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Schematic of custom tripartite microfluidic device used in the study of synaptic events. This microfluidic device contains three channels separated by microgrooves (M), which creates both fluidic and physical isolation between channels. When neurons are cultured in channels 1 and 3, channel 2 (middle channel) becomes enriched with dendrites and axons. As the microgrooves that separate channels 1 and 3 from the middle channel are of different lengths, dendrites of neurons cultured only in channel 1 (postsynaptic) can extend to the synaptic channel located in the middle of the device. At DIV21, immunostaining for the synaptic marker SV2 shows that the synaptic channel is enriched with synapses. 

RNA regulation in synaptic plasticity and cognitive function: Our research focuses on novel mechanisms of RNA regulation and how they control neuronal development in normal and disease states. Local mRNA translation has been implicated in synaptogenesis, synaptic plasticity as well as learning and memory. Most work in this field has focused on understanding the pathways that activate mRNA translation in dendrites. We are interested in exploring the role of mRNA degradation pathways in synaptic regions and their role in synaptic plasticity. mRNA degradation pathways have been linked to various neurodevelopmental diseases including mental retardation, autism and schizophrenia. To determine the local function of mRNA degradation in dendrites, we use a novel microfluidic device to uniquely compartmentalize synapses. To study the contribution of the mRNA-degradation pathways into synaptic plasticity and cognitive function, we employ genetic mouse models in combination with electrophysiology experiments and behavioral tests.

 
 
 

75 days old cerebral organoid

Footprint of more than 400 organoids

GFP-positive human astrocyte transplantation into neonatal mouse cortex, imaged 2 months post-transplantation

Studying developmental pathology of neuropsychiatric diseases: Cognitive dysfunction is a core feature of neuropsychiatric diseases. We are interested in understanding the cellular mechanisms underlying the cognitive dysfunction seen in autism and schizophrenia, with a special focus on glial cells. Existing animal models do not capture the genetic heterogeneity of these polygenetic diseases, and human postmortem studies offer very limited insight into the time course of disease progression. Patient-derived induced pluripotent stem cells (iPSCs) provide the best experimental system to identify the underlying molecular and cellular defects in polygenic diseases. iPSCs can be manipulated to form brain-like structures termed cerebral organoids. This culture system recapitulates the spontaneous generation of glial cells, providing a unique opportunity to study glial-cell abnormalities using patient cerebral organoids. We use cerebral organoids derived from patient iPSCs in combination with cell sorting, transplantation, electrophysiology and mouse behavioral assays to study the role of glial cells in characteristic deficits of both autism and schizophrenia such as defective synaptic plasticity and cognitive function.

We employ control and patient cerebral organoids to spontaneously generate disease astrocytes. Cell fate specification is temporally regulated in cortical development and is defined by the sequential appearance of neurons and glia. Cerebral organoids recapitulate the temporal sequence of cortical development seen in developing embryos. Importantly, the organoid system also allows us to populate disease astrocytes in an environment that mimics the early brain pathology. Therefore, cerebral organoids are likely to serve as a more representative system to preserve disease-specific features in patient astrocytes compared to directed differentiation protocols.

Techniques we use to study developmental pathology of neuropsychiatric diseases:

Patient iPSC-derived cerebral organoids

Cell sorting

2-photon Calcium imaging

Multielectrode arrays

Proteomics and single-cell RNA sequencing

Cell transplantation 

Stereological cell counting

Electrophysiology (E-LTP, L-LTP and LTD)

Behavioral assays

Spontaneous and ATP-evoked calcium activity of astrocytes in human cerebral organoids

Fluo-4 AM: Calcium sensor; SR-101; Astrocyte-specific dye

Our lab is more than 800 square feet and located at the Center for Neurogenetics on the 10th floor in the newly constructed Belfer building of Weill Cornell Medical College in New York City. We have access to two confocal microscopes (Olympus FV1000 and Zeiss 510), a 2-photon microscopy (Olympus), a Multi-Electrode Array (MEA, Axion BioSystems) and Illumina NextSeq 500 sequencing platform at no cost. The Belfer vivarium has two rooms specially equipped for behavioral phenotyping with brand-new equipment, purchased in 2016, and is managed by three recently established laboratories, including our own.

