High-plex imaging of RNA and proteins at subcellular resolution in fixed tissue by spatial molecular imaging (2024)

  • Garon, E. B. et al. Pembrolizumab for the treatment of non-small-cell lung cancer. N. Engl. J. Med. 372, 2018–28 (2015).

    Article Google Scholar

  • Yu, H. et al. PD-L1 expression by two complementary diagnostic assays and mRNA in situ hybridization in small cell lung cancer. J. Thorac. Oncol. 12, 110–120 (2017).

    Article Google Scholar

  • Yu, H., Boyle, T. A., Zhou, C., Rimm, D. L. & Hirsch, F. R. PD-L1 expression in lung cancer. J .Thorac. Oncol. 11, 964–975 (2016).

    Article Google Scholar

  • Ting, D. T. et al. Aberrant overexpression of satellite repeats in pancreatic and other epithelial cancers. Science 331, 593–596 (2011).

    Article CAS Google Scholar

  • Garber, K. Oncologists await historic first: a pan-tumor predictive marker, for immunotherapy. Nat. Biotechnol. 35, 297–298 (2017).

    Article CAS Google Scholar

  • Sokolenko, A. P. & Imyanitov, E. N. Molecular tests for the choice of cancer therapy. Curr. Pharm. Des. 23, 4794–4806 (2017).

    Article CAS Google Scholar

  • Dereli, A. S., Bailey, E. J. & Kumar, N. N. Combining multiplex fluorescence in situ hybridization with fluorescent immunohistochemistry on fresh frozen or fixed mouse brain sections. J. Vis. Exp. https://doi.org/10.3791/6170910.3791/61709 (2021).

  • Taube, J. M. et al. The Society for Immunotherapy of Cancer statement on best practices for multiplex immunohistochemistry (IHC) and immunofluorescence (IF) staining and validation. J. Immunother. Cancer 8, e000155 (2020).

  • Hirsch, F. R. et al. PD-L1 immunohistochemistry assays for lung cancer: results from Phase 1 of the Blueprint PD-L1 IHC Assay Comparison Project. J. Thorac. Oncol. 12, 208–222 (2017).

    Article Google Scholar

  • Udall, M. et al. PD-L1 diagnostic tests: a systematic literature review of scoring algorithms and test-validation metrics. Diagn. Pathol. 13, 12 (2018).

    Article Google Scholar

  • Halse, H. et al. Multiplex immunohistochemistry accurately defines the immune context of metastatic melanoma. Sci. Rep. 8, 11158 (2018).

    Article CAS Google Scholar

  • Macosko Evan, Z. et al. Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets. Cell. 161, 1202–1214 (2015).

    Article CAS Google Scholar

  • Zilionis, R. et al. Single-cell barcoding and sequencing using droplet microfluidics. Nat. Protoc. 12, 44–73 (2017).

    Article CAS Google Scholar

  • Wang, X., He, Y., Zhang, Q., Ren, X. & Zhang, Z. Direct comparative analyses of 10X Genomics Chromium and Smart-seq2. Genomics Proteomics Bioinformatics 19, 253–266 (2021).

  • See, P., Lum, J., Chen, J. & Ginhoux, F. A single-cell sequencing guide for immunologists. Front. Immunol. 9, 2425 (2018).

    Article Google Scholar

  • Ståhl, P. L. et al. Visualization and analysis of gene expression in tissue sections by spatial transcriptomics. Science 353, 78–82 (2016).

    Article Google Scholar

  • Stickels, R. R. et al. Highly sensitive spatial transcriptomics at near-cellular resolution with Slide-seqV2. Nat. Biotechnol. 39, 313–319 (2021).

    Article CAS Google Scholar

  • Fu, X. et al. Continuous polony gels for tissue mapping with high resolution and RNA capture efficiency. Preprint at bioRxiv https://doi.org/10.1101/2021.03.17.435795 (2021).

  • Liu, Y. et al. High-spatial-resolution multi-omics sequencing via deterministic barcoding in tissue. Cell 183, 1665–1681 (2020).

    Article CAS Google Scholar

  • Merritt, C. R. et al. Multiplex digital spatial profiling of proteins and RNA in fixed tissue. Nat. Biotechnol. 38, 586–599 (2020).

    Article CAS Google Scholar

  • Wu, Q. et al. Poly A – transcripts expressed in HeLa cells. PLoS ONE 3, e2803 (2008).

    Article Google Scholar

  • Moffitt, J. R. et al. High-throughput single-cell gene-expression profiling with multiplexed error-robust fluorescence in situ hybridization. Proc. Natl Acad. Sci. USA 113, 11046–11051 (2016).

