Ginsberg Lab

Head of Lab

Stephen D. Ginsberg, PhD

Ginsberg Lab Members

Melissa J. Alldred, PhD - Research Scientist/NKI; Research Assistant Professor, Dept of Psychiatry/NYULMC [email]

Judah Beilin - Undergraduate participant in the Summer Undergraduate Research Program (SURP) [email]

Tatyana Budylin, PhD - Research Technician/ NKI [email]

Shaoli Che, MD, PhD - Research Scientist/ NKI; Research Assistant Professor, Department of Psychiatry/ NYULMC [email] [CV]

Irina Elarova, MS - Research Technician/ NKI [email]

Shaona Fang, BS - Research Technician/ NKI [email]

Abigail Mariga - Graduate student, Cell and Molecular Biology Program (CMB)/ NYULMC [email]

Arthur Saltzman, MS - Research Technician / NKI [email]

Publications

All publications

 

About the Ginsberg Lab

Led by Stephen D. Ginsberg, Ph.D., the principal focus of the Ginsberg laboratory in the Ginsberg LabCenter for Dementia Research (CDR) is to delineate cellular and molecular mechanisms underlying cellular, synaptic, and dendritic reorganization following neurodevelopmental and neurodegenerative brain insults. The Ginsberg laboratory employs the use of animal and cellular models of neurodegeneration as well as human postmortem brain tissues for functional genomic and proteomic based studies. Steve’s underlying hypothesis is that individual cell types are likely to have unique patterns of gene and protein expression under normative conditions that are altered in pathological states, which drives subsequent neurodegeneration. Indeed, the molecular and cellular basis of why certain neuronal populations are vulnerable to neurodegeneration, often termed “selective vulnerability”, can be elucidated by discrete cell analysis more readily than by utilizing regional and total brain preparations. The hippocampal formation and cholinergic basal forebrain, brain regions critical for learning and memory, are the main structures analyzed, with particular emphasis given to identifying mechanisms that underlie changes within specific cell types, including cholinergic basal forebrain (CBF) neurons, dentate gyrus granule cells, CA1 & CA3 pyramidal neurons, and entorhinal cortex stellate cells. Experiments are conducted on animal and cellular models of neurodegeneration, including mouse models of amyloid overexpression, Down syndrome (DS), and tauopathy. The Ginsberg lab also conducts parallel studies on postmortem human brain tissues accrued from subjects diagnosed with Alzheimer’s disease (AD), DS, mild cognitive impairment (MCI), and nondemented controls with no cognitive impairment (NCI). Dr. Ginsberg is also spearheading a program to investigate selective vulnerability of specific pyramidal neurons and GABAergic interneurons in schizophrenia (SZ) and major depressive disorder (MDD).

The Ginsberg Laboratory has provided essential data in human and relevant mouse models that compare and contrast cells that degenerate (e.g., CBF neurons, CA1 hippocampal pyramidal neurons, and glutamatergic neocortical pyramidal neurons) versus cells that are relatively spared within these specific paradigms (e.g., dentate gyrus granule cells). Dr. Ginsberg is one of the relatively few neuroscientists that conduct expression profiling research at the single cell level consistently. Dr. Ginsberg developed his own RNA amplification technology termed terminal continuation (TC) RNA amplification which is employed in conjunction with microarray and qPCR based investigations of gene expression at the single cell level. The Ginsberg laboratory has just developed a new technology for the amplification of microRNAs termed miRNA signature sequence amplification (SSAM) for biomarker discovery science. miRNAs are a short 17-25 nucleotide class of non-protein coding RNAs (ncRNAs) that have been shown to have critical functions in a wide variety of biological processes. One major obstacle when profiling miRNAs is their low expression level. miRNAs are estimated to constitute only 0.01% of total RNA. As a result, large quantities of starting materials were required for miRNA profiling until the advent of the developing SSAM technology.

Recent research achievements include:
Postmortem single cell gene expression analyses in hippocampal CA1 pyramidal neurons demonstrating up regulation of endosomal markers (including rab GTPases rab5 and rab7) with concomitant down regulation of the BDNF receptor TrkB in AD and mild cognitive impairment (MCI). Based on these postmortem human microarray, qPCR, and protein-based observations, we were able to determine in vitro that rab5 down regulates TrkB expression, providing a potential mechanism for lack of neurotrophic support during the progression of AD.

