Ernest Arenas Lab


Karolinska Institutet

Department of Medical Biochemistry and Biophysics

Division of Molecular Neurobiology


Lab News:


  • Two articles in the same issue of Science provide two new single cell atlases describing the development of the human midbrain and the subtypes of midbrain dopaminergic neurons in the adult human brain, respectively. These results are part of a true collaborative effort between Sten Linnarsson and Ernest Arenas groups, and part of a broader analysis of the human brain and of a large collection of articles published in Science and Science Advances simultaneously.
  • The Human brain cell census

    Sten Linnarsson & Ernest Arenas

  • Comprehensive cell atlas of the first-trimester developing human brain

    Emelie Braun, Miri Danan-Gotthold, Lars E. Borm, Elin Vinsland, Ka Wai Lee, Peter Lonnerberg, Lijuan Hu, Xiaofei Li, Xiaoling He, Zaneta Andrusivova, Joakim Lundeberg, Roger A. Barker, Ernest Arenas, Erik Sundstrom, Sten Linnarsson*

    Published in Science
    October 13, 2023. DOI: 10.1126/science.adf1226

  • Transcriptomic diversity of cell types across the adult human brain

    Kimberly Siletti, Rebecca Hodge#, Alejandro Mossi Albiach#, Ka Wai Lee, Song-Lin Ding, Lijuan Hu, Peter Lönnerberg, Trygve Bakken, Tamara Casper, Michael Clark, Nick Dee, Jessica Gloe, Daniel Hirschstein, Nadiya V Shapovalova, C. Dirk Keene, Julie Nyhus, Herman Tung, Anna Marie Yanny, Ernest Arenas, Ed S Lein, Sten Linnarsson*

    Published in Science
    October 13, 2023. DOI: 10.1126/science.add7046





  • Review article on midbrain dopaminergic Neuron Development at the Single Cell Level in Frontiers in Cell and Developmental Biology

  • Collaborative article with the group of Jens Hjerling-Leffler on genetic identification of cell types underlying brain complex traits of Parkinson's disease in Nature Genetics

  • Original article in Cell Reports on the role of Srebf1 in controlling midbrain dopaminergic neurogenesis
  • Srebf1 Controls Midbrain Dopaminergic Neurogenesis

    Toledo EM et al.

    Liver X receptors (LXRs) and their ligands are potent regulators of midbrain dopaminergic (mDA) neurogenesis and differentiation. However, the molecular mechanisms by which LXRs control these functions remain to be elucidated. Here, we perform a combined transcriptome and chromatin immunoprecipitation sequencing (ChIP-seq) analysis of midbrain cells after LXR activation, followed by bioinformatic analysis to elucidate the transcriptional networks controlling mDA neurogenesis. Our results identify the basic helix-loop-helix transcription factor sterol regulatory element binding protein 1 (SREBP1) as part of a cluster of proneural transcription factors in radial glia and as a regulator of transcription factors controlling mDA neurogenesis, such as Foxa2. Moreover, loss- and gain-of-function experiments in vitro and in vivo demonstrate that Srebf1 is both required and sufficient for mDA neurogenesis. Our data, thus, identify Srebf1 as a central player in mDA neurogenesis.


  • Summary of the project: By mapping the dopaminergic cells, which are attacked and lost in the brain of patient with Parkinson's disease, at a molecular level using single-cell RNA sequencing, amongst other tools, our research group hopes to have sufficient information to create new ones, either by using stem cells that are then transplanted into the patient, or by reprogramming existing brain cells in vivo. The project can lead to more exact methods involving designing the right cell types for therapeutic intervention from the start.

    More information

    KI press release


  • New Postdoctoral Researcher Positions Available.
  • The Arenas lab is looking for Postdoctoral researchers in the following areas:

  • OPEN NOW. Deadline March 25th.
    Single nuclei RNA-sequencing of Parkinson’s disease and cell replacement therapy

  • All applications are to be submitted via the Karolinska Institute web recruitment system.