    Article CAS Google Scholar

  • Moffitt, J. R. & Zhuang, X. in Methods in Enzymology (eds Filonov, G. S. & Jaffrey, S. R.) 1–49 (Academic Press, 2016).

  • Groiss, S. et al. Highly resolved spatial transcriptomics for detection of rare events in cells. Preprint at bioRxiv https://doi.org/10.1101/2021.10.11.463936 (2021).

  • Lee, J. H. et al. Fluorescent in situ sequencing (FISSEQ) of RNA for gene expression profiling in intact cells and tissues. Nat. Protoc. 10, 442–458 (2015).

    Article CAS Google Scholar

  • Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by RNA seqFISH+. Nature 568, 235–239 (2019).

    Article CAS Google Scholar

  • Xia, C., Fan, J., Emanuel, G., Hao, J. & Zhuang, X. Spatial transcriptome profiling by MERFISH reveals subcellular RNA compartmentalization and cell cycle-dependent gene expression. Proc. Natl Acad. Sci. USA 116, 19490–19499 (2019).

    Article CAS Google Scholar

  • Goltsev, Y. et al. Deep profiling of mouse splenic architecture with CODEX multiplexed imaging. Cell 174, 968–981 (2018).

    Article CAS Google Scholar

  • Lin, J. R., Fallahi-Sichani, M. & Sorger, P. K. Highly multiplexed imaging of single cells using a high-throughput cyclic immunofluorescence method. Nat. Commun. 6, 8390 (2015).

    Article CAS Google Scholar

  • Giesen, C. et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nat. Methods 11, 417–422 (2014).

    Article CAS Google Scholar

  • Chen, K. H., Boettiger, A. N., Moffitt, J. R., Wang, S. & Zhuang, X. RNA imaging. Spatially resolved, highly multiplexed RNA profiling in single cells. Science 348, aaa6090 (2015).

    Article Google Scholar

  • Mercer, T. R. et al. The human mitochondrial transcriptome. Cell 146, 645–658 (2011).

    Article CAS Google Scholar

  • Gudenas, B. L. & Wang, L. Prediction of LncRNA subcellular localization with deep learning from sequence features. Sci. Rep. 8, 16385 (2018).

    Article Google Scholar

  • Baker, S. C. et al. The External RNA Controls Consortium: a progress report. Nat. Methods 2, 731–734 (2005).

    Article CAS Google Scholar

  • Ghandi, M. et al. Next-generation characterization of the Cancer Cell Line Encyclopedia. Nature 569, 503–508 (2019).

    Article CAS Google Scholar

  • Nusinow, D. P. et al. Quantitative proteomics of the Cancer Cell Line Encyclopedia. Cell 180, 387–402 (2020).

    Article CAS Google Scholar

  • National Cancer Institute. NCI-60 Human Tumor Cell Lines Screen https://dtp.cancer.gov/discovery_development/nci-60/ (2020).

  • Kinker, G. S. et al. Pan-cancer single-cell RNA-seq identifies recurring programs of cellular heterogeneity. Nat. Genet. 52, 1208–1218 (2020).

    Article CAS Google Scholar

  • Liu, J. et al. Concordance of MERFISH spatial transcriptomics with bulk and single-cell RNA sequencing. Preprint at bioRxiv https://doi.org/10.1101/2022.03.04.483068 (2022).

  • Leader, A. M. et al. Single-cell analysis of human non-small cell lung cancer lesions refines tumor classification and patient stratification. Cancer Cell 39, 1594–1609 (2021).

    Article CAS Google Scholar

  • Danaher, P. et al. Advances in mixed cell deconvolution enable quantification of cell types in spatially-resolved gene expression data. Nat. Commun. 13, 385 (2022).

  • Illumina. Evaluating RNA quality from FFPE samples. https://www.illumina.com/content/dam/illumina-marketing/documents/products/technotes/evaluating-rna-quality-from-ffpe-samples-technical-note-470-2014-001.pdf (2021).

  • Leica Biosystems. OND-III fully automated IHC and ISH staining system. https://www.leicabiosystems.com/ihc-ish-fish/fully-automated-ihc-ish-instruments/bond-iii/ (2021).

  • Qiu, P. Embracing the dropouts in single-cell RNA-seq analysis. Nat. Commun. 11, 1169 (2020).

    Article CAS Google Scholar

  • Lin, J. R., Fallahi-Sichani, M., Chen, J. Y. & Sorger, P. K. Cyclic immunofluorescence (CycIF), a highly multiplexed method for single-cell imaging. Curr. Protoc. Chem. Biol. 8, 251–264 (2016).

