Expanding the CRISPR imaging toolset with Staphylococcus aureus Cas9 for simultaneous imaging of multiple genomic loci.

In order to elucidate the functional organization of the genome, it is vital to directly visualize the interactions between genomic elements in living cells. For this purpose, we engineered the Cas9 protein from Staphylococcus aureus (SaCas9) for the imaging of endogenous genomic loci, which showed a similar robustness and efficiency as previously reported for Streptococcus pyogenes Cas9 (SpCas9). Imaging readouts allowed us to characterize the DNA-binding activity of SaCas9 and to optimize its sgRNA scaffold. Combining SaCas9 and SpCas9, we demonstrated two-color CRISPR imaging with the capability to resolve genomic loci spaced by <300 kb. Combinatorial color-mixing further enabled us to code multiple genomic elements in the same cell. Our results highlight the potential of combining SpCas9 and SaCas9 for multiplexed CRISPR-Cas9 applications, such as imaging and genome engineering.

Tracking Multiple Genomic Elements Using Correlative CRISPR Imaging and Sequential DNA FISH.

Live imaging of genome has offered important insights into the dynamics of the genome organization and gene expression. The demand to image simultaneously multiple genomic loci has prompted a flurry of exciting advances in multicolor CRISPR imaging, although color-based multiplexing is limited by the need for spectrally distinct fluorophores. Here we introduce an approach to achieve highly multiplexed live recording via correlative CRISPR imaging and sequential DNA fluorescence in situ hybridization (FISH). This approach first performs one-color live imaging of multiple genomic loci and then uses sequential rounds of DNA FISH to determine the loci identity. We have optimized the FISH protocol so that each round is complete in 1 min, demonstrating the identification of seven genomic elements and the capability to sustain reversible staining and washing for up to 20 rounds. We have also developed a correlation-based algorithm to faithfully register live and FISH images. Our approach keeps the rest of the color palette open to image other cellular phenomena of interest, as demonstrated by our simultaneous live imaging of genomic loci together with a cell cycle reporter. Furthermore, the algorithm to register faithfully between live and fixed imaging is directly transferrable to other systems such as multiplex RNA imaging with RNA-FISH and multiplex protein imaging with antibody-staining.

Identification of environmental stressors and validation of light preference as a measure of anxiety in larval zebrafish.

BACKGROUND: Larval zebrafish, with a simple and transparent vertebrate brain composed of ~100 K neurons, is well suited for deciphering entire neural circuit activity underlying behavior. Moreover, their small body size (~4-5 mm in length) is compatible with 96-well plates, making larval zebrafish amenable to high content screening. Despite these attractive features, there is a scarcity of behavioral characterizations in larval zebrafish compared to other model organisms as well as adult zebrafish. RESULTS: In this study, we have characterized the physiological and behavioral responses of larval zebrafish to several easily amenable stimuli, including heat, cold, UV, mechanical disturbance (MD), and social isolation (SI). These stimuli are selected based on their perceived aversive nature to larval zebrafish. Using a light/dark choice paradigm, in which larval zebrafish display an innate dark avoidance behavior (i.e. scotophobia), we find that heat, cold and UV stimuli significantly enhance their dark avoidance with heat having the most striking effect, whereas MD and SI have little influence on the behavior. Surprisingly, using the cortisol assay, a physiological measure of stress, we uncover that all stimuli but heat and SI significantly increase the whole body cortisol levels. CONCLUSION: These results identify a series of stressors that can be easily administered to larval zebrafish. Those stimuli that elicit differential responses at behavioral and physiological levels warrant further studies at circuit levels to understand the underlying mechanisms. The findings that various stressors enhance while anxiolytics attenuate dark avoidance further reinforce that the light/dark preference behavior in larval zebrafish is fear/anxiety-associated.

Open-top selective plane illumination microscope for conventionally mounted specimens.

