Nature Search

FXR inhibition may protect from SARS-CoV-2 infection by reducing ACE2

FXR regulates the levels of ACE2 in tissues of the respiratory and gastrointestinal systems that are affected by COVID-19, and inhibiting FXR with ursodeoxycholic acid downregulates ACE2 and reduces susceptibility to SARS-CoV-2 infection.

Teresa Brevini
Mailis Maes
Fotios Sampaziotis
ResearchOpen Access05 Dec 2022
Nature

Volume: 615, P: 134-142
Single-cell atlas of human liver development reveals pathways directing hepatic cell fates

Wesley et al. describe the developmental trajectories of human foetal liver cell types at single-cell resolution and generate bipotential hepatoblast organoids, which can serve as a new platform to investigate human liver development.

Brandon T. Wesley
Alexander D. B. Ross
Ludovic Vallier
Research15 Sept 2022
Nature Cell Biology

Volume: 24, P: 1487-1498
The SMAD2/3 interactome reveals that TGFβ controls m⁶A mRNA methylation in pluripotency

The SMAD2 and SMAD3 protein interactome links TGFβ signalling to diverse effectors including m⁶A methyltransferase, which has a role in regulating differentiation of human pluripotent stem cells.

Alessandro Bertero
Stephanie Brown
Ludovic Vallier
Research28 Feb 2018
Nature

Volume: 555, P: 256-259
Acquisition of epithelial plasticity in human chronic liver disease

Single-cell RNA sequencing and 3D imaging have revealed the cellular changes and structural reorganization that occur during the progression of human chronic liver disease and as the liver attempts to regenerate.

Christopher Gribben
Vasileios Galanakis
Ludovic Vallier
ResearchOpen Access22 May 2024
Nature

Volume: 630, P: 166-173
Single-cell RNA-sequencing of differentiating iPS cells reveals dynamic genetic effects on gene expression

Studying the genetic effects on early stages of human development is challenging due to a scarcity of biological material. Here, the authors utilise induced pluripotent stem cells from 125 donors to track gene expression changes and expression quantitative trait loci at single cell resolution during in vitro endoderm differentiation.

Anna S. E. Cuomo
Daniel D. Seaton
Oliver Stegle
ResearchOpen Access10 Feb 2020
Nature Communications

Volume: 11, P: 1-14
Erratum: Genome editing reveals a role for OCT4 in human embryogenesis

Norah M. E. Fogarty
Afshan McCarthy
Kathy K. Niakan
Amendments and Corrections04 Oct 2017
Nature

Volume: 551, P: 256
Correction: Corrigendum: Common genetic variation drives molecular heterogeneity in human iPSCs

Helena Kilpinen
Angela Goncalves
Daniel J. Gaffney
Amendments and Corrections14 Jun 2017
Nature

Volume: 546, P: 686
Author Correction: A single-cell comparison of adult and fetal human epicardium defines the age-associated changes in epicardial activity

Vincent R. Knight-Schrijver
Hongorzul Davaapil
Sanjay Sinha
Amendments and CorrectionsOpen Access11 Apr 2023
Nature Cardiovascular Research

Volume: 2, P: 486
Reconstruction of the mouse extrahepatic biliary tree using primary human extrahepatic cholangiocyte organoids

Repair of defects in the common bile duct is hampered by a lack of healthy donor tissue. Developing human extrahepatic cholangiocyte organoids and testing them in mouse models may provide a way to overcome this limitation.

Fotios Sampaziotis
Alexander W Justin
Ludovic Vallier
Research03 Jul 2017
Nature Medicine

Volume: 23, P: 954-963
Publisher Correction: GDF15 mediates the effects of metformin on body weight and energy balance

Anthony P. Coll
Michael Chen
Stephen O’Rahilly
Amendments and Corrections13 Feb 2020
Nature

Volume: 578, P: E24
Cell therapy for liver disorders: past, present and future

The burden of liver disorders increases worldwide as does the necessity for new treatments. This Review discusses cell therapy as an alternative therapeutic strategy for liver transplantation, the pros and cons, and the future technological potential.

