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Human and mouse adrenal glands are characterized by species-specific steroidogenic states and tissue turnover.

Code ↔ Paper

8 matches between paragraphs of the paper and lines of its authors' code, computed by the harvester (lexical-v1). Click a colored paragraph or line to see its counterpart.

The 8 matches
  1. [1] § Methods › Cholesterol balance analysis in bulk scRNA-seq and Visium data ↔ notebooks/human_cortex_endothelium_blood.ipynb, lines 77–154 · score 0.91 · Cyp11a1, Cyp21a2, Cyb5a, Sult2a1, Cyp17a1, Cyp11b1
  2. [2] § Results › Comparison of adult and fetal human adrenal cortex ↔ Adrenal2/AdultMouseHuman/Figures/Figure_AdultMouseHumanSpatialExpression_R.ipynb, lines 545–549 · score 0.80 · CYB5A, SULT2A1, CYP17A1, CYP11B1, HSD3B2, CYP11B2
  3. [3] § Results › Comparison of human and mouse adult adrenal cortex ↔ Adrenal2/AdultMouseHuman/Figures/Figure_AdultMouseHumanSpatialExpression_R.ipynb, lines 545–549 · score 0.77 · LY6D, CYB5A, SULT2A1, CYP17A1, CYP11B1, Ptn
  4. [4] § Results › Comparison of human and mouse adult adrenal cortex ↔ Adrenal2/AdultMouseHuman/Figures/Figure_AdultMouseHumanSpatialExpression_R.ipynb, lines 574–575 · score 0.73 · Ly6d, Sult2a1, Cyp17a1, Cyp11b1, Ptn, VCAN
  5. [5] § Methods › Tissue-pattern identification in high-resolution spatial transcriptomics data ↔ notebooks/human_cortex_endothelium_blood.ipynb, lines 176–184 · score 0.70 · RunUMAP, FindClusters, FindNeighbors, resolution, human
  6. [6] § Results › Steroidogenic cell states within the human adrenal cortex ↔ notebooks/human_cortex_endothelium_blood.ipynb, lines 77–154 · score 0.70 · Cyb5a, Cyp17a1, Cyp11b1, Hsd3b2, Cyp11b2, STAR
  7. [7] § Methods › Tissue-pattern identification in high-resolution spatial transcriptomics data ↔ notebooks/adrenal_mouse.ipynb, lines 20–25 · score 0.57 · FindClusters, FindNeighbors, resolution
  8. [8] § Methods › Cycling cell identification in high-resolution spatial transcriptomics data ↔ notebooks/human_adrenal_medulla.ipynb, lines 317–318 · score 0.51 · cell cycle scores, G2M, CC, genes, adrenal, humans

Paper

Loaded from Europe PMC by your browser, not stored by OSCR: doi.org · Europe PMC

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The authors' code

Jupyter notebook · 460 lines · 6.5 MB · no license · 3 matches

The registry keeps no copy of this file: its repository has no license, so its authors keep all their rights to it. Your browser shows it from its source, with JavaScript.

It can be read at the source: notebooks/human_cortex_endothelium_blood.ipynb.

