Evidence map›Paper›PMID 38712088›Full record

ArticlebioRxiv : the preprint server for biology2024

Tissue and cellular spatiotemporal dynamics in colon aging.

Aidan C Daly, Francesco Cambuli, Tarmo Äijö, Britta Lötstedt, Nemanja Marjanovic, Olena Kuksenko, Matthew Smith-Erb, Sara Fernandez, Daniel Domovic, Nicholas Van Wittenberghe and 6 more

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

16 authors.

Aidan C DalyNew York Genome Center, New York, NY, USA.ORCID 0000-0003-4447-8623
Francesco CambuliNew York Genome Center, New York, NY, USA.
Tarmo ÄijöCenter for Computational Biology, Flatiron Institute, New York, NY, USA.
Britta LötstedtNew York Genome Center, New York, NY, USA.
Nemanja MarjanovicKlarman Cell Observatory Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Olena KuksenkoKlarman Cell Observatory Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Matthew Smith-ErbNew York Genome Center, New York, NY, USA.
Sara FernandezNew York Genome Center, New York, NY, USA.
Daniel DomovicNew York Genome Center, New York, NY, USA.
Nicholas Van WittenbergheKlarman Cell Observatory Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Eugene DrokhlyanskyKlarman Cell Observatory Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Gabriel K GriffinKlarman Cell Observatory Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Hemali PhatnaniNew York Genome Center, New York, NY, USA.
Richard BonneauCenter for Computational Biology, Flatiron Institute, New York, NY, USA.
Aviv RegevKlarman Cell Observatory Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Sanja VickovicNew York Genome Center, New York, NY, USA.

Funding

Center for Integrated Cellular Analysis - Valeria A. Sanchez EstradaRM1HG011014 · NHGRI · NEW YORK GENOME CENTER · PI LANDAU, DAN, SATIJA, RAHUL · 2020 to 2025
$22.1M
Data Analysis CoreU54AG076040 · NIA · COLUMBIA UNIVERSITY HEALTH SCIENCES · PI PHATNANI, HEMALI · 2021 to 2025
$13.1M
Integrating Spatial Multi-omics and Clinical Covariates to Identify Mechanisms of Disease in ALS-FTDR01NS118183 · NINDS · NEW YORK GENOME CENTER · PI Hemali Phatnani · 2020 to 2026
$4.7M
Spatially Resolved Dynamics of Molecular Pathology and Intercellular Interactions in Amytrophic Lateral SclerosisR01NS116350 · NINDS · NEW YORK GENOME CENTER · PI Hemali Phatnani · 2020 to 2026
$3.6M
NHGRI NIH HHS RM1 HG011014NIA NIH HHS U54 AG076040
6 · The paper itself

Abstract

Tissue structure and molecular circuitry in the colon can be profoundly impacted by systemic age-related effects, but many of the underlying molecular cues remain unclear. Here, we built a cellular and spatial atlas of the colon across three anatomical regions and 11 age groups, encompassing ~1,500 mouse gut tissues profiled by spatial transcriptomics and ~400,000 single nucleus RNA-seq profiles. We developed a new computational framework, cSplotch, which learns a hierarchical Bayesian model of spatially resolved cellular expression associated with age, tissue region, and sex, by leveraging histological features to share information across tissue samples and data modalities. Using this model, we identified cellular and molecular gradients along the adult colonic tract and across the main crypt axis, and multicellular programs associated with aging in the large intestine. Our multi-modal framework for the investigation of cell and tissue organization can aid in the understanding of cellular roles in tissue-level pathology.

Identifiers

PMID38712088
PMCPMC11071407

What OpenQuestion holds

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LicenceCC BY
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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.