Publications

Nghia Millard, Jonathan H. Chen, Mukta G. Palshikar, Karin Pelka, Maxwell Spurrell, Colles Price, Jiang He, Nir Hacohen, Soumya Raychaudhuri, Ilya Korsunsky. Integrating spatial transcriptomics count data with Crescendo improves visualization and detection of spatial gene patterns. bioRxiv 2024.03.07.583997; doi: https://doi.org/10.1101/2024.03.07.583997

 

Dietl A, Ralser A, Pelka K. Dual Checkpoint t(H1)Eamwork Makes the Anti-Cancer Dream Work. Immunity, Cell Press, 12 Mar. 2024. https://doi.org/10.1016/j.immuni.2024.02.015

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 [Preprint]. 2023 Apr 6:2023.04.04.535379. doi: 10.1101/2023.04.04.535379. PMID: 37066412; PMCID: PMC10104028.

 

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 Feb 15. doi: 10.1038/s41596-022-00795-3. Epub ahead of print. PMID: 36792778.

 

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 Feb;29(2):458-466. doi: 10.1038/s41591-022-02181-8. Epub 2023 Jan 26. PMID: 36702949; PMCID: PMC9941044.

 

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 Mar;615(7950):158-167. doi: 10.1038/s41586-023-05704-6. Epub 2023 Jan 12. PMID: 36634707.

Albers JJ, Pelka K. Listening in on Multicellular Communication in Human Tissue Immunology. Front Immunol. 2022 May 13;13:884185. doi: 10.3389/fimmu.2022.884185. PMID: 35634333; PMCID: PMC9136009.

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. Cell2021 Dec 22;184(26):6262-6280.e26doi: 10.1016/j.cell.2021.11.031. Epub 2021 Dec 14. PubMed PMID: 34910928; PubMed Central PMCID: PMC8941949.

 

Pelka K*, Hofree M*, Chen J*, 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 M, 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; 184:4734-4752.e20.

 

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 May 18;2(5):100287.

 

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; 22(4):1560.

 

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 Apr;39(4):451-461.

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; 182:1474-1489.e23.

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; 176: 1325-1339.e22.

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; 172: 162-175.e1.

 

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; 48: 911-922.e7.

 

Pelka K, De Nardo D. Emerging Concepts in Innate Immunity. Methods Mol Biol 2018; 1714: 1-18.

Chen JH, Pelka K, Haohen N. Heavy Metal Enlightens Tumor Immunity. Cell 2017; 169: 567-569.

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; 197: 1044-53.

Eigenbrod T, Pelka K, Latz E, Kreikemeyer B, Dalpke AH. TLR8 senses Bacterial RNA in Human Monocytes and Plays a Nonredundant Role for Recognition of Streptococcus pyogenes. J Immunol 2015; 195: 1092-9.

 

Geyer M, Pelka K, Latz E. Synergistic activation of Toll-like receptor 8 by two RNA degradation products. Nat Struct Mol Biol 2015; 22: 99-101.

 

Pelka K, Shibata T, Miyake K, Latz E. Nucleic acid sensing TLRs and autoimmunity: novel insights from structural and cell biology. Immunol Rev 2015; 269: 60-75.

Schmid-Burgk JL*, Schmidt T*, Gaidt MM, Pelka K, Latz E, Ebert TS, Hornung V. OutKnocker: a web tool for rapid and simple genotyping of designer nuclease edited cell lines. Genome Res 2014; 24: 1719-23.

 

Pelka K, Phulphagar K, Zimmermann J, Stahl R, Schmid-Burgk JL, Schmidt T, Spille J-H, Labzin LI, Agrawal S, Kandimalla ER, Casanova J-L, Hornung V, Marshak-Rothstein A, Höning S, Latz E. Cutting edge: the UNC93B1 tyrosine-based motif regulates trafficking and TLR responses via separate mechanisms. J Immunol 2014; 193: 3257-61.

 

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-S, Chowdhury PS, Sims GP, Kolbeck R, Coyle AJ, Humbles AA, Xiao TS, Latz E. RAGE is a nucleic acid receptor that promotes inflammatory responses to DNA. J Exp Med 2013; 210: 2447-63.

 

Pelka K, Latz E. IRF5, IRF8, and IRF7 in human pDCs – the good, the bad, and the insignificant? Eur J Immunol 2013; 43: 1693–7.

 

Lennartsson J*, Ma H*, Wardega P, Pelka K, Engstrom U, Hellberg C, & Heldin CH. The Fer tyrosine kinase is important for platelet-derived growth factor-BB-induced Stat3 phosphorylation, colony formation in soft agar and tumor growth in vivo. J Biol Chem 2013; 288: 15736–44.

 

Pelka K, Latz E. Getting closer to the dirty little secret. Immunity 2011; 34: 455-8.

News

Media highlights of Pelka Lab's research.
Juggling Motherhood and Science
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Cancer Immunologist Karin Pelka Joins Gladstone Institutes
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Researchers discover immune cell “hubs” hiding in tumors
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SU2C Peggy Prescott Early Career Scientist Award in Colorectal Cancer Research
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Stand Up to Cancer Awards $1.1 Million in Grants to Research Teams
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Faith Fight Finish Foundation Gala
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‘Goodness, I’m getting emotional’: How Cowboys QB Dak Prescott brought Jerry Jones to tears at gala
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Stand Up to Cancer Grants First Peggy Prescott Award in Colorectal Cancer Research
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