We have developed a new open-top selective plane illumination microscope (SPIM) compatible with microfluidic devices, multi-well plates, and other sample formats used in conventional inverted microscopy. Its key element is a water prism that compensates for the aberrations introduced when imaging at 45 degrees through a coverglass. We have demonstrated its unique high-content imaging capability by recording Drosophila embryo development in environmentally-controlled microfluidic channels and imaging zebrafish embryos in 96-well plates. We have also shown the imaging of C. elegans and moving Drosophila larvae on coverslips.

Inducing primary brainstem gliomas in genetically engineered mice using RCAS/TVA retroviruses and Cre/loxP recombination.

Genetically engineered mice are commonly used to model brainstem gliomas in pre-clinical research. One technique for inducing primary tumors in these genetically engineered mice involves delivering viral vectors containing the code for gene-editing proteins. We present a protocol for generating primary brainstem gliomas using the RCAS-TVA retroviral delivery system and the Cre/loxP gene editing system. We describe steps for transfecting and harvesting chicken fibroblast cells, intracranially injecting cells into mice, imaging primary tumors, and treating primary tumors with focal, image-guided brain irradiation. For complete details on the use and execution of this protocol, please refer to Deland et al. (2021).1.

A Novel Preclinical Murine Model to Monitor Inflammatory Breast Cancer Tumor Growth and Lymphovascular Invasion.

Inflammatory breast cancer (IBC), an understudied and lethal breast cancer, is often misdiagnosed due to its unique presentation of diffuse tumor cell clusters in the skin and dermal lymphatics. Here, we describe a window chamber technique in combination with a novel transgenic mouse model that has red fluorescent lymphatics (ProxTom RFP Nu/Nu) to simulate IBC clinicopathological hallmarks. Various breast cancer cells stably transfected to express green or red fluorescent reporters were transplanted into mice bearing dorsal skinfold window chambers. Intravital fluorescence microscopy and the in vivo imaging system (IVIS) were used to serially quantify local tumor growth, motility, length density of lymph and blood vessels, and degree of tumor cell lymphatic invasion over 0-140 h. This short-term, longitudinal imaging time frame in studying transient or dynamic events of diffuse and collectively migrating tumor cells in the local environment and quantitative analysis of the tumor area, motility, and vessel characteristics can be expanded to investigate other cancer cell types exhibiting lymphovascular invasion, a key step in metastatic dissemination. It was found that these models were able to effectively track tumor cluster migration and dissemination, which is a hallmark of IBC clinically, and was recapitulated in these mouse models.

Ataxia-telangiectasia mutated ( Atm ) disruption sensitizes spatially-directed H3.3K27M/TP53 diffuse midline gliomas to radiation therapy.

Diffuse midline gliomas (DMGs) are lethal brain tumors characterized by p53-inactivating mutations and oncohistone H3.3K27M mutations that rewire the cellular response to genotoxic stress, which presents therapeutic opportunities. We used RCAS/tv-a retroviruses and Cre recombinase to inactivate p53 and induce K27M in the native H3f3a allele in a lineage- and spatially-directed manner, yielding primary mouse DMGs. Genetic or pharmacologic disruption of the DNA damage response kinase Ataxia-telangiectasia mutated (ATM) enhanced the efficacy of focal brain irradiation, extending mouse survival. This finding suggests that targeting ATM will enhance the efficacy of radiation therapy for p53-mutant DMG but not p53-wildtype DMG. We used spatial in situ transcriptomics and an allelic series of primary murine DMG models with different p53 mutations to identify transactivation-independent p53 activity as a key mediator of such radiosensitivity. These studies deeply profile a genetically faithful and versatile model of a lethal brain tumor to identify resistance mechanisms for a therapeutic strategy currently in clinical trials.

An intertidal snail shows a dramatic size increase over the past century.

