; PMCID: PMC11673812.
      View in: PubMed   Mentions: 4     Fields:    
    3. Human lung cancer harbors spatially organized stem-immunity hubs associated with response to immunotherapy. Nat Immunol. 2024 Apr; 25(4):644-658. Chen JH, Nieman LT, Spurrell M, Jorgji V, Elmelech L, Richieri P, Xu KH, Madhu R, Parikh M, Zamora I, Mehta A, Nabel CS, Freeman SS, Pirl JD, Lu C, Meador CB, Barth JL, Sakhi M, Tang AL, Sarkizova S, Price C, Fernandez NF, Emanuel G, He J, Van Raay K, Reeves JW, Yizhak K, Hofree M, Shih A, Sade-Feldman M, Boland GM, Pelka K, Aryee MJ, Mino-Kenudson M, Gainor JF, Korsunsky I, Hacohen N. PMID: 38503922.
      View in: PubMed   Mentions: 20     Fields:    Translation:HumansCells
    4. Dual checkpoint T(h1)eamwork makes the anti-cancer dream work. Immunity. 2024 03 12; 57(3):406-408. Dietl A, Ralser A, Pelka K. PMID: 38479356.
      View in: PubMed   Mentions:    Fields:    
    5. Author Correction: Massively parallel single-cell mitochondrial DNA genotyping and chromatin profiling. Nat Biotechnol. 2023 Sep; 41(9):1345. Lareau CA, Ludwig LS, Muus C, Gohil SH, Zhao T, Chiang Z, Pelka K, Verboon JM, Luo W, Christian E, Rosebrock D, Getz G, Boland GM, Chen F, Buenrostro JD, Hacohen N, Wu CJ, Aryee MJ, Regev A, Sankaran VG. PMID: 37653227.
      View in: PubMed   Mentions:    Fields:    
    6. Spatial analysis of human lung cancer reveals organized immune hubs enriched for stem-like CD8 T cells and associated with immunotherapy response. bioRxiv. 2023 Apr 06. Chen JH, Nieman LT, Spurrell M, Jorgji V, Richieri P, Xu KH, Madhu R, Parikh M, Zamora I, Mehta A, Nabel CS, Freeman SS, Pirl JD, Lu C, Meador CB, Barth JL, Sakhi M, Tang AL, Sarkizova S, Price C, Fernandez NF, Emanuel G, He J, Raay KV, Reeves JW, Yizhak K, Hofree M, Shih A, Sade-Feldman M, Boland GM, Pelka K, Aryee M, Korsunsky I, Mino-Kenudson M, Gainor JF, Hacohen N. PMID: 37066412; PMCID: PMC10104028.
      View in: PubMed   Mentions:
    7. Mitochondrial single-cell ATAC-seq for high-throughput multi-omic detection of mitochondrial genotypes and chromatin accessibility. Nat Protoc. 2023 05; 18(5):1416-1440. Lareau CA, Liu V, Muus C, Praktiknjo SD, Nitsch L, Kautz P, Sandor K, Yin Y, Gutierrez JC, Pelka K, Satpathy AT, Regev A, Sankaran VG, Ludwig LS. PMID: 36792778; PMCID: PMC10317201.
      View in: PubMed   Mentions: 16     Fields:    Translation:HumansAnimalsCells
    8. Combined PD-1, BRAF and MEK inhibition in BRAFV600E colorectal cancer: a phase 2 trial. Nat Med. 2023 02; 29(2):458-466. Tian J, Chen JH, Chao SX, Pelka K, Giannakis M, Hess J, Burke K, Jorgji V, Sindurakar P, Braverman J, Mehta A, Oka T, Huang M, Lieb D, Spurrell M, Allen JN, Abrams TA, Clark JW, Enzinger AC, Enzinger PC, Klempner SJ, McCleary NJ, Meyerhardt JA, Ryan DP, Yurgelun MB, Kanter K, Van Seventer EE, Baiev I, Chi G, Jarnagin J, Bradford WB, Wong E, Michel AG, Fetter IJ, Siravegna G, Gemma AJ, Sharpe A, Demehri S, Leary R, Campbell CD, Yilmaz O, Getz GA, Parikh AR, Hacohen N, Corcoran RB. PMID: 36702949; PMCID: PMC9941044.