Overview

Authors: Maria E Kastriti1, Denis Maksimov2, Julia Krupinova3, Marina Utkina4, Dmitry Beltsevich4, Anna Roslyakova4, Olga Glazova2,3, Samira Kaziakhmedova4, Alina Ryabova4, Anna Kuznetsova4, Anastasia Shcherbakova4, Ekaterina Bondarenko4, Zoia Antysheva2, Eugene Albert2, Lilia Urusova4, Anastasia Lapshina4, Anastassia Chevais4, Ekaterina Avsievich3, Valentin Trofimov4, Galina Melnichenko4
and 10 other authorsNatalya Mokrysheva4, Ivan Dedov4, Lukas Englmaier5, Julian Petersen6, Oleg Gusev7,8,9, Andreas Heinzel10, Rainer Oberbauer10, Pavel Volchkov2,3,11,12, Peter V Kharchenko1,13, Igor Adameyko1,14
ORCID iDs: Maria E Kastriti, Denis Maksimov, Marina Utkina, Alina Ryabova, Anastasia Shcherbakova, Ekaterina Bondarenko, Anastassia Chevais, Ekaterina Avsievich, Lukas Englmaier, Julian Petersen, Oleg Gusev, Rainer Oberbauer, Pavel Volchkov, Peter V Kharchenko, Igor Adameyko
14 affiliations
  1. Medical University of Vienna, Center for Brain Research, Department of Neuroimmunology, Vienna, Austria
  2. Lomonosov Moscow State University, Moscow, Russia
  3. Moscow Clinical Scientific Center named after A.S. Loginov, Moscow, Russia
  4. Endocrinology Research Centre, Moscow, Russia
  5. CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
  6. Department of Orthodontics, University of Leipzig Medical Center, Leipzig, Germany
  7. Intractable Disease Research Center, Graduate School of Medicine, Juntendo University, Tokyo, Japan
  8. Life Improvement by Future Technologies (LIFT) Center, Moscow, Russia
  9. Federal Center of Brain Research and Neurotechnologies, Моscow, Russia
  10. Department of Nephrology, Internal Medicine III, Medical University of Vienna, Vienna, Austria
  11. National Medical Research Centre of Cardiology named after Academician E.I. Chazov, Moscow, Russia
  12. Almazov National Medical Research Centre, St Petersburg, Russia
  13. Department of Biomedical Informatics, Harvard Medical School, Boston, MA USA
  14. Department of Physiology and Pharmacology, Karolinska Institutet, Solna, Sweden
Institutions: Medical University of Vienna (Austria); Lomonosov Moscow State University (Russia); Moscow Clinical Scientific Center (Russia); Endocrinology Research Center (Russia); Austrian Academy of Sciences (Austria); CeMM Research Center for Molecular Medicine (Austria); University Hospital Leipzig (Germany); Leipzig University (Germany); Juntendo University (Japan); Federal Almazov North-West Medical Research Centre (Russia); National Medical Research Center of Cardiology (Russia); Harvard University (United States); Karolinska Institutet (Sweden)
Journal: Nature genetics, volume 58, issue 9, pages 2270-2283
Dates: received 9 February 2024; accepted 1 August 2026; published online 8 September 2026; in print 2026
Type: Research article · Language: English
License: CC BY
Identifiers: DOI 10.1038/s41588-026-02737-1 · PMID 42711427 · PMCID PMC13553300 · OpenAlex W7211966900
Open access: hybrid, a free copy (OpenAlex)
Status: code verified
Categories: genetics / omics (modality), human (organism), mouse (organism), cellular / molecular (subfield)
Methods: Connectivity, Statistics, Smoothing, state filtering, decompositions, Machine learning, Preprocessing, fMRI & imaging
Keywords: Transcriptomics, Stem cells
MeSH: Adrenal Glands*, Adrenal Cortex, Adult, Aldosterone, Animals, Cell Proliferation, Female, Humans, Hydrocortisone, Male, Mice, Species Specificity, Transcriptome, Wnt4 Protein, Zona Glomerulosa (* major topic)
Topic: Single-cell and spatial transcriptomics (Molecular Biology, Biochemistry, Genetics and Molecular Biology), according to OpenAlex
Funding: Vienna Science and Technology Fund (Wiener Wissenschafts-, Forschungs- und Technologiefonds) (WWTF Genomics based immunologic risk stratification, grant number 10.47379/LS20081)); Riksbankens Jubileumsfond (Stiftelsen Riksbankens Jubileumsfond) (none); Novo Nordisk Fonden (Novo Nordisk Foundation) (NNF17OC0026874)
Citations: cited by 1 paper (Europe PMC); 78 references in the paper

Abstract

The adult adrenal cortex undergoes constant renewal, yet underlying human-specific mechanisms remain poorly understood. Here we generated single-cell and spatial transcriptomic atlases of adult human and mouse adrenal glands, leveraging single-cell-resolution spatial data and a rare clonal mosaic case for lineage inference. In humans, we identified age-associated zona glomerulosa (ZG) cell states with direct cortisol synthesis capacity and sex-specific differences in inferred cholesterol balance. Cross-species comparison revealed conserved aldosterone-producing ZG but notable divergence in zona fasciculata markers, absence of zona reticularis homologs in mice and differential SHH–WNT4 signaling in proliferating cells. We uncovered human WT1− capsule-to-ZG transition and vascular smooth muscle cell-to-steroidogenic transitions supported by mosaic lineage evidence. We revealed dispersed proliferating cortical SF1+EZH2+ cells throughout the human cortex in contrast with ZG restriction in mice. Taken together, our data expand the centripetal renewal model and establish a comparative framework for human adrenocortical biology.

Reproduced under the paper's license (CC BY), from the paper cited above.

