targeted-studies-using-serial-block-face-focused-ion-beam-scan

Targeted Studies Using Serial Block Face and Focused Ion Beam Scan Electron Microscopy

This protocol allows for the efficient and effective imaging of cell or tissue samples in three dimensions at the resolution level of electron microscopy. ...

VIB Bio Imaging Core

VIB Inflammation Research Center

UGent

Sox9 is a transcription factor expressed in most solid tumors. However, the molecular mechanisms underlying Sox9 function during tumorigenesis remain unclear. Here, using a genetic mouse model of basal cell carcinoma (BCC), the most frequent cancer in humans, we show that Sox9 is expressed from the earliest step of tumor formation in a Wnt/β-catenin-dependent manner. Deletion of Sox9 together with the constitutive activation of Hedgehog signaling completely prevents BCC formation and leads to a progressive loss of oncogene-expressing cells. Transcriptional profiling of oncogene-expressing cells with Sox9 deletion, combined with in vivo ChIP sequencing, uncovers a cancer-specific gene network regulated by Sox9 that promotes stemness, extracellular matrix deposition, and cytoskeleton remodeling while repressing epidermal differentiation. Our study identifies the molecular mechanisms regulated by Sox9 that link tumor initiation and invasion.

Sox9 Controls Self-Renewal of Oncogene Targeted Cells and Links Tumor Initiation and Invasion.

There is a growing appreciation that membrane-bound organelles in eukaryotic cells communicate directly with one another through direct membrane contact sites. Mitochondria-associated membranes are specialized subdomains of the endoplasmic reticulum that function as membrane contact sites between the endoplasmic reticulum and mitochondria. These sites have emerged as major players in lipid metabolism and calcium signaling. More recently also autophagy and mitochondrial dynamics have been found to be regulated at ER-mitochondria contact sites. Neurons critically depend on mitochondria-associated membranes as a means to exchange metabolites and signaling molecules between these organelles. This is underscored by the fact that genes affecting mitochondrial and endoplasmic reticulum homeostasis are clearly overrepresented in several hereditary neurodegenerative disorders. Conversely, the processes affected by the contact sites between the endoplasmic reticulum and mitochondria are widely implicated in neurodegeneration. This review will focus on the most recent data addressing the structural composition and function of the mitochondria-associated membranes. In addition, the 3D morphology of the contact sites as observed using volume electron microscopy is discussed. Finally, it will highlight the role of several key proteins associated with these contact sites that are involved not only in dementias, amyotrophic lateral sclerosis and Parkinson's disease, but also in axonopathies such as hereditary spastic paraplegia and Charcot-Marie-Tooth disease. 

Mitochondria-associated membranes as hubs for neurodegeneration.

Self-renewing tissue-resident macrophages are thought to be exclusively derived from embryonic progenitors. However, whether circulating monocytes can also give rise to such macrophages has not been formally investigated. Here we use a new model of diphtheria toxin-mediated depletion of liver-resident Kupffer cells to generate niche availability and show that circulating monocytes engraft in the liver, gradually adopt the transcriptional profile of their depleted counterparts and become long-lived self-renewing cells. Underlining the physiological relevance of our findings, circulating monocytes also contribute to the expanding pool of macrophages in the liver shortly after birth, when macrophage niches become available during normal organ growth. Thus, like embryonic precursors, monocytes can and do give rise to self-renewing tissue-resident macrophages if the niche is available to them. 

Bone marrow-derived monocytes give rise to self-renewing and fully differentiated Kupffer cells.

Microglia, the mononuclear phagocytes of the central nervous system (CNS), are important for the maintenance of CNS homeostasis, but also critically contribute to CNS pathology. Here we demonstrate that the nuclear factor kappa B (NF-κB) regulatory protein A20 is crucial in regulating microglia activation during CNS homeostasis and pathology. In mice, deletion of A20 in microglia increases microglial cell number and affects microglial regulation of neuronal synaptic function. Administration of a sublethal dose of lipopolysaccharide induces massive microglia activation, neuroinflammation, and lethality in mice with microglia-confined A20 deficiency. Microglia A20 deficiency also exacerbates multiple sclerosis (MS)-like disease, due to hyperactivation of the Nlrp3 inflammasome leading to enhanced interleukin-1β secretion and CNS inflammation. Finally, we confirm a Nlrp3 inflammasome signature and IL-1β expression in brain and cerebrospinal fluid from MS patients. Collectively, these data reveal a critical role for A20 in the control of microglia activation and neuroinflammation.

A20 critically controls microglia activation and inhibits inflammasome-dependent neuroinflammation.

There are different technologies that can be used to obtain a 3D image at nanometer resolution. Over the past decade, there has been a growing interest in applying Serial Block Face Scanning Electron Microscopy (SBF-SEM) in different fields of life science research. This technology has the advantage that it can cover a range of volumes, going from monolayers to multiple tissue layers in all three dimensions. SBF-SEM was originally used in neuroscience and then expanded to other research domains. The whole process of sample preparation for SBF-SEM is very long and consists of many steps, which makes adjustment of a given workflow very challenging. Here we describe the SBF-SEM workflow and those steps in the process that can be tweaked for any sample.

Serial block face-scanning electron microscopy for volume electron microscopy.

Volume electron microscopy allows for the automated acquisition of serial-section imaging data that can be reconstructed in three-dimensions (3D) to provide a detailed, geometrically accurate view of cellular ultrastructure. Two, volume electron microscopy (EM) techniques, serial block face scanning electron microscopy (SBF-SEM) and focused ion beam scanning electron microscopy (FIB-SEM), use a similar slice-and-view approach but differ in their fields of view and 3D resolution. This chapter highlights a workflow where the ability of SBF-SEM to image a large field of view is combined with the precise sectioning capability of FIB-SEM to first locate a rare cellular event in a large tissue volume and then inspect the event with higher resolution. Using these two EM platforms in synergy is a powerful technique and can be useful for both simple structural studies as well as correlative studies using both light and electron microscopy.

Article	Year
Sox9 Controls Self-Renewal of Oncogene Targeted Cells and Links Tumor Initiation and Invasion. Cell stem cell\| PubMed ID: 26095047	2015
Mitochondria-associated membranes as hubs for neurodegeneration. Acta neuropathologica\| PubMed ID: 26744348	2016
Bone marrow-derived monocytes give rise to self-renewing and fully differentiated Kupffer cells. Nature communications\| PubMed ID: 26813785	2016
A20 critically controls microglia activation and inhibits inflammasome-dependent neuroinflammation. Nature communications\| PubMed ID: 29789522	2018
Serial block face-scanning electron microscopy for volume electron microscopy. Methods in cell biology\| PubMed ID: 31326027	2019
Combining serial block face and focused ion beam scanning electron microscopy for 3D studies of rare events. Methods in cell biology\| PubMed ID: 31326028	2019

Saskia Lippens

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