    Apply here:

    Requirements: We are looking for candidates with experience in single-cell/nuclei technologies (such as 10X genomics, ATAC-seq or in situ transcriptomics), single cell data analysis, computational biology tools (Linux, R, Python), imaging (in situ hybridization and confocal microscopy), molecular biology, FACS and previous work in the area of neuroscience. Experience in working with human pluripotent stem cells, gene editing, cellular reprogramming, genetics and epigenetics and/or previous work on midbrain development and/or neurodegenerative diseases, such as PD, will be considered as additional merits.

    Project: Work in this project will involve the use of diverse single cell technologies and bioinformatics tools in order to profile and define PD and cell replacement strategies for PD at the single cell level. Our overall goal is to understand disease mechanisms and develop better cell replacement therapies for PD.

    Documents to be submitted (English or Swedish):

    • A complete curriculum vitae, including date of the thesis defense, title of the thesis, previous academic positions, academic title, current position, academic distinctions, and committee work
    • A complete list of publications
    • A summary of current work (no more than one page)
    • A personal letter with motivation
    • The name, e-mail and phone of two recent group leaders to provide reference letters


    1. Position in “Reprogramming astrocytes into disease resistant dopaminergic neurons

    2. Position in “Computational biology/Bioinformatics analysis of single cell data in Parkinson’s disease and regenerative medicine

    For more information, please contact


  • NEWS: A New Horizon 2020 project of the EU, Novel Strategies for Cell-based Neural Reconstruction (NSC-Reconstruct), has been granted to Ernest Arenas as a partner.
  • Summary of the project: Neurodegenerative diseases and brain injuries affect large patient groups and carry large unmet clinical needs. NSC-Reconstruct will respond to these needs by developing innovative therapies based on cell replacement, cell reprogramming and circuit reconstruction that have the potential to transform how we treat a wide range of neurological diseases and disorders. In this area of clinical science European research has generated groundbreaking knowledge that has resulted in a pioneering human embryonic stem cell-derived product that is now entering clinical trials for Parkinson’s Disease (PD). In NSC-Reconstruct we will move beyond the replacement of a single neuronal type towards future cell therapies with enhanced authenticity, functions and compositions. NSC-Reconstruct will address PD as an example of disorder for which single neuron replacement has been developed. Our focus in PD will be on incorporating improved cell types and on local network reconstruction. We will also work on repairing long distance networks such as those affected in Huntington’s disease and finally in restoring the complex networks and projections of the cerebral cortex to achieve effective repair in conditions known to affect this structure, such as trauma or stroke.

    More information: Horizon 2020

    KI press release


  • Collaborative article with the group of Charles ffrench-Constant on how Laminin α2 controls stem cell behaviour during midbrain dopaminergic neuron development in Development

  • Original article in Nature Communications on the transportation of Wnt5a in the cerebrospinal fluid via lipoporotein particles
  • WNT5A is transported via lipoprotein particles in the cerebrospinal fluid to regulate hindbrain morphogenesis

    Kaiser K et al.

    WNTs are lipid-modified proteins that control multiple functions in development and disease via short- and long-range signaling. However, it is unclear how these hydrophobic molecules spread over long distances in the mammalian brain. Here we show that WNT5A is produced by the choroid plexus (ChP) of the developing hindbrain, but not the telencephalon, in both mouse and human. Since the ChP produces and secretes the cerebrospinal fluid (CSF), we examine the presence of WNT5A in the CSF and find that it is associated with lipoprotein particles rather than exosomes. Moreover, since the CSF flows along the apical surface of hindbrain progenitors not expressing Wnt5a, we examined whether deletion of Wnt5a in the ChP controls their function and find that cerebellar morphogenesis is impaired. Our study thus identifies the CSF as a route and lipoprotein particles as a vehicle for long-range transport of biologically active WNT in the central nervous system.