      View in: PubMed   Mentions: 41     Fields:    Translation:HumansCTClinical Trials
    9. Targeting TBK1 to overcome resistance to cancer immunotherapy. Nature. 2023 03; 615(7950):158-167. Sun Y, Revach OY, Anderson S, Kessler EA, Wolfe CH, Jenney A, Mills CE, Robitschek EJ, Davis TGR, Kim S, Fu A, Ma X, Gwee J, Tiwari P, Du PP, Sindurakar P, Tian J, Mehta A, Schneider AM, Yizhak K, Sade-Feldman M, LaSalle T, Sharova T, Xie H, Liu S, Michaud WA, Saad-Beretta R, Yates KB, Iracheta-Vellve A, Spetz JKE, Qin X, Sarosiek KA, Zhang G, Kim JW, Su MY, Cicerchia AM, Rasmussen MQ, Klempner SJ, Juric D, Pai SI, Miller DM, Giobbie-Hurder A, Chen JH, Pelka K, Frederick DT, Stinson S, Ivanova E, Aref AR, Paweletz CP, Barbie DA, Sen DR, Fisher DE, Corcoran RB, Hacohen N, Sorger PK, Flaherty KT, Boland GM, Manguso RT, Jenkins RW. PMID: 36634707; PMCID: PMC10171827.
      View in: PubMed   Mentions: 34     Fields:    Translation:HumansCells
    10. Listening in on Multicellular Communication in Human Tissue Immunology. Front Immunol. 2022; 13:884185. Albers JJ, Pelka K. PMID: 35634333; PMCID: PMC9136009.
      View in: PubMed   Mentions: 2     Fields:    Translation:Humans
    11. Differential pre-malignant programs and microenvironment chart distinct paths to malignancy in human colorectal polyps. Cell. 2021 12 22; 184(26):6262-6280.e26. Chen B, Scurrah CR, McKinley ET, Simmons AJ, Ramirez-Solano MA, Zhu X, Markham NO, Heiser CN, Vega PN, Rolong A, Kim H, Sheng Q, Drewes JL, Zhou Y, Southard-Smith AN, Xu Y, Ro J, Jones AL, Revetta F, Berry LD, Niitsu H, Islam M, Pelka K, Hofree M, Chen JH, Sarkizova S, Ng K, Giannakis M, Boland GM, Aguirre AJ, Anderson AC, Rozenblatt-Rosen O, Regev A, Hacohen N, Kawasaki K, Sato T, Goettel JA, Grady WM, Zheng W, Washington MK, Cai Q, Sears CL, Goldenring JR, Franklin JL, Su T, Huh WJ, Vandekar S, Roland JT, Liu Q, Coffey RJ, Shrubsole MJ, Lau KS. PMID: 34910928; PMCID: PMC8941949.
      View in: PubMed   Mentions: 108     Fields:    Translation:HumansAnimalsCells
    12. Spatially organized multicellular immune hubs in human colorectal cancer. Cell. 2021 09 02; 184(18):4734-4752.e20. Pelka K, Hofree M, Chen JH, Sarkizova S, Pirl JD, Jorgji V, Bejnood A, Dionne D, Ge WH, Xu KH, Chao SX, Zollinger DR, Lieb DJ, Reeves JW, Fuhrman CA, Hoang ML, Delorey T, Nguyen LT, Waldman J, Klapholz M, Wakiro I, Cohen O, Albers J, Smillie CS, Cuoco MS, Wu J, Su MJ, Yeung J, Vijaykumar B, Magnuson AM, Asinovski N, Moll T, Goder-Reiser MN, Applebaum AS, Brais LK, DelloStritto LK, Denning SL, Phillips ST, Hill EK, Meehan JK, Frederick DT, Sharova T, Kanodia A, Todres EZ, Jané-Valbuena J, Biton M, Izar B, Lambden CD, Clancy TE, Bleday R, Melnitchouk N, Irani J, Kunitake H, Berger DL, Srivastava A, Hornick JL, Ogino S, Rotem A, Vigneau S, Johnson BE, Corcoran RB, Sharpe AH, Kuchroo VK, Ng K, Giannakis M, Nieman LT, Boland GM, Aguirre AJ, Anderson AC, Rozenblatt-Rosen O, Regev A, Hacohen N. PMID: 34450029; PMCID: PMC8772395.
