CAJAL Neuroscience Training Course Bordeaux School of ... files/CAJAL/2020... · the goal to decode the mechanistic molecular alterations which lead to psychiatric diseases such as

CAJAL Neuroscience Training Course

Single cell profiling and analysis in neuroscience Bordeaux School of Neuroscience – June 15 to July 3, 2020

The CAJAL Advanced Neuroscience Training Programme www.cajal-training.org

1

Instructors

Lisa BAST, PhD | Karolinska Institutet, Sweden

Lisa Bast is a postdoctoral researcher in the Hjerling-Leffler Lab at Karolinska Institutet. Lisa studied Mathematics in Bioscience at Koblenz University of Applied Sciences and Technical University Munich and has ever since been fascinated by solving biological or medical problems with computational methods. Her previous research focused on data-driven modeling of cell division and differentiation processes, such as computationally modeling adult neurogenesis in the subependymal zone of the murine brain to infer cell type specific changes that explain the agerelated

decline in neurogenesis. She is about to finish her Ph.D. at Technical University Munich in close collaboration with the Helmholtz Center Munich (Institute of Computational Biology), under the supervision of Dr. Carsten Marr and Prof. Fabian Theis. Her current postdoctoral work relates to gene regulatory network inference from single cell RNA sequencing data with the goal to decode the mechanistic molecular alterations which lead to psychiatric diseases such as schizophrenia.

Selected publication: - L. Bast, F. Calzolari, M. K. Strasser, J. Hasenauer, F. J. Theis, J. Ninkovic, C. Marr, Increasing Neural

Stem Cell Division Asymmetry and Quiescence Are Predicted to Contribute to the Age-Related Decline in Neurogenesis. Cell reports 25 (12), 32313240 (2018)

Song CHEN, PhD | University of California San Diego, USA

My current research focuses on the development of massive parallel multi-omics single-cell sequencing methods to simultaneously measure the dynamics of genetic, epigenetic and transcriptome changes to help to illustrate the decisive mechanism of tissue heterogeneity during normal development and disease progression, and by leveraging these knowledges, guide the design of targeted molecular and cellular therapies. My postdoctoral research focuses on the development of novel massively parallel single-cell sequencing technologies and the application of these

methods to decipher tissue heterogeneity on an unprecedented resolution and scale. To achieve this goal, we developed the high-throughput single-nucleus droplet-based sequencing (snDrop-seq) method to acquire nuclear transcriptomics from frozen archived samples, and the single-cell transposome hypersensitive site sequencing method (scTHS-seq) to capture chromatin regulatory regions. Employing these methods, we generated more than 60,000 datasets across several human adult brain regions. And with a joint analysis of this dual-omics profiling, we identified 35 and 11 distinct cell types within the cerebral and

http://www.cajal-training.org/




2

cerebellar cortex, respectively, revealed cell-type specific regulatory program and recovered disease-relevant risk variants that could connect specific cell types to certain brain diseases and disorders. The integration of single-cell measurements of different omics techniques requires significant computational strategies and effort while may miss crucial intrinsic linkages between different modalities. To overcome this limitation, we took a step further and developed the joint single-nucleus chromatin accessibility and mRNA expression sequencing method (SNARE-seq) to link transcriptome with regulatory chromatin regions from the same cells. By matching transcriptional regulation directly to its output using this method, we reconstructed the transcriptome and epigenetic landscapes of various cell types in the mouse brain, uncovered lineage-specific accessible sites, and connected the dynamics of promoter accessibility with transcription during neurogenesis. Applying our single-nucleus transcriptome profiling method, we also established a robust tissue processing and profiling pipeline to investigate cell-type diversity within fetal and adult human kidney clinical samples. My Ph.D. study focused on the discovery of signaling transduction and transcription regulation that controls hepatic and pancreatic fate determination and maturation, and we developed an in vitro differentiation system that allows us to produce metabolically functional hepatocytes that could be used for drug toxicity screening. Selected publications: - Chen S, Lake BB, Zhang K. High-throughput sequencing of the transcriptome and chromatin

accessibility in the same cell. Nature Biotechnology, 2019; 37,1452-1457. - Lake BB*, Chen S*, Hoshi M*, Plongthongkum N*, Salamon D, Knoten A, Vijayan A, Venkatesh R,