Postmortem single cell gene expression analyses in cholinergic basal forebrain (CBF) neurons demonstrating down regulation of nerve growth factor receptor TrkA, BDNF receptor TrkB, and neurotrophin-3 receptor TrkC, but not the pan-nerve growth factor receptor p75 in AD and MCI.

Correlation of antemortem cognitive decline with postmortem down regulation of TrkB and up regulation of rab5 and rab7 expression within individual CBF and CA1 neurons in normal control, MCI, and AD patients.

Identifying a shift in the expression of 3-repeat tau (3Rtau) relative to 4-repeat tau (4Rtau) within individual CBF neurons and CA1 pyramidal cells in MCI and AD as compared to normal controls.

Characterizing transcripts and proteins in adult mice that are differentially regulated in the dentate gyrus (granule cells as well as granule cell dendrites) following perforant path lesions over a 6 month postlesion time course including specific NMDA receptors and AMPA glutamate receptors.

Demonstrating specific transcripts are differentially regulated in hippocampal CA1 neurons that bear neurofibrillary tangles (NFTs) in AD versus non-tangle bearing CA1 neurons in normal control brains.

Illustrating that classes of transcripts within single CA1 pyramidal neurons tended to be genes related to neuronal communication, whereas glial-associated markers were under represented in CA1 pyramidal neurons relative to regional hippocampal dissections. These observations highlight a dilution effect that is likely to occur in conventional regional microarray and qPCR studies.

Current research endeavors include:
Expression profiling of neocortical pyramidal neurons as well as calbindin-immunoreactive and parvalbumin-immunoreactive interneurons within the auditory cortex of schizophrenics compared to age-matched normal controls.

Molecular fingerprinting of hippocampal CA1 pyramidal neurons throughout the lifespan of a mouse model of tauopathy (hTau mice).

Expression profiling of hippocampal and basal forebrain circuits at time points before and following cholinergic neurodegeneration a mouse model of Down’s syndrome and AD (Ts65Dn mice).

Assessment of hippocampal pyramidal neurons and entorhinal cortex stellate cells in mouse models of AD and DS (Tg2576 mouse and Ts65Dn mouse) following caloric restriction.

Single cell expression profiling of the six isoforms of tau as well as truncated tau isoforms within vulnerable cell types in postmortem human brains in AD and related tauopathies as well as tauopathy animal models.

Future endeavors include:
Nanotechnology development of RNA amplification to facilitate expression profiling of processes (including dendritic spines and developing axonal profiles) and subcellular elements (including mitochondria and lysosomes) that can test the overriding hypothesis of selective vulnerability within specific forebrain circuits.

Subcellular fractionation (including synaptic, postsynaptic density, and mitochondrial fractions) of tissue homogenates for discrete proteomic evaluations including tandem MS/MS and MALDI-TOF assessments in postmortem hippocampus in normal, MCI, and AD as well as analysis of subcellular fractions in normal mice and transgenic models subjected to perforant path transections.

Ginsberg Lab TC RNA Amplification Protocol
Click here to view protocol or click the icon to download as a PDF.

Selected publications since 2008 (from a total of 75 peer-reviewed manuscripts and 23 book chapters)

Ginsberg, S.D.: Transcriptional profiling of small samples in the central nervous system. Methods Mol. Biol., 439: 147-158, 2008. PMID: 18370101. PMCID: PMC2648843.

Levine, S., Saltzman, A., and Ginsberg, S.D.: Different inflammatory reactions to vitamin D(3) among the lateral, third and fourth ventricular choroid plexuses of the rat. Exp. Mol. Pathol., 85: 117-121, 2008. PMID: 18675267.

Mufson, E.J., Counts, S.E., Perez, S., and Ginsberg, S.D.: Cholinergic system during the progression of Alzheimer’s disease: therapeutic implications. Expert Rev. Neurother., 8: 1703-1718, 2008. PMID: 18986241. PMCID: PMC2631573.

Alldred, M.J., Che, S., and Ginsberg, S.D.: Terminal continuation (TC) RNA amplification enables expression profiling using minute RNA input obtained from mouse brain. Int. J. Mol. Sci., 9: 2091-2104, 2008. PMID: 19165351. PMCID: PMC2629436.

