Spatially visualized single-cell pathology of highly multiplexed protein profiles in health and disease

Allam, Mayar; Hu, Thomas; Cai, Shuangyi; Laxminarayanan, Krishnan; Hughley, Robert B.; Coşkun, Ahmet F.

doi:10.1038/s42003-021-02166-2

Cited by 7 publications

(3 citation statements)

References 43 publications

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“…In the pancreas as many as ten structures (normal ductal epithelium, pancreatic precancers, pancreatic cancer, islets of Langerhans, vessels, nerves, acini, stroma, lymph nodes, and fat) have been labeled to a resolution of 1-2 microns (Kiemen et al). Unused intervening sections can be used for immunohistochemistry, imaging mass cytometry, somatic sequencing and spatial transcriptomics, creating 3D integrations of histologic, gene, protein and immune features (Allam et al, 2021;Black et al, 2021;Giesen et al, 2014;Ho et al, 2020;Kiemen et al;Korehisa et al, 2018;Liu et al, 2020;Rao et al, 2021).…”

Section: D Reconstruction Of Digitized Serial Microscope Slidesmentioning

confidence: 99%

Tissue clearing and 3D reconstruction of digitized, serially sectioned slides provide novel insights into pancreatic cancer

Kiemen¹,

Damanakis²,

Braxton³

et al. 2023

Med

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Section: D Reconstruction Of Digitized Serial Microscope Slidesmentioning

confidence: 99%

Tissue clearing and 3D reconstruction of digitized, serially sectioned slides provide novel insights into pancreatic cancer

Kiemen¹,

Damanakis²,

Braxton³

et al. 2023

Med

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“…IMC has also been used to further characterize hepatitis B virus-associated liver disease and most recently, COVID-19-associated organ manifestations including lung disease ( Wang et al, 2020 ; Zhang et al, 2020 ; Melms et al, 2021 ; Rendeiro et al, 2021 ), brain injury ( Schwabenland et al, 2021 ), and small intestinal infection ( Lehmann et al, 2021 ). Allam et al (2021) analyzed tonsillitis samples, while at the same time introducing a new algorithm to explore spatial relationships in diverse multiplexed tissue imaging data. In these publications, the corresponding antibody panels reflected potentially relevant signaling pathways in addition to immune cell composition and cross talk.…”

Section: Applications Of Imcmentioning

confidence: 99%

Using Imaging Mass Cytometry to Define Cell Identities and Interactions in Human Tissues

2021

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In the evolving landscape of highly multiplexed imaging techniques that can be applied to study complex cellular microenvironments, this review characterizes the use of imaging mass cytometry (IMC) to study the human kidney. We provide technical details for antibody validation, cell segmentation, and data analysis specifically tailored to human kidney samples, and elaborate on phenotyping of kidney cell types and novel insights that IMC can provide regarding pathophysiological processes in the injured or diseased kidney. This review will provide the reader with the necessary background to understand both the power and the limitations of IMC and thus support better perception of how IMC analysis can improve our understanding of human disease pathogenesis and can be integrated with other technologies such as single cell sequencing and proteomics to provide spatial context to cellular data.

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“…Multiple factors, such as microenvironment variability, differences in the cellular stages, genetics or epigenetics, or fluctuations in gene expression levels, can cause this heterogeneity. Single-cell analysis approaches are thus useful in investigating aspects of cellular mechanisms that are not revealed in bulk-level studies 4 , 5 .…”

Section: Introductionmentioning

confidence: 99%

Spatial subcellular organelle networks in single cells

Venkatesan

Zhang

Marteau

et al. 2023

Sci Rep

Self Cite

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Organelles play important roles in human health and disease, such as maintaining homeostasis, regulating growth and aging, and generating energy. Organelle diversity in cells not only exists between cell types but also between individual cells. Therefore, studying the distribution of organelles at the single-cell level is important to understand cellular function. Mesenchymal stem cells are multipotent cells that have been explored as a therapeutic method for treating a variety of diseases. Studying how organelles are structured in these cells can answer questions about their characteristics and potential. Herein, rapid multiplexed immunofluorescence (RapMIF) was performed to understand the spatial organization of 10 organelle proteins and the interactions between them in the bone marrow (BM) and umbilical cord (UC) mesenchymal stem cells (MSCs). Spatial correlations, colocalization, clustering, statistical tests, texture, and morphological analyses were conducted at the single cell level, shedding light onto the interrelations between the organelles and comparisons of the two MSC subtypes. Such analytics toolsets indicated that UC MSCs exhibited higher organelle expression and spatially spread distribution of mitochondria accompanied by several other organelles compared to BM MSCs. This data-driven single-cell approach provided by rapid subcellular proteomic imaging enables personalized stem cell therapeutics.

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Spatially visualized single-cell pathology of highly multiplexed protein profiles in health and disease

Cited by 7 publications

References 43 publications

Tissue clearing and 3D reconstruction of digitized, serially sectioned slides provide novel insights into pancreatic cancer

Tissue clearing and 3D reconstruction of digitized, serially sectioned slides provide novel insights into pancreatic cancer

Using Imaging Mass Cytometry to Define Cell Identities and Interactions in Human Tissues

Spatial subcellular organelle networks in single cells

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