Neurogenomics Seminar

28 June, 16:00-17:00

Dr Jacob Schreiber

Stanford University

Navigating the Pitfalls of Applying Machine Learning in Genomics

The recent surge in the scale and scope of genomics data has prompted the development of computational methods for integration and analysis. However, when these methods involve machine learning, they run the risk of being improperly applied and silently yielding insights or results that are completely incorrect. This talk will describe five interrelated statistical pitfalls one might encounter when applying machine learning in practice and strategies for avoiding them. Although these pitfalls are general, examples will be drawn from genomics. The overarching gist is: be more skeptical of your results, particularly when they're good.

Neurogenomics Seminar

14 June, 15:00-16:00

Kaya Matson & Dr Archana Yadav

Columbia University

An atlas of adult human spinal cord reveals molecular basis for motoneuron disease susceptibility

In neurodegenerative diseases of the human spinal cord, such as amyotrophic lateral sclerosis (ALS), motoneurons are particularly vulnerable to degeneration. It is hypothesized that their large size contributes to disease susceptibility, but the link between genetic variants associated with disease and cell-type specific degeneration is not clear. We characterized human spinal cord cells using single-nucleus RNA-sequencing and protein profiling. We found that human motoneurons displayed a unique expression profile characterized by factors involved in cytoskeletal structure, cell size, and degenerative disease (including ALS-associated genes SOD1, NEFH, OPTN, TUBA4A, PRPH, and STMN2) and that protein expression of these genes correlated with larger cell size in tissue. This work suggests a motoneuron-specific signature underlies their selective vulnerability to neurodegeneration.

Neurogenomics Seminar

31 May, 15:00-16:00

Dr Kiran Girdhar

Icahn School of Medicine

Chromatin domain alterations linked to 3D genome organization in a large cohort of schizophrenia and bipolar disorder brains

Chromosomal organization, scaling from the 147-base pair (bp) nucleosome to megabase-ranging domains encompassing multiple transcriptional units, including heritability loci for psychiatric traits, remains largely unexplored in the human brain. In this study, we constructed promoter- and enhancer-enriched nucleosomal histone modification landscapes for adult prefrontal cortex from H3-lysine 27 acetylation and H3-lysine 4 trimethylation profiles, generated from 388 controls and 351 individuals diagnosed with schizophrenia (SCZ) or bipolar disorder (BD) (n = 739). We mapped thousands of cis-regulatory domains (CRDs), revealing fine-grained, 104-106-bp chromosomal organization, firmly integrated into Hi-C topologically associating domain stratification by open/repressive chromosomal environments and nuclear topography. Large clusters of hyper-acetylated CRDs were enriched for SCZ heritability, with prominent representation of regulatory sequences governing fetal development and glutamatergic neuron signaling. Therefore, SCZ and BD brains show coordinated dysregulation of risk-associated regulatory sequences assembled into kilobase- to megabase-scaling chromosomal domains.

Neurogenomics seminar

17 May, 16:00-17:00

Dr Andrew C Yang

Dr Andrew C Yang, who recently started his own research group at UCSF, will present exciting work on gene expression in cells of the brain vasculature and their links to Alzheimer’s disease. Check out his impressive recently published atlas of the brain vasculature here: https://www.nature.com/articles/s41586-021-04369-3

Molecular approaches to decode the human blood-brain barrier

The brain vasculature is of vast medical importance: its dysfunction is a leading cause of death and its specialization—the blood-brain barrier (BBB)—impedes treatment of nearly all brain disorders. Yet so far, we have no molecular map of the human brain vasculature. We recently developed a method, vessel isolation and nuclei extraction for sequencing (VINE-seq), to provide molecular definitions for human brain vascular, perivascular, and immune cell types in health and Alzheimer’s disease (AD). Intriguingly, we find several AD risk genes expressed in the human brain vasculature, many microglia-specific in mice. Future work will explore how human brain vascular cells and genes may be causally linked to AD pathology, cognitive dysfunction, and risk.

Neurogenomics seminar

3 May, 15:00-16:00

Dr Elizabeta Gjoneska

National Institute of Environmental Health Sciences (NIEHS) and NIH

Dissecting Mechanisms of Microglia Dysfunction in Alzheimer’s Disease

Microglia, the resident immune cells of the brain, are not just sensors of pathological events as initially described, but rather play an active role as drivers of neurological disease.  Using high-throughput sequencing to profile chromatin and transcriptional changes in mouse models of Alzheimer’s disease (AD), we previously identified AD-relevant noncoding DNA regulatory regions and demonstrated that genetic predisposition to the disease is encoded in the regions that regulate microglia function.  We also identified key proteins, such as transcription factors and chromatin modifiers that target these regulatory regions and mediate gene expression changes during AD. Ongoing studies in the group are aimed at dissecting the mechanisms by which genetic and environmental risk factors alter the function of regulatory regions and proteins, and lead to microglia dysfunction and increasing susceptibility to AD. These studies will provide greater insight into the molecular and cellular basis of AD and facilitate the development of novel therapeutic strategies for the treatment of this disorder.   