Ginsberg, S.D., Che, S., Counts, S.E., and Mufson, E.J.: Gene expression abnormalities mark the progression of Alzheimer's disease. In Sun, M.K. (ed): Research Progress in Alzheimer's Disease and Dementia, Volume 3, Hauppauge: Nova Science Publishing, pp. 25-58, 2008. ISBN-13: 978-1-60021-960-3.

Ginsberg, S.D.: Single and rare cell analysis-amplification methods. T7 based amplification protocols. In Bosio, A. and Gerstmayer, B. (eds): Microarrays in Inflammation. Progress in Inflammation Research, Basel: Birkhäuser-Verlag, pp. 81-94, 2008. ISBN-13: 978-3-7643-8333-6.

Altar, C.A., Vawter, M., and Ginsberg, S.D.: Target identification for CNS diseases by transcriptional profiling. Neuropsychopharmacology, 34: 18-54, 2009. PMID: 18923405. PMCID: PMC2675576.

Alldred, M.J., Che, S., and Ginsberg, S.D.: Terminal continuation (TC) RNA amplification without second strand synthesis. J. Neurosci. Meth., 177: 381-385, 2009. PMID: 19026688. PMCID: PMC2659495.

Levine, S., Saltzman, A., Levy, E., and Ginsberg, S.D.: Systemic pathology in aged mouse models of Down's syndrome and Alzheimer's disease. Exp. Mol. Pathol., 86: 18-22, 2009. PMID: 19041304. PMCID: PMC2659493.

Choi, J.H.K., Berger, J.D., Mazzella, M.J., Morales-Corraliza, J., Nixon, R.A., Ginsberg, S.D., Levy, E., and Mathews, P.M.: Age-dependent dysregulation of brain amyloid precursor protein in the Ts65Dn Down syndrome mouse model. J. Neurochem., 110: 1818-1827, 2009. PMID: 19619138. PMCID: PMC2744432.

Jiang, Y., Mullaney, K.A., Peterhoff, C.M., Che, S., Schmidt, S.D., Boyer-Boiteau, A., Ginsberg, S.D., Cataldo, A.M., Mathews, P.M., and Nixon, R.A.: Alzheimer’s-related endosome dysfunction in Down syndrome is Abeta-independent but requires APP and is reversed by BACE-1 inhibition. Proc. Natl. Acad. Sci. USA, 107: 1630-1635, 2010. PMID: 20080541. PMCID: PMC2824382.

Ginsberg, S.D.: Alterations in discrete glutamate receptor subunits in adult mouse dentate gyrus granule cells following perforant path transection. Anal. Bioanal. Chem., 397: 3349-3358, 2010. PMID: 20577723. PMCID: PMC3149099.

Levine, S., Saltzman, A., and Ginsberg, S.D.: Mitotic figures in the median eminence of the hypothalamus. Neurochem. Res., 35: 1743-1746, 2010. PMID: 20680457. PMCID: PMC3148030.

Haskew-Layton, R.E., Payappilly, J.B., Smirnova, N.A., Ma, T.C., Chan, K.K., Murphy, T.H., Guo, H., Langley, B., Sultana, R., Butterfield, D.A., Santagata, S., Alldred, M.J., Gazaryan, I.G., Bell, G.W., Ginsberg, S.D., and Ratan, R.R.: Controlled enzymatic production of astrocytic hydrogen peroxide protects neurons from oxidative stress via an Nrf2 independent pathway. Proc. Natl. Acad. Sci. USA, 107: 17385-17390, 2010. PMID: 20855618. PMCID: PMC2951414.

Ginsberg, S.D., Alldred, M.J., Counts, S.E., Cataldo, A.M., Neve, R.L., Jiang, Y., Wuu, J., Chao, M.V., Mufson, E.J., Nixon, R.A., and Che, S.: Microarray analysis of hippocampal CA1 neurons implicates early
 endosomal dysfunction during Alzheimer’s disease progression. Biol. Psychiatry, 68: 885-893, 2010. PMID: 20655510. PMCID: PMC2965820.

Kaur, G., Mohan, P., Pawlik, M., DeRosa, S., Fajiculay, J., Che, S., Grubb, A., Ginsberg, S.D., Nixon, R.A., and Levy, E: Cystatin C rescues degenerating neurons in a cystatin B-knockout mouse model of progressive myoclonus epilepsy. Am. J. Pathol., 177: 2256-2267, 2010. PMID: 20889561. PMCID: PMC2966785.

