{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,21]],"date-time":"2025-02-21T18:54:36Z","timestamp":1740164076354,"version":"3.37.3"},"reference-count":15,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2024,6,3]],"date-time":"2024-06-03T00:00:00Z","timestamp":1717372800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2024,6,3]],"date-time":"2024-06-03T00:00:00Z","timestamp":1717372800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"name":"NIA","award":["AG000114"],"award-info":[{"award-number":["AG000114"]}]},{"DOI":"10.13039\/100000057","name":"NIGMS","doi-asserted-by":"crossref","award":["1R35GM142561"],"award-info":[{"award-number":["1R35GM142561"]}],"id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100000957","name":"Alzheimer's Association","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000957","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100002690","name":"Ruth K Broad Foundation","doi-asserted-by":"crossref","id":[{"id":"10.13039\/100002690","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Sci Rep"],"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Comprehensive characterization of protein networks in mounted brain tissue represents a major challenge in brain and neurodegenerative disease research. In this study, we develop a simple staining method, called TSWIFT, to iteratively stain pre-mounted formalin fixed, paraffin embedded (FFPE) brain sections, thus enabling high-dimensional sample phenotyping. We show that TSWIFT conserves tissue architecture and allows for relabeling a single mounted FFPE sample more than 10 times, even after prolonged storage at 4\u00a0\u00b0C. Our results establish TSWIFT as an efficient method to obtain integrated high-dimensional knowledge of cellular proteomes by analyzing mounted FFPE human brain tissue.<\/jats:p>","DOI":"10.1038\/s41598-024-63152-2","type":"journal-article","created":{"date-parts":[[2024,6,3]],"date-time":"2024-06-03T12:02:14Z","timestamp":1717416134000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["TSWIFT, a novel method for iterative staining of embedded and mounted human brain sections"],"prefix":"10.1038","volume":"14","author":[{"given":"Corey M.","family":"Porter","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sarah","family":"Tabler","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sooin","family":"Choi","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Matthias C.","family":"Truttmann","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2024,6,3]]},"reference":[{"key":"63152_CR1","doi-asserted-by":"publisher","DOI":"10.1038\/s41596-021-00644-9","author":"J Andrea","year":"2022","unstructured":"Andrea J et al (2022) IBEX: An iterative immunolabeling and chemical bleaching method for high-content imaging of diverse tissues. Nat Protoc. https:\/\/doi.org\/10.1038\/s41596-021-00644-9","journal-title":"Nat. Protoc."},{"key":"63152_CR2","doi-asserted-by":"publisher","DOI":"10.1038\/s41596-021-00556-8","author":"B Sarah","year":"2021","unstructured":"Sarah B et al (2021) CODEX multiplexed tissue imaging with DNA-conjugated antibodies. Nat Protoc. https:\/\/doi.org\/10.1038\/s41596-021-00556-8","journal-title":"Nat. Protoc."},{"key":"63152_CR3","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-021-03135-9","author":"A Jocelyn","year":"2021","unstructured":"Jocelyn A et al (2021) Oligonucleotide conjugated antibody strategies for cyclic immunostaining. Sci Rep. https:\/\/doi.org\/10.1038\/s41598-021-03135-9","journal-title":"Sci. Rep."},{"key":"63152_CR4","doi-asserted-by":"publisher","DOI":"10.1002\/cbic.202000727","author":"S Jonathan","year":"2021","unstructured":"Jonathan S et al (2021) Site-specific antibody fragment conjugates for reversible staining in fluorescence microscopy. Chembiochem Eur J Chem Biol. https:\/\/doi.org\/10.1002\/cbic.202000727","journal-title":"Chembiochem Eur. J. Chem. Biol."},{"key":"63152_CR5","doi-asserted-by":"publisher","first-page":"73","DOI":"10.1038\/nbt.4281","volume":"37","author":"Y-G Park","year":"2018","unstructured":"Park Y-G et al (2018) Protection of tissue physicochemical properties using polyfunctional crosslinkers. Nat. Biotechnol. 37:73\u201383. https:\/\/doi.org\/10.1038\/nbt.4281","journal-title":"Nat. Biotechnol."