Kim EH, Gao D, Gaut J, Zhang K, Jain S. A single-nucleus RNA-sequencing pipeline to decipher the molecular anatomy and pathophysiology of human kidneys. Nature Communications, 2019; 10(1):2832. (Co-first author)

- Lake BB*, Chen S*, Sos BC*, Fan J*, Kaeser GE, Yung YC, Duong TE, Gao D, Chun J, Kharchenko PV, Zhang K. Integrative single-cell analysis of transcriptional and epigenetic states in the human adult brain. Nature Biotechnology, 2018; 36(1):70-80. (Co-first author)

- Zhao D*, Chen S*, Duo S, Xiang C, Jia J, Guo M, Lai W, Lu S, Deng H. Promotion of the efficient metabolic maturation of human pluripotent stem cell-derived hepatocytes by correcting specification defects. Cell research 2013; 23 (1), 157. (Co-first author)

Martin HARING, PhD | Medical University of Vienna (MedUni Vienna), Austria

I am a senior postdoc at the Center for Brain Research at the Medical University of Vienna. My main research experience during my education comprise pharmacology, mouse behavior, molecular neurobiology and cancer biology. My main research interest is to understand specific physiological functions of the serotonergic system. Due to the plethora of behaviors influences be serotonergic signaling I try to focus on how serotonin influences sensory signaling. I address this task by combining intersectional genetics, mouse behavior, various staining methods and viral injections.

Selected publications:





3

- Häring, M, Kaiser, N., Monory, K., & Lutz, B. (2011). Circuit specific functions of cannabinoid CB1 receptor in the balance of investigatory drive and exploration. PloS One, 6(11), e26617. https://doi.org/10.1371/journal.pone.0026617

- Häring, M, Grieb, M., Monory, K., Lutz, B., & Moreira, F. A. (2013). Cannabinoid CB₁ receptor in the modulation of stress coping behavior in mice: the role of serotonin and different forebrain neuronal subpopulations. Neuropharmacology, 65, 83–89. https://doi.org/10.1016/j.neuropharm.2012.09.002

- Häring, M, Enk, V., Aparisi Rey, A., Loch, S., Ruiz de Azua, I., Weber, T., … Lutz, B. (2015). Cannabinoid type-1 receptor signaling in central serotonergic neurons regulates anxiety-like behavior and sociability. Frontiers in Behavioral Neuroscience, 9, 235. https://doi.org/10.3389/fnbeh.2015.00235

- Häring, M, Zeisel, A., Hochgerner, H., Rinwa, P., Jakobsson, J. E. T., Lönnerberg, P., … Ernfors, P. (2018). Neuronal atlas of the dorsal horn defines its architecture and links sensory input to transcriptional cell types. Nature Neuroscience, 21(6), 869–880. https://doi.org/10.1038/s41593-018-0141-1

- Kupari, J., Häring, M., Agirre, E., Castelo-Branco, G., & Ernfors, P. (2019). An Atlas of Vagal Sensory Neurons and Their Molecular Specialization. Cell Reports, 27(8), 2508-2523.e4. https://doi.org/10.1016/j.celrep.2019.04.096

