Kirkeby Group - Human Neural Development 

Human neurons generated from pluripotent stem cells

The Kirkeby group studies the factors involved in human neural subtype specification in order to enable production of specific neurons for understanding and treating neurological diseases.

The group uses stem cells to produce specific subtypes of human neurons. The aim of our work is to develop novel stem cell transplantation therapies for neurodegenerative diseases as well as to use the stem cells as a tool to understand the pathogenesis of brain disorders.



Creating a human fetal brain in the dish with microfluidics (the MiSTR model)

This project is an interdisciplinary collaboration joining forces from the fields of bioengineering and stem cell biology with the aim of producing a novel model of early human neural tube patterning. Through microfluidic engineering techniques, we expose hESCs to morphogenic gradients in vitro, thereby building a microenvironment in which the stem cells are patterned into structures resembling the early stages of the rostral-to-caudal regionalised human neural tube. With this technique, we produce an anatomically relevant 3D in vitro model of the developing human neural tube corresponding to around weeks 2-10 of fetal development – read more here.

Mapping human neural subtype identities through single cell RNAseq

Using the MiSTR model described above, we apply single cell RNA sequencing to map the complexity of human neural subtypes present during early and late neural specification. By mapping cells at a single cell level at several different time points, we identify the unique molecular signatures of different human neural subtypes and aim to dissect the trajectories underlying the regionalisation and subregionalisation of human neural progenitors and neurons during embryo development.

Identifying secreted factors from different human brain regions through proteomics

For this project, we use our MISTR model to search for human-specific patterns of developmental growth factors through unbiased mass-spec (MS) proteomic analysis of the secreted proteins produced from different neural regions during development. Novel candidates identified from this approach are explored for their biological function in directing neural cells towards specific neuronal subtypes and for inducing neuronal subtype maturation.

Studying the functions of long non-coding RNAs in human neural cells

Long non-coding RNAs (lncRNAs) are highly abundant in the human genome, and for the vast majority of these their functions are unknown. Here, we apply CRISPR gene editing techniques in human pluripotent cells (CRISPR knockout, CRISPR activation and CRISPR inhibition) to investigate the functions of novel lncRNAs during human neural specification and differentiation. We aim to uncover both general functions in neural differentiation as well as more specific functions in regional subtype specification.

Generating human hypothalamic neurons for studying neuronal control of appetite and metabolism

The hypothalamus is important for regulating appetite, metabolism and sleep, and hypothalamic neuronal dysfunction is coupled to obesity, type 2 diabetes and narcolepsy. As such, access to functional human hypothalamic neurons is of great interest to pharma, biotech and academia for use in disease modelling, drug screening and cell replacement therapies. However, protocols for generation of subtype-specific hypothalamic neurons are still suboptimal, partly due to a lack of knowledge on the developmental trajectories giving rise to each specific neuronal subtype of the hypothalamus. In this project, we generate protocols for subtype-specific differentiation of hESCs into different subregions of the hypothalamus, and we investigate the neuronal lineages through single cell RNA sequencing. We focus in particular on hypothalamic neuronal subtypes which are important for the regulation of appetite, metabolism and sleep

Generating human hypocretin (HCRT) neurons for treatment of narcolepsy

Narcolepsy is a chronic, neurological disease affecting approximately 20-50 out of 100,000 individuals. The disease onset is typically during adolescence or early adulthood, and symptoms include excessive daytime sleepiness, cataplexy, hypnagogic hallucinations and sleep paralysis. The most common form of the disease, Type 1 narcolepsy, is caused by the selective loss of HCRT neurons in the hypothalamus of the patients. In this project, we generate protocols for production of HCRT neurons from hESCs, and we investigate in animal models the potential of these neurons to be used as a transplantation therapy for narcolepsy, by regenerating the HCRT sleep circuit

Generating human basal forebrain cholinergic neurons for treatment of dementia

Neurodegenerative disorders such as Alzheimer’s Disease, Parkinson’s Disease and Lewy body disease are associated with the loss of basal forebrain cholinergic neurons, which can lead to memory loss and dementia. In this project, we develop protocols for generating cultures of human basal forebrain cholinergic neurons from stem cells and through animal models, we assess the potential of these cells to be used as a transplantation cell therapy for treatment of cognitive deficits. This project is part of the EU H2020 consortium NSC-Reconstruct.

Studying neuroinflammation in in vitro stem cell models of Parkinson’s Disease

Recent studies in the field of Parkinson’s Disease has put increased focus on the role of neuroinflammation in the pathogenesis of the disease. In this project, we study the factors involved in neuroinflammation in Parkinson’s Disease through the use of complex in vitro models containing human neurons, astrocytes and microglia. This work is funded as a Michael J Fox Foundation/ASAP Research consortium

STEM-PD: developing a stem cell therapy for treatment of Parkinson’s Disease

In our lab at Lund University, together with the lab of Malin Parmar, we work in a long-standing collaboration to develop a cell therapy for treatment of Parkinson’s Disease. In this project, we produce human dopaminergic progenitor cells from human embryonic stem cells for transplantation therapy to replace the dopamine neurons which are lost in the brains of Parkinson’s Disease patients. This work has resulted in the development of a clinical stem cell product (STEM-PD), which is anticipated to go into clinical trial in Parkinson’s Disease patients in late 2021/early 2022.  