Changes in the shell architecture of marine snails enhance defenses and greatly improve survival against predators. In the northwest Atlantic Ocean, shorter and thicker shells have been reported for several species following the introduction of predatory Carcinus maenas crabs early in the 20th century. But we report that the shell lengths of Nucella lapillus actually increased by an average of 22.6% over the past century, with no evidence of shell thickening after correcting for shell length. The increases in shell length were greatest on sheltered shores, highlighting the interaction between wave exposure and the sampling period. Comparisons were based on archived shells collected in 1915-1922 from sites that were resampled in 2007. N. lapillus is an important member of North Atlantic marine ecosystems, and our results suggest that the impacts of historical changes in species' key morphological traits on marine ecosystems remain underappreciated.

In Vivo Dopamine Neuron Imaging-Based Small Molecule Screen Identifies Novel Neuroprotective Compounds and Targets.

Parkinson's disease (PD) is the second most common neurodegenerative disorder with prominent dopamine (DA) neuron degeneration. PD affects millions of people worldwide, but currently available therapies are limited to temporary relief of symptoms. As an effort to discover disease-modifying therapeutics, we have conducted a screen of 1,403 bioactive small molecule compounds using an in vivo whole organism screening assay in transgenic larval zebrafish. The transgenic model expresses the bacterial enzyme nitroreductase (NTR) driven by the tyrosine hydroxylase (th) promotor. NTR converts the commonly used antibiotic pro-drug metronidazole (MTZ) to the toxic nitroso radical form to induce DA neuronal loss. 57 compounds were identified with a brain health score (BHS) that was significantly improved compared to the MTZ treatment alone after FDR adjustment (padj<0.05). Independently, we curated the high throughput screening (HTS) data by annotating each compound with pharmaceutical classification, known mechanism of action, indication, IC50, and target. Using the Reactome database, we performed pathway analysis, which uncovered previously unknown pathways in addition to validating previously known pathways associated with PD. Non-topology-based pathway analysis of the screening data further identified apoptosis, estrogen hormone, dipeptidyl-peptidase 4, and opioid receptor Mu1 to be potentially significant pathways and targets involved in neuroprotection. A total of 12 compounds were examined with a secondary assay that imaged DA neurons before and after compound treatment. The z'-factor of this secondary assay was determined to be 0.58, suggesting it is an excellent assay for screening. Etodolac, nepafenac, aloperine, protionamide, and olmesartan showed significant neuroprotection and was also validated by blinded manual DA neuronal counting. To determine whether these compounds are broadly relevant for neuroprotection, we tested them on a conduritol-b-epoxide (CBE)-induced Gaucher disease (GD) model, in which the activity of glucocerebrosidase (GBA), a commonly known genetic risk factor for PD, was inhibited. Aloperine, olmesartan, and nepafenac showed significant protection of DA neurons in this assay. Together, this work, which combines high content whole organism in vivo imaging-based screen and bioinformatic pathway analysis of the screening dataset, delineates a previously uncharted approach for identifying hit-to-lead candidates and for implicating previously unknown pathways and targets involved in DA neuron protection.

Alkali metal salts of 4-hydroxybenzoic acid: a structural and educational study.

