Research Summary

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.

Research Funding

  • April 8, 2021 - August 31, 2024 - Malignant Cell Engagement in Immune Circuits of Human Microsatellite-stable and Microsatellite-instable Colorectal Cancer , Principal Investigator . Sponsor: NIH, Sponsor Award ID: R00CA259511
  • July 1, 2020 - June 30, 2022 - Can scRNAseq-derived gene programs predict anti-PD-1 response in high TMB CRC and NSCLC patients? , Principal Investigator . Sponsor: , Sponsor Award ID: SU2C-AACR-PS-32
  • June 1, 2019 - November 30, 2021 - Exploiting myeloid cells to gain immune control of human colorectal cancer , Principal Investigator . Sponsor: SU2C Peggy Prescott Early Career Scientist Award, Sponsor Award ID: PA-6146
  • April 1, 2021 - August 31, 2021 - Malignant Cell Engagement in Immune Circuits of Human Microsatellite-stable and Microsatellite-instable Colorectal Cancer , Principal Investigator . Sponsor: NIH, Sponsor Award ID: K99CA259511
  • April 1, 2019 - March 31, 2021 - , Principal Investigator . Sponsor: BroadIgnite Award, Sponsor Award ID:
  • April 1, 2018 - March 31, 2020 - Studying the co-evolution of malignant cells and anti-tumor immunity , Principal Investigator . Sponsor: German Research Foundation (DFG), Sponsor Award ID: PE 2842/1-1

Education

  • Leibniz Kolleg, Tübingen, Germany, 2005, Interdisciplinary Studies
  • University of Bonn, Germany, MS, 2010, Molecular Biomedicine
  • University of Bonn, Germany, PhD, 2016, Innate Immunity
  • UMass Medical School, Worcester, Research Fellow, 2016, Innate Immunity
  • Broad Institute of MIT and Harvard, Cambridge, Postdoctoral Fellow, 2021, Cancer immunology, Systems biology

Honors & Awards

  • 2021
    NIH Pathway to Independence Award K99/R00, NCI
  • 2020
    SU2C Phillip A. Sharp Innovation in Collaboration Award
  • 2019
    SU2C Peggy Prescott Early Career Scientist Award in Colorectal Cancer Research
  • 2019
    BroadIgnite Award supporting bold ideas of early-career scientists
  • 2018 – 2020
    Research fellowship of the German Research Foundation
  • 2018
    Poster award for the best poster at the MGH Cancer Center retreat
  • 2013 – 2015
    German Academic Exchange Service (DAAD) and BFB travel awards
  • 2005 – 2010
    Scholar of the German Academic Scholarship Foundation

Selected Publications

  1. 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. Author Correction: Massively parallel single-cell mitochondrial DNA genotyping and chromatin profiling. Nat Biotechnol. 2023 Sep; 41(9):1345.  View on PubMed
  2. 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. 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.  View on PubMed
  3. 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. 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.  View on PubMed
  4. 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. Combined PD-1, BRAF and MEK inhibition in BRAFV600E colorectal cancer: a phase 2 trial. Nat Med. 2023 02; 29(2):458-466.  View on PubMed
  5. 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. Targeting TBK1 to overcome resistance to cancer immunotherapy. Nature. 2023 03; 615(7950):158-167.  View on PubMed
  6. Albers JJ, Pelka K. Listening in on Multicellular Communication in Human Tissue Immunology. Front Immunol. 2022; 13:884185.  View on PubMed
  7. 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. Differential pre-malignant programs and microenvironment chart distinct paths to malignancy in human colorectal polyps. Cell. 2021 12 22; 184(26):6262-6280.e26.  View on PubMed
  8. 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. Spatially organized multicellular immune hubs in human colorectal cancer. Cell. 2021 09 02; 184(18):4734-4752.e20.  View on PubMed
  9. 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. 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.  View on PubMed
  10. 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. Interaction of TLR4 and TLR8 in the Innate Immune Response against Mycobacterium Tuberculosis. Int J Mol Sci. 2021 Feb 04; 22(4).  View on PubMed
  11. 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. Plasma proteomics reveals tissue-specific cell death and mediators of cell-cell interactions in severe COVID-19 patients. bioRxiv. 2020 Nov 03.  View on PubMed
  12. 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. Large-Scale Topological Changes Restrain Malignant Progression in Colorectal Cancer. Cell. 2020 09 17; 182(6):1474-1489.e23.  View on PubMed
  13. 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. Massively parallel single-cell mitochondrial DNA genotyping and chromatin profiling. Nat Biotechnol. 2021 04; 39(4):451-461.  View on PubMed
  14. 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. Lineage Tracing in Humans Enabled by Mitochondrial Mutations and Single-Cell Genomics. Cell. 2019 03 07; 176(6):1325-1339.e22.  View on PubMed
  15. 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. The Chaperone UNC93B1 Regulates Toll-like Receptor Stability Independently of Endosomal TLR Transport. Immunity. 2018 05 15; 48(5):911-922.e7.  View on PubMed
  16. 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. Western Diet Triggers NLRP3-Dependent Innate Immune Reprogramming. Cell. 2018 01 11; 172(1-2):162-175.e14.  View on PubMed
  17. Pelka K, De Nardo D. Emerging Concepts in Innate Immunity. Methods Mol Biol. 2018; 1714:1-18.  View on PubMed
  18. Chen JH, Pelka K, Hacohen N. Heavy Metal Enlightens Tumor Immunity. Cell. 2017 05 04; 169(4):567-569.  View on PubMed
  19. 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. 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.  View on PubMed
  20. Pelka K, Shibata T, Miyake K, Latz E. Nucleic acid-sensing TLRs and autoimmunity: novel insights from structural and cell biology. Immunol Rev. 2016 Jan; 269(1):60-75.  View on PubMed

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