Markus HILSCHER, PhD | Science for Life Laboratory (SciLifeLab), Sweden

Markus Hilscher is senior researcher at the Science for Life Laboratory in Sweden. He uses In situ sequencing to study the genetic architecture of nervous tissue. Markus has a PhD in Neuroscience, focusing on the electrophysiological and morphological characterization of specific interneurons (defined by the cholinergic receptor nicotinic alpha 2 subunit - Chrna2) as well as the functional output of neural circuits when manipulating selected cell types. His current research tries to link transcriptomic profiles to cell types to better understand cell type diversity and the spatial organization of

cells in the brain. Markus has also experience in the pharma industry where he used genomic approaches to identify new drug targets for the treatment of neurodevelopmental disorders. His studies on the developing or diseased brain thus incorporate spatial transcriptomic approaches to better understand how spatially resolved omics technologies could help to advance our knowledge of the various brain disorders. Selected publications: - M. M. Hilscher, R. N. Leão, S. J. Edwards, K. E. Leão, K. Kullander, Chrna2-Martinotti cells

synchronize layer 5 type A pyramidal cells via rebound excitation. PLoS biology 15 (2), e2001392 (2017).





4

- M. M. Hilscher, I. Nogueira, S. Mikulovic, K. Kullander, R. N. Leão, K. E. Leão, Chrna2‐OLM interneurons display different membrane properties and h‐current magnitude depending on dorsoventral location Hippocampus. Dec;29(12):1224-1237 (2019).

- S. Siwani, A. S. C. França, S. Mikulovic, A. Reis, M. M. Hilscher, S. J. Edwards, R. N. Leão, A. B. L. Tort, K. Kullander, OLMα2 cells bidirectionally modulate learning. Neuron 99 (2), 404-412. e3 (2018).

- K. Tiklová, Å. K. Björklund, L. Lahti, A. Fiorenzano, S. Nolbrant, L. Gillberg, N. Volakakis, C. Yokota, M. M. Hilscher, T. Hauling, F. Holmström, E. Joodmardi, M. Nilsson, M. Parmar, T. Perlmann, Single-cell RNA sequencing reveals midbrain dopamine neuron diversity emerging during mouse brain development. Nature Communications 10 (1), 581 (2019).

- R. Soldatov, M. Kaucka, M. E. Kastriti, J. Petersen, T. Chontorotzea, L. Englmaier, N. Akkuratova, Y. Yang, M. Häring, V. Dyachuk, C. Bock, M. Farlik, M. L. Piacentino, F. Boismoreau, M. M. Hilscher, C. Yokota, X. Qian, M. Nilsson, M. E. Bronner, L. Croci, W.-Y. Hsiao, D. A. Guertin, J.-F. Brunet, G. G. Consalez, P. Ernfors, K. Fried, P. V. Kharchenko, I. Adameyko, Spatiotemporal structure of cell fate decisions in murine neural crest. Science. 364, eaas9536 (2019).

Danny KITSBERG, PhD | Hebrew University of Jerusalem, Israel

Dr. Danny Kitsberg is a senior research scientist at the Hebrew University of Jerusalem. He is currently the lab manager of the laboratory of Dr. Naomi Habib at the Center for Brain Sciences. The main interest of the lab is using single nuclear sequencing (sNuc-seq) to study cellular interactions and molecular changes underlying aging related neurodegenerative diseases, such as Alzheimer’s Disease. Danny is an experienced molecular and cell biologist. After undergraduate studies in biology at the University of Cambridge, he completed his PhD at the Hebrew University on mammalian origins of replication

working with Prof. Howard Cedar. He did his postdoctoral training with Prof. Phil Leder at Harvard Medical School, investigating mouse models of breast and prostate cancer. He has also worked in biotech Industry, running the molecular biology division of a neuroscience company and later as chief scientific officer of a knockout mouse company in Australia. More recently, Danny had worked both in academia and in a commercial company researching various aspects of human embryonic stem cells. His passion for biology has lead him to impart his enthusiasm and excitement further by teaching both undergraduate students in the lab and in more formal teaching of biology students in high school in his spare time. Selected publications :