As part of an educational exercise designed to introduce school students to the technique of single-crystal X-ray diffraction and enhance their understanding of primary and secondary bonding, a group of nine secondary school students was given the opportunity to prepare new compounds and to solve and refine data collected on the crystalline materials they had prepared. Their investigation of the alkali metal salts of 4-hydroxybenzoic acid (H2hba) yielded nine new compounds and their structures are described in this article. Whilst the salts might be expected to have similar atomic arrangements, there are significant differences in their structures. Although H2hba is a relatively simple organic molecule, it displays remarkable coordinative flexibility, forming ionic solids containing the uncharged molecule, the monoanion Hhba- or the dianion hba2-. A common feature of the structures is their layered arrangement: alternating hydrophilic layers made up of closely packed metal-oxygen polyhedra separated by the hydrophobic component of the hydroxybenzoate linking units. Close packing of these units seems to be a dominant influence in determining the overall structure. The hydroxybenzoate units are usually both parallel and antiparallel with their immediate neighbours, with packing that can be edge-to-face, face-to-face or a mixture of the two. Hydrogen bonding plays a key role in the structure of most compounds and a short strong hydrogen bond (SSHB) is observed in two of the networks. The compounds of 4-hydroxybenzoic acid, C7H6O3, described here are: poly[di-µ-aqua-µ-4-oxidobenzoato-dilithium], [Li2(C7H4O3)(H2O)2]n, 1, poly[triaqua-µ-4-oxidobenzoato-dilithium], [Li2(C7H4O3)(H2O)3]n, 2, poly[µ-4-hydroxybenzoato-lithium], [Li(C7H5O3)]n, 3, catena-poly[4-hydroxybenzoate [[diaquasodium]-di-µ-aqua]], {[Na(H2O)4](C7H5O3)}n, 4, poly[di-µ-aqua-aqua-µ-4-hydroxybenzoato-potassium], [K(C7H5O3)(H2O)3]n, 5, poly[µ-aqua-µ-4-hydroxybenzoato-potassium], [K(C7H5O3)(H2O)]n, 6, poly[aqua-µ-4-hydroxybenzoato-rubidium], [Rb(C7H5O3)(H2O)]n, 7, poly[aqua-µ-4-hydroxybenzoato-caesium], [Cs(C7H5O3)(H2O)]n, 8, poly[[µ-aqua-aqua(µ-4-hydroxybenzoato)(4-hydroxybenzoic acid)sodium] monohydrate], {[Na(C7H5O3)(C7H6O3)(H2O)2]·H2O}n, 9, poly[[(µ-4-hydroxybenzoato)(µ-4-hydroxybenzoic acid)rubidium] monohydrate], {[K(C7H5O3)(C7H6O3)]·H2O}n, 10, and poly[[(µ-4-hydroxybenzoato)(µ-4-hydroxybenzoic acid)rubidium] monohydrate], {[Rb(C7H5O3)(C7H6O3)]·H2O}n, 11.

A zebrafish screen reveals Renin-angiotensin system inhibitors as neuroprotective via mitochondrial restoration in dopamine neurons.

Parkinson's disease (PD) is a common neurodegenerative disorder without effective disease-modifying therapeutics. Here, we establish a chemogenetic dopamine (DA) neuron ablation model in larval zebrafish with mitochondrial dysfunction and robustness suitable for high-content screening. We use this system to conduct an in vivo DA neuron imaging-based chemical screen and identify the Renin-Angiotensin-Aldosterone System (RAAS) inhibitors as significantly neuroprotective. Knockdown of the angiotensin receptor 1 (agtr1) in DA neurons reveals a cell-autonomous mechanism of neuroprotection. DA neuron-specific RNA-seq identifies mitochondrial pathway gene expression that is significantly restored by RAAS inhibitor treatment. The neuroprotective effect of RAAS inhibitors is further observed in a zebrafish Gaucher disease model and Drosophila pink1-deficient PD model. Finally, examination of clinical data reveals a significant effect of RAAS inhibitors in delaying PD progression. Our findings reveal the therapeutic potential and mechanisms of targeting the RAAS pathway for neuroprotection and demonstrate a salient approach that bridges basic science to translational medicine.