    Article Google Scholar

  • Caruthers, M. H. et al. Chemical synthesis of deoxyoligonucleotides by the phosphoramidite method. Methods Enzymol. 154, 287–313 (1987).

    Article CAS Google Scholar

  • Zhang, Z., Revyakin, A., Grimm, J. B., Lavis, L. D. & Tjian, R. Single-molecule tracking of the transcription cycle by sub-second RNA detection. eLife 3, e01775 (2014).

    Article Google Scholar

  • Wagle, M.-C. et al. A transcriptional MAPK Pathway Activity Score (MPAS) is a clinically relevant biomarker in multiple cancer types. NPJ Precis. Oncol. 2, 7 (2018).

    Article Google Scholar

  • Son, Y. H. et al. Roles of MAPK and NF-kappaB in interleukin-6 induction by lipopolysaccharide in vascular smooth muscle cells. J. Cardiovasc. Pharmacol. 51, 71–77 (2008).

    Article CAS Google Scholar

  • Kang, H. B., Kim, Y. E., Kwon, H. J., Sok, D. E. & Lee, Y. Enhancement of NF-kappaB expression and activity upon differentiation of human embryonic stem cell line SNUhES3. Stem Cells Dev. 16, 615–623 (2007).

    Article CAS Google Scholar

  • Hiscott, J. et al. Induction of human interferon gene expression is associated with a nuclear factor that interacts with the NF-kappa B site of the human immunodeficiency virus enhancer. J. Virol. 63, 2557–2566 (1989).

    Article CAS Google Scholar

  • Kitamura, A., Takahashi, K., Okajima, A. & Kitamura, N. Induction of the human gene for p44, a hepatitis-C-associated microtubular aggregate protein, by interferon-alpha/beta. Eur. J. Biochem. 224, 877–883 (1994).

    Article CAS Google Scholar

  • Kim, J. H., Park, S. Y., Jun, Y., Kim, J. Y. & Nam, J. S. Roles of Wnt target genes in the journey of cancer stem cells. Int. J. Mol. Sci. 18, 1604 (2017).

  • Jho, E. H. et al. Wnt/beta-catenin/Tcf signaling induces the transcription of Axin2, a negative regulator of the signaling pathway. Mol. Cell. Biol. 22, 1172–1183 (2002).

    Article CAS Google Scholar

  • Lustig, B. et al. Negative feedback loop of Wnt signaling through upregulation of conductin/axin2 in colorectal and liver tumors. Mol. Cell. Biol. 22, 1184–1193 (2002).

    Article CAS Google Scholar

  • Yan, D. et al. Elevated expression of axin2 and hnkd mRNA provides evidence that Wnt/beta–catenin signaling is activated in human colon tumors. Proc. Natl Acad. Sci. USA 98, 14973–14978 (2001).

    Article CAS Google Scholar

  • Ramakrishnan, A. B. & Cadigan, K. M. Wnt target genes and where to find them. F1000Res 6, 746 (2017).

    Article Google Scholar

  • Barker, N. et al. Identification of stem cells in small intestine and colon by marker gene Lgr5. Nature 449, 1003–1007 (2007).

    Article CAS Google Scholar

  • He, T. C. et al. Identification of c-MYC as a target of the APC pathway. Science 281, 1509–1512 (1998).

    Article CAS Google Scholar

  • Shtutman, M. et al. The cyclin D1 gene is a target of the beta-catenin/LEF-1 pathway. Proc. Natl Acad. Sci. USA 96, 5522–5527 (1999).

    Article CAS Google Scholar

  • Katoh, Y. & Katoh, M. Hedgehog target genes: mechanisms of carcinogenesis induced by aberrant hedgehog signaling activation. Curr. Mol. Med. 9, 873–886 (2009).

    Article CAS Google Scholar

  • Danaher, P. et al. Gene expression markers of Tumor Infiltrating Leukocytes. J. Immunother. Cancer 5, 18 (2017).

    Article Google Scholar

  • Nguyen, Q. H. et al. Profiling human breast epithelial cells using single cell RNA sequencing identifies cell diversity. Nat. Commun. 9, 2028 (2018).

    Article Google Scholar

  • Barneda, D. et al. The brown adipocyte protein CIDEA promotes lipid droplet fusion via a phosphatidic acid-binding amphipathic helix. eLife 4, e07485 (2015).

    Article Google Scholar

  • Ussar, S. et al. ASC-1, PAT2, and P2RX5 are cell surface markers for white, beige, and brown adipocytes. Sci. Transl. Med. 6, 247ra103 (2014).