5

- Habib N, McCabe C, Medina S, Varshavsky M, Kitsberg D, Dvir R, Green G, Dionne D, Nguyen L,. Marshall J, Chen F, Zhang F, Kaplan T, Regev A, Schwartz M. Unique disease-associated astrocytes in Alzheimer’s disease Nat. Neurosci 2019 In press

- Levy G, Habib N, Guzzardi MA, Kitsberg D, Bomze D, Ezra E, Uygun BE, Uygun K, Trippler M, Schlaak JF, Shibolet O, Sklan EH, Cohen M, Timm J, Friedman N, Nahmias Y. Nuclear receptors control pro-

viral and antiviral metabolic responses to hepatitis C virus infection. Nat Chem Biol. 2016 Dec;12(12):1037-1045.

- Moussaieff A, Rouleau M, Kitsberg D, Cohen M, Levy G, Barasch D, Nemirovski A, Shen-Orr S, Laevsky I, Amit M, Bomze D, Elena-Herrmann B, Scherf T, Nissim-Rafinia M, Kempa S, Itskovitz-Eldor J, Meshorer E, Aberdam D, Nahmias Y. Glycolysis-mediated changes in acetyl-CoA and histone

acetylation control the early differentiation of embryonic stem cells. Cell Metab. 2015 Mar 3;21(3):392-402.

- Fishman B, Segev H, Kopper O, Nissenbaum J, Schulman M, Benvenisty N, Itskovitz-Eldor J, Kitsberg D.

- Targeting pancreatic progenitor cells in human embryonic stem cell differentiation for the identification of novel cell surface markers. Stem Cell Rev. 2012 Sep;8(3):792-802.

- Kitsberg D, Selig S, Keshet I, Cedar H. Replication structure of the human beta-globin gene domain. Nature. 1993 Dec 9;366(6455):588-90.

Gioele LA MANNO, PhD | École polytechnique fédérale de Lausanne (EPFL),

Switzerland

Gioele La Manno leads the laboratory of Neurodevelopmental Systems biology at the Brain and Mind Institute of the Swiss Federal Institute of Technology Lausanne (EPFL). Dr. La Manno holds a Bachelor degree in Biotechnology from University of Palermo and Master in Biomedicine from Karolinska Institute. He obtained his Ph.D. at Karolinska Institutet, working on single-cell transcriptomics analyses under the supervision of Sten Linnarsson. Dr. La Manno research spans from technique development in molecular biology to computational analysis of different kinds of genomics data. His research is

characterized by the use of high throughput data to understand the development of the nervous system. He has discovered new cell types in both the sympathetic system and ventral midbrain. He has also developed computational tools and analysis techniques, including RNA Velocity. La Manno’s lab overarching goal is the description and modeling of the cell fate commitment processes taking place during the embryonic development of the brain and the retina. Selected publications: - RNA velocity of single cells. Nature. 2018 Aug 08. La Manno G, Soldatov R, Zeisel A, [...] Linnarsson

S*, Kharchenko P*


https://www.ncbi.nlm.nih.gov/pubmed/27723751




http://www.ncbi.nlm.nih.gov/pubmed/22592939

http://www.ncbi.nlm.nih.gov/pubmed/22592939




6

- Single-cell transcriptional logic of cell-fate specification and axon guidance in early-born retinal neurons. Development. 2019 Sep 1. Lo Giudice Q, Leleu M, La Manno G, Fabre PJ.

- Spatial organization of the somatosensory cortex revealed by cyclic smFISH. Nature Methods. 2018 Oct 30. Codeluppi S, Borm LE, Zeisel A, La Manno G, van Lunteren JA, Svensson CI, Linnarsson S

- Molecular Diversity of Midbrain Development in Mouse, Human, and Stem Cells. Cell. 2016 Oct 6. La Manno G*, Gyllborg D*, Codeluppi S, [...], Barker RA, Arenas E, Linnarsson S.

- Quantitative single-cell RNA-seq with unique molecular identifiers. Nature Methods 2014 February. Islam S, Zeisel A, Joost S, La Manno G, Zajac P, Kasper M, Lönnerberg P, Linnarsson S.