Neurogenomics Seminar

22 February, 15:00-16:00

Dr Francesca Giannese & Dr Davide Cittaro

Dr Francesca Giannese and Dr Davide Cittaro will present their recent work profiling open and closed chromatin at the single cell level, and deriving epigenetic trajectories using Chromatin Velocity. https://www.nature.com/articles/s41587-021-01031-1

Sketching chromatin dynamics in single cells

Recent efforts have succeeded in surveying open chromatin at the single-cell level, but high-throughput, single-cell assessment of heterochromatin and its underlying genomic determinants remains challenging. We engineered a hybrid transposase including the chromodomain (CD) of the heterochromatin protein-1α (HP-1α), which is involved in heterochromatin assembly and maintenance through its binding to trimethylation of the lysine 9 on histone 3 (H3K9me3), and developed a single-cell method, single-cell genome and epigenome by transposases sequencing (scGET-seq), that, unlike single-cell assay for transposase-accessible chromatin with sequencing (scATAC-seq), comprehensively probes both open and closed chromatin and concomitantly records the underlying genomic sequences. We tested scGET-seq in cancer-derived organoids and human-derived xenograft (PDX) models and identified genetic events and plasticity-driven mechanisms contributing to cancer drug resistance. Next, building upon the differential enrichment of closed and open chromatin, we devised a strategy that identifies the trajectories of epigenetic modifications at the single-cell level. Our approach is able to uncover paths of epigenetic reorganization during stem cell reprogramming and identified key transcription factors driving these developmental processes. scGET-seq reveals the dynamics of genomic and epigenetic landscapes underlying any cellular processes.

Neurogenomics seminar

8 February, 15:00-16:00

Professor Morten Scheibye-Knudsen

University of Copenhagen

"Targeting Aging"

The process of aging is characterized by an accumulation of DNA damage likely contributing to the many pathologies observed in the elderly population. Indeed, recent findings suggest that we can intervene in the DNA damage response and thereby alleviate features of aging. In this lecture, I will describe our in silico, in vitro and in vivo methodologies aimed at understanding the basic mechanisms underlying the aging process, and how we can use this knowledge to develop interventions. Our goal, to allow everyone to live healthier and longer lives. 

Neurogenomics seminar

25 January, 15:00-16:00

Dr Samuel Marsh

Harvard and Boston Children’s Hospital

"The power and pitfalls of single cell genomics: Dissection of artifactual and confounding signatures by single cell sequencing of the mouse and human brain"

In my talk I will be discussing the power and potential pitfalls of using single cell genomics to gain better understanding of multiple CNS cell types but with a focus on microglia. I will be discussing both work in preprint (currently in press) as well as new unpublished work in both the control/healthy brain as well as in neurodegenerative disease/disease models. Below is a more detailed abstract for the first part of my talk which will focus on our recent preprint (now in press).

A key aspect of nearly all single-cell sequencing experiments is dissociation of intact tissues into single-cell suspensions.  While many protocols have been optimized for optimal cell yield, they have often overlooked the effects that dissociation can have on ex vivo gene expression. We demonstrate that use of enzymatic dissociation on brain tissue induces an aberrant ex vivo gene expression signatures, most prominently in microglia. Such signatures are widespread in published literature and can significantly confound downstream analyses. To address this issue, we present a rigorously validated protocol that preserves both in vivo transcriptional profiles and cell-type diversity and yield across tissue types and species. We also identify a similar signature in post-mortem human brain single-nucleus RNA-sequencing datasets, and show that this signature is induced in freshly-isolated human tissue by exposure to elevated temperatures ex vivo. Together our results provide a methodological solution for preventing artifactual gene expression changes during fresh tissue digestion and a reference for future deeper analysis of the potential confounding states present in post-mortem human samples.

Neurogenomics seminar

11 January, 15:00-16:00

Easwaran Ramamurthy

Carnegie Mellon University

"Using computational models and cell type-specific epigenomics to identify variants that influence Alzheimer's predisposition"

Genome wide associations studies (GWAS) are revealing an increasing number of variants associated with Alzheimer's Disease (AD) risk. These variants have been found to be enriched in regulatory genomic regions. However, identification of causal variants (or “finemapping”) and impacted cellular mechanisms remains an open problem, due to non-random association or linkage disequilibrium (LD) between variants in the population and incomplete knowledge of the cell type-specificity of regulatory region activity. In the first part of this talk, I will present our work on analyzing new epigenomic maps of 3 major brain cell types generated from the hippocampi and dorsolateral prefrontal cortices of Alzheimer’s Disease brains. We confirm that variants associated with late onset AD (LOAD) show a strong tendency to reside in microglia-specific gene regulatory elements. Strikingly, microglia do not harbor strong epigenomic differences associated with amyloid beta (Aβ) pathology. In contrast, an oligodendrocyte-enriched glial (OEG) population contains the majority of differential epigenomic peaks associated with Aβ load. These differential peaks reside near early onset risk genes, late onset AD risk loci, Aβ processing genes as well as genes involved in myelinating and oligodendrocyte development processes. These findings implicate oligodendrocyte gene regulation as a potential mechanism by which early onset and late onset AD risk genes mediate their effects, and highlight the deregulation of myelinating processes in AD. 