Parkinson's disease is caused by the slow death and deterioration of brain cells, in particular of the neurons that produce a chemical messenger known as dopamine. Certain drugs can mitigate the resulting drop in dopamine levels and help to manage symptoms, but they cause dangerous side-effects. There is no treatment that can slow down or halt the progress of the condition, which affects 0.3% of the population globally. Many factors, both genetic and environmental, contribute to the emergence of Parkinson's disease. For example, dysfunction of the mitochondria, the internal structures that power up cells, is a known mechanism associated with the death of dopamine-producing neurons. Zebrafish are tiny fish which can be used to study Parkinson's disease, as they are easy to manipulate in the lab and share many characteristics with humans. In particular, they can be helpful to test the effects of various potential drugs on the condition. Here, Kim et al. established a new zebrafish model in which dopamine-producing brain cells die due to their mitochondria not working properly; they then used this assay to assess the impact of 1,403 different chemicals on the integrity of these cells. A group of molecules called renin-angiotensin-aldosterone (RAAS) inhibitors was shown to protect dopamine-producing neurons and stopped them from dying as often. These are already used to treat high blood pressure as they help to dilate blood vessels. In the brain, however, RAAS worked by restoring certain mitochondrial processes. Kim et al. then investigated whether these results are relevant in other, broader contexts. They were able to show that RAAS inhibitors have the same effect in other animals, and that Parkinson's disease often progresses more slowly in patients that already take these drugs for high blood pressure. Taken together, these findings therefore suggest that RAAS inhibitors may be useful to treat Parkinson's disease, as well as other brain illnesses that emerge because of mitochondria not working properly. Clinical studies and new ways to improve these drugs are needed to further investigate and capitalize on these potential benefits.

Cherenkov emissions for studying tumor changes during radiation therapy: An exploratory study in domesticated dogs with naturally-occurring cancer.

PURPOSE: Real-time monitoring of physiological changes of tumor tissue during radiation therapy (RT) could improve therapeutic efficacy and predict therapeutic outcomes. Cherenkov radiation is a normal byproduct of radiation deposited in tissue. Previous studies in rat tumors have confirmed a correlation between Cherenkov emission spectra and optical measurements of blood-oxygen saturation based on the tissue absorption coefficients. The purpose of this study is to determine if it is feasible to image Cherenkov emissions during radiation therapy in larger human-sized tumors of pet dogs with cancer. We also wished to validate the prior work in rats, to determine if Cherenkov emissions have the potential to act an indicator of blood-oxygen saturation or water-content changes in the tumor tissue-both of which have been correlated with patient prognosis. METHODS: A DoseOptics camera, built to image the low-intensity emission of Cherenkov radiation, was used to measure Cherenkov intensities in a cohort of cancer-bearing pet dogs during clinical irradiation. Tumor type and location varied, as did the radiation fractionation scheme and beam arrangement, each planned according to institutional standard-of-care. Unmodulated radiation was delivered using multiple 6 MV X-ray beams from a clinical linear accelerator. Each dog was treated with a minimum of 16 Gy total, in ≥3 fractions. Each fraction was split into at least three subfractions per gantry angle. During each subfraction, Cherenkov emissions were imaged. RESULTS: We documented significant intra-subfraction differences between the Cherenkov intensities for normal tissue, whole-tumor tissue, tissue at the edge of the tumor and tissue at the center of the tumor (p<0.05). Additionally, intra-subfraction changes suggest that Cherenkov emissions may have captured fluctuating absorption properties within the tumor. CONCLUSION: Here we demonstrate that it is possible to obtain Cherenkov emissions from canine cancers within a fraction of radiotherapy. The entire optical spectrum was obtained which includes the window for imaging changes in water and hemoglobin saturation. This lends credence to the goal of using this method during radiotherapy in human patients and client-owned pets.

Covalent Modification and Regulation of the Nuclear Receptor Nurr1 by a Dopamine Metabolite.

Nurr1, a nuclear receptor essential for the development, maintenance, and survival of midbrain dopaminergic neurons, is a potential therapeutic target for Parkinson's disease, a neurological disorder characterized by the degeneration of these same neurons. Efforts to identify Nurr1 agonists have been hampered by the recognition that it lacks several classic regulatory elements of nuclear receptor function, including the canonical ligand-binding pocket. Here we report that the dopamine metabolite 5,6-dihydroxyindole (DHI) binds directly to and modulates the activity of Nurr1. Using biophysical assays and X-ray crystallography, we show that DHI binds to the ligand-binding domain within a non-canonical pocket, forming a covalent adduct with Cys566. In cultured cells and zebrafish, DHI stimulates Nurr1 activity, including the transcription of target genes underlying dopamine homeostasis. These findings suggest avenues for developing synthetic Nurr1 ligands to ameliorate the symptoms and progression of Parkinson's disease.