Dilek Colak, PI: Dilek is an Assistant Professor in the Brain and Mind Research Institute (BMRI). She earned her PhD degree from the Ludwig Maximilian University in Munich, Germany. Her PhD studies showed that neurogenesis in adult neural stem cells can be initiated upon inhibition of the apparent default pathway that is oligodendrogenesis. During  her PhD, Dilek was also actively involved in projects that aimed to re-instruct neurogenesis after brain injury. During her postdoc studies in New York, she explored the physiological role of local mRNA translation. Her study identified RNA degradation pathway nonsense-mediated mRNA decay (NMD) as a mechanism that regulates axon guidance in vivo. During this time, she also became interested in the mechanism of FMR1 gene silencing in Fragile X Syndrome (FXS), which is a trinucleotide repeat expansion disease and the most common monogenic cause of autism. Using FXS human embryonic stem cells, she discovered that the expanded repeats of the FMR1 mRNA interacts with the genomic DNA that then triggers FMR1 promoter repression. Her studies showed for the first time that a coding RNA could bind DNA to induce epigenetic silencing.

Michael Notaras, Postdoctoral fellow: Michael comes from Australia and holds a PhD in neuroscience from the University of Melbourne, Australia, where he studied the role of a neurotrophin coding polymorphism in sensitivity to stress and stress-induced brain remodelling. His work has led to five first author publications, including two in Molecular Psychiatry (Notaras et al., Molecular Psychiatry 2015; Notaras et al., Molecular Psychiatry 2016). He joined the Colak laboratory in 2016 to obtain postdoctoral training in the use of induced-pluripotent stem cells, 3D organotypic culturing methods, transplantation, microfluidic devices, and synaptic biology. Michael’s primary academic interest is the neurobiology of mental disorders, and he currently works on projects that seek to elucidate the mechanisms of brain aberrations that lead to schizophrenia and autism. When not in the laboratory, you may see Michael exploring New York’s food scene or find him writing in one of the many cafés on the Upper East Side of Manhattan.

Megan Allen, Postdoctoral fellow: Megan recently finished her PhD studies in Georgetown University, Washington-DC, in the neuroscience program. Her work revealed that the protease MMP-1 regulates synaptic plasticity through increases in intracellular Ca2+ concentrations and dendritic arborization in hippocampal neurons in vitro and in vivo (Allen et al., Scientific Reports 2016). In addition to her first author paper, she has published five co-author papers during her PhD studies. Megan is currently working on projects that explore the role of glial cells in idiopathic autism. The techniques she mastered make her an excellent fit to the lab: Primary hippocampal cultures, receptor internalization, live cell Calcium imaging, SDS-PAGE, dendritic Sholl analysis, in vivo spine analysis, and network activity recording with multielectrode arrays.

Nicole Volk, Research technician: Nicole received her BS degree in Biochemistry at Rutgers, State University of New Jersey. During her undergrad research assistant studies, she studied post-transcriptional regulatory elements of neocortical neurogenesis; specifically focusing on RNA binding proteins CUGBP1 and HuD. During her first laboratory technician appointment, and expanding upon her undergraduate studies, Nicole investigated the role of mRNA decapping enzymes, DcpS and Dcp2, in neocortical neurogenesis. She joined the Colak laboratory in May 2016. In addition to routinely preparing microfluidic devices, Nicole is responsible for ordering, perfusion, tissue sectioning, maintaining mouse colonies and genotyping.

Aiman Lodhi, research volunteer: Aiman is an undergrtad student in the Biochemistry Department of Hunter College, NY. To broaden her knowledge and skills in neuroscience, she has been volunteering in our lab since August 2018 . Aiman performs cryosectioning of cerebral organoids as well as stereological countings in mice transplanted with human astrocytes. 

Former members

Nicole Sayles, rotation student

Shellie Ann Dick, rotation student

Jacques Lara, research volunteer

July 30, 2018,              Dilek is giving a talk for the Department of Neurosurgery Grand Rounds at WCM

June 29,  2018,            Mike is giving a talk for the BMRI Progress Report Seminar Series at MSKCC 

February 2018,           Dilek received her first R01

January 2018,              Mike received the NHMRC CJ Martin Biomedical Fellowship

Dec 12, 2017,              Mike is giving a talk for the Neurodevelopmental Group Meeting at MSKCC 

April 21, 2016,             Dilek is giving a talk at the Leon Levy Symposium at Columbia University

February 2016,            Dilek received the Leon Levy Foundation Junior Investigator Grant 