In the second part of my talk, I will present unpublished work on using convolutional neural network (CNN) model to finemap AD GWAS signal. We train CNN regression models that relate genome sequence to open chromatin signal in cell types relevant to disease. We validate and refine our models on massively parallel reporter assay (MPRA) data, which do not suffer from the confounds introduced by LD. Then, using in silico mutagenesis, we predict the impact of AD associated variants on open chromatin signal. Using this framework, we identify which of multiple variants in LD are likely to influence AD predisposition along with the associated cell types in which they have predicted impact on regulatory activity. Overall, we report a library of computational models which can be used to study AD regulatory variants as well as regulatory variants associated with other immune and neurological disorders.

Neurogenomics seminar

14 December, 15:00-16:00

Dr Anaelle Dumas

University of Freiburg

"Current tools to interrogate microglia biology in brain tumours"

Microglial cells perform a plethora of functions in the central nervous system (CNS), which have emerged as particularly critical in the development and progression of brain tumours. As the prominent immune cell type in the tumour microenvironment, microglia tumour-associated profile and activity has become a major focus in the field. Significant technical advancements have prompted the development of novel systems adapted to analyze microglia with increasing specificity and intricacy. The advent of single-cell technologies combined with targeted mouse models has been decisive in deciphering microglia phenotypic and functional heterogeneity. However sophisticated these tools have become, clear limitations remain. Understanding their pitfalls and advantages ensures their correct application. Therefore, we provide a guide to the cutting-edge methods currently available to dissect microglial biology.

Virtual Brain Meeting Seminar

2nd December 2021 4-5pm

Julieta Camino De La Llosa

University of East Anglia

A different and tidier kitchen: can people with dementia perform tasks in a new environment?

Neurogenomics seminar

30th november 2021

Dr Nina Dräger

UCSF

"A CRISPRi/a platform in iPSC-derived microglia uncovers regulators of disease states"

Microglia are emerging as key drivers of neurological diseases. However, we lack a systematic understanding of the underlying mechanisms. In this talk, I present a screening platform to systematically elucidate functional consequences of genetic perturbations in human iPSC-derived microglia. We developed an efficient eight-day protocol for the generation of microglia-like cells based on the inducible expression of six transcription factors. We established inducible CRISPR interference and activation in this system and conducted three screens targeting the “druggable genome”. These screens uncovered genes controlling microglia survival, activation, and phagocytosis, including neurodegeneration-associated genes. A screen with single-cell RNA sequencing as the readout revealed that these microglia adopt a spectrum of states mirroring those observed in human brains and identified regulators of these states. A disease-associated state characterized by SPP1 expression was selectively depleted by CSF1R inhibition. Thus, our platform can systematically uncover regulators of microglia states, enabling their functional characterization and therapeutic targeting.

Neurogenomics Seminar

16th November, 3-4pm

Dr Greg Findlay

Francis Crick Institute

'Linking Variants to Functional Effects with Saturation Genome Editing'

Our incomplete understanding of how rare variants contribute to disease phenotypes substantially limits the clinical utility of genetic data. To help address the challenge of variant interpretation, we’ve developed a CRISPR/Cas9-based approach called saturation genome editing (SGE) in which we engineer and assay all possible single nucleotide variants across targeted genomic regions. In this talk, I will describe the optimisation of SGE and its application to study ~5,000 variants in the tumour suppressor BRCA1. The resulting functional data reveal the diverse genetic mechanisms through which variants exert phenotypic effects and predict with high accuracy which variants predispose patients to cancer. Ongoing work in the laboratory centres on scaling SGE and related technologies to enable systematic interrogation of variants across many additional disease loci. 

