NEU2004 Neuroanatomy Workshop 2 Gene expression profiling, structural and functional connectivity

NEU2004 Neuroanatomy Workshop 2 Gene expression profiling, structural and functional connectivity.

Learning Objectives. To understand the major methods for exploring gene expression in the brain. To describe the major brain-imaging technologies that have developed to explore the structure, connectivity and function of the living brain. To understand the contribution of computerized tomography (CT) to defining brain structure. To characterize the major magnetic resonance imaging (MRI) methods that are being used to explore structure, function, and connectivity in health, disease and experimental paradigms. To describe the methods of p ositron emission tomography and its application to understanding brain function in health and disease. To be aware of the advantages and limitations of different neuroimaging methods..

Multiscale organization of human brain structure, function, behaviour, and disorders.

Electrophysiological techniques to localize function and impute connectivity.

Gene Expression – Fluorescent in situ hybridization (FISH).

Single gene expression profiling of miRNA-101 (an autopahagy regulator) in a mouse model of AD ( in situ hybridization).

Gene expression (transcriptomics) in human brain tissue Transcriptome analysis shows that 74% (n=14,518) of all human proteins (n=19,613) are expressed in the brain 1,460 of these genes show an elevated expression in brain compared to other tissue types In situ hybridization RNAscope ISH (Single-cell quantification of mRNA in many genes) DNA microarray (binds to labelled cDNA (from mRNA)(25-70 bases used as hybridization probes) High-throughput sequencing or RNA- Seq (global gene expression studies - next-generation sequencing).

Lake BB et al. Nat Biotechnol. 2018;36:70–80.. Sample Archived Brain Tissues Frontal Cortex Cryosectjon Cerebellar Hemtsphere Nuclei Run Single Nucleus Assays snDrop-seq scTHS-seq Annotate Cell expression gone/access& site map chromatin Discover Cell Type-Spectt•c Profiles expression Markers.TFs. TF Targets Disease Relevance regulation.

Neurons in different nuclei have variable patterns of gene expression.

Of a Brain Cell-type Transcriptomic Reference Panel Micro glia Astro Oligo Panel C uration Aleorithm Evalu•tior Ssn* estimat•on Micr%lia with ure Estimation Accuracy Gene Specific Study Cellular Population Structure in Neurodegenerative Disorders Preprocessing Pipeline Extensive QC Salmon Quantification DIAN ADRC MSB8 MSBB DIAN Analysis Of Differential Distribution Mayo PA PLD3 TREM2 Knight ADRC.

13.1 78.4 100% 36.5 50.6 Disease Type 36.8 50.4 63.5 Braak Stage ß = -0.03 p-value = 8.51 xlO-C6 37.4 52.8 31.3 50.9 23.5 66. 25.7 = 31 63.9 52.3 ß = 0.03 p-value = 2.66x10-02 p-value = 3.83xIO-Ø LOAD 31 59.6 CDR 26.2 60.5 LOAD Variants 18 Cell 64.4 ß = 0.03 p-value = 5.48x10,03 100% 23.2 -64.9 AD Neuron 25.7 64.5 PLD3 30.3 59.7 TREM2 19 71.6 36.8 = 16 Cmtrol.

Pathophysiology A+: brain amyloidosis T+: tau pathology N+: neurodegeneration Detection Methods Amyloid PET Tau PET FOG PET Structural MRI CSF AßQ or Aß42 / APO ratio CSF p-tau181 CSF t-tau or.

Biomarker 1 Biomarker 2 Biomarker I biomarker Biomarker Biomarker 1 Biomarker 2 arker Biomarker 1 arkef Multidimensional Space Dimensionality Reduction.

Neuroimaging - Visualizing the Human Brain Biological psychology has been revolutionized by recently developed brain-imaging technologies: Computerized tomography, Magnetic resonance imaging, Positron emission tomography. These techniques make possible the study of both brain anatomy and patterns of brain activation in living, healthy human beings. Bain imaging is playing a major role in the study of the neural basis of human thought and language..

Computerized Tomography Computerized tomography (CT) introduced in 1973. CT is an enhancement of the familiar X-ray procedure. In CT, narrow X-ray beams are passed through the head in a particular cross-sectional slice from a wide variety of angles. The amount of radiation absorbed along each line is measured. From the measurements associated with each beam, a computer program can determine the density of tissue at each point in the slice. The resulting image is the CT scan. CT is most commonly indicated in the emergency room evaluation of patients with acute head trauma and acute neurological dysfunction (intracranial or subarachnoid hemorrhage ). E xtremely rapid acquisition time and sensitivity of detecting hemorrhage makes it the modality of choice in the acute setting..

