spatial transcriptomics

Novel Tools for Spatial and Temporal Genomics

The precise spatial localization of molecular signals within tissues richly informs the mechanisms of tissue formation and function. Here, we’ll introduce Slide-seq, a technology which enables transcriptome-wide measurements with near-single cell spatial resolution. We’ll describe recent experimental and computational advances to enable Slide-seq in biological contexts in biological contexts where high detection sensitivity is important. More broadly, we’ll discuss the promise and challenges of spatial transcriptomics for tissue genomics. Lastly, we’ll touch upon novel molecular recording technologies, which allows recording of the absolute time dynamics of gene expression in live systems into DNA sequences.

Microglia function and dysfunction in Alzheimer’s disease

Emerging genetic studies of late-onset Alzheimer’s Disease implicate the brain’s resident macrophages in the pathogenesis of AD. More than half the risk genes associated with late-onset AD are selectively expressed in microglia and peripheral myeloid cells; yet we know little about the underlying biology or how myeloid cells contribute to AD pathogenesis. Using single-cell RNA sequencing and spatial transcriptomics we identified molecular signatures that can be used to localize and monitor distinct microglia functional states in the human and mouse brain. Our results show that microglia assume diverse functional states in development, aging and injury, including populations corresponding to known microglial functions including proliferation, migration, inflammation, and synaptic phagocytosis. We identified several innate immune pathways by which microglia recognize and prune synapses during development and in models of Alzheimer’s disease, including the classical complement cascade. Illuminating the mechanisms by which developing synaptic circuits are sculpted is providing important insight on understanding how to protect synapses in Alzheimer’s and other neurodegenerative diseases of synaptic dysfunction.

MULTIMODAL SPATIAL TRANSCRIPTOMICS DETERMINES REPEAT EXPANSION, HUNTINGTIN AGGREGATION, AND SELECTIVE CORTICAL NEURON LOSS IN HUNTINGTON’S DISEASE

FENS Forum 2026

LEVERAGING SPATIAL TRANSCRIPTOMICS AND MACHINE LEARNING TO CRACK THE SPATIAL CODE OF NEURAL STEM CELL NICHES IN THE ADULT BRAIN

FENS Forum 2026

A SPATIAL TRANSCRIPTOMICS ATLAS OF THE ADULT MOUSE BRAIN

FENS Forum 2026

DEMOCRATISING SPATIAL TRANSCRIPTOMICS WITH AUTOMATED IN SITU SEQUENCING

FENS Forum 2026

SPATIAL TRANSCRIPTOMICS REVEALS DISTINCT MOLECULAR SIGNATURE OF MOTOR NEURONS AND INTERNEURONS IN CONTROL AND PRE-SYMPTOMATIC STAGES OF AN ALS MOUSE MODEL

FENS Forum 2026

SINGLE-CELL AND SPATIAL TRANSCRIPTOMICS REVEAL NEURONAL AND REGIONAL VULNERABILITY IN THE HUMAN DORSAL STRIATUM IN PARKINSON’S DISEASE

FENS Forum 2026

SUPER-RESOLVED SPATIAL TRANSCRIPTOMICS REVEALS EARLY HIPPOCAMPAL RNA LOCALIZATION CHANGES IN A MOUSE MODEL OF ALZHEIMER’S DISEASE

FENS Forum 2026

HIGH-THROUGHPUT SPATIAL TRANSCRIPTOMICS ON 50 UM-THICK VIBRATOME SECTIONS TO ENABLE INTEGRATION WITH TWO-PHOTON CALCIUM IMAGING

FENS Forum 2026

Single nucleus and spatial transcriptomics of human hippocampus from people with major depression and controls

Tracing Glia-into-Neuron Conversion in the Aged Mouse Brain using Single Cell Spatial Transcriptomics

Spatial transcriptomics-correlated electron microscopy integrates transcriptional and ultrastructural responses to brain injury

FENS Forum 2024

Spatial transcriptomics reveals common pathways in Alzheimer's disease and Down syndrome

FENS Forum 2024