MAP2 and TAU stainings, hippocampal neurons in a tripartite device

Presynaptic channel

Postsynaptic channel

Techniques we use in RNA and synaptic plasticity studies:

Mouse hippocampal cultures

 

Microfluidic devices

CLICK chemistry

Mouse models

Electrophysiology (E-LTP, L-LTP and LTD)

Behavioral assays

75 days old cerebral organoid

Footprint of more than 400 organoids

GFP-positive human astrocyte transplantation into neonatal mouse cortex, imaged 2 months post-transplantation

Studying developmental pathology of neuropsychiatric diseases: Cognitive dysfunction is a core feature of neuropsychiatric diseases. We are interested in understanding the cellular mechanisms underlying the cognitive dysfunction seen in autism and schizophrenia, with a special focus on glial cells. Existing animal models do not capture the genetic heterogeneity of these polygenetic diseases, and human postmortem studies offer very limited insight into the time course of disease progression. Patient-derived induced pluripotent stem cells (iPSCs) provide the best experimental system to identify the underlying molecular and cellular defects in polygenic diseases. iPSCs can be manipulated to form brain-like structures termed cerebral organoids. This culture system recapitulates the spontaneous generation of glial cells, providing a unique opportunity to study glial-cell abnormalities using patient cerebral organoids. We use cerebral organoids derived from patient iPSCs in combination with cell sorting, transplantation, electrophysiology and mouse behavioral assays to study the role of glial cells in characteristic deficits of both autism and schizophrenia such as defective synaptic plasticity and cognitive function.

We employ control and patient cerebral organoids to spontaneously generate disease astrocytes. Cell fate specification is temporally regulated in cortical development and is defined by the sequential appearance of neurons and glia. Cerebral organoids recapitulate the temporal sequence of cortical development seen in developing embryos. Importantly, the organoid system also allows us to populate disease astrocytes in an environment that mimics the early brain pathology. Therefore, cerebral organoids are likely to serve as a more representative system to preserve disease-specific features in patient astrocytes compared to directed differentiation protocols.

Techniques we use to study developmental pathology of neuropsychiatric diseases:

Patient iPSC-derived cerebral organoids

Cell sorting

2-photon Calcium imaging

Multielectrode arrays

Proteomics and single-cell RNA sequencing

Cell transplantation 

Stereological cell counting

Electrophysiology (E-LTP, L-LTP and LTD)

Behavioral assays

Spontaneous and ATP-evoked calcium activity of astrocytes in human cerebral organoids

Fluo-4 AM: Calcium sensor; SR-101; Astrocyte-specific dye

Our lab is more than 800 square feet and located at the Center for Neurogenetics on the 10th floor in the newly constructed Belfer building of Weill Cornell Medical College in New York City. We have access to two confocal microscopes (Olympus FV1000 and Zeiss 510), a 2-photon microscopy (Olympus), a Multi-Electrode Array (MEA, Axion BioSystems) and Illumina NextSeq 500 sequencing platform at no cost. The Belfer vivarium has two rooms specially equipped for behavioral phenotyping with brand-new equipment, purchased in 2016, and is managed by three recently established laboratories, including our own.

Dilek Colak, PI: Dilek is an Assistant Professor in the Brain and Mind Research Institute (BMRI). She earned her PhD degree from the Ludwig Maximilian University in Munich, Germany. Her PhD studies showed that neurogenesis in adult neural stem cells can be initiated upon inhibition of the apparent default pathway that is oligodendrogenesis. During  her PhD, Dilek was also actively involved in projects that aimed to re-instruct neurogenesis after brain injury. During her postdoc studies in New York, she explored the physiological role of local mRNA translation. Her study identified RNA degradation pathway nonsense-mediated mRNA decay (NMD) as a mechanism that regulates axon guidance in vivo. During this time, she also became interested in the mechanism of FMR1 gene silencing in Fragile X Syndrome (FXS), which is a trinucleotide repeat expansion disease and the most common monogenic cause of autism. Using FXS human embryonic stem cells, she discovered that the expanded repeats of the FMR1 mRNA interacts with the genomic DNA that then triggers FMR1 promoter repression. Her studies showed for the first time that a coding RNA could bind DNA to induce epigenetic silencing.