    Article Google Scholar

  • Min, S. Y. et al. Diverse repertoire of human adipocyte subtypes develops from transcriptionally distinct mesenchymal progenitor cells. Proc. Natl Acad. Sci. USA 116, 17970–17979 (2019).

    Article CAS Google Scholar

  • Shan, T., Liu, W. & Kuang, S. Fatty acid binding protein 4 expression marks a population of adipocyte progenitors in white and brown adipose tissues. FASEB J. 27, 277–287 (2013).

    Article CAS Google Scholar

  • Bradley, D. & Roth, G. Adaptive thresholding using the integral image. J. Graph. Tools 12, 13–21 (2007).

    Article Google Scholar

  • Krishnamoorthy, A. & Menon, D. Matrix inversion using Cholesky decomposition. In 2013 Signal Processing: Algorithms, Architectures, Arrangements, and Applications (SPA) (IEEE, 2013).

  • Stringer, C., Wang, T., Michaelos, M. & Pachitariu, M. Cellpose: a generalist algorithm for cellular segmentation. Nat. Methods 18, 100–106 (2021).

    Article CAS Google Scholar

  • High-plex imaging of RNA and proteins at subcellular resolution in fixed tissue by spatial molecular imaging (2024)
    Top Articles
    PhD candidate within the Academic Collaborative Center on Sustainable Care Limburg
    PhD position on understanding, supporting and guiding medical residents' career choices
    Mopaga Game
    Bucks County Job Requisitions
    Bluegabe Girlfriend
    Our History | Lilly Grove Missionary Baptist Church - Houston, TX
    Citi Card Thomas Rhett Presale
    Tiraj Bòlèt Florida Soir
    Brenna Percy Reddit
    Signs Of a Troubled TIPM
    How Many Slices Are In A Large Pizza? | Number Of Pizzas To Order For Your Next Party
    Oscar Nominated Brings Winning Profile to the Kentucky Turf Cup
    Charmeck Arrest Inquiry
    Michaels W2 Online
    I Wanna Dance with Somebody : séances à Paris et en Île-de-France - L'Officiel des spectacles
    Tvtv.us Duluth Mn
    iZurvive DayZ & ARMA Map
    How To Cancel Goodnotes Subscription
    Lehmann's Power Equipment
    *Price Lowered! This weekend ONLY* 2006 VTX1300R, windshield & hard bags, low mi - motorcycles/scooters - by owner -...
    Vegas7Games.com
    Parc Soleil Drowning
    Sef2 Lewis Structure
    Aol News Weather Entertainment Local Lifestyle
    Sherburne Refuge Bulldogs
    Beaufort 72 Hour
    Xxn Abbreviation List 2017 Pdf
    Till The End Of The Moon Ep 13 Eng Sub
    FREE Houses! All You Have to Do Is Move Them. - CIRCA Old Houses
    Missing 2023 Showtimes Near Mjr Southgate
    Miss America Voy Board
    Mg Char Grill
    Palmadise Rv Lot
    24 slang words teens and Gen Zers are using in 2020, and what they really mean
    October 31St Weather
    2024 Ford Bronco Sport for sale - McDonough, GA - craigslist
    Eleceed Mangaowl
    Skill Boss Guru
    Latest Nigerian Music (Next 2020)
    Crazy Balls 3D Racing . Online Games . BrightestGames.com
    Ticket To Paradise Showtimes Near Regal Citrus Park
    Stanley Steemer Johnson City Tn
    Craigslist Ludington Michigan
    140000 Kilometers To Miles
    Aurora Il Back Pages
    Stewartville Star Obituaries
    The Largest Banks - ​​How to Transfer Money With Only Card Number and CVV (2024)
    Tricare Dermatologists Near Me
    A rough Sunday for some of the NFL's best teams in 2023 led to the three biggest upsets: Analysis
    Ajpw Sugar Glider Worth
    Denys Davydov - Wikitia
    Latest Posts
    Article information

    Author: Ms. Lucile Johns

    Last Updated:

    Views: 5652

    Rating: 4 / 5 (61 voted)

    Reviews: 92% of readers found this page helpful

    Author information

    Name: Ms. Lucile Johns

    Birthday: 1999-11-16

    Address: Suite 237 56046 Walsh Coves, West Enid, VT 46557

    Phone: +59115435987187

    Job: Education Supervisor

    Hobby: Genealogy, Stone skipping, Skydiving, Nordic skating, Couponing, Coloring, Gardening

    Introduction: My name is Ms. Lucile Johns, I am a successful, friendly, friendly, homely, adventurous, handsome, delightful person who loves writing and wants to share my knowledge and understanding with you.