Literature DB >> 28784428

Large-scale 3-dimensional quantitative imaging of tissues: state-of-the-art and translational implications.

Seth Winfree1, Michael J Ferkowicz2, Pierre C Dagher3, Katherine J Kelly4, Michael T Eadon4, Timothy A Sutton4, Troy A Markel5, Mervin C Yoder2, Kenneth W Dunn6, Tarek M El-Achkar7.   

Abstract

Recent developments in automated optical sectioning microscope systems have enabled researchers to conduct high resolution, three-dimensional (3D) microscopy at the scale of millimeters in various types of tissues. This powerful technology allows the exploration of tissues at an unprecedented level of detail, while preserving the spatial context. By doing so, such technology will also enable researchers to explore cellular and molecular signatures within tissue and correlate with disease course. This will allow an improved understanding of pathophysiology and facilitate a precision medicine approach to assess the response to treatment. The ability to perform large-scale imaging in 3D cannot be realized without the widespread availability of accessible quantitative analysis. In this review, we will outline recent advances in large-scale 3D imaging and discuss the available methodologies to perform meaningful analysis and potential applications in translational research. Published by Elsevier Inc.

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Year:  2017        PMID: 28784428      PMCID: PMC5659947          DOI: 10.1016/j.trsl.2017.07.006

Source DB:  PubMed          Journal:  Transl Res        ISSN: 1878-1810            Impact factor:   7.012


  69 in total

1.  Optical sectioning deep inside live embryos by selective plane illumination microscopy.

Authors:  Jan Huisken; Jim Swoger; Filippo Del Bene; Joachim Wittbrodt; Ernst H K Stelzer
Journal:  Science       Date:  2004-08-13       Impact factor: 47.728

2.  Dynamic in situ cytometry uncovers T cell receptor signaling during immunological synapses and kinapses in vivo.

Authors:  Hélène D Moreau; Fabrice Lemaître; Emmanuel Terriac; Georges Azar; Matthieu Piel; Ana-Maria Lennon-Dumenil; Philippe Bousso
Journal:  Immunity       Date:  2012-06-07       Impact factor: 31.745

3.  Advanced CUBIC protocols for whole-brain and whole-body clearing and imaging.

Authors:  Etsuo A Susaki; Kazuki Tainaka; Dimitri Perrin; Hiroko Yukinaga; Akihiro Kuno; Hiroki R Ueda
Journal:  Nat Protoc       Date:  2015-10-08       Impact factor: 13.491

Review 4.  Selective plane illumination microscopy techniques in developmental biology.

Authors:  Jan Huisken; Didier Y R Stainier
Journal:  Development       Date:  2009-06       Impact factor: 6.868

Review 5.  High-resolution imaging of entire organs by 3-dimensional imaging of solvent cleared organs (3DISCO).

Authors:  Ali Ertürk; Frank Bradke
Journal:  Exp Neurol       Date:  2012-11-01       Impact factor: 5.330

Review 6.  Nanobodies: natural single-domain antibodies.

Authors:  Serge Muyldermans
Journal:  Annu Rev Biochem       Date:  2013-03-13       Impact factor: 23.643

7.  Estrogen receptor status by immunohistochemistry is superior to the ligand-binding assay for predicting response to adjuvant endocrine therapy in breast cancer.

Authors:  J M Harvey; G M Clark; C K Osborne; D C Allred
Journal:  J Clin Oncol       Date:  1999-05       Impact factor: 44.544

8.  Ultramicroscopy: three-dimensional visualization of neuronal networks in the whole mouse brain.

Authors:  Hans-Ulrich Dodt; Ulrich Leischner; Anja Schierloh; Nina Jährling; Christoph Peter Mauch; Katrin Deininger; Jan Michael Deussing; Matthias Eder; Walter Zieglgänsberger; Klaus Becker
Journal:  Nat Methods       Date:  2007-03-25       Impact factor: 28.547

9.  Histo-cytometry: a method for highly multiplex quantitative tissue imaging analysis applied to dendritic cell subset microanatomy in lymph nodes.