      View in: PubMed   Mentions: 232     Fields:    Translation:HumansCells
    13. Longitudinal proteomic analysis of severe COVID-19 reveals survival-associated signatures, tissue-specific cell death, and cell-cell interactions. Cell Rep Med. 2021 05 18; 2(5):100287. Filbin MR, Mehta A, Schneider AM, Kays KR, Guess JR, Gentili M, Fenyves BG, Charland NC, Gonye ALK, Gushterova I, Khanna HK, LaSalle TJ, Lavin-Parsons KM, Lilley BM, Lodenstein CL, Manakongtreecheep K, Margolin JD, McKaig BN, Rojas-Lopez M, Russo BC, Sharma N, Tantivit J, Thomas MF, Gerszten RE, Heimberg GS, Hoover PJ, Lieb DJ, Lin B, Ngo D, Pelka K, Reyes M, Smillie CS, Waghray A, Wood TE, Zajac AS, Jennings LL, Grundberg I, Bhattacharyya RP, Parry BA, Villani AC, Sade-Feldman M, Hacohen N, Goldberg MB. PMID: 33969320; PMCID: PMC8091031.
      View in: PubMed   Mentions: 134     Fields:    
    14. Interaction of TLR4 and TLR8 in the Innate Immune Response against Mycobacterium Tuberculosis. Int J Mol Sci. 2021 Feb 04; 22(4). Thada S, Horvath GL, Müller MM, Dittrich N, Conrad ML, Sur S, Hussain A, Pelka K, Gaddam SL, Latz E, Slevogt H, Schumann RR, Burkert S. PMID: 33557133; PMCID: PMC7913854.
      View in: PubMed   Mentions: 10     Fields:    Translation:HumansCells
    15. Plasma proteomics reveals tissue-specific cell death and mediators of cell-cell interactions in severe COVID-19 patients. bioRxiv. 2020 Nov 04. Filbin MR, Mehta A, Schneider AM, Kays KR, Guess JR, Gentili M, Fenyves BG, Charland NC, Gonye ALK, Gushterova I, Khanna HK, LaSalle TJ, Lavin-Parsons KM, Lilly BM, Lodenstein CL, Manakongtreecheep K, Margolin JD, McKaig BN, Rojas-Lopez M, Russo BC, Sharma N, Tantivit J, Thomas MF, Gerszten RE, Heimberg GS, Hoover PJ, Lieb DJ, Lin B, Ngo D, Pelka K, Reyes M, Smillie CS, Waghray A, Wood TE, Zajac AS, Jennings LL, Grundberg I, Bhattacharyya RP, Parry BA, Villani AC, Sade-Feldman M, Hacohen N, Goldberg MB. PMID: 33173871; PMCID: PMC7654866.
      View in: PubMed   Mentions: 7  
    16. Large-Scale Topological Changes Restrain Malignant Progression in Colorectal Cancer. Cell. 2020 09 17; 182(6):1474-1489.e23. Johnstone SE, Reyes A, Qi Y, Adriaens C, Hegazi E, Pelka K, Chen JH, Zou LS, Drier Y, Hecht V, Shoresh N, Selig MK, Lareau CA, Iyer S, Nguyen SC, Joyce EF, Hacohen N, Irizarry RA, Zhang B, Aryee MJ, Bernstein BE. PMID: 32841603; PMCID: PMC7575124.
