Evidence map›Paper›PMID 38351241›Full record

ArticleScientific reports2024

Technical optimization of spatially resolved single-cell transcriptomic datasets to study clinical liver disease.

Brittany Rocque, Kate Guion, Pranay Singh, Sarah Bangerth, Lauren Pickard, Jashdeep Bhattacharjee, Sofia Eguizabal, Carly Weaver, Shefali Chopra, Shengmei Zhou and 5 more

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Scientific reports, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.

0numbers the graph read from it
0cells of the map it votes in
4citing papers in PubMed
0.7field-weighted citation impact, top 33% of its field
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

4 citing papers in PubMed, 3 citations in OpenAlex.

  1. Article
  2. Review
  3. Review
  4. Review
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

15 authors at 3 institutions in 1 country.

Brittany RocqueDivision of Abdominal Organ Transplantation and Hepatobiliary Surgery, Department of Surgery, Keck School of Medicine, University of Southern California, 1510 San Pablo Street, Suite 412, Los Angeles, CA, 90033, USA.ORCID http://orcid.org/0000-0002-3664-4946
Kate GuionDivision of Abdominal Organ Transplantation and Hepatobiliary Surgery, Department of Surgery, Keck School of Medicine, University of Southern California, 1510 San Pablo Street, Suite 412, Los Angeles, CA, 90033, USA.ORCID http://orcid.org/0000-0002-3859-7573
Pranay SinghDivision of Abdominal Organ Transplantation and Hepatobiliary Surgery, Department of Surgery, Keck School of Medicine, University of Southern California, 1510 San Pablo Street, Suite 412, Los Angeles, CA, 90033, USA.
Sarah BangerthDivision of Abdominal Organ Transplantation and Hepatobiliary Surgery, Department of Surgery, Keck School of Medicine, University of Southern California, 1510 San Pablo Street, Suite 412, Los Angeles, CA, 90033, USA.ORCID http://orcid.org/0000-0002-7952-0679
Lauren PickardDivision of Abdominal Organ Transplantation and Hepatobiliary Surgery, Department of Surgery, Keck School of Medicine, University of Southern California, 1510 San Pablo Street, Suite 412, Los Angeles, CA, 90033, USA.
Jashdeep BhattacharjeeDivision of Gastroenterology, Hepatology and Nutrition, Children's Hospital Los Angeles, Los Angeles, CA, USA.
Sofia EguizabalDivision of Abdominal Organ Transplantation and Hepatobiliary Surgery, Department of Surgery, Keck School of Medicine, University of Southern California, 1510 San Pablo Street, Suite 412, Los Angeles, CA, 90033, USA.
Carly WeaverDivision of Abdominal Organ Transplantation, Children's Hospital Los Angeles, Los Angeles, CA, USA.
Shefali ChopraDepartment of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
Shengmei ZhouDepartment of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Keck School of Medicine, University of Southern California Los Angeles, Los Angeles, CA, USA.
Rohit KohliDivision of Gastroenterology, Hepatology and Nutrition, Children's Hospital Los Angeles, Los Angeles, CA, USA.ORCID http://orcid.org/0000-0002-0198-7703
Linda SherDivision of Abdominal Organ Transplantation and Hepatobiliary Surgery, Department of Surgery, Keck School of Medicine, University of Southern California, 1510 San Pablo Street, Suite 412, Los Angeles, CA, 90033, USA.
Omid AkbariDepartment of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.ORCID http://orcid.org/0000-0002-6853-9884
Burcin EkserDivision of Transplant Surgery, Department of Surgery, Indiana University School of Medicine, Indiana University, Indianapolis, IN, USA.ORCID http://orcid.org/0000-0003-0741-8007
Juliet A EmamaulleeDivision of Abdominal Organ Transplantation and Hepatobiliary Surgery, Department of Surgery, Keck School of Medicine, University of Southern California, 1510 San Pablo Street, Suite 412, Los Angeles, CA, 90033, USA. Juliet.emamaullee@med.usc.edu.ORCID http://orcid.org/0000-0003-4238-3057
University of Southern California · USChildren's Hospital of Los Angeles · USIndiana University School of Medicine

Funding

Study the link of autophagy dysfunction to allergic and neutrophilic asthma onsetR01HL151493 · NHLBI · UNIVERSITY OF SOUTHERN CALIFORNIA · PI AKBARI, OMID · 2020 to 2024
$3.6M
Role of TNF receptor 2 on Pulmonary Group 2 Innate Lymphoid CellsR01HL159804 · NHLBI · UNIVERSITY OF SOUTHERN CALIFORNIA · PI AKBARI, OMID · 2022 to 2025
$3.0M
Induction of cells and pathways that promote respiratory tolerance in allergic asthmaR01HL144790 · NHLBI · UNIVERSITY OF SOUTHERN CALIFORNIA · PI AKBARI, OMID · 2019 to 2022
$2.6M
Transcriptional and metabolomic regulation of IL-10 in pulmonary ILC2sR01AI169687 · NIAID · UNIVERSITY OF SOUTHERN CALIFORNIA · PI OMID AKBARI · 2022 to 2026
$2.1M
Immunologic Biomarkers of Rejection in Clinical Liver TransplantationK08CA245220 · NCI · UNIVERSITY OF SOUTHERN CALIFORNIA · PI EMAMAULLEE, JULIET · 2020 to 2024
$1.3M
NCI NIH HHS K08 CA245220NCI NIH HHS K08CA245220NHLBI NIH HHS R01 HL144790NHLBI NIH HHS R01 HL151493NHLBI NIH HHS R01 HL159804NIAID NIH HHS R01 AI169687
6 · The paper itself

Abstract

Single cell and spatially resolved 'omic' techniques have enabled deep characterization of clinical pathologies that remain poorly understood, providing unprecedented insights into molecular mechanisms of disease. However, transcriptomic platforms are costly, limiting sample size, which increases the possibility of pre-analytical variables such as tissue processing and storage procedures impacting RNA quality and downstream analyses. Furthermore, spatial transcriptomics have not yet reached single cell resolution, leading to the development of multiple deconvolution methods to predict individual cell types within each transcriptome 'spot' on tissue sections. In this study, we performed spatial transcriptomics and single nucleus RNA sequencing (snRNAseq) on matched specimens from patients with either histologically normal or advanced fibrosis to establish important aspects of tissue handling, data processing, and downstream analyses of biobanked liver samples. We observed that tissue preservation technique impacts transcriptomic data, especially in fibrotic liver. Single cell mapping of the spatial transcriptome using paired snRNAseq data generated a spatially resolved, single cell dataset with 24 unique liver cell phenotypes. We determined that cell-cell interactions predicted using ligand-receptor analysis of snRNAseq data poorly correlated with cellular relationships identified using spatial transcriptomics. Our study provides a framework for generating spatially resolved, single cell datasets to study gene expression and cell-cell interactions in biobanked clinical samples with advanced liver disease.

Indexed as

Digestive System DiseasesLiver DiseasesGene Expression ProfilingHumansLiver CirrhosisSingle-Cell AnalysisTranscriptomeBiliary atresiaCirrhosisLiver diseaseSingle-cell spatial mappingSpatial transcriptomics

Identifiers

PMID38351241
PMCPMC10864257
OpenAlexW4391780455

What OpenQuestion holds

Textmetadata
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.