Zoom meeting ID    814 1666 7061
Password                 124233  
https://ukdri.zoom.us/j/81416667061?pwd=Um5GTmZlZ2w0SnNSSnppV3hyNDJHdz09

Neurogenomics Seminar

5th November 2021- 3-4pm

Dr Renzo Mancuso

VIB – University of Antwerp

"Human microglia xenotransplantation models to study genetic risk for neurodegeneration"

Neuroinflammation and microglial activation are significant processes during Alzheimer’s disease (AD) pathology. Recent transcriptomic profiling from experimental AD models sheds light on the changes undergone by microglia during the pathological process in mice. Nevertheless, determining the role of microglia in human AD comes with technical challenges, including lack of homology between mouse and humans, and limited expression of AD risk genes in mouse microglia. To address this important question, we have generated a novel model of human-mouse chimera that consist of the engraftment of iPSC-derived human microglia into the mouse brain. We first validated this model by comparing the gene expression profile of iPSC-derived to primary human microglia isolated from surgical resected tissue and investigated the response of iPSC-derived microglia to oligomeric Aβ in vivo. We also investigated the role of different genetic risk factors in human microglia in vivo. We found that altering microglial genetics affects the response of human microglia to amyloid beta plaques, with significant changes in their phenotypic transition from homeostatic to activation states. This novel platform will help us to understand the role of human microglia in AD and will give insights into the potential of new therapeutic routes based on the modulation of microglia and neuroinflammation. 

Neurogenomics Seminar

19th October- 4-5pm

Tara Chari

California Institute of Technology

"The Specious Art of Single-Cell Genomics"

Dimensionality reduction is standard practice for filtering noise and identifying relevant dimensions in large-scale data analyses. In biology, single-cell expression studies almost always begin with reduction to two or three dimensions to produce ‘all-in-one’ visuals of the data that are amenable to the human eye, and these are subsequently used for qualitative and quantitative analysis of cell relationships. However, there is little theoretical support for this practice. We examine the theoretical and practical implications of low-dimensional embedding of single-cell data, and find extensive distortions incurred on the global and local properties of biological patterns relative to the high-dimensional, ambient space. In lieu of this, we propose semi-supervised dimension reduction to higher dimension, and show that such targeted reduction guided by the metadata associated with single-cell experiments provides useful latent space representations for hypothesis-driven biological discovery.

Neurogenomics seminar

5 October, 15:00-16:00

Dr Hamish King

"Mapping dynamic cell states and gene regulatory networks with single-cell genomics: lessons from the immune system"

B cell-mediated immune responses and memory form in secondary lymphoid organs, such as the tonsils, lymph nodes or spleen and form a major arm of the adaptive immune system to fight and remember infections. During this process, B cells undergo affinity maturation in the germinal centre reaction before differentiation into memory or plasma cells. However, many questions remain about the dynamic cellular states involved, including the gene regulatory networks that underlie key cell fate decisions and phenotypes. We generated a comprehensive roadmap of humaueiran B cell maturation in a model secondary lymphoid organ by defining the gene expression, antibody repertoires, and chromatin accessibility of diverse B cell states at single-cell resolution. We reconstruct gene expression and transcription factor dynamics during B cell activation to identify a novel pre-germinal centre state and use spatial transcriptomics to map this population in human tissue. Finally, we leverage our single cell transcriptomic and epigenomic maps to interpret potential regulatory impact of genetic variants implicated in autoimmunity. We find that many autoimmune-linked fine-mapped GWAS variants exhibit their greatest regulatory potential in germinal centre-associated cell populations, providing new insights into the cellular and genetic causes that may underpin autoimmune disease.

Zoom meeting ID      837 2803 4677
Password                     842186
https://ukdri.zoom.us/j/83728034677?pwd=NFVSUVp3MENvdXkrVGNEMU1JN2RWdz09

Neurogenomics seminar

21st September, 4-5pm

Dr Claudia Han

"Decoding of gene regulatory networks underlying human microglia maturation"

Microglia, as the resident macrophages of the brain, engage in a variety of processes essential for brain development and homeostasis. In the human brain, microglia infiltrate the fetal brain as early as the fourth gestational week with microglia colonization of the brain preceding waves of neuro-, astro-, and oligodendro-genesis, myelination, etc, suggesting an ever-evolving environmental milieu that can influence cellular phenotypes. Many lines of evidence indicate that mis-regulation of microglia functions contributes to the pathogenesis of neurodegenerative diseases and in neurodevelopment disorders. Here, utilization of both bulk and single-cell assessment of gene expression and open chromatin profiles between human fetal and postnatal microglia reveal that changing brain environmental signals have a significant impact on the maturing transcriptome and predicted gene regulatory network of human microglia during development. Additionally, development of a new computational approach that integrates epigenomic and single-cell RNA-seq data allows the decoding of cellular heterogeneity with inference of subtype- and development stage-specific transcriptional regulators. Lastly, our collective data integrated with existing iPSC-microglia models provide a roadmap for the interrogation of human fetal and postnatal microglia phenotypes in the future. 

Zoom meeting ID      820 9289 0565
Password                     522151
https://ukdri.zoom.us/j/82092890565?pwd=emNTMndsVFgvMEdad3VCM1NKV2VhUT09