  • NEWS: Ernest Arenas has been appointed Wallenberg Scholar from the Wallenberg Foundations in 2019.
  • Short description about the project: Parkinson’s disease is a very common neurodegenerative disorder. However, current therapies neither cure, nor slow down disease. Clinical trials have shown that it is possible to transplant and replace brain cells lost by the disease with cells from a fetus – but this approach poses several technical and ethical challenges. Ernest Arenas and his colleagues aim to identify the combination of genes controlling development of dopamine-producing neurons in the substantia nigra (SN), the cell type mainly affected by Parkinson’s disease. For this purpose they will use new methodologies such as single-cell RNA-sequencing and CRISPR/cas9 genome editing. They will apply the new knowledge to develop two methods to genetically control the formation of SN neurons.

    More information: Knut and Alice Wallenberg Foundation

    KI press release


  • Collaborative article with the group of Per Uhlén on the role of a type of calcium channel Cav3.2 in regulation of cortical neurogenesis in Neuroscience

  • Original article in Journal of Biological Chemistry on role of Lxr ligands in dopaminergic neurogenesis and differentiation
  • 24(S),25-Epoxycholesterol and cholesterol 24S-hydroxylase (CYP46A1) overexpression promote midbrain dopaminergic neurogenesis in vivo

    Theofilopoulos S et al.

    The liver X receptors Lxrα/NR1H3 and Lxrβ/NR1H2 are ligand-dependent nuclear receptors critical for midbrain dopaminergic (mDA) neuron development. We previously found that 24(S),25-epoxycholesterol (24,25-EC), the most potent and abundant Lxr ligand in the developing mouse midbrain, promotes mDA neurogenesis in vitro. In this study, we demonstrate that 24,25-EC promotes mDA neurogenesis in an Lxr-dependent manner, in the developing mouse midbrain in vivo and also prevents toxicity induced by the Lxr inhibitor geranylgeranyl pyrophosphate. Furthermore, using MS we show that overexpression of human cholesterol 24S-hydroxylase (CYP46A1) increases the levels of both 24(S)-hydroxycholesterol (24-HC) and 24,25-EC in the developing midbrain, resulting in a specific increase in mDA neurogenesis in vitro and in vivo, but has no effect on occulomotor or red nucleus neurogenesis. 24-HC, unlike 24,25-EC, did not affect in vitro neurogenesis, indicating that the neurogenic effect of 24,25-EC on mDA neurons is specific. Combined, our results indicate that increased levels of 24,25-EC in vivo, by intracerebroventricular delivery in wild-type mice or by overexpression of its biosynthetic enzyme CYP46A1, specifically promote mDA neurogenesis. We propose that increasing the levels of 24,25-EC in vivo may be a useful strategy to combat the loss of mDA neurons in Parkinson’s disease.


  • NEWS: Chan Zuckerberg Initiative award for Neurodegeneration Challenge Network to profile and define Parkinson's disease
  • The group of Ernest Arenas has been awarded a grant from CZI to systematically analyze and provide an unbiased understanding of the cell types and molecular mechanisms involved in Parkinson's disease. The project will be performed in collaboration with Per Svenningsson (KI), Sten Linnarsson (KI), and Mats Nilsson (SU).

    More information: CZI Neurodegeneration Challenge Network

    SciLife Lab press release


  • Collaborative article with the group of William Griffiths and Yuqin Wang on pathways of sterol metabolism in Biochimica et Biophysica Acta (BBA) - Molecular and Cell Biology of Lipids

  • Collaborative article with the group of Per Uhlén on identity of a novel platinum resistance gene COX7B in Cancer Medicine

  • Original article in Stem Cell Reports on role of R-Spondin 2 in dopaminergic neurogenesis and differentiation
  • The Matricellular Protein R-Spondin 2 Promotes Midbrain Dopaminergic Neurogenesis and Differentiation

    Gyllborg D et al.

