Our Publications

  1. Färkkilä A, Gulhan DC, Casado J, Jacobson CA, Nguyen H, Kochupurakkal B, Maliga Z, Yapp C, Chen YA, Schapiro D, Zhou Y. Immunogenomic profiling determines responses to combined PARP and PD-1 inhibition in ovarian cancer. Nat Commun. 2020 Mar 19;11(1):1-3. PMCID: PMC7081234

  2. Gaglia G, Rashid R, Yapp C, Joshi GN, Li CG, Lindquist SL, Sarosiek KA, Whitesell L, Sorger PK, Santagata S. HSF1 phase transition mediates stress adaptation and cell fate decisions. Nat Cell Biol. 2020 Feb;22(2):151-8. PMID: 32015439.

  3. Rashid R, Gaglia G, Chen YA, Lin JR, Du Z, Maliga Z, Schapiro D, Yapp C, Muhlich J, Sokolov A, Sorger P. Highly multiplexed immunofluorescence images and single-cell data of immune markers in tonsil and lung cancer. Sci Data. 2019 Dec 17;6(1):1-0. PMCID: PMC6917801

  4. Du Z, Lin JR, Rashid R, Maliga Z, Wang S, Aster JC, Izar B, Sorger PK, Santagata S. Qualifying antibodies for image-based immune profiling and multiplexed tissue imaging. Nat Protoc. 2019 Oct;14(10):2900-30. PMCID: PMC6959005

  5. Lin J-R, Izar B, Wang S, Yapp C, Mei S, Shah P, Santagata S, Sorger PK. Highly multiplexed immunofluorescence imaging of human tissues and tumors using t-CyCIF and conventional optical microscopes. eLife. 2018 Jul 11;7:e31657. PMCID: PMC6075866
    Publication summary | Available images

  6. Coy S, Rashid R, Lin J-R, Du Z, Donson AM, Hankinson TC, Foreman NK, Manley PE, Kieran MW, Reardon DA, Sorger PK, Santagata S. Multiplexed immunofluorescence reveals potential PD-1/PD-L1 pathway vulnerabilities in craniopharyngioma. Neuro Oncol. 2018 Jul 5;20(8):1101-1112. PMCID: PMC6280314

  7. Lin J-R, Fallahi-Sichani M, Chen J-Y, Sorger PK. Cyclic Immunofluorescence (CyCIF), A Highly Multiplexed Method for Single-cell Imaging. Curr Protoc Chem Biol. 2016 Dec 7;8(4):251-264. PMCID: PMC5233430

  8. Lin J-R, Fallahi-Sichani M, Sorger PK. Highly multiplexed imaging of single cells using a high-throughput cyclic immunofluorescence method. Nat Commun. 2015 Sep 24;6:8390. PMCID: PMC4587398
    Publication summary


Key References on Multi-round (Cyclic) IF

  1. Gerdes MJ, Sevinsky CJ, Sood A, Adak S, Bello MO, Bordwell A, Can A, Corwin A, Dinn S, Filkins RJ, Hollman D, Kamath V, Kaanumalle S, Kenny K, Larsen M, Lazare M, Li Q, Lowes C, McCulloch CC, McDonough E, Montalto MC, Pang Z, Rittscher J, Santamaria-Pang A, Sarachan BD, Seel ML, Seppo A, Shaikh K, Sui Y, Zhang J, Ginty F. Highly multiplexed single-cell analysis of formalin-fixed, paraffin-embedded cancer tissue. Proc Natl Acad Sci U S A. 2013 Jul 16;110(29):11982-7. doi: 10.1073/pnas.1300136110. Epub 2013 Jul 1. PMCID: PMC3718135.

  2. Gerdes MJ, Gökmen-Polar Y, Sui Y, Pang AS, LaPlante N, Harris AL, Tan PH, Ginty F, Badve SS. Single-cell heterogeneity in ductal carcinoma in situ of breast. Mod Pathol. 2018 Mar;31(3):406-417. PMID: 29148540.

  3. Graf JF, Zavodszky MI. Characterizing the heterogeneity of tumor tissues from spatially resolved molecular measures. PLoS One. 2017 Nov 30;12(11):e0188878. PMCID: PMC5708750.

  4. Uhlik MT, Liu J, Falcon BL, Iyer S, Stewart J, Celikkaya H, O’Mahony M, Sevinsky C, Lowes C, Douglass L, Jeffries C, Bodenmiller D, Chintharlapalli S, Fischl A, Gerald D, Xue Q, Lee JY, Santamaria-Pang A, Al-Kofahi Y, Sui Y, Desai K, Doman T, Aggarwal A, Carter JH, Pytowski B, Jaminet SC, Ginty F, Nasir A, Nagy JA, Dvorak HF, Benjamin LE. Stromal-Based Signatures for the Classification of Gastric Cancer. Cancer Res. 2016 May 1;76(9):2573-86. PMID: 27197264.


Other Approaches to Multi-channel Tissue Imaging

  1. Gut G, Herrmann MD, Pelkmans L. Multiplexed protein maps link subcellular organization to cellular states. Science. 2018 Aug 3;361(6401). PMID: 30072512.

  2. Giesen C, Wang HA, Schapiro D, Zivanovic N, Jacobs A, Hattendorf B, Schüffler PJ, Grolimund D, Buhmann JM, Brandt S, Varga Z, Wild PJ, Günther D, Bodenmiller B. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nat Methods. 2014 Apr;11(4):417-22. PMID: 24584193.

  3. Angelo M, Bendall SC, Finck R, Hale MB, Hitzman C, Borowsky AD, Levenson RM, Lowe JB, Liu SD, Zhao S, Natkunam Y, Nolan GP. Multiplexed ion beam imaging of human breast tumors. Nat Med. 2014 Apr;20(4):436-42. PMCID: PMC4110905.

  4. Tsujikawa T, Kumar S, Borkar RN, Azimi V, Thibault G, Chang YH, Balter A, Kawashima R, Choe G, Sauer D, El Rassi E, Clayburgh DR, Kulesz-Martin MF, Lutz ER, Zheng L, Jaffee EM, Leyshock P, Margolin AA, Mori M, Gray JW, Flint PW, Coussens LM. Quantitative Multiplex Immunohistochemistry Reveals Myeloid-Inflamed Tumor-Immune Complexity Associated with Poor Prognosis. Cell Rep. 2017 Apr 4;19(1):203-217. PMID: 28380359

  5. Goltsev Y, Samusik N, Kennedy-Darling J, Bhate S, Hale M, Vazquez G, Black S, Nolan GP. Deep Profiling of Mouse Splenic Architecture with CODEX Multiplexed Imaging. Cell. 2018 Aug 9;174(4):968-981.e15. PMCID: PMC6086938.