Romain LOPEZ, PhD student | University of California Berkeley (UCB), USA

Romain Lopez is a Ph.D. candidate in the Department of Electrical Engineering and Computer Sciences at UC Berkeley, advised by Prof. Michael I. Jordan and Prof. Nir Yosef. His research lies at the intersection of machine learning, applied statistics and computational biology. In particular, Romain's research overarching goal is to develop statistically-grounded algorithmic tools to investigate biomedical data with factual or causal queries. His current research focus is to build deep generative model for single-cell transcriptomics data. Prior to his Ph.D., he visited the Harvard Medical School where he

worked on methodology for scRNA-seq data analysis with Prof. Allon Klein. More recently, Romain collaborated with Prof. Le Song at Ant Financial on structured counterfactual inference and with Prof. Inderjit Dhillon at Amazon on reinforcement learning applied to ranking problems in online search. Selected publications : - Romain Lopez, Jeffrey Regier, Michael I. Jordan, Nir Yosef. Information Constraints on Auto-

Encoding Variational Bayes. Advances in Neural Information Processing Systems, 2018. - Romain Lopez, Jeffrey Regier, Michael B. Cole, Michael I. Jordan, Nir Yosef. Deep generative

modeling for single-cell transcriptomics. Nature Methods, 2018. - Samuel L. Wolock, Romain Lopez, Allon M. Klein. Scrublet: computational identification of cell

doublets in single-cell transcriptomic data. Cell Systems, 2019. - Chenling Xu*, Romain Lopez*, Edouard Mehlman*, Jeffrey Regier, Michael I. Jordan, Nir Yosef.

Probabilistic Harmonization and Annotation of Single-cell Transcriptomics data with Deep Generative Models. bioRxiv, 2019.

- Romain Lopez, Chenchen Li, Xiang Yan, Junwu Xiong, Michael I. Jordan, Yuan Qi, Le Song. Cost-Effective Incentive Allocation via Structured Counterfactual Inference. Association for the Advancement of Artificial Intelligence (AAAI), 2020

Malte LUCKEN, PhD | Institute of computational biology (ICB), Germany


https://www.berkeley.edu/

https://www.berkeley.edu/




7

Malte Lücken is a postdoctoral researcher in the Theis lab at the Helmholtz Center Munich. After a PhD in network biology at the University of Oxford, he now works at the interface of machine learning and single-cell analysis. His interests range from the interpretability of neural network methods to building analysis pipelines for complex datasets. Previously he developed a best-practices tutorial for the analysis of single-cell data, which he is currently using to study diseases including Parkinson's disease, COPD, and depression. Furthermore, Malte is actively contributing to the Human Cell

Atlas efforts to generate an integrated lung cell atlas. For this purpose he has been researching data integration and batch correction for large cell atlases. Selected publications: - Luecken MD, Theis FJ, Current best practices in single‐cell RNA‐seq analysis: a tutorial, Molecular

Systems Biology (2019) - Luecken MD, Page MJT, Crosby AJ, Mason S, Reinert G, Deane CM, CommWalker: correctly

evaluating modules in molecular networks in light of annotation bias, Bioinformatics (2018)

Christian MAYER, PhD | Max Planck Institute of Neurobiology, Germany

Christian Mayer is a native of Germany and first became interested in how intrinsic and extrinsic processes cooperate to establish the adult form of brain connectivity and behaviour control as an undergraduate at the University of Konstanz, Germany. Dr. Mayer received his PhD from the University of Hamburg, Germany, where his thesis work at the ZMNH on the neuronal mechanisms of pubertal maturation was awarded the Gebhard Koch PhD prize for biochemistry and neurobiology. As an EMBO Long-Term Fellow at the NYU Neuroscience Institute, USA, Dr. Mayer pioneered the use of

single cell RNA sequencing to study how developmental gene expression results in the generation of cortical interneuron diversity. In 2018 Dr. Mayer moved to Munich, Germany, to start his independent laboratory at the Max Planck Institut of Neurobiology. His lab combines lineage tracing methods, genetics, physiology and computational methods to understand how different interneuron types emerge during development and integrate into functional circuits. Dr. Mayer recently received a Starting Grant from the European Research Council.