    The development of midbrain dopaminergic (mDA) neurons is controlled by multiple morphogens and transcription factors. However, little is known about the role of extracellular matrix proteins in this process. Here we examined the function of roof plate-specific spondins (RSPO1-4) and the floor plate-specific, spondin 1 (SPON1). Only RSPO2 and SPON1 were expressed at high levels during mDA neurogenesis, and the receptor LGR5 was expressed by midbrain floor plate progenitors. Surprisingly, RSPO2, but not SPON1, specifically promoted the differentiation of mDA neuroblasts into mDA neurons in mouse primary cultures and embryonic stem cells (ESCs). In addition, RSPO2 was found to promote not only mDA differentiation, but also mDA neurogenesis in human ESCs. Our results thus uncover an unexpected function of the matricellular protein RSPO2 and suggest an application to improve mDA neurogenesis and differentiation in human stem cell preparations destined to cell replacement therapy or drug discovery for Parkinson disease.


  • Collaborative article with the group of Sten Linnarsson on RNA sequencing of half a million cells in the mouse central nervous system published in Cell
  • Molecular Architecture of the Mouse Nervous System

    Zeisel A et al., wiki page for visualization of data


  • Collaborative article with the group of Antonio del Sol on synergistic activity of transcription factors for subpopulation identity in Nature Communications

  • Original article in Communications Biology on role of Zeb2 in dopaminergic neurogenesis and migration
  • A Zeb2-miR-200c loop controls midbrain dopaminergic neuron neurogenesis and migration

    Yang S et al.

    Zeb2 is a homeodomain transcription factor that plays pleiotropic functions during embryogenesis, but its role for midbrain dopaminergic (mDA) neuron development is unknown. Here we report that Zeb2 is highly expressed in progenitor cells in the ventricular zone of the midbrain floor plate and downregulated in postmitotic neuroblasts. Functional experiments show that Zeb2 expression in the embryonic ventral midbrain is dynamically regulated by a negative feedback loop that involves miR-200c. We also find that Zeb2 overexpression reduces the levels of CXCR4, NR4A2, and PITX3 in the developing ventral midbrain in vivo, resulting in migration and mDA differentiation defects. This phenotype was recapitulated by miR-200c knockdown, suggesting that the Zeb2-miR-200c loop prevents the premature differentiation of mDA progenitors into postmitotic cells and their migration. Together, our study establishes Zeb2 and miR-200c as critical regulators that maintain the balance between mDA progenitor proliferation and neurogenesis.


  • NEWS: Division of Molecular Neurobiology has moved to the new Biomedicum building.

  • Collaborative article as Preprint at BioRxiv with the group of Sten Linnarsson on RNA sequencing of half a million cells in the mouse central nervous system
  • Molecular Architecture of the Mouse Nervous System

    Zeisel A et al., wiki page for visualization of data


  • Postdoctoral fellow position available in Computational Biology of Single Cell and CRISPR Genomics
  • A postdoctoral fellow position is available in our lab. The position is in Computational Biology of Single Cell and CRISPR Genomics in Dopamine Neurons.

    More information and announcement of position.

    Apply here!


  • NEWS: Division of Molecular Neurobiology is moving in April 2018 to the new Biomedicum building.
  • Karolinska Institutet is building an ultramodern, purpose-built facility for experimental medical research, Biomedicum. The new laboratory gives Karolinska Institutet more research space and new opportunities to make more effective use of shared infrastructure.

    The department of MBB will be relocated to Biomedicum in April 2018.

    More information: Biomedicum - Laboratory of the future


  • Original article in Science Signaling on role of YAP in dopaminergic differentiation and survival
  • Niche-derived laminin-511 promotes midbrain dopaminergic neuron survival and differentiation through YAP

    Zhang D, et al.

    Parkinson’s disease (PD) is a neurodegenerative disorder marked by progressive loss of dopaminergic neurons and motor control. Various factors promote or inhibit neuronal survival. Zhang et al. found that a prosurvival signal was mediated by the transcription cofactor YAP. YAP was activated in midbrain dopaminergic neurons in culture and in mice through an interaction between an integrin and the extracellular matrix protein laminin-511. YAP then transcriptionally activated dopaminergic neuron differentiation factors and a microRNA that decreased the synthesis of the apoptotic protein PTEN. The findings uncover a new role for YAP in neurons and a pathway that might be explored for the purpose of promoting dopaminergic neuron survival in PD patients.


