Our Publications

  1. 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. PMID: 29993362
    Publication summary | Available images

  2. 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. PMID: 29509940.

  3. 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

  4. 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.


Highly multiplexed immunofluorescence imaging of human tissues and tumors using t-CyCIF and conventional optical microscopes

Lin JR, Izar B, Wang S, Yapp C, Mei S, Shah P, Santagata S, Sorger PK.
eLife. 2018 Jul 11;7:e31657. PMID: 29993362

Publication summary

Available images

figure2.jpg
Figure 2

Representative t-CyCIF staining of a large metastatic melanoma lesion and adjacent benign tissue stitched together using the Ashlar software from 165 successive CyteFinder fields using a 20X/0.8NA objective.

Melanoma mosaic
figure5.jpg
Figure 5 and 6

Representative images of Slide A (top panels) and Slide B specimens (bottom panels) after each t-CyCIF cycle. The color coding highlighting specific cycles is the same as in A.

Tonsil A mossaic Tonsil B mossaic
figure7.jpg
Figure 7 and 8

t-CyCIF of a large resection specimen from a patient with pancreatic cancer. The entire sample comprising 143 stitched 10X fields of view is shown.

PDAC mosaic
figure10.jpg
Figure 10

Eight-cycle t-CyCIF of a tissue microarray (TMA) including 13 normal tissues and corresponding tumor types. The TMA includes normal tissue types, and corresponding high and low grade tumors, for a total of 39 specimens.

TMA mosaic
figure11.jpg
Figure 11 and 12

Molecular heterogeneity in a single GBM tumor. (A) Representative low magnification image of a GBM specimen generated from 221 stitched 10X frames; the sample was subjected to 10 rounds of t-CyCIF.

GBM mosaic