Research Profile

Agnete Kirkeby has founded her research on applying human pluripotent stem cells to generate subtype-specific neural cells for developmental studies and regenerative therapy. During her time at Lund University, Agnete has been heavily involved in developing protocols for producing dopaminergic progenitor cells as a cell therapy for Parkinson’s Disease patients. This work has led to the development of a stem cell product which is currently in preparation for clinical trial. Moreover, Agnete has focused on producing novel tools for studying human neural development through modelling of neural tube patterning with microfluidic morphogenic gradients. The main focus of Agnete Kirkeby’s group is to use these 3D in vitro models of human brain development to map and understand human neural subtype specification and maturation.

Curriculum Vitae

2022- : Group leader, Associate Prof, Novo Nordisk Foundation Center for Stem Cell Medicine, reNEW

2019 - 2021: Group leader, Associate Prof., Department of Neuroscience, University of Copenhagen

2019 - : Group leader, WCMM fellow, Wallenberg Center for Regenerative Medicine, Lund University, Sweden

2017-19: Group leader, Associate Prof., Novo Nordisk Foundation Center for Stem Cell Biology, DanStem, University of Copenhagen

2015-2019 : Group leader, Research Scientist, Medical Faculty, Lund University, Sweden

2009-2015: Postdoc/Research scientist, Lund University, Dept. Developmental and Regenerative Neurobiology. (Malin Parmar group), Lund University, Sweden

2006-2009: Ph.D in Neurobiology, Performed at Sloan Kettering Institute, New York and H. Lundbeck A/S. Title: Studying the effects of low oxygen on stem cells. PhD Institution: Faculty of Health and Medical Sciences, University of Copenhagen, Denmark. Supervisors: Prof. Jan Sap and Dr. Lorenz Studer. Doctoral degree obtained Sept. 2009. 

2003-2006: MSc in Human Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark. Masters project performed at H. Lundbeck A/S.

Read about the Kirkeby lab at Lund University here  



  • Human pluripotent stem cells: Culturing and neural differentiation of human pluripotent stem cells to subtype-specific neural cells.
  • 3D stem cell models: Applying 3D models for neural differentiation of human stem cells into regionalised neural subtypes.
  • Microfluidic cell culturing: Development and use of microfluidic culturing devices to control regionalisation of human stem cells during differentiation
  • Proteomics: Shotgun proteomics (LC-MS/MS) for identifying proteins in cells and cell culture medium from human stem cells.
  • Molecular biology: Generation of CRISPR/Cas9 reporter cell lines, generation of lentiviral constructs, high-throughput qRT-PCR analysis
  • Bioinformatics: Single cell RNAsequencing using the 10X Chromium platform and lineage trajectory analysis by bioinformatics
  • In vivo transplantation: Rat models for stereotaxic xeno-transplantation of human neural cells
  • Imaging: Confocal fluorescence microscopy and immunohistochemistry


Staff List - Kirkeby Group

Name Title Job responsibilities Phone E-mail
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Abay-Nørgaard, Zehra Caldwell PhD Student Kirkeby Lab +4535325894 E-mail
Aldrin Kirk, Patrick Anders Postdoc Kirkeby Lab +4535337477 E-mail
Ankjær, Matias Heide Master-Student Kirkeby Lab   E-mail
Asenjo Martinez, Andrea Postdoc PhD student +4535331080 E-mail
Baungaard, Sara Olivia Master-Student Kirkeby Lab   E-mail
Brun, Ida Sophie Master-Student Kirkeby Lab   E-mail
Christensen, Jens Bager Master-Student Kirkeby Lab   E-mail
Dubonyte, Ugne PhD Fellow Kirkeby Lab +4535325174 E-mail
Essenbæk, David Nørgaard Bachelor student Kirkeby Lab   E-mail
Finlay, Brenda Master-Student Kirkeby Lab   E-mail
Holm, Amalie Research Assistant Kirkeby Lab   E-mail
Kirkeby, Agnete Associate Professor, Group Leader Kirkeby Lab +4551685353 E-mail
Larsen, Jette Pia Laboratory Technician. Lab technician   E-mail
Müller, Anika Research Assistant Kirkeby Lab   E-mail
Rathore, Gaurav Singh Research Assistant Kirkeby Lab   E-mail
Reis Rifes, Pedro Goncalo Assistant Professor Kirkeby Lab   E-mail
Saietz, Sarah Kieler Master-Student Kirkeby Lab   E-mail
Salvador, Alison Master-Student Kirkeby Lab   E-mail
Schörling, Alrik Guest Researcher Kirkeby Lab   E-mail
Thiruvalluvan, Arun Postdoc Kirkeby Lab   E-mail
Zhang, Yu Guest Researcher Kirkeby Lab   E-mail