  • Original article in Molecular Neurodegeneration on binding partners of LRRK2
  • A proteomic analysis of LRRK2 binding partners reveals interactions with multiple signaling components of the WNT/PCP pathway

    Salašová A, et al.

    Autosomal-dominant mutations in the Park8 gene encoding Leucine-rich repeat kinase 2 (LRRK2) have been identified to cause up to 40% of the genetic forms of Parkinson’s disease. However, the function and molecular pathways regulated by LRRK2 are largely unknown. It has been shown that LRRK2 serves as a scaffold during activation of WNT/β-catenin signaling via its interaction with the β-catenin destruction complex, DVL1-3 and LRP6. In this study, we examine whether LRRK2 also interacts with signaling components of the WNT/Planar Cell Polarity (WNT/PCP) pathway, which controls the maturation of substantia nigra dopaminergic neurons, the main cell type lost in Parkinson’s disease patients.


  • Collaborative article with the group of Gunnar Schulte on Frizzled recruitment of Disheveled in Cellular Signalling

  • Original article as Preprint at BioRxiv on the ventral midbrain dopaminergic niche
  • Molecular analysis of the midbrain dopaminergic niche during neurogenesis

    Toledo EM, et al.

    Midbrain dopaminergic (mDA) neurons degenerate in Parkinson's disease and are one of the main targets for cell replacement therapies. However, a comprehensive view of the signals and cell types contributing to mDA neurogenesis is not yet available. By analyzing the transcriptome of the mouse ventral midbrain at a tissue and single-cell level during mDA neurogenesis we found that three recently identified radial glia types 1-3 (Rgl1-3) contribute to different key aspects of mDA neurogenesis. While Rgl3 expressed most extracellular matrix components and multiple ligands for various pathways controlling mDA neuron development, such as Wnt and Shh, Rgl1-2 expressed most receptors. Moreover, we found that specific transcription factor networks explain the transcriptome and suggest a function for each individual radial glia. A network controlling neurogenesis was found in Rgl1, progenitor maintenance in Rgl2 and the secretion of factors forming the mDA niche by Rgl3. Our results thus uncover a broad repertoire of developmental signals expressed by each midbrain cell type during mDA neurogenesis. Cells identified for their emerging importance are Rgl3, a niche cell type, and Rgl1, a neurogenic progenitor that expresses ARNTL, a transcription factor that we find is required for mDA neurogenesis.


  • Review article on Wnts in human development in British Journal of Pharmacology

  • Nature Biotechnology has a News and Views article about our recent publication on reprogramming astrocytes
  • Reprogramming the diseased brain

    Dunnett SB and Rosser AE

    Original publication by Rivetti di Val Cervo P, et al.
    Link to original publication

  • Collaborative article with the group of Per Uhlén on mapping genes for calcium signaling in Bioinformatics

  • Collaborative article with the group of Igor Adameyko on growth and shaping of vertebrate cartilage in eLife

  • Original article in Nature Biotechnology on reprogrammed astrocytes to dopaminergic neurons
  • Induction of functional dopamine neurons from human astrocytes in vitro and mouse astrocytes in a Parkinson's disease model

    Rivetti di Val Cervo P, et al.

    Cell replacement therapies for neurodegenerative disease have focused on transplantation of the cell types affected by the pathological process. Here we describe an alternative strategy for Parkinson's disease in which dopamine neurons are generated by direct conversion of astrocytes. Using three transcription factors, NEUROD1, ASCL1 and LMX1A, and the microRNA miR218, collectively designated NeAL218, we reprogram human astrocytes in vitro, and mouse astrocytes in vivo, into induced dopamine neurons (iDANs). Reprogramming efficiency in vitro is improved by small molecules that promote chromatin remodeling and activate the TGFβ, Shh and Wnt signaling pathways. The reprogramming efficiency of human astrocytes reaches up to 16%, resulting in iDANs with appropriate midbrain markers and excitability. In a mouse model of Parkinson's disease, NeAL218 alone reprograms adult striatal astrocytes into iDANs that are excitable and correct some aspects of motor behavior in vivo, including gait impairments. With further optimization, this approach may enable clinical therapies for Parkinson's disease by delivery of genes rather than cells.