},{"key":"63152_CR6","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.68000","author":"C John Darby","year":"2022","unstructured":"John Darby C et al (2022) Characterization of the neurogenic niche in the aging dentate gyrus using iterative immunofluorescence imaging. elife. https:\/\/doi.org\/10.7554\/eLife.68000","journal-title":"elife"},{"key":"63152_CR7","doi-asserted-by":"publisher","DOI":"10.1126\/science.aar7042","author":"G Gut","year":"2018","unstructured":"Gut G, Herrmann MD, Pelkmans L (2018) Multiplexed protein maps link subcellular organization to cellular states. Science. https:\/\/doi.org\/10.1126\/science.aar7042","journal-title":"Science"},{"key":"63152_CR8","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.2019","author":"S Johannes","year":"2012","unstructured":"Johannes S et al (2012) Fiji: An open-source platform for biological-image analysis. Nat Methods. https:\/\/doi.org\/10.1038\/nmeth.2019","journal-title":"Nat. Methods"},{"key":"63152_CR9","doi-asserted-by":"publisher","DOI":"10.1007\/s00018-014-1610-7","author":"S Tim","year":"2014","unstructured":"Tim S, Eckhard M (2014) Transport and diffusion of Tau protein in neurons. Cell Mol Life Sci CMLS. https:\/\/doi.org\/10.1007\/s00018-014-1610-7","journal-title":"Cell. Mol. Life Sci. CMLS"},{"issue":"2","key":"63152_CR10","doi-asserted-by":"publisher","first-page":"42","DOI":"10.32607\/20758251-2015-7-2-42-47","volume":"7","author":"VV Gusel\u2019nikova","year":"2015","unstructured":"Gusel\u2019nikova VV, Korzhevskiy DE (2015) NeuN as a neuronal nuclear antigen and neuron differentiation marker. Acta Nat. 7(2):42\u201347","journal-title":"Acta Nat."},{"key":"63152_CR11","doi-asserted-by":"publisher","DOI":"10.1002\/cac2.12023","author":"T Wei Chang Colin","year":"2020","unstructured":"Wei Chang Colin T et al (2020) Overview of multiplex immunohistochemistry\/immunofluorescence techniques in the era of cancer immunotherapy. Cancer Commun (Lond Engl). https:\/\/doi.org\/10.1002\/cac2.12023","journal-title":"Cancer Commun. (Lond. Engl.)"},{"key":"63152_CR12","doi-asserted-by":"publisher","DOI":"10.1369\/jhc.2009.953240","author":"P Daniel","year":"2009","unstructured":"Daniel P et al (2009) Antibody elution method for multiple immunohistochemistry on primary antibodies raised in the same species and of the same subtype. J Histochem Cytochem Off J Histochem Soc. https:\/\/doi.org\/10.1369\/jhc.2009.953240","journal-title":"J. Histochem. Cytochem. Off. J. Histochem. Soc."},{"key":"63152_CR13","doi-asserted-by":"publisher","DOI":"10.1016\/j.jneumeth.2020.108708","author":"J Alexander","year":"2020","unstructured":"Alexander J et al (2020) A manual multiplex immunofluorescence method for investigating neurodegenerative diseases. J Neurosci Methods. https:\/\/doi.org\/10.1016\/j.jneumeth.2020.108708","journal-title":"J. Neurosci. Methods"},{"issue":"1","key":"63152_CR14","doi-asserted-by":"publisher","first-page":"3","DOI":"10.1111\/jmi.12928","volume":"280","author":"F Rohde","year":"2020","unstructured":"Rohde F, Braumann UD, Schmidt M (2020) Correlia: An ImageJ plug-in to co-register and visualise multimodal correlative micrographs. J. Microsc. 280(1):3\u201311","journal-title":"J. Microsc."},{"key":"63152_CR15","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-021-21735-x","author":"M Dragan","year":"2021","unstructured":"Dragan M et al (2021) Whole-brain tissue mapping toolkit using large-scale highly multiplexed immunofluorescence imaging and deep neural networks. Nat Commun. https:\/\/doi.org\/10.1038\/s41467-021-21735-x","journal-title":"Nat. Commun."}],"container-title":["Scientific Reports"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s41598-024-63152-2.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41598-024-63152-2","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41598-024-63152-2.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,6,3]],"date-time":"2024-06-03T12:12:56Z","timestamp":1717416776000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s41598-024-63152-2"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,6,3]]},"references-count":15,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2024,12]]}},"alternative-id":["63152"],"URL":"https:\/\/doi.org\/10.1038\/s41598-024-63152-2","relation":{},"ISSN":["2045-2322"],"issn-type":[{"type":"electronic","value":"2045-2322"}],"subject":[],"published":{"date-parts":[[2024,6,3]]},"assertion":[{"value":"19 September 2023","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"25 May 2024","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"3 June 2024","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The authors declare no competing interests.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"12688"}}