Selected publications: - C. Mayer, and G. Fishell (2018). “Developing neurons are innately inclined to learn on the job,”

Nature, vol. 21, p. 920. doi: 10.1038/d41586-018-05737-2 - C. Mayer*, C. Hafemeister*, R. C. Bandler*, R. Machold, R. Batista-Brito, X. Jaglin, K. Allaway, A.

Butler, G. Fishell and R. Satija (2018). “Developmental diversification of cortical inhibitory interneurons,” Nature, vol. 555, 457–462. doi:10.1038/nature25999

- C. Mayer, R. C. Bandler, and G. Fishell (2016). “Lineage Is a Poor Predictor of Interneuron Positioning within the Forebrain.,” Neuron, vol. 92, no. 1, pp. 45–51, Oct. 2016





8

- C. Mayer, X. H. Jaglin, L. V. Cobbs, R. C. Bandler, C. Streicher, C. L. Cepko, S. Hippenmeyer, and G. Fishell (2015). “Clonally Related Forebrain Interneurons Disperse Broadly across Both Functional Areas and Structural Boundaries,” Neuron, vol. 87, no. 5, pp. 989–998

- C. Mayer and U. Boehm (2011) .“Female reproductive maturation in the absence of kisspeptin/GPR54 signaling,” Nature Neuroscience, vol. 14, no. 6, pp. 704–710

Fatima MEMIC, PhD | Karolinska Institute, Sweden

Dr Fatima Memic, PhD is a Research Coordinator in Jens Hjerling-Leffler lab at Karolinska Institutet, Stockholm, Sweden. She received her PhD in Neuroscience at Uppsala University in 2012 focusing on the development of neuronal networks in the spinal cord. During her postdoctoral training at Karolinska institutet she worked on cell type specific development of the enteric nervous system. The focus of her research today is in single-cell transcriptomic analysis of cell type specific changes in schizophrenia, both in human tissue and genetic mouse models. Her expertise lies in molecular

biology, tissue dissection, dissociation, nuclei isolation and 10x Chromium library preparation. Selected publications: - Zeisel A.#, Hochgerner H.#, Lönnerberg P., Johnsson A., Memic F., van der Zwan J., Häring M.,

Braun E., Borm L., La Manno G., Codeluppi S., Furlan A., Lee K., Skene N., Harris K., Hjerling-Leffler J., Arenas E., Ernfors P., Marklund U and Linnarsson S. Molecular architecture of the mouse nervous system. Cell 2018 August 174:4, 999-1014e22

- Memic F, Knoflach V, Morarach K, Sadler R, Laranjeira C, Hjerling-Leffler J, Sundström E, Pachnis V, Marklund U. Transcription and Signaling Regulators in Developing Neuronal Subtypes of Mouse and Human Enteric Nervous System. Gastroenterology, 2018 154:624-636

- Memic F, Knoflach V, Sadler R, Tegerstedt G, Sundström E, Guillemot F, Pachnis V, Marklund U. Ascl1 is required for the development of specific neuronal subtypes in the enteric nervous system. J Neurosci. 2016 April 13:36(15):4339-4350

- Dyachuk V, Furlan A, Shahidi MK, Giovenco M, Kaukua N, Konstantinidou C, Pachnis V, Memic F, Marklund U, Müller T, Birchmeier C, Fried K, Ernfors P, Adameyko I. Parasympathetic neurons originate from nerve-associated peripheral glial progenitors. Science 2014 Jul 4;345(6192):82-7

- Andersson LS#, Larhammar M#, Memic F,# Wootz H#, Schwochow D, Rubin CJ, Patra K, Arnason T, Wellbring L, Hjälm G, Imsland F, Petersen JL, McCue ME, Mickelson JR, Cothran G, Ahituv N, Roepstorff L, Mikko S, Vallstedt A, Lindgren G, Andersson L, Kullander K. Mutations in DMRT3 affect locomotion in horses and spinal circuit function in mice. Nature 2012 Aug 30;488(7413):642-6 (# equal contribution).