Ginsberg, S.D.: Microarray use for the analysis of the CNS. In Squire, L.R. (ed): Encyclopedia of Neuroscience, Volume 5, Oxford: Academic Press, pp. 835-841, 2009. ISBN-13: 978-0-08-045046-9.

Ginsberg, S.D.: Gene microarrays. In Kompoliti, K., and Verhagen Metman, L. (eds): Encyclopedia of Movement Disorders. Oxford: Academic Press, pp. 538-540, 2010. ISBN: 978-0-12-374101-1.

Mufson, E.J., Counts, S.E., Perez, S.E., and Ginsberg, S.D.: Cholinergic systems in aging and Alzheimer’s disease: neurotrophic and molecular analysis. In Koob, G.F., Le Moal, M., and Thompson, R.F. (eds): Encyclopedia of Behavioral Neuroscience, Volume 1, Oxford: Academic Press, pp. 249-256, 2010. ISBN-13: 978-0-08-044732-2.

Devi, L., Alldred, M.J., Ginsberg, S.D., and Ohno, M.: Sex- and brain region-specific acceleration of beta-amyloidogenesis following behavioral stress in a mouse model of Alzheimer's disease. Molecular Brain, 3: 34, 2010. PMID: 21059265. PMCID: PMC2988063.

Ginsberg, S.D., Mufson, E.J., Counts, S.E., Wuu, J., Alldred, M.J., Nixon, R.A., and Che, S.: Regional selectivity of rab5 and rab7 protein upregulation in mild cognitive impairment and Alzheimer’s disease. J. Alzheimers Dis., 22: 631-639, 2010. PMID: 20847427. PMCID: PMC3031860.

Counts, S.E., Perez, S.E., Ginsberg, S.D., and Mufson, E.J.: Neuroprotective role for galanin in Alzheimer’s disease. EXS, 102: 143-162, 2010. PMID: 21299067. PMCID: PMC3117305.

Levine, S., Saltzman, A., and Ginsberg, S.D.: Vacuolar pathology in the median eminence of the hypothalamus after hyponatremia. J. Neuropathol. Exp. Neurol., 70: 151-156, 2011. PMID: 21343884. PMCID: PMC3074179.

Ginsberg, S.D., Mufson, E.J., Alldred, M.J., Counts, S.E., Wuu, J., Nixon, R.A., and Che, S.: Upregulation of select rab GTPases in cholinergic basal forebrain neurons in mild cognitive impairment and Alzheimer's disease. J. Chem. Neuroanat., 42: 102-110, 2011. PMID: 21669283. PMCID: PMC3163754.

Counts, S.E., Che, S., Ginsberg, S.D., and Mufson, E.J.: Gender differences in neurotrophin and glutamate receptor expression in cholinergic nucleus basalis neurons during the progression of Alzheimer's disease. J. Chem. Neuroanat., 42: 111-117, 2011. PMID: 21397006. PMCID: PMC3155625.

Ginsberg, S.D., Che, S., Hashim, A., Zavadil, J., Cancro, R., Lee, S.H., Petkova, E., Sershen, H.W., and Volavka, J.: Differential regulation of catechol-O-methyltransferase expression in a mouse model of aggression. Brain Struct. Funct., 216(4):347-56, 2011. PMID: 21512897. PMCID: PMC3199365.

Mufson, E.J., Perez, S., Kelley, C.M., Chu, S., Galarza, A., Blakely, S., and Ginsberg, S.D.: Fixation protocols for neurohistology: neurons to genes. In Walz, C.M., and Doucette, R. (eds): Neurohistology and Imaging: Basic Techniques, Totowa: Humana Press, in press.

Ginsberg, S.D., Alldred, M.J., and Che, S.: Gene expression profiling using the terminal continuation (TC) RNA amplification method for small input samples in neuroscience. In Karamanos, Y. (ed): Expression Profiling in Neuroscience, Neuromethods, Volume 64. New York: Humana Press, 2012. ISBN 978-1-61779-447-6.

Ginsberg, S.D., Alldred, M.J., and Che, S.: Gene expression levels assessed by CA1 pyramidal neuron and regional hippocampal dissections in Alzheimer's disease. Neurobiol. Dis., 45(1):99-107, 2012. PMID: 21821124. PMCID: PMC3220746.