M. Carmen Ortuño-Costela
Massimo Pinzani
Ludovic Vallier
Reviews18 Mar 2025
Nature Reviews Gastroenterology & Hepatology

Volume: 22, P: 329-342
Putting induced pluripotent stem cells to the test

Human induced pluripotent stem cells are found to be nearly identical to embryonic stem cells, supporting their suitability for clinical applications.

Ludovic Vallier
News & Views06 Nov 2015
Nature Biotechnology

Volume: 33, P: 1145-1146
Cholangiocytes derived from human induced pluripotent stem cells for disease modeling and drug validation

A protocol for generating biliary epithelial cells from human pluripotent stem cells facilitates disease modeling and drug screening.

Fotios Sampaziotis
Miguel Cardoso de Brito
Ludovic Vallier
Research13 Jul 2015
Nature Biotechnology

Volume: 33, P: 845-852
Non-CG DNA methylation is a biomarker for assessing endodermal differentiation capacity in pluripotent stem cells

The methylation of non-CpG residues is a poorly understood marker of pluripotent cells, gradually lost as cells differentiate. Here the authors show non-CG methylation can be used as a marker of differentiation potential.

Lee M. Butcher
Mitsuteru Ito
Stephan Beck
ResearchOpen Access29 Jan 2016
Nature Communications

Volume: 7, P: 1-8
Derivation of pluripotent epiblast stem cells from mammalian embryos

A study revealing that pluripotent stem cells (EpiSCs) can be derived from the late epiblast layer of post-implantation mouse and rat embryos. To achieve this, a chemically defined, activin-containing culture medium known to be sufficient for long-term maintenance of human embryonic stem cells is used. These findings will help to understand the biological provenance of human embryonic stem cells.

I. Gabrielle M. Brons
Lucy E. Smithers
Ludovic Vallier
Research27 Jun 2007
Nature

Volume: 448, P: 191-195
SARS-CoV-2 entry factors are highly expressed in nasal epithelial cells together with innate immune genes

An analysis of single-cell transcriptomics datasets from different tissues shows that ACE2 and TMPRSS2 are co-expressed in respiratory, corneal and intestinal epithelial cell populations, and that respiratory expression of ACE2 is associated with genes involved in innate immunity.

Waradon Sungnak
Ni Huang
Francisco Figueiredo
Research23 Apr 2020
Nature Medicine

Volume: 26, P: 681-687
Single-cell transcriptomic characterization of a gastrulating human embryo

The single-cell transcriptional profile of a human embryo between 16 and 19 days after fertilization reveals parallels and differences in gastrulation in humans as compared with mouse and non-human primate models.

Richard C. V. Tyser
Elmir Mahammadov
Shankar Srinivas
Research17 Nov 2021
Nature

Volume: 600, P: 285-289
Publisher Correction: Single-cell RNA-sequencing of differentiating iPS cells reveals dynamic genetic effects on gene expression

Anna S. E. Cuomo
Daniel D. Seaton
Oliver Stegle
Amendments and CorrectionsOpen Access23 Mar 2020
Nature Communications

Volume: 11, P: 1
GDF15 mediates the effects of metformin on body weight and energy balance

In mouse studies, metformin treatment results in increased secretion of growth/differentiation factor 15 (GDF15), which prevents weight gain in response to high-fat diet, and GDF15-independent lowering of circulating blood glucose.

Anthony P. Coll
Michael Chen
Stephen O’Rahilly
Research25 Dec 2019
Nature

Volume: 578, P: 444-448
Platelet function is modified by common sequence variation in megakaryocyte super enhancers

Numerous genetic variants, including those located in the non-coding regions of the genome, are known to be associated with blood cells traits. Here, Frontini and colleagues investigate their potential regulatory functions using epigenomic data and promoter long-range interactions.

Romina Petersen
John J. Lambourne
Mattia Frontini
ResearchOpen Access13 Jul 2017
Nature Communications

Volume: 8, P: 1-12
Targeted gene correction of α₁-antitrypsin deficiency in induced pluripotent stem cells

Kosuke Yusa
S. Tamir Rashid
Ludovic Vallier
Research12 Oct 2011
Nature

Volume: 478, P: 391-394
Genome editing reveals a role for OCT4 in human embryogenesis

Genome editing in human zygotes shows that OCT4 is required for normal development at an earlier stage in humans than in mice.