Ana MUNOZ MANCHADO, PhD | University of Cádiz, Spain





9

I am a biologist with a strong interest in genetics and neuroscience. I recently established my own research line focusing in the specific transcriptional changes behind the pathology of Parkinson’s disease and other neurodegenerative disorders. For that, I combined my expertise from my PhD (University of Seville, 2011) and my postdoc (Karolinska Institutet). During my thesis, I investigated the mechanisms behind the benefitial effects of intrastriatal carotid body transplants as a potential antiparkinsonian cell therapies, and during my postdoc, I

investigated the cellular diversity of different brain areas using RNA single cell sequencing to define the molecular identity, and Patch-seq to link that identity with the firing properties. Selected publications: - Muñoz-Manchado AB, Bengtsson-Gonzales C*, Zeisel A*, Munguba H, Bekkouche B, Skene NG,

Lonnerberg P, Ryge J, Harris K, Linnarsson, S, Hjerling-Leffler J. Diversity of interneurons in the dorsal striatum revealed by single-cell RNA-sequencing and PatchSeq. Cell Reports 2018, 21;24(8):2179-2190.e7. PMID: 30134177.

- Muñoz-Manchado AB, Foldi C, Szydlowski S*, Sjulson L, Farries M, Wilson C, Silberberg G, Hjerling-Leffler J. Novel Striatal GABAergic Interneuron Populations Labeled in the 5HT3a(EGFP) Mouse. Cerebral cortex, 2016, 26;1 96-105. PMID: 25146369.

- Marques S, Zeisel A, Codeluppi S, van Bruggen D, Mendanha Falcão A, Xiao L, Li H, Häring M, Hochgerner H, Romanov RA, Gyllborg D, Muñoz-Manchado AB, La Manno G, Lönnerberg P, Floriddia EM, Rezayee F, Ernfors P, Arenas E, Hjerling-Leffler J, Harkany T, Richardson WD, Linnarsson S, Castelo-Branco G. Oligodendrocyte heterogeneity in the mouse juvenile and adult central nervous system. Science, 2016, 352; 6291 1326-9. PMID: 27284195.

- Zeisel A, Muñoz-Manchado AB, Codeluppi S, Lönnerberg P, La Manno G, Juréus A, Marques S, Munguba H, He L, Betsholtz C, Rolny C, Castelo-Branco G, Hjerling-Leffler J, Linnarsson S. Brain structure. Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq. Science, 2015, 347; 6226 1138-42. PMID: 25700174.

- Muñoz-Manchado AB, Villadiego J, Suarez-Luna N, Bermejo-Navas A, Garrido-Gil P, Labandeira-Garcia JL, Echevarria M, Lopez-Barneo J, Toledo-Aral JJ. Neuroprotective and reparative effects of carotid body grafts in a chronic MPTP model of Parkinson's disease. Neurobiology of Aging, 2013, 34;3 902-15. PMID: 22743091.

