Molecular cartography uncovers evolutionary and microenvironmental dynamics in sporadic colorectal tumors

Heiser, Cody N.; Simmons, Alan J.; Revetta, Frank; McKinley, Eliot T.; Ramirez‐Solano, Marisol; Wang, Jiawei; Shao, Justin; Ayers, Gregory D.; Wang, Yu; Glass, Sarah E.; Kaur, Harsimran; Rolong, Andrea; Chen, Bob; Vega, Paige N.; Drewes, Julia L.; Saleh, Nabil; Vandekar, Simon; Jones, Angela L.; Washington, Mary Kay; Roland, Joseph T.; Sears, Cynthia L.; Liu, Qi; Shrubsole, Martha J.; Coffey, Robert J.; Lau, Ken S.

doi:10.1101/2023.03.09.530832

Cited by 4 publications

(9 citation statements)

References 108 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Spatial transcriptomics was performed using the Human FFPE Visium platform, as described previously (Heiser et al, 2023). FFPE sections (5 µm) of biospies were cut directly into 6.5mm × 6.5mm capture areas of Visium FFPE spatial gene expression slides (10X Genomics).…”

Section: Methodsmentioning

confidence: 99%

A Specialized Epithelial Cell Type Regulating Mucosal Immunity and Driving Human Crohn’s Disease

Li,

Simmons,

Chiron

et al. 2023

Preprint

Self Cite

View full text Add to dashboard Cite

Crohn’s disease (CD) is a complex chronic inflammatory disorder that may affect any part of gastrointestinal tract with extra-intestinal manifestations and associated immune dysregulation. To characterize heterogeneity in CD, we profiled single-cell transcriptomics of 170 samples from 65 CD patients and 18 non-inflammatory bowel disease (IBD) controls in both the terminal ileum (TI) and ascending colon (AC). Analysis of 202,359 cells identified a novel epithelial cell type in both TI and AC, featuring high expression ofLCN2,NOS2, andDUOX2, and thus is named LND. LND cells, confirmed by high-resolution in-situ RNA imaging, were rarely found in non-IBD controls, but expanded significantly in active CD. Compared to other epithelial cells, genes defining LND cells were enriched in antimicrobial response and immunoregulation. Moreover, multiplexed protein imaging demonstrated that LND cell abundance was associated with immune infiltration. Cross-talk between LND and immune cells was explored by ligand-receptor interactions and further evidenced by their spatial colocalization. LND cells showed significant enrichment of expression specificity of IBD/CD susceptibility genes, revealing its role in immunopathogenesis of CD. Investigating lineage relationships of epithelial cells detected two LND cell subpopulations with different origins and developmental potential, early and late LND. The ratio of the late to early LND cells was related to anti-TNF response. These findings emphasize the pathogenic role of the specialized LND cell type in both Crohn’s ileitis and Crohn’s colitis and identify novel biomarkers associated with disease activity and treatment response.

show abstract

Section: Methodsmentioning

confidence: 99%

A Specialized Epithelial Cell Type Regulating Mucosal Immunity and Driving Human Crohn’s Disease

Li,

Simmons,

Chiron

et al. 2023

Preprint

Self Cite

View full text Add to dashboard Cite

show abstract

“…Semi-automated marker gating results are obtained using GammaGateR as described in Section 2.3, with monotonically adjusted posterior probability and marginal probability thresholded at 0.5 to define marker positive cells. The same phenotype definitions used for ASTIR are used to define phenotypes from marker positive labels using GammaGateR and manual marker gating as well [5,7]. Each cell belongs to a given phenotype if it is marker positive for combinations of markers for that phenotype (Tables S1, S2).…”

Section: Methods and Phenotyping Evaluationmentioning

confidence: 99%

“…We use three single-cell imaging datasets to evaluate model performance and demonstrate the use of the GammaGateR analysis pipeline (Table 1): the Colorectal Molecular Atlas Project (Colon MAP) dataset [5], the Spatial Colorectal Cancer (CRC) Atlas dataset [7] and Ovarian Cancer dataset [32,33]. Dataset-specific acquisition and processing are described below and in prior work [5,7,33]. After processing and prior to analysis, cell expression values were normalized by first mean division then log10 transformation to reduce slide-to-slide variation [14]…”