Norah M. E. Fogarty
Afshan McCarthy
Kathy K. Niakan
Research20 Sept 2017
Nature

Volume: 550, P: 67-73
Common genetic variation drives molecular heterogeneity in human iPSCs

Genetic and phenotypic analysis reveals expression quantitative trait loci in human induced pluripotent stem cell lines associated with cancer and disease.

Helena Kilpinen
Angela Goncalves
Daniel J. Gaffney
Research10 May 2017
Nature

Volume: 546, P: 370-375
Human iPSC-derived motoneurons harbouring TARDBP or C9ORF72 ALS mutations are dysfunctional despite maintaining viability

Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease that affects spinal cord motor neurons. Here the authors use induced pluripotent stem cell-derived motor neurons obtained from patients with ALS-linked mutations, and find functional deficits resulting from a progressive decrease in voltage-activated Na⁺ and K⁺currents that occur in the absence of cell death.

Anna-Claire Devlin
Karen Burr
Gareth B. Miles
ResearchOpen Access12 Jan 2015
Nature Communications

Volume: 6, P: 1-12
TEAD and YAP regulate the enhancer network of human embryonic pancreatic progenitors

By deciphering the transcriptional network of human embryonic pancreatic progenitors, Ferrer and colleagues identify the Hippo-responsive transcription factor TEAD1 as a regulator of the pancreatic progenitor enhancer programme.

Inês Cebola
Santiago A. Rodríguez-Seguí
Jorge Ferrer
Research27 Apr 2015
Nature Cell Biology

Volume: 17, P: 615-626
Isolation and propagation of primary human cholangiocyte organoids for the generation of bioengineered biliary tissue

Bioengineered biliary tissue suitable for biliary reconstruction is obtained from cholangiocyte organoids derived from human primary extra- or intrahepatic duct cholangiocytes.

Olivia C. Tysoe
Alexander W. Justin
Fotios Sampaziotis
Protocols20 May 2019
Nature Protocols

Volume: 14, P: 1884-1925
A single-cell comparison of adult and fetal human epicardium defines the age-associated changes in epicardial activity

Knight-Schrijver et al. use single-cell and single-nuclei RNA sequencing to profile the human fetal and adult epicardium in homeostatic conditions. The analysis shows fetal-specific epicardial gene programs that could support heart regeneration.

Vincent R. Knight-Schrijver
Hongorzul Davaapil
Sanjay Sinha
ResearchOpen Access21 Dec 2022
Nature Cardiovascular Research

Volume: 1, P: 1215-1229
Directed differentiation of human induced pluripotent stem cells into functional cholangiocyte-like cells

This protocol describes how to recapitulate biliary development by differentiation of hPSCs into endoderm, foregut progenitor cells, hepatoblasts, cholangiocyte progenitors and mature 3D cholangiocyte-like cell organoids.

Fotios Sampaziotis
Miguel Cardoso de Brito
Ludovic Vallier
Protocols23 Mar 2017
Nature Protocols

Volume: 12, P: 814-827
Recessive mutations in a distal PTF1A enhancer cause isolated pancreatic agenesis

Andrew Hattersley, Jorge Ferrer and colleagues use epigenomic annotation of pancreatic progenitor cells to guide the interpretation of whole-genome sequences from individuals with isolated pancreatic agenesis. They show that recessive mutations in a distal developmental enhancer of PTF1A cause pancreatic agenesis and abolish enhancer activity.

Michael N Weedon
Inês Cebola
Andrew T Hattersley
Research10 Nov 2013
Nature Genetics

Volume: 46, P: 61-64
Cardelino: computational integration of somatic clonal substructure and single-cell transcriptomes

Cardelino leverages variant information from single-cell RNA-seq data for inferring clonal tree configuration and mapping cells to their clone of origin.

Davis J. McCarthy
Raghd Rostom
Sarah A. Teichmann
Research16 Mar 2020
Nature Methods

Volume: 17, P: 414-421
Defining murine organogenesis at single-cell resolution reveals a role for the leukotriene pathway in regulating blood progenitor formation

Ibarra-Soria et al. study cellular diversity, transcriptional signatures, lineage specification and somitogenesis on a single-cell level in E8.25 mouse embryos, and reveal the regulation of blood progenitor formation by the leukotriene pathway.