Michael Notaras, Postdoctoral fellow: Michael comes from Australia and holds a PhD in neuroscience from the University of Melbourne, Australia, where he studied the role of a neurotrophin coding polymorphism in sensitivity to stress and stress-induced brain remodelling. His work has led to five first author publications, including two in Molecular Psychiatry (Notaras et al., Molecular Psychiatry 2015; Notaras et al., Molecular Psychiatry 2016). He joined the Colak laboratory in 2016 to obtain postdoctoral training in the use of induced-pluripotent stem cells, 3D organotypic culturing methods, transplantation, microfluidic devices, and synaptic biology. Michael’s primary academic interest is the neurobiology of mental disorders, and he currently works on projects that seek to elucidate the mechanisms of brain aberrations that lead to schizophrenia and autism. When not in the laboratory, you may see Michael exploring New York’s food scene or find him writing in one of the many cafés on the Upper East Side of Manhattan.

Megan Allen, Postdoctoral fellow: Megan recently finished her PhD studies in Georgetown University, Washington-DC, in the neuroscience program. Her work revealed that the protease MMP-1 regulates synaptic plasticity through increases in intracellular Ca2+ concentrations and dendritic arborization in hippocampal neurons in vitro and in vivo (Allen et al., Scientific Reports 2016). In addition to her first author paper, she has published five co-author papers during her PhD studies. Megan is currently working on projects that explore the role of glial cells in idiopathic autism. The techniques she mastered make her an excellent fit to the lab: Primary hippocampal cultures, receptor internalization, live cell Calcium imaging, SDS-PAGE, dendritic Sholl analysis, in vivo spine analysis, and network activity recording with multielectrode arrays.

Estibaliz Barrio Alonso, Postdoctoral fellow: Estibaliz comes from Spain and received her PhD from the Cajal Institute in Madrid. Her PhD studies focused on revealing how an aberrant re-entry in cell cycle by a differentiated neuron can affect its synaptic and functional properties. Her results showed that cell cycle reentry in neurons might contribute to cognitive impairment in early stages of Alzheimer’s disease and neuronal death susceptibility at later stages. Estibaliz has expertise in patch clamp technique. She will join the Colak lab in October 2019. Her studies will focus on the role of circadian rhythm proteins in synaptic plasticity and cognitive function.

Nicole Volk, Research technician: Nicole received her BS degree in Biochemistry at Rutgers, State University of New Jersey. During her undergrad research assistant studies, she studied post-transcriptional regulatory elements of neocortical neurogenesis; specifically focusing on RNA binding proteins CUGBP1 and HuD. During her first laboratory technician appointment, and expanding upon her undergraduate studies, Nicole investigated the role of mRNA decapping enzymes, DcpS and Dcp2, in neocortical neurogenesis. She joined the Colak laboratory in May 2016. In addition to routinely preparing microfluidic devices, Nicole is responsible for ordering, perfusion, tissue sectioning, maintaining mouse colonies and genotyping.

Tanya Jain, Rotation student:  Tanya jopined the Neuroscience Graduate program of Weill Cornell Medical College in September 2018. She worked at the New York Stem Cell Foundation (NYSCF) as a technician for two years before joining Weill Conrell's Graduate Program. At the NYSCF, she gained expertise in developing glia differentiation protocols from induced stem cells. In the Colak Lab, Tanya has learnt mouse behavioral tests. 

Aiman Lodhi, research volunteer: Aiman is an undergrtad student in the Biochemistry Department of Hunter College, NY. To broaden her knowledge and skills in neuroscience, she has been volunteering in our lab since August 2018 . Aiman performs cryosectioning of cerebral organoids as well as stereological countings in mice transplanted with human astrocytes. 

Former members

Nicole Sayles, rotation student

Shellie Ann Dick, rotation student

Jacques Lara, research volunteer

Sept 18, 2019,            Dilek is giving a talk for the Department of Biological Sciences at St. John's University

August 2019,              Mike's paper got accepted at Molecular Psychiatry!! This is the first paper from our lab.

June 2019,                   We got the second R01 grant!!!!!  

