Spatial host-microbiome sequencing

Lötstedt, Britta; Stražar, Martin; Xavier, Ramnik J.; Regev, Aviv; Vicković, Sanja

doi:10.1101/2022.07.18.500470

Cited by 11 publications

(13 citation statements)

References 99 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Using scRNA-seq, we were able to reconstruct cell type-specific effects that occur post-pathobiont exposure. However, recently developed approaches that enable combined host transcriptomics with microbiome species mapping 137,138…”

Section: Discussionmentioning

confidence: 99%

Keystone pathobionts associated with colorectal cancer promote oncogenic reprograming

Jones

Shi

Nath

et al. 2023

Preprint

View full text Add to dashboard Cite

Fusobacterium nucleatum (Fn) and enterotoxigenic Bacteroides fragilis (ETBF) are two pathobionts consistently enriched in the gut microbiomes of patients with colorectal cancer (CRC) compared to healthy counterparts and frequently observed for their direct association within tumors. Although several molecular mechanisms have been identified that directly link these organisms to features of CRC in specific cell types, their specific effects on the epithelium and local immune compartment are not well-understood. To fill this gap, we leveraged single-cell RNA sequencing (scRNA-seq) on wildtype mice and mouse model of CRC. We find that Fn and ETBF exacerbate cancer-like transcriptional phenotypes in transit-amplifying and mature enterocytes in a mouse model of CRC. We also observed increased T cells in the pathobiont-exposed mice, but these pathobiont-specific differences observed in wildtype mice were abrogated in the mouse model of CRC. Although there are similarities in the responses provoked by each organism, we find pathobiont-specific effects in Myc-signaling and fatty acid metabolism. These findings support a role for Fn and ETBF in potentiating tumorigenesis via the induction of a cancer stem cell-like transit-amplifying and enterocyte population and the disruption of CTL cytotoxic function.

show abstract

Section: Discussionmentioning

confidence: 99%

Keystone pathobionts associated with colorectal cancer promote oncogenic reprograming

Jones

Shi

Nath

et al. 2023

Preprint

View full text Add to dashboard Cite

show abstract

“…Optimized methodologies for histone removal and Tn5 treatments for a variety of tumor tissue types have been shown to prevent potential bias in DNA capture. More recently, spatial host-microbiome sequencing (SHM-seq) has been reported [63]. SHM-seq is an adapted version from Spatial Transcriptomics, where mRNA probes for transcript captures are modified to DNA capture probes so that they can obtain both polyadenylated transcripts and 16S rRNA hypervariable regions.…”

Section: Other Spatial Omics Technologies For Multi-modal Studymentioning

confidence: 99%

Spatial omics technologies at multimodal and single cell/subcellular level

et al. 2022

View full text Add to dashboard Cite

Spatial omics technologies enable a deeper understanding of cellular organizations and interactions within a tissue of interest. These assays can identify specific compartments or regions in a tissue with differential transcript or protein abundance, delineate their interactions, and complement other methods in defining cellular phenotypes. A variety of spatial methodologies are being developed and commercialized; however, these techniques differ in spatial resolution, multiplexing capability, scale/throughput, and coverage. Here, we review the current and prospective landscape of single cell to subcellular resolution spatial omics technologies and analysis tools to provide a comprehensive picture for both research and clinical applications.

show abstract

“…Even mental illnesses can be exacerbated after gut malfunctions. New techniques such as spatially resolved single-cell multi-omics have recently been applied to gut research [ 27 ]. The human cell atlas will inevitably identify some rare new cell types.…”

Section: Introductionmentioning

confidence: 99%

“…When chronic inflammation is caused in the large intestines and colon area ulcerative colitis may develop. The proliferation of lymphatic and blood vessels, the so-called lymphangiogenesis is correlated to the expression of vascular endothelial growth factors (VEGFs) [ 27 ]. It seems that nanocarriers loaded with polyphenols interact with the VEGFs and nanobubbles and polyphenols have already shown their potential to inhibition of lymphatic vessel formation in the large intestine [ 28 ].…”

Section: Introductionmentioning

confidence: 99%

Enhancing the bioavailability and activity of natural antioxidants with nanobubbles and nanoparticles

Čolić,

Kraljević Pavelić,

Peršurić

et al. 2024

Redox Report

View full text Add to dashboard Cite

Objectives: Many polyphenols such as EGCG from green tea, curcumin, apigenin, resveratrol or the alkaloid berberine show in-vitro activity that is much higher than FDA and EU approved drugs. And yet, while mice studies show excellent results, human clinical trials have so far been quite disappointing. Methods: In this review paper we accordingly present data from scientific literature and publicly available databases that support further development of nanoformulations for enhanced natural antioxidants bioavailability and activity. Results: Nanobubbles, and nanoparticles may enhance the polyphenols bioavailability and special coatings can be used to avoid liver fast inactivation. Zeolites have also been tested as carriers for bioactive compounds from the Mediterranean food. Other polyphenols can be used with nanoemulsions for synergistic antioxidants treatment. Finally, nanobubbles in the presence of ferric or copper ions at low pH as in human stomach or lysosomes can produce small amount of hydroxyl radicals, stimulating activation of Nrf2 transcription factor and detox enzymes. Discussion: A number of nanoformulations, including nanobubbles loaded with natural antioxidants may be used with low carbs and protein diet as a support to chemotherapy or treatment of advanced tumors. Good results in animal studies of neurodegenerative diseases and type II diabetes were also observed. KEY POLICY HIGHLIGHTS Nanobubbles and nanoparticles may enhance the polyphenols’ bioavailability Nanobubbles may stimulate the activation of Nrf2 and detox enzymes Armoured oxygen nanobubbles may enhance radiotherapy or chemotherapy effects

show abstract

Spatial host-microbiome sequencing

Cited by 11 publications

References 99 publications

Keystone pathobionts associated with colorectal cancer promote oncogenic reprograming

Keystone pathobionts associated with colorectal cancer promote oncogenic reprograming

Spatial omics technologies at multimodal and single cell/subcellular level

Enhancing the bioavailability and activity of natural antioxidants with nanobubbles and nanoparticles

Contact Info

Product

Resources

About