Ximena Ibarra-Soria
Wajid Jawaid
John C. Marioni
Research08 Jan 2018
Nature Cell Biology

Volume: 20, P: 127-134
Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics

An integrated analysis of over 100 single-cell and single-nucleus transcriptomics studies illustrates severe acute respiratory syndrome coronavirus 2 viral entry gene coexpression patterns across different human tissues, and shows association of age, smoking status and sex with viral entry gene expression in respiratory cell populations.

Christoph Muus
Malte D. Luecken
Xiaohui Zhang
Research02 Mar 2021
Nature Medicine

Volume: 27, P: 546-559
Production of hepatocyte-like cells from human pluripotent stem cells

Nicholas R F Hannan
Charis-Patricia Segeritz
Ludovic Vallier
Protocols31 Jan 2013
Nature Protocols

Volume: 8, P: 430-437
A proteomic time course through the differentiation of human induced pluripotent stem cells into hepatocyte-like cells

Tracey Hurrell
Charis-Patricia Segeritz
Allan D. Cromarty
ResearchOpen Access01 Mar 2019
Scientific Reports

Volume: 9, P: 1-11

Search

FXR inhibition may protect from SARS-CoV-2 infection by reducing ACE2

Single-cell atlas of human liver development reveals pathways directing hepatic cell fates

The SMAD2/3 interactome reveals that TGFβ controls m⁶A mRNA methylation in pluripotency

Acquisition of epithelial plasticity in human chronic liver disease

Single-cell RNA-sequencing of differentiating iPS cells reveals dynamic genetic effects on gene expression

Erratum: Genome editing reveals a role for OCT4 in human embryogenesis

Correction: Corrigendum: Common genetic variation drives molecular heterogeneity in human iPSCs

Author Correction: A single-cell comparison of adult and fetal human epicardium defines the age-associated changes in epicardial activity

Reconstruction of the mouse extrahepatic biliary tree using primary human extrahepatic cholangiocyte organoids

Publisher Correction: GDF15 mediates the effects of metformin on body weight and energy balance

Cell therapy for liver disorders: past, present and future

Putting induced pluripotent stem cells to the test

Cholangiocytes derived from human induced pluripotent stem cells for disease modeling and drug validation

Non-CG DNA methylation is a biomarker for assessing endodermal differentiation capacity in pluripotent stem cells

Derivation of pluripotent epiblast stem cells from mammalian embryos

SARS-CoV-2 entry factors are highly expressed in nasal epithelial cells together with innate immune genes

Single-cell transcriptomic characterization of a gastrulating human embryo

Publisher Correction: Single-cell RNA-sequencing of differentiating iPS cells reveals dynamic genetic effects on gene expression

GDF15 mediates the effects of metformin on body weight and energy balance

Platelet function is modified by common sequence variation in megakaryocyte super enhancers

Targeted gene correction of α₁-antitrypsin deficiency in induced pluripotent stem cells

Genome editing reveals a role for OCT4 in human embryogenesis

Common genetic variation drives molecular heterogeneity in human iPSCs

Human iPSC-derived motoneurons harbouring TARDBP or C9ORF72 ALS mutations are dysfunctional despite maintaining viability

TEAD and YAP regulate the enhancer network of human embryonic pancreatic progenitors

Isolation and propagation of primary human cholangiocyte organoids for the generation of bioengineered biliary tissue

A single-cell comparison of adult and fetal human epicardium defines the age-associated changes in epicardial activity

Directed differentiation of human induced pluripotent stem cells into functional cholangiocyte-like cells

Recessive mutations in a distal PTF1A enhancer cause isolated pancreatic agenesis

Cardelino: computational integration of somatic clonal substructure and single-cell transcriptomes

Defining murine organogenesis at single-cell resolution reveals a role for the leukotriene pathway in regulating blood progenitor formation

Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics

Production of hepatocyte-like cells from human pluripotent stem cells

A proteomic time course through the differentiation of human induced pluripotent stem cells into hepatocyte-like cells

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