Feb 11, 2019,              Megan is giving a talk for the Stem Cell Forum supported by the Tri-

                                      Institutional Stem Cell Initiative, 12:30pm Room ZRC-136

Dec 18, 2018,              Megan is giving a talk for the Neurodevelopmental Group Meeting at MSKCC, 4:30pm

                                      Room RRL-117 

July 30, 2018,              Dilek is giving a talk for the Department of Neurosurgery Grand Rounds at WCM

June 29,  2018,            Mike is giving a talk for the BMRI Progress Report Seminar Series at WCM

May 4, 2018,               Dilek is giving a talk for the Molecular Biology Special Seminar Series at MSKCC 

February 2018,           Dilek received her first R01

January 2018,              Mike received the NHMRC CJ Martin Biomedical Fellowship

Dec 12, 2017,              Mike is giving a talk for the Neurodevelopmental Group Meeting at MSKCC 

April 21, 2016,            Dilek is giving a talk at the Leon Levy Symposium at Columbia University

February 2016,           Dilek received the Leon Levy Foundation Junior Investigator Grant 

Deglincerti, A., Liu, Y., Colak, D., Hengst, U., Xu, G., Jaffrey, S.R. Coupled local translation and degradation regulate growth cone collapse. Nat Commun 6:6888 (2015).

Colak, D., Zaninovic, N., Cohen, M.S., Rosenwaks, Z., Yang, W.Y., Gerhardt, J., Disney, M.D., Jaffrey, S.R.  Promoter-bound trinucleotide repeat mRNA drives epigenetic silencing in Fragile X syndrome.  Science 343:1002-5 (2014).

Gerhardt, J., Tomishima, M., Zaninovic, N., Colak, D., Yan, Z., Zhan, Q., Rosenwaks, Z., Jaffrey, S.R., Schildkraut, C.L.  The DNA replication program is altered at the FMR1 locus in fragile X embryonic stem cells. Mol Cell 53:19-31 (2014).

Colak, D., Ji, S.-J., Porse B.T., Jaffrey, S.R.  Regulation of axon guidance by compartmentalized nonsense-mediated mRNA decay. Cell 153:1252-65 (2013) (Previewed by Nicolas Preitner, Jie Quan and John G. Flanagan, Cell 153:1185-7).

Sirko, S., Behrendt, G., Johansson, P.A., Tripathi, P., Costa, M., Bek, S., Heinrich, C., Tiedt, S., Colak, D., Dichgans, M., Fischer, I.R., Plesnila, N., Staufenbiel, M., Haass, C., Snapyan, M., Saghatelyan, A., Tsai, L.H., Fischer, A., Grobe, K., Dimou, L., Götz, M.  Reactive glia in the injured brain acquire stem cell properties in response to sonic hedgehog.  Cell Stem Cell 12:426-39 (2013).

Mira, H., Andreu, Z., Suh, H., Lie, C.D., Jessberger, S., Emeterio, J.S., Hortigüela, R., Marqués-Torrejón, M.A., Nakashima, K., Consiglio, A., Colak, D., Götz, M., Fariñas, I., and Gage, F.H.  Signalling through BMPR-IA regulates quiescence and long-term activity of neural stem cells in the adult hippocampus. Cell Stem Cell 7:78-89 (2010).

Jawerka, M., Colak, D., Dimou, L., Spiller, C., Lagger, S., Montgomery, R.L., Olson, E.N., Wurst, W., Göttlicher, M., Götz, M.  The specific role of histone deacetylase 2 in adult neurogenesis.  Neuron Glia Biol 6:93-107 (2010).

Colak, D., Mori, T., Brill, M.S., Pfeifer, A., Falk, S., Deng, C., Monteiro, R., Mummery C., Sommer, L., Götz, M.  Adult neurogenesis requires Smad4-mediated bone morphogenic protein signaling in stem cells.  J Neurosci 28:434-46 (2008).

Buffo, A., Rite, I., Tripathi, P., Lepier, A., Colak, D., Horn, A.P., Mori, T., Götz, M. Origin and progeny of reactive gliosis - a novel source of multipotent cells in the injured brain.  Proc Natl Acad Sci U S A 105:3581-6 (2008).

Ma, L., Cantrup, R., Varrault, A., Colak, D., Klenin, N., Götz, M., McFarlane, S., Journot, L., Schuurmans, C. Zac1 functions through TGFbetaII to negatively regulate cell number in the developing retina.  Neural Develop 2:11 (2007).

Buffo, A., Vosko, MR., Erturk*, D., Hamann, GF., Jucker, M., Rowitch, D., Götz, M.  Expression pattern of the transcription factor Olig2 in response to brain injuries: implications for neuronal repair.  Proc Natl Acad Sci U S A 102:18183-8 (2005). * Erturk: Previously used last name.