Evidence map›Paper›PMID 37260295›Full record

ArticleDisease models & mechanisms2023

deCLUTTER2+ - a pipeline to analyze calcium traces in a stem cell model for ventral midbrain patterned astrocytes.

Martyna M Grochowska, Federico Ferraro, Ana Carreras Mascaro, Domenico Natale, Amber Winkelaar, Valerie Boumeester, Guido J Breedveld, Vincenzo Bonifati, Wim Mandemakers

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

Article in Disease models & mechanisms, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
0.2field-weighted citation impact, top 46% 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

1 citing paper in PubMed, 1 citations in OpenAlex.

  1. Review
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

9 authors at 1 institution in 1 country.

Martyna M GrochowskaErasmus MC, University Medical Center Rotterdam, Department of Clinical Genetics, P.O. Box 2040, 3000 CA Rotterdam, Netherlands.ORCID 0000-0002-1234-4105
Federico FerraroErasmus MC, University Medical Center Rotterdam, Department of Clinical Genetics, P.O. Box 2040, 3000 CA Rotterdam, Netherlands.ORCID 0000-0003-1365-2529
Ana Carreras MascaroErasmus MC, University Medical Center Rotterdam, Department of Clinical Genetics, P.O. Box 2040, 3000 CA Rotterdam, Netherlands.ORCID 0000-0002-8962-755X
Domenico NataleErasmus MC, University Medical Center Rotterdam, Department of Clinical Genetics, P.O. Box 2040, 3000 CA Rotterdam, Netherlands.ORCID 0000-0002-2830-3412
Amber WinkelaarErasmus MC, University Medical Center Rotterdam, Department of Clinical Genetics, P.O. Box 2040, 3000 CA Rotterdam, Netherlands.
Valerie BoumeesterErasmus MC, University Medical Center Rotterdam, Department of Clinical Genetics, P.O. Box 2040, 3000 CA Rotterdam, Netherlands.
Guido J BreedveldErasmus MC, University Medical Center Rotterdam, Department of Clinical Genetics, P.O. Box 2040, 3000 CA Rotterdam, Netherlands.ORCID 0000-0002-4392-5906
Vincenzo BonifatiErasmus MC, University Medical Center Rotterdam, Department of Clinical Genetics, P.O. Box 2040, 3000 CA Rotterdam, Netherlands.ORCID 0000-0002-9334-1263
Wim MandemakersErasmus MC, University Medical Center Rotterdam, Department of Clinical Genetics, P.O. Box 2040, 3000 CA Rotterdam, Netherlands.ORCID 0000-0003-2673-5972
Erasmus MC · NL

Funding

Erasmus MCStichting ParkinsonFonds 110875
6 · The paper itself

Abstract

Astrocytes are the most populous cell type of the human central nervous system and are essential for physiological brain function. Increasing evidence suggests multiple roles for astrocytes in Parkinson's disease, nudging a shift in the research focus, which historically pivoted around ventral midbrain dopaminergic neurons (vmDANs). Studying human astrocytes and other cell types in vivo remains challenging. However, in vitro-reprogrammed human stem cell-based models provide a promising alternative. Here, we describe a novel protocol for astrocyte differentiation from human stem cell-derived vmDAN-generating progenitors. This protocol simulates the regionalization, gliogenic switch, radial migration and final differentiation that occur in the developing human brain. We characterized the morphological, molecular and functional features of these ventral midbrain patterned astrocytes with a broad palette of techniques and identified novel candidate midbrain-astrocyte specific markers. In addition, we developed a new pipeline for calcium imaging data analysis called deCLUTTER2+ (deconvolution of Ca2+ fluorescent patterns) that can be used to discover spontaneous or cue-dependent patterns of Ca2+ transients. Altogether, our protocol enables the characterization of the functional properties of human ventral midbrain patterned astrocytes under physiological conditions and in disease.

Indexed as

Parkinson DiseasePluripotent Stem CellsAstrocytesCalciumCalcium, DietaryCell DifferentiationHumansMesencephalonCalciumCalcium, DietaryCalcium imaging data analysisDisease modelingHuman astrocytesHuman stem cell-based modelsInduced pluripotent stem cellsParkinson's diseaseVentral midbrain

Identifiers

PMID37260295
PMCPMC10309582
OpenAlexW4378952426

What Socratic holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

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 Socratic graph.