Viktor PETUKHOV, PhD | University of Copenhagen, Denmark





10

Viktor Petukhov finished Master’s programme in Applied Math and Informatics in St. Petersburg Polytechnic University. There, at 2016 he started working on low-level processing of scRNA-seq data under supervision of Peter Kharchenko (HMS). In 2018 he joined Khodosevich group in University of Copenhagen as a PhD student with co-supervision from Peter Kharchenko. There started working on application of scRNA-seq to investigation of neuronal development. Currently he works on method development for comparative analysis of transcriptional changes of cell types across conditions, as well

as low-level processing of spatial transcriptomics data. Selected publications: - Barkas, N., Petukhov, V., Nikolaeva, D. et al. Joint analysis of heterogeneous single-cell RNA-seq

dataset collections. Nat Methods 16, 695–698 (2019) doi:10.1038/s41592-019-0466-z - Petukhov, V., Guo, J., Baryawno, N. et al. dropEst: pipeline for accurate estimation of molecular

counts in droplet-based single-cell RNA-seq experiments. Genome Biol 19, 78 (2018) doi:10.1186/s13059-018-1449-6

Xiaoyan QIAN, PhD | Cartana, Sweden

I am co-founder and senior scientist at Cartana AB. Cartana is a spin-off from Mats Nilsson’s lab at Stockholm University. We provide service and kits for in situ sequencing (ISS), a technology for spatially resolved gene expression profiling directly inside a tissue section. I developed probabilistic cell typing by in situ sequencing (pciSeq) during my PhD in Nilsson lab. Using ISS and pciSeq, we successfully localized scRNA-seq defined cell types in mouse hippocampus, cortex and human fetal heart. My research focuses on method development, image analysis and data visualization, aiming to provide novel

tools for researchers to bring new knowledge. Selected publications: - X. Qian, K. D. Harris, T. Hauling, D. Nicoloutsopoulos, A. B. Muñoz-Manchado, N. Skene, J. Hjerling-

Leffler, M. Nilsson, Probabilistic cell typing enables fine mapping of closely related cell types in situ. Nat Methods, 1–6 (2019).

- B. Carow, T. Hauling, X. Qian, I. Kramnik, M. Nilsson, M. E. Rottenberg, Spatial and temporal localization of immune transcripts defines hallmarks and diversity in the tuberculosis granuloma. Nature Communications. 10, 1823 (2019).

- M. Asp, S. Giacomello, L. Larsson, C. Wu, D. Fürth, X. Qian, E. Wärdell, J. Custodio, J. Reimegård, F. Salmén, C. Österholm, P. L. Ståhl, E. Sundström, E. Åkesson, O. Bergmann, M. Bienko, A. Månsson-Broberg, M. Nilsson, C. Sylvén, J. Lundeberg, A Spatiotemporal Organ-Wide Gene Expression and Cell Atlas of the Developing Human Heart. Cell. 179, 1647-1660.e19 (2019).

- R. Soldatov, M. Kaucka, M. E. Kastriti, J. Petersen, T. Chontorotzea, L. Englmaier, N. Akkuratova, Y. Yang, M. Häring, V. Dyachuk, C. Bock, M. Farlik, M. L. Piacentino, F. Boismoreau, M. M. Hilscher, C. Yokota, X. Qian, M. Nilsson, M. E. Bronner, L. Croci, W.-Y. Hsiao, D. A. Guertin, J.-F. Brunet, G. G.





11

Consalez, P. Ernfors, K. Fried, P. V. Kharchenko, I. Adameyko, Spatiotemporal structure of cell fate decisions in murine neural crest. Science. 364, eaas9536 (2019).

- W.-T. Chen, A. Lu, K. Craessaerts, B. Pavie, C. S. Frigerio, R. Mancuso, X. Qian, J. Lalakova, M. Kühnemund, I. Voytyuk, L. Wolfs, A. Snellinx, S. Munck, A. Jurek, J. F. Navarro, T. C. Saido, J. Lundeberg, M. Fiers, B. D. Strooper, Spatial and temporal transcriptomics reveal microglia-astroglia crosstalk in the amyloid-β plaque cell niche of Alzheimer’s disease. bioRxiv, 719930 (2019).


Documents

CAJAL Neuroscience Training Course Bordeaux School of ... files/CAJAL/2020... · the goal to decode the mechanistic molecular alterations which lead to psychiatric diseases such as