High-throughput screens using photo-highlighting discover BMP signaling in mitochondrial lipid oxidation.

High-throughput screens at microscopic resolution can uncover molecular mechanisms of cellular dynamics, but remain technically challenging in live multicellular organisms. Here we present a genetic screening method using photo-highlighting for candidate selection on microscopes. We apply this method to stimulated Raman scattering (SRS) microscopy and systematically identify 57 Caenorhabditis elegans mutants with altered lipid distribution. Four of these mutants target the components of the Bone Morphogenetic Protein (BMP) signaling pathway, revealing that BMP signaling inactivation causes exhaustion of lipid reserves in somatic tissues. Using SRS-based isotope tracing assay to quantitatively track lipid synthesis and mobilization, we discover that the BMP signaling mutants have increased rates of lipid mobilization. Furthermore, this increase is associated with the induction of mitochondrial ß-oxidation and mitochondrial fusion. Together these studies demonstrate a photo-highlighting microscopic strategy for genome-scale screens, leading to the discovery of new roles for BMP signaling in linking mitochondrial homeostasis and lipid metabolism.High-throughput genetic screens in animals could benefit from an easy way to mark positive hits. Here the authors introduce photo-highlighting using a photoconvertible fluorescent protein, and in combination with stimulated Raman scattering (SRS) microscopy, define a role for BMP signaling in lipid metabolism in C. elegans.

A High-Content Larval Zebrafish Brain Imaging Method for Small Molecule Drug Discovery.

Drug discovery in whole-organisms such as zebrafish is a promising approach for identifying biologically-relevant lead compounds. However, high content imaging of zebrafish at cellular resolution is challenging due to the difficulty in orienting larvae en masse such that the cell type of interest is in clear view. We report the development of the multi-pose imaging method, which uses 96-well round bottom plates combined with a standard liquid handler to repose the larvae within each well multiple times, such that an image in a specific orientation can be acquired. We have validated this method in a chemo-genetic zebrafish model of dopaminergic neuron degeneration. For this purpose, we have developed an analysis pipeline that identifies the larval brain in each image and then quantifies neuronal health in CellProfiler. Our method achieves a SSMD* score of 6.96 (robust Z'-factor of 0.56) and is suitable for screening libraries up to 105 compounds in size.

Coimmunization with an optimized IL15 plasmid adjuvant enhances humoral immunity via stimulating B cells induced by genetically engineered DNA vaccines expressing consensus JEV and WNV E DIII.

The Japanese encephalitis virus (JEV) and West Nile virus (WNV) are responsible for a large proportion of viral encephalitis in humans. Currently, there is no FDA approved specific treatment for either, though there are attempts to develop vaccines against both viruses. In this study, we proposed novel genetically engineered DNA vaccines against these two neurotrophic flaviviruses. The structural domain III (DIII) of E protein from these viruses is reported to carry dominant epitopes that induce neutralizing antibodies. Therefore we created consensus sequence of DIII domain across numerous strains of JEV and WNV. Based on the consensus amino acid sequence, synthetic codon and RNA optimized DIII-expressing DNA vaccine constructs with an efficient leader sequence were synthesized for immunization studies. In addition, we also constructed a genetically engineered IL15 DNA vaccine molecular adjuvant for co-stimulating the immune response against DIII clones. Vaccine constructs were delivered into BALB/C mice intramuscularly followed by electroporation using the CELLECTRA in vivo electroporator. We have observed that the combined delivery of both WNV DIII and IL15-ECRO DNA vaccine constructs resulted in not only the highest level of antibody against DIII, but also enhanced cross reactivity with two other antigens tested. Also, coimmunization with IL15 plasmid further increased the immune response by four- to five-fold. Importantly, we have shown that IL15 coimmunization adjuvanted humoral responses against DIII antigens by elevating the level of antibody secreting B cells. Such a DNA vaccine approach may better help to control potential travel related infectious agents such as JEV.