      View in: PubMed   Mentions: 86     Fields:    Translation:HumansCells
    17. Massively parallel single-cell mitochondrial DNA genotyping and chromatin profiling. Nat Biotechnol. 2021 04; 39(4):451-461. Lareau CA, Ludwig LS, Muus C, Gohil SH, Zhao T, Chiang Z, Pelka K, Verboon JM, Luo W, Christian E, Rosebrock D, Getz G, Boland GM, Chen F, Buenrostro JD, Hacohen N, Wu CJ, Aryee MJ, Regev A, Sankaran VG. PMID: 32788668; PMCID: PMC7878580.
      View in: PubMed   Mentions: 105     Fields:    Translation:HumansCells
    18. Lineage Tracing in Humans Enabled by Mitochondrial Mutations and Single-Cell Genomics. Cell. 2019 03 07; 176(6):1325-1339.e22. Ludwig LS, Lareau CA, Ulirsch JC, Christian E, Muus C, Li LH, Pelka K, Ge W, Oren Y, Brack A, Law T, Rodman C, Chen JH, Boland GM, Hacohen N, Rozenblatt-Rosen O, Aryee MJ, Buenrostro JD, Regev A, Sankaran VG. PMID: 30827679; PMCID: PMC6408267.
      View in: PubMed   Mentions: 223     Fields:    Translation:HumansCells
    19. The Chaperone UNC93B1 Regulates Toll-like Receptor Stability Independently of Endosomal TLR Transport. Immunity. 2018 05 15; 48(5):911-922.e7. Pelka K, Bertheloot D, Reimer E, Phulphagar K, Schmidt SV, Christ A, Stahl R, Watson N, Miyake K, Hacohen N, Haas A, Brinkmann MM, Marshak-Rothstein A, Meissner F, Latz E. PMID: 29768176; PMCID: PMC6482051.
      View in: PubMed   Mentions: 63     Fields:    Translation:HumansAnimalsCells
    20. Western Diet Triggers NLRP3-Dependent Innate Immune Reprogramming. Cell. 2018 01 11; 172(1-2):162-175.e14. Christ A, Günther P, Lauterbach MAR, Duewell P, Biswas D, Pelka K, Scholz CJ, Oosting M, Haendler K, Baßler K, Klee K, Schulte-Schrepping J, Ulas T, Moorlag SJCFM, Kumar V, Park MH, Joosten LAB, Groh LA, Riksen NP, Espevik T, Schlitzer A, Li Y, Fitzgerald ML, Netea MG, Schultze JL, Latz E. PMID: 29328911; PMCID: PMC6324559.
      View in: PubMed   Mentions: 468     Fields:    Translation:HumansAnimalsCells
    21. Emerging Concepts in Innate Immunity. Methods Mol Biol. 2018; 1714:1-18. Pelka K, De Nardo D. PMID: 29177852.
      View in: PubMed   Mentions: 6     Fields:    Translation:HumansAnimals
    22. Heavy Metal Enlightens Tumor Immunity. Cell. 2017 05 04; 169(4):567-569. Chen JH, Pelka K, Hacohen N. PMID: 28475889; PMCID: PMC6597172.
      View in: PubMed   Mentions: 2     Fields:    Translation:Humans
    23. TLR9 Deficiency Leads to Accelerated Renal Disease and Myeloid Lineage Abnormalities in Pristane-Induced Murine Lupus. J Immunol. 2016 08 15; 197(4):1044-53. Bossaller L, Christ A, Pelka K, Nündel K, Chiang PI, Pang C, Mishra N, Busto P, Bonegio RG, Schmidt RE, Latz E, Marshak-Rothstein A. PMID: 27354219; PMCID: PMC5266544.
