Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Homing pigeon navigation relies on superparamagnetic macrophages under overcast conditions.

Science (New York, N.Y.)·2026
Same author

Integrative omics and phase IIa clinical trial identify TNF as key node in autoimmune hepatitis.

Journal of hepatology·2026
Same author

Urinary CD4<sup>+</sup> T helper cells are a potential biomarker for tubulointerstitial nephritis in Sjögren's disease.

Scientific reports·2026
Same author

SCALE: unsupervised multiscale domain identification in spatial omics data.

Nucleic acids research·2026
Same author

Subcellular glycan-mannose receptor binding kinetics correlate with myeloid cell function.

Nature communications·2025
Same author

High-salt diet induces immune-independent re-differentiation, metabolic shut down and cell cycle arrest of melanoma.

Cell death & disease·2025
Same journal

Learning Moisture-Induced Damage From Vision: Diffusion Models for Real-Time Monitoring of Additive Manufacturing Processes.

Advanced science (Weinheim, Baden-Wurttemberg, Germany)·2026
Same journal

Intrinsic Dual-Phase Regulated GeSe<sub>2</sub> Nanoparticles Triggered by Ball-Milling Treatment for Photonic Multi-Valued Logic Circuits.

Advanced science (Weinheim, Baden-Wurttemberg, Germany)·2026
Same journal

A Plant Photoregulator-Inspired S-Type Heterojunction System for Diabetic Keratopathy via Tri-Modal Light-Driven Immunometabolic Reprogramming, Tissue Repair, and Antibacterial Activity.

Advanced science (Weinheim, Baden-Wurttemberg, Germany)·2026
Same journal

eEF1G Orchestrates Translation to Ensure Meiotic Progression in Transcriptionally Quiescent Spermatocytes.

Advanced science (Weinheim, Baden-Wurttemberg, Germany)·2026
Same journal

Ultrasound-Recharged Sub-Nanometer Palladium Catalysts for on-Demand and Self-Terminating Bioorthogonal Prodrug Activation in Cancer Therapy.

Advanced science (Weinheim, Baden-Wurttemberg, Germany)·2026
Same journal

Graphene Aerogels With Spherical Pore Structure for Broad Frequency Regulation and Enhanced Low-Frequency Response.

Advanced science (Weinheim, Baden-Wurttemberg, Germany)·2026
See all related articles

Related Experiment Video

Updated: Mar 2, 2026

Isolation of Region-specific Microglia from One Adult Mouse Brain Hemisphere for Deep Single-cell RNA Sequencing
09:49

Isolation of Region-specific Microglia from One Adult Mouse Brain Hemisphere for Deep Single-cell RNA Sequencing

Published on: December 3, 2019

11.7K

Predicting Macrophage Spatial Localization from Single-Cell Transcriptomes to Uncover Disease Mechanisms.

Junping Yin1, Qi Mei2,3, Hans-Joachim Paust4

  • 1Institute of Molecular Medicine and Experimental Immunology (IMMEI), University Hospital Bonn, 53127, Bonn, Germany.

Advanced Science (Weinheim, Baden-Wurttemberg, Germany)
|February 28, 2026
PubMed
Summary
This summary is machine-generated.

MERLIN, a new algorithm, reconstructs lost cell positions from single-cell RNA sequencing data in organs like the kidney. It accurately predicts macrophage locations, aiding disease mechanism discovery.

Keywords:
inflammationkidney diseasemacrophagesmicrogliaspatial immunology

More Related Videos

Droplet Barcoding-Based Single Cell Transcriptomics of Adult Mammalian Tissues
10:12

Droplet Barcoding-Based Single Cell Transcriptomics of Adult Mammalian Tissues

Published on: January 10, 2019

19.2K
Comprehensive Spatial Profiling of Species-agnostic Transcriptomes via Stereo-seq
10:22

Comprehensive Spatial Profiling of Species-agnostic Transcriptomes via Stereo-seq

Published on: October 31, 2025

655

Related Experiment Videos

Last Updated: Mar 2, 2026

Isolation of Region-specific Microglia from One Adult Mouse Brain Hemisphere for Deep Single-cell RNA Sequencing
09:49

Isolation of Region-specific Microglia from One Adult Mouse Brain Hemisphere for Deep Single-cell RNA Sequencing

Published on: December 3, 2019

11.7K
Droplet Barcoding-Based Single Cell Transcriptomics of Adult Mammalian Tissues
10:12

Droplet Barcoding-Based Single Cell Transcriptomics of Adult Mammalian Tissues

Published on: January 10, 2019

19.2K
Comprehensive Spatial Profiling of Species-agnostic Transcriptomes via Stereo-seq
10:22

Comprehensive Spatial Profiling of Species-agnostic Transcriptomes via Stereo-seq

Published on: October 31, 2025

655

Area of Science:

  • Genomics
  • Computational Biology
  • Immunology

Background:

  • Single-cell RNA sequencing (scRNA-seq) loses crucial spatial information when cells are isolated.
  • Organs with compartmentalized anatomy, like the kidney, present unique challenges for spatial reconstruction.
  • Understanding cell location is vital for interpreting cellular function and disease pathology.

Purpose of the Study:

  • To develop and validate an algorithm (MERLIN) for reconstructing positional information from scRNA-seq data in compartmentalized organs.
  • To investigate the predictability of immune cell localization within the kidney.
  • To explore the functional and disease-specific transcriptomic signatures associated with cell position.

Main Methods:

  • Generation of independent immune cell scRNA-seq datasets from distinct renal compartments.
  • Training and evaluation of machine learning algorithms, including a modified multi-layer Perceptron.
  • Application of MERLIN to predict cell positions in healthy and disease models (crescentic glomerulonephritis, acute kidney injury, diabetic nephropathy).
  • Analysis of positional transcriptomic fingerprints and enrichment pathways.

Main Results:

  • MERLIN achieved over 75% accuracy in predicting the positions of resident macrophages in murine and human kidneys.
  • Motile immune cells, such as lymphocytes, were not accurately predictable by position.
  • Positional transcriptomic data revealed enrichment in microenvironmental response and adaptation pathways, with a notable sex bias.
  • MERLIN successfully predicted macrophage localization in kidney disease models and aligned with known pathology and therapeutic efficacy in specific compartments.
  • The algorithm was also trained to predict spatial distribution of brain microglia.

Conclusions:

  • MERLIN enables the spatial interpretation of scRNA-seq data in anatomically defined organs.
  • The algorithm enhances mechanistic insights into disease processes by linking cell location to function and response.
  • MERLIN provides a powerful tool for spatial transcriptomics in complex tissues.