Magnetic Resonance Imaging Magnetic resonance imaging (MRI) provides a reconstructed image of slices of living tissue. MRI exploits a phenomenon known as nuclear magnetic resonance, in which radio-frequency energy in a strong magnetic field is used to generate signals from a particular atom - usually hydrogen - contained within the tissue. Advantages over CT: N o ionizing radiation is employed. MRI images have fine spatial resolution. I t is possible to obtain slices at any angle, not just in the horizontal plane, as is the case with CT. Three-dimensional images of the brain may also be generated. A dvanced MRI methods have recently permitted the imaging of brain function as well as structure , measuring both brain blood flow and oxidative metabolism..

The neural origins of the fMRI BOLD signal. (1) Neuronal activity (2) Neurovascular (3) Haemodynamic response fMRI BOLD response Stimulus or modulation in background activity - Excitatory activity and inhibitory activity - Anaesthetic influence coupling - Metabolic Signal unknown - Anaesthetic influence O O o - Blood flow - Blood oxygenation level - Blood volume - Haematocrit (4) Detection by MRI scanner - Magnetic field strength - TR. repetition time - TE, echo time - Spin or gradient echo EPI.

Tractography - Diffusion Tensor Imaging. CSF Isotropic High diffusivity Grey matter Isotropic Low diffusivity White matter Anisotropic High diffusivity.

Differences among the imaging techniques, MRI, fMRI, and DTI.

Positron Emission Tomography Provide images indicating the functional or physiological properties of the living human brain. PET involves the injection of a tracer substance labeled with a positron-emitting radionuclide. One common tracer is labeled fluorodeoxyglucose (FDG) that is taken up by cells when they need glucose for nutrition. Over the course of a few minutes, metabolically active portions of the brain accumulate more FDG than less active regions. By determining where FDG is accumulating in the brain, patterns of differential brain activation can be mapped. PET scanning is now widely used to study patterns of brain activity that underlie higher mental functions..

Aβ Deposition detected by PET in Autosomal Dominant Alzheimer’s Disease Years before Expected Clinical Symptoms.

PIB Binding t CSF Tau Hippocampal Volume Brain Metabolism Episodic Memory -25 CSF Aß -20 -15 -10 Years -5 t CDR +5 Estimated Age at Onset of Symptoms.

PET-PiB b -Amyloid Imaging in AD. T. Benzinger, DIAN.

Summary. There are several methods that may be used to explore patterns of gene expression both within a single neuron and in anatomical regions. A number of major brain-imaging technologies have been developed to explore the structure, connectivity and function of the living brain. Computerized tomography (CT) has contributed to defining brain structure in health and disease. Several magnetic resonance imaging (MRI) methods have been developed that are being used to explore structure (MRI), function (fMRI), and connectivity (DTI) in health, disease and experimental paradigms. Positron emission tomography (PET) imaging has been used to further understand brain function in health and disease. Neuroimaging methods have many advantages over other more invasive methods to investigate structure, function and connectivity; however, there are and limitations too each of the different neuroimaging methods and these limitations may be overcome partially by using batteries of methods covering different attributes of brain activity..

Workshop 2 Journal Review Prevention of tau seeding and propagation by immunotherapy with a central tau epitope antibody. Albert M, Mairet-Coello G, Danis C, Lieger S, Caillierez R, Carrier S, Skrobala E, Landrieu I, Michel A, Schmitt M, Citron M, Downey P, Courade JP, Buée L, Colin M. Brain. 2019;142(6):1736-1750. doi : 10.1093/brain/awz100..

26. Misfolded proteins (tau and A b ) in AD brain.

Protein Misfolding Diseases. 27. Other proteins (1 ) Chaperones (3) Aggregation Folded protein Lag phase Misfolded protein (2) Degradation Growth phase Oligomer Plateau phase Fibril Soluble Amyloids Aggregate Liquid phase.

Potential mechanisms for trans-cellular propagation of misfolded proteins.

Trans -cellular propagation of misfolded proteins – target for immunotherapy.