Repositories

Its files are read in the Code ↔ Paper reader above, with 8 matches between paragraphs and lines of code.

artem-artemov/adrenal

License: none: the authors keep all their rights
State: the link answers, verified on 26 September 2026
Evidence: files inventoried
Commit: b17096bfee5acce26c43c61d164f2743870a3852, 27 April 2021
Languages: Jupyter (8), R (3)
Size: 18 files, 11 scripts
Software Heritage: archived
Found in: “Data availability”
Holds: README, 8 notebooks
Not found: license file, CITATION.cff, environment file, tests, continuous integration, documentation
Tools: igraph (3 files), tidyverse (3 files), ggplot2 (2 files), Seurat (2 files), cowplot (1 file), Matplotlib (1 file), Monocle 3 (1 file), pandas (1 file), pheatmap (1 file), Scanpy (1 file), scVelo (1 file)
Availability: 1 check, the latest on 26 September 2026: the link answers
  • 26 September 2026: the link answers
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At the source: github.com/artem-artemov/adrenal

MaksimovDenis/adrenalglandscatlas

License: MIT
State: the link answers, verified on 26 September 2026
Evidence: files inventoried
Commit: 5eb548cf9eaa330819fe6441bebefdacbb2dfbf1, 9 July 2026
Languages: R (80), Jupyter (37)
Size: 183 files, 117 scripts
Software Heritage: not archived
Found in: “Code availability”
Holds: README, 117 notebooks
Not found: license file, CITATION.cff, environment file, tests, continuous integration, documentation
Tools: ComplexHeatmap (1 file), ggplot2 (1 file), patchwork (1 file), Seurat (1 file)
Availability: 1 check, the latest on 26 September 2026: the link answers
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At the source: gitlab.com/MaksimovDenis/adrenalglandscatlas

Zenodo 20258071

License: CC-BY-4.0
State: the link answers, verified on 26 September 2026
Evidence: files inventoried
Size: 1 file
Software Heritage: not checked
Found in: “Code availability”
Not found: README, license file, CITATION.cff, environment file, tests, continuous integration, documentation
Availability: 1 check, the latest on 26 September 2026: the link answers (HTTP 200)
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At the source:

Code availability

Source code is available via GitLab at https://gitlab.com/MaksimovDenis/adrenalglandscatlas and via Zenodo at https://doi.org/10.5281/zenodo.20258071(ref. 78).

Reproduced under the paper's license (CC BY), from the paper cited above.

Tracing map

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What the map holds:

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Data

Datasets cited

Data Availability Statement

Sequenced reads of mouse scRNA-seq and Visium HD samples, h5 files with gene counts in individual cells or spots and all data related to Visium, Visium HD or Stereo-Seq spatial transcriptomics (coordinate matrices, slide images and so on) were deposited under the Gene Expression Omnibus (GEO) accession no. GSE253852 (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE253852). Sequenced reads of human scRNA-seq, Visium and Stereo-seq spatial transcriptomics were deposited under European Genome–phenome Archive (EGA) controllable accession no. EGAC00001003383 (http://www.ebi.ac.uk/ena/data/view/EGAC00001003383). The EGA provides a managed access framework in which human data are archived under controlled conditions and released only to approved applicants through a Data Access Committee (DAC) review process. Researchers wishing to access the raw data may submit a data access request to the DAC via the EGA portal (https://ega-archive.org/datasets/EGAC00001003383), describing their intended use. Requests are evaluated only against the original ethical framework and, if approved according to the ethical criteria, access is granted subject to a Data Use Agreement that legally binds the recipient to the approved terms of use. Controlled access via the EGA is not intended to restrict scientific use, but to ensure that human raw sequencing data cannot be repurposed in ways that would violate donor privacy or applicable ethical regulations. The contact details for the DAC and expected response timelines are available on the EGA dataset page. We provide interactive access to the data via CellxGene74–76 (detailed list and links in Supplementary Information) and PDF versions of all Extended Data figures and Supplementary figures are available via figshare at https://adameykolab.hifo.meduniwien.ac.at/cellxgene_public/filecrawl/2026_NatGen_Kastriti_Maksimov (ref. 77). Human fetal scRNA-seq data were obtained from the following sources: Kameneva et al.22 processed Seurat object via the link from github: https://github.com/artem-artemov/adrenal (http://pklab.med.harvard.edu/artem/adrenal/data/Seurat/adrenal.human.seurat.scrublet.rds); Jansky et al.23 counted matrix and annotation from: https://adrenal.kitz-heidelberg.de/developmental_programs_NB_viz/; Kildisiute et al.24 processed Seurat object from: https://www.neuroblastomacellatlas.org/, Han et al.25 samples counted matrices from GEO accession no. GSE134355 (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE134355). Previously published mouse adult scRNA-seq sample count matrices were downloaded from GEO accession nos. GSE134355 (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE134355) and GSE161751 (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE161751) (refs. 25,31). Normal adrenal gland bulk RNA-seq data from the Genotype-Tissue Expression cohort15 were obtained via the recount3 v1.0.7R package65. Adrenocortical carcinoma bulk RNA-seq and metadata were downloaded from the TCGA portal: https://portal.gdc.cancer.gov/projects/TCGA-ACC.