      View in: PubMed   Mentions: 37     Fields:    Translation:AnimalsCells
    24. Nucleic acid-sensing TLRs and autoimmunity: novel insights from structural and cell biology. Immunol Rev. 2016 Jan; 269(1):60-75. Pelka K, Shibata T, Miyake K, Latz E. PMID: 26683145.
      View in: PubMed   Mentions: 60     Fields:    Translation:HumansAnimalsCells
    25. TLR8 Senses Bacterial RNA in Human Monocytes and Plays a Nonredundant Role for Recognition of Streptococcus pyogenes. J Immunol. 2015 Aug 01; 195(3):1092-9. Eigenbrod T, Pelka K, Latz E, Kreikemeyer B, Dalpke AH. PMID: 26101323.
      View in: PubMed   Mentions: 40     Fields:    Translation:HumansAnimalsCells
    26. Synergistic activation of Toll-like receptor 8 by two RNA degradation products. Nat Struct Mol Biol. 2015 Feb; 22(2):99-101. Geyer M, Pelka K, Latz E. PMID: 25650902.
      View in: PubMed   Mentions: 10     Fields:    Translation:HumansAnimals
    27. OutKnocker: a web tool for rapid and simple genotyping of designer nuclease edited cell lines. Genome Res. 2014 Oct; 24(10):1719-23. Schmid-Burgk JL, Schmidt T, Gaidt MM, Pelka K, Latz E, Ebert TS, Hornung V. PMID: 25186908; PMCID: PMC4199374.
      View in: PubMed   Mentions: 72     Fields:    Translation:HumansCells
    28. Cutting edge: the UNC93B1 tyrosine-based motif regulates trafficking and TLR responses via separate mechanisms. J Immunol. 2014 Oct 01; 193(7):3257-61. Pelka K, Phulphagar K, Zimmermann J, Stahl R, Schmid-Burgk JL, Schmidt T, Spille JH, Labzin LI, Agrawal S, Kandimalla ER, Casanova JL, Hornung V, Marshak-Rothstein A, Höning S, Latz E. PMID: 25187660; PMCID: PMC4170058.
      View in: PubMed   Mentions: 20     Fields:    Translation:HumansCells
    29. RAGE is a nucleic acid receptor that promotes inflammatory responses to DNA. J Exp Med. 2013 Oct 21; 210(11):2447-63. Sirois CM, Jin T, Miller AL, Bertheloot D, Nakamura H, Horvath GL, Mian A, Jiang J, Schrum J, Bossaller L, Pelka K, Garbi N, Brewah Y, Tian J, Chang C, Chowdhury PS, Sims GP, Kolbeck R, Coyle AJ, Humbles AA, Xiao TS, Latz E. PMID: 24081950; PMCID: PMC3804942.
      View in: PubMed   Mentions: 101     Fields:    Translation:HumansAnimalsCells
    30. IRF5, IRF8, and IRF7 in human pDCs - the good, the bad, and the insignificant? Eur J Immunol. 2013 Jul; 43(7):1693-7. Pelka K, Latz E. PMID: 23828296.
      View in: PubMed   Mentions: 18     Fields:    Translation:HumansCells
    31. The Fer tyrosine kinase is important for platelet-derived growth factor-BB-induced signal transducer and activator of transcription 3 (STAT3) protein phosphorylation, colony formation in soft agar, and tumor growth in vivo. J Biol Chem. 2013 May 31; 288(22):15736-44. Lennartsson J, Ma H, Wardega P, Pelka K, Engström U, Hellberg C, Heldin CH. PMID: 23589302; PMCID: PMC3668732.
      View in: PubMed   Mentions: 19     Fields:    Translation:HumansAnimalsCells
    32. Getting closer to the dirty little secret. Immunity. 2011 Apr 22; 34(4):455-8. Pelka K, Latz E. PMID: 21511178; PMCID: PMC3128920.
      View in: PubMed   Mentions: 12     Fields:    
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