    News article at Karolinska Institutet

    Press article in TheScientist

    Press article in Scientific American


  • Original article in Cell on single-cell in the developing ventral midbrain
  • Molecular Diversity of Midbrain Development in Mouse, Human, and Stem Cells

    La Manno G, Gyllborg D, et al.

    Understanding human embryonic ventral midbrain is of major interest for Parkinson’s disease. However, the cell types, their gene expression dynamics, and their relationship to commonly used rodent models remain to be defined. We performed single-cell RNA sequencing to examine ventral midbrain development in human and mouse. We found 25 molecularly defined human cell types, including five subtypes of radial glia-like cells and four progenitors. In the mouse, two mature fetal dopaminergic neuron subtypes diversified into five adult classes during postnatal development. Cell types and gene expression were generally conserved across species, but with clear differences in cell proliferation, developmental timing, and dopaminergic neuron development. Additionally, we developed a method to quantitatively assess the fidelity of dopaminergic neurons derived from human pluripotent stem cells, at a single-cell level. Thus, our study provides insight into the molecular programs controlling human midbrain development and provides a foundation for the development of cell replacement therapies.

    News article at Karolinska Institutet

    Supporing Information and Visualization


  • Original article in EMBO on role of Pbx1 in the ventral midbrain
  • A PBX1 transcriptional network controls dopaminergic neuron development and is impaired in Parkinson's disease

    Villaescusa JC, et al.

    Pre‐B‐cell leukemia homeobox (PBX) transcription factors are known to regulate organogenesis, but their molecular targets and function in midbrain dopaminergic neurons (mDAn) as well as their role in neurodegenerative diseases are unknown. Here, we show that PBX1 controls a novel transcriptional network required for mDAn specification and survival, which is sufficient to generate mDAn from human stem cells. Mechanistically, PBX1 plays a dual role in transcription by directly repressing or activating genes, such as Onecut2 to inhibit lateral fates during embryogenesis, Pitx3 to promote mDAn development, and Nfe2l1 to protect from oxidative stress. Notably, PBX1 and NFE2L1 levels are severely reduced in dopaminergic neurons of the substantia nigra of Parkinson's disease (PD) patients and decreased NFE2L1 levels increases damage by oxidative stress in human midbrain cells. Thus, our results reveal novel roles for PBX1 and its transcriptional network in mDAn development and PD, opening the door for new therapeutic interventions.


    About the lab:

      The Arenas Laboratory aims at developing regenerative therapies for Parkinson's disease. Work in this area integrates molecular, cellular, and biochemical techniques, and involves both in vitro and in vivo studies. Of particular interest are specific aspects of midbrain and dopamine neuron development, Wnt signaling, biotechnology, stem cell biology and regenerative medicine for Parkinson's disease.

      At Karolinska Institutet, the laboratory is situated in the new Biomedicum building as part of the Division of Molecular Neurobiology within the Department of Medical Biochemistry and Biophysics (MBB). MBB is a department consisting of 12 research divisions within the fields of protein chemistry, redox biochemistry, metabolism, lipid research, inflammation research, structural biochemistry, molecular biochemistry, tissue biology, and developmental biology.

      Karolinska Institutet is Sweden’s single largest centre of medical academic research and one of the world’s foremost medical universities with a vision is to make a significant contribution to the improvement of human health. Since 1901 the Nobel Assembly at Karolinska Institutet awards the Nobel prize in Physiology or Medicine.



    Contact Information

      Visiting address:

      Karolinska Institutet
      Biomedicum, C6
      Solnavägen 9
      171 65 Solna, Sweden

      Mailing address:

      Karolinksa Institutet
      171 77 Stockholm, Sweden

      For deliveries:

      Karolinska Institutet
      Biomedicum, C6
      Tomtebodavägen 16
      171 65 Solna, Sweden