Combined protein and nucleic acid staining in tissues with PANINI

Deisher, Addison; Yeo, Yao Yu; Jiang, Sizun

doi:10.1016/j.xpro.2022.101663

Cited by 2 publications

(1 citation statement)

References 9 publications

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“…The bacterial pellets were then fixed using methacarn and subsequently fixed in methacarn and formalin. To further maintain the structural integrity of the fixed bacteria pellets, we embedded them in Histogel (33). The fixed and histogel-embedded bacteria pellets across different species were finally arranged in an array format in a tissue cassette, and embedded in paraffin to create a methacarn and formalin-fixed, paraffin embedded (MFPE) Bacteria MicroArray (BMA).…”

Section: Resultsmentioning

confidence: 99%

A Spatial Multi-Modal Dissection of Host-Microbiome Interactions within the Colitis Tissue Microenvironment

Zhu,

Bai,

Yeo

et al. 2024

Preprint

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The intricate and dynamic interactions between the host immune system and its microbiome constituents undergo dynamic shifts in response to perturbations to the intestinal tissue environment. Our ability to study these events on the systems level is significantly limited by in situ approaches capable of generating simultaneous insights from both host and microbial communities. Here, we introduce Microbiome Cartography (MicroCart), a framework for simultaneous in situ probing of host features and its microbiome across multiple spatial modalities. We demonstrate MicroCart by comprehensively investigating the alterations in both gut host and microbiome components in a murine model of colitis by coupling MicroCart with spatial proteomics, transcriptomics, and glycomics platforms. Our findings reveal a global but systematic transformation in tissue immune responses, encompassing tissue-level remodeling in response to host immune and epithelial cell state perturbations, and bacterial population shifts, localized inflammatory responses, and metabolic process alterations during colitis. MicroCart enables a deep investigation of the intricate interplay between the host tissue and its microbiome with spatial multi-omics.

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Section: Resultsmentioning

confidence: 99%