Authors:  Michael Y Gerner; Wolfgang Kastenmuller; Ina Ifrim; Juraj Kabat; Ronald N Germain
Journal:  Immunity       Date:  2012-08-02       Impact factor: 31.745

10.  Cell distance mapping identifies functional T follicular helper cells in inflamed human renal tissue.

Authors:  Vladimir M Liarski; Natalya Kaverina; Anthony Chang; Daniel Brandt; Denisse Yanez; Lauren Talasnik; Gianluca Carlesso; Ronald Herbst; Tammy O Utset; Christine Labno; Yahui Peng; Yulei Jiang; Maryellen L Giger; Marcus R Clark
Journal:  Sci Transl Med       Date:  2014-04-02       Impact factor: 17.956

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  16 in total

1.  Tamm-Horsfall Protein Regulates Mononuclear Phagocytes in the Kidney.

Authors:  Radmila Micanovic; Shehnaz Khan; Danielle Janosevic; Maya E Lee; Takashi Hato; Edward F Srour; Seth Winfree; Joydeep Ghosh; Yan Tong; Susan E Rice; Pierre C Dagher; Xue-Ru Wu; Tarek M El-Achkar
Journal:  J Am Soc Nephrol       Date:  2017-11-27       Impact factor: 10.121

Review 2.  Quantitative Large-Scale Three-Dimensional Imaging of Human Kidney Biopsies: A Bridge to Precision Medicine in Kidney Disease.

Authors:  Seth Winfree; Pierre C Dagher; Kenneth W Dunn; Michael T Eadon; Michael Ferkowicz; Daria Barwinska; Katherine J Kelly; Timothy A Sutton; Tarek M El-Achkar
Journal:  Nephron       Date:  2018-06-05       Impact factor: 2.847

Review 3.  Cellular and molecular interrogation of kidney biopsy specimens.

Authors:  Michael T Eadon; Pierre C Dagher; Tarek M El-Achkar
Journal:  Curr Opin Nephrol Hypertens       Date:  2022-03-01       Impact factor: 2.894

Review 4.  Profiling Immune Cells in the Kidney Using Tissue Cytometry and Machine Learning.

Authors:  Seth Winfree; Mohammad Al Hasan; Tarek M El-Achkar
Journal:  Kidney360       Date:  2022-03-28

5.  VEGFR3 tyrosine kinase inhibition aggravates cisplatin nephrotoxicity.

Authors:  Laurence M Black; Elisa R Farrell; Daria Barwinska; Gunars Osis; Anna A Zmijewska; Amie M Traylor; Stephanie K Esman; Subhashini Bolisetty; Grace Whipple; Malgorzata M Kamocka; Seth Winfree; Daryll R Spangler; Shehnaz Khan; Abolfazl Zarjou; Tarek M El-Achkar; Anupam Agarwal
Journal:  Am J Physiol Renal Physiol       Date:  2021-10-18

6.  Kidney Histopathology and Prediction of Kidney Failure: A Retrospective Cohort Study.

Authors:  Michael T Eadon; Tae-Hwi Schwantes-An; Carrie L Phillips; Anna R Roberts; Colin V Greene; Ayman Hallab; Kyle J Hart; Sarah N Lipp; Claudio Perez-Ledezma; Khawaja O Omar; Katherine J Kelly; Sharon M Moe; Pierre C Dagher; Tarek M El-Achkar; Ranjani N Moorthi
Journal:  Am J Kidney Dis       Date:  2020-04-24       Impact factor: 8.860

Review 7.  The Indiana O'Brien Center for Advanced Renal Microscopic Analysis.

Authors:  Kenneth W Dunn; Bruce A Molitoris; Pierre C Dagher
Journal:  Am J Physiol Renal Physiol       Date:  2021-03-08

8.  Large-scale, three-dimensional tissue cytometry of the human kidney: a complete and accessible pipeline.

Authors:  Michael J Ferkowicz; Seth Winfree; Angela R Sabo; Malgorzata M Kamocka; Suraj Khochare; Daria Barwinska; Michael T Eadon; Ying-Hua Cheng; Carrie L Phillips; Timothy A Sutton; Katherine J Kelly; Pierre C Dagher; Tarek M El-Achkar; Kenneth W Dunn
Journal:  Lab Invest       Date:  2021-01-06       Impact factor: 5.662

9.  In Situ Classification of Cell Types in Human Kidney Tissue Using 3D Nuclear Staining.

Authors:  Andre Woloshuk; Suraj Khochare; Aljohara F Almulhim; Andrew T McNutt; Dawson Dean; Daria Barwinska; Michael J Ferkowicz; Michael T Eadon; Katherine J Kelly; Kenneth W Dunn; Mohammad A Hasan; Tarek M El-Achkar; Seth Winfree
Journal:  Cytometry A       Date:  2020-12-13       Impact factor: 4.714

10.  A Precision Medicine Approach Uncovers a Unique Signature of Neutrophils in Patients With Brushite Kidney Stones.

Authors:  Mohammad Shahidul Makki; Seth Winfree; James E Lingeman; Frank A Witzmann; Elaine M Worcester; Amy E Krambeck; Fredric L Coe; Andrew P Evan; Sharon Bledsoe; Kristin J Bergsland; Suraj Khochare; Daria Barwinska; James C Williams; Tarek M El-Achkar
Journal:  Kidney Int Rep       Date:  2020-02-20
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