Single-cell integration and multi-modal profiling reveals phenotypes and spatial organization of neutrophils in colorectal cancer

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Авг. 26, 2024

SUMMARY The immune composition of the tumor microenvironment (TME) has a major impact on therapeutic response and clinical outcome in patients with colorectal cancer (CRC). Here, we comprehensively characterize TME at single-cell level by first building large-scale atlas that integrates 4.27 million single cells from 1,670 patient samples. We then complemented profiles four CRC cohorts 266 patients, including low mRNA content, spatial transcriptional 3.7 cells, protein 0.7 cells. analysis allows refined classification into phenotypes: desert, B cell enriched, T myeloid enriched subtypes. Within compartment uncover distinct subpopulations neutrophils acquire new functional properties blood TME, anti-tumorigenic capabilities. Further, multimodal profiling reveals are organized clusters within niches. Finally, using an orthotopic mouse model show cancer-derived systemic signals modify neutrophil production bone marrow, providing evidence for tumor-induced granulopoiesis. Our study provides big data resource suggests novel strategies targeting neutrophils.

Язык: Английский

More is better: A simple antibody-based strategy for recovering all major mouse brain cell types from multiplexed single-cell RNAseq samples

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Июнь 12, 2024

ABSTRACT Single-cell RNA sequencing (scRNAseq) is a powerful yet costly technique for studying cellular diversity within the complexity of organs and tissues. Here, we sought to establish an effective multiplexing strategy adult mouse brain that could allow multiple experimental groups be pooled into single sample sequencing, reducing costs, increasing data yield, eliminating batch effects. We first describe optimized cold temperature single-cell dissociation protocol permits isolation high yield viability cells from mouse. Cells isolated using this were then screened by flow cytometry panel antibodies, allowing identification antibody, anti-Thy1.2, can tag vast majority cells. used primary antibody against “universal” neural target, together with secondary antibodies carrying sample-specific oligonucleotides BD Rhapsody system show samples multiplexed run scRNAseq. Bioinformatic analyses enable efficient demultiplexing sequenced sample, tagging efficiency precise annotation clustering cell populations. The flexibility two-step simplifies design, optimizes reagent usage, eliminates effects reduces overall costs.

Язык: Английский

Potential role of liver resident CD3+ macrophages in HBV clearance in a mouse hepatitis B model

JHEP Reports, Год журнала: 2024, Номер 7(4), С. 101323 - 101323

Опубликована: Дек. 31, 2024

Язык: Английский