Source code is available via GitLab at https://gitlab.com/MaksimovDenis/adrenalglandscatlas and via Zenodo at https://doi.org/10.5281/zenodo.20258071(ref. 78).

Reproduced under the paper's license (CC BY), from the paper cited above.

Versions

The history of this record: each version stored by the harvester or made by a correction of its authors or of the maintainers of its code, and what changed in its facts. The texts of the paper (its abstract, its availability statements) are not part of it; versions that changed only those are not listed.

Version 3, 28 September 2026

  • Publisher: — → Nature Portfolio

Version 1, 27 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 30 authors, 2 keywords, 15 MeSH terms, 3 funders, 75 references.

Cite

This paper

Kastriti, M. E., Maksimov, D., Krupinova, J., Utkina, M., Beltsevich, D., Roslyakova, A., Glazova, O., Kaziakhmedova, S., Ryabova, A., Kuznetsova, A., Shcherbakova, A., Bondarenko, E., Antysheva, Z., Albert, E., Urusova, L., Lapshina, A., Chevais, A., Avsievich, E., Trofimov, V., . . . Adameyko, I. (2026). Human and mouse adrenal glands are characterized by species-specific steroidogenic states and tissue turnover. Nature genetics, 58(9), 2270-2283. https://doi.org/10.1038/s41588-026-02737-1

BibTeX

@article{kastriti2026human,
author = {Kastriti, Maria E and Maksimov, Denis and Krupinova, Julia and Utkina, Marina and Beltsevich, Dmitry and Roslyakova, Anna and Glazova, Olga and Kaziakhmedova, Samira and Ryabova, Alina and Kuznetsova, Anna and Shcherbakova, Anastasia and Bondarenko, Ekaterina and Antysheva, Zoia and Albert, Eugene and Urusova, Lilia and Lapshina, Anastasia and Chevais, Anastassia and Avsievich, Ekaterina and Trofimov, Valentin and Melnichenko, Galina and Mokrysheva, Natalya and Dedov, Ivan and Englmaier, Lukas and Petersen, Julian and Gusev, Oleg and Heinzel, Andreas and Oberbauer, Rainer and Volchkov, Pavel and Kharchenko, Peter V and Adameyko, Igor},
title = {{Human and mouse adrenal glands are characterized by species-specific steroidogenic states and tissue turnover}},
journal = {Nature genetics},
year = {2026},
month = sep,
volume = {58},
number = {9},
pages = {2270--2283},
publisher = {Nature Portfolio},
issn = {1061-4036},
doi = {10.1038/s41588-026-02737-1},
url = {https://doi.org/10.1038/s41588-026-02737-1},
pmid = {42711427},
pmcid = {PMC13553300}
}

RIS

TY - JOUR
AU - Kastriti, Maria E
AU - Maksimov, Denis
AU - Krupinova, Julia
AU - Utkina, Marina
AU - Beltsevich, Dmitry
AU - Roslyakova, Anna
AU - Glazova, Olga
AU - Kaziakhmedova, Samira
AU - Ryabova, Alina
AU - Kuznetsova, Anna
AU - Shcherbakova, Anastasia
AU - Bondarenko, Ekaterina
AU - Antysheva, Zoia
AU - Albert, Eugene
AU - Urusova, Lilia
AU - Lapshina, Anastasia
AU - Chevais, Anastassia
AU - Avsievich, Ekaterina
AU - Trofimov, Valentin
AU - Melnichenko, Galina
AU - Mokrysheva, Natalya
AU - Dedov, Ivan
AU - Englmaier, Lukas
AU - Petersen, Julian
AU - Gusev, Oleg
AU - Heinzel, Andreas
AU - Oberbauer, Rainer
AU - Volchkov, Pavel
AU - Kharchenko, Peter V
AU - Adameyko, Igor
TI - Human and mouse adrenal glands are characterized by species-specific steroidogenic states and tissue turnover
T2 - Nature genetics
J2 - Nat Genet
PY - 2026
DA - 2026/09/08
VL - 58
IS - 9
SP - 2270
EP - 2283
SN - 1061-4036
PB - Nature Portfolio
DO - 10.1038/s41588-026-02737-1
UR - https://doi.org/10.1038/s41588-026-02737-1
LA - en
ER -

CSL-JSON

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