Section: Datasets and Preprocessingmentioning

confidence: 99%

“…The CRC atlas dataset includes 16 samples that represent various stages of human colon cancer [7]. The goal of this study was to investigate the co-evolution of tumor and immune microenvironments in microsatellite-stable and chromosomally-unstable tumors.…”

Section: Crc Atlas Datamentioning

confidence: 99%

“…mIF is advantageous over other single-cell assays that disaggregate the tissue because it can reveal insights about the spatial interactions between tissue and cell types in situ and offers a subcellular spatial resolution that is higher than other spatial assays. mIF has already revealed valuable spatial insights into the tumor microenvironment [5][6][7][8]. For example, recent findings demonstrate differences in immune cell infiltration of colorectal precancerous polyps such as a higher concentration of CD8+ T-cells in the epithelium of sessile serrated lesions (SSL) than that of conventional adenomas and higher CD68+ macrophages concentration at the luminal surface in SSL, but more randomly distributed in adenomas [5].…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

GammaGateR: semi-automated marker gating for single-cell multiplexed imaging

Xiong,

Kaur,

Heiser

et al. 2023

Preprint

Self Cite

View full text Add to dashboard Cite

Multiplexed immunofluorescence (mIF) is an emerging assay for multichannel protein imaging that can decipher cell-level spatial features in tissues. However, existing automated cell phenotyping methods, such as clustering, face challenges in achieving consistency across experiments and often require subjective evaluation. As a result, mIF analyses often revert to marker gating based on manual thresholding of raw imaging data. To address the need for an evaluable semi-automated algorithm, we developed GammaGateR, an R package for interactive marker gating designed specifically for segmented cell-level data from mIF images. Based on a novel closed-form gamma mixture model, GammaGateR provides estimates of marker-positive cell proportions and soft clustering of marker-positive cells. The model incorporates user-specified constraints that provide a consistent but slide-specific model fit. We compared GammaGateR against the newest unsupervised approach for annotating mIF data, employing two colon datasets and one ovarian cancer dataset for the evaluation. We showed that GammaGateR produces highly similar results to a silver standard established through manual annotation. Furthermore, we demonstrated its effectiveness in identifying biological signals, achieved by mapping known spatial interactions between CD68 and MUC5AC cells in the colon and by accurately predicting survival in ovarian cancer patients using the phenotype probabilities as input for machine learning methods. GammaGateR is a highly efficient tool that can improve the replicability of marker gating results, while reducing the time of manual segmentation.

show abstract

Temporal recording of mammalian development and precancer

Islam,

Yang,

Simmons

et al. 2023

Preprint

Self Cite

View full text Add to dashboard Cite

Key to understanding many biological phenomena is knowing the temporal ordering of cellular events, which often require continuous direct observations [1, 2]. An alternative solution involves the utilization of irreversible genetic changes, such as naturally occurring mutations, to create indelible markers that enables retrospective temporal ordering [3-8]. Using NSC-seq, a newly designed and validated multi-purpose single-cell CRISPR platform, we developed a molecular clock approach to record the timing of cellular events and clonalityin vivo, while incorporating assigned cell state and lineage information. Using this approach, we uncovered precise timing of tissue-specific cell expansion during murine embryonic development and identified new intestinal epithelial progenitor states by their unique genetic histories. NSC-seq analysis of murine adenomas and single-cell multi-omic profiling of human precancers as part of the Human Tumor Atlas Network (HTAN), including 116 scRNA-seq datasets and clonal analysis of 418 human polyps, demonstrated the occurrence of polyancestral initiation in 15-30% of colonic precancers, revealing their origins from multiple normal founders. Thus, our multimodal framework augments existing single-cell analyses and lays the foundation forin vivomultimodal recording, enabling the tracking of lineage and temporal events during development and tumorigenesis.

show abstract

Molecular cartography uncovers evolutionary and microenvironmental dynamics in sporadic colorectal tumors

Cited by 4 publications

References 108 publications

A Specialized Epithelial Cell Type Regulating Mucosal Immunity and Driving Human Crohn’s Disease

A Specialized Epithelial Cell Type Regulating Mucosal Immunity and Driving Human Crohn’s Disease

GammaGateR: semi-automated marker gating for single-cell multiplexed imaging

Temporal recording of mammalian development and precancer

Contact Info

Product

Resources

About