Stochastic Optical Reconstruction Microscopy Research Articles

Decreasing microtubule detyrosination by parthenolide restores sodium current in mdx cardiomyocytes

Abstract Funding Acknowledgements Type of funding sources: None. Background The cardiac sodium channel Nav1.5 is transported to the membrane by the microtubule network. Alterations in microtubule dynamics are known to impact on ion channel trafficking. Pathophysiological conditions such as heart failure and Duchenne muscular dystrophy (DMD) are associated with an increase in microtubule detyrosination as well as a decreased sodium current (INa) and pro-arrhythmia. Parthenolide, a compound that decreases the fraction of detyrosinated microtubules, has been shown to have beneficial effects on cardiac function in DMD mice, but its impact on INa has not been investigated. Methods and Results Cardiomyocytes (CMs) from wild type (WT) and mdx (DMD) mice were used to investigate the effect of parthenolide. Cells were incubated with either 10 µM parthenolide or DMSO for 3-5 hours. INa and action potential (AP) characteristics were assessed using the patch-clamp technique, while immunofluorescence and stochastic optical reconstruction microscopy (STORM), were used to investigate microtubule detyrosination and Nav1.5 cluster density, respectively. In accordance with previous studies, we observed increased levels of detyrosinated microtubules and decreased INa in mdx CMs compared to WT. Treatment with parthenolide decreased the fraction of detyrosinated microtubules and significantly increased INa magnitude in mdx CMs, but had no effect on INa in WT CMs. Accordingly, parthenolide significantly increased AP maximal upstroke velocity in mdx CMs, without affecting other AP properties. Parthenolide did not affect INa gating properties, indicating that it increased INa by enhancing Nav1.5 membrane trafficking. Indeed, STORM analysis showed that parthenolide increased Nav1.5 cluster density at both the lateral membrane (crest) and intercalated disc region in mdx CMs while it had no effect on WT CMs. Conclusions Parthenolide restores INa and Nav1.5 membrane expression in mdx CMs, and may be of potential benefit in other pathophysiological conditions associated with increased microtubule detyrosination and reduced INa. Further elucidation of the impact of microtubule dynamics on Nav1.5 may identify additional therapeutic targets for restoring conduction and preventing arrhythmias.

Super-resolution imaging pinpoints the periodic ultrastructure at the human node of Ranvier and its disruption in patients with polyneuropathy

The node of Ranvier is the key element in saltatory conduction along myelinated axons, but its specific protein organization remains elusive in the human species. To shed light on nanoscale anatomy of the human node of Ranvier in health and disease, we assessed human nerve biopsies of patients with polyneuropathy by super-resolution fluorescence microscopy. We applied direct stochastic optical reconstruction microscopy (dSTORM) and supported our data by high-content confocal imaging combined with deep learning-based analysis. As a result, we revealed a ∼ 190 nm periodic protein arrangement of cytoskeletal proteins and axoglial cell adhesion molecules in human peripheral nerves. In patients with polyneuropathy, periodic distances increased at the paranodal region of the node of Ranvier, both at the axonal cytoskeleton and at the axoglial junction. In-depth image analysis revealed a partial loss of proteins of the axoglial complex (Caspr-1, neurofascin-155) in combination with detachment from the cytoskeletal anchor protein ß2-spectrin. High content analysis showed that such paranodal disorganization occurred especially in acute and severe axonal neuropathy with ongoing Wallerian degeneration and related cytoskeletal damage. We provide nanoscale and protein-specific evidence for the prominent, but vulnerable role of the node of Ranvier for axonal integrity. Furthermore, we show that super-resolution imaging can identify, quantify and map elongated periodic protein distances and protein interaction in histopathological tissue samples. We thus introduce a promising tool for further translational applications of super resolution microscopy.

Thyroid hormone maintains cardiac dyadic structures by regulating junctophilin-2 localization to ryanodine clusters

Overt and subclinical hypothyroidism are associated with increased risk of cardiovascular disease and mortality. In pre-clinical studies, supplementation with triiodo-L-thyronine (T3) has been shown to regulate cardiomyocyte T-tubule (TT) organization, and thereby maintain ryanodine receptor-2 and L-type Ca 2+ channel (RyR-LTCC) clusters in dyadic structures necessary for efficient excitation-contraction (EC) coupling. We hypothesized that the TT-sarcoplasmic reticulum (SR)-spanning protein Junctophilin-2 (Jph) is regulated by T3. Thyroid hormone (TH) deficiency was induced in 12 adult female Sprague-Dawley rats by oral propyl-thiouracil (PTU; 0.025%) treatment for 8 weeks. Rats were then randomized to continued PTU treatment or with T3 (10 μg/kg/day) supplementation for 2 weeks (PTU+T3). Untreated rats served as euthyroid (EU) controls. Thyroid status was confirmed by plasma T3 and T4 levels. Left ventricular cardiomyocytes (CM) were isolated by collagenase digestion for single molecule imaging of Jph2, RyR2 and LTCC proteins using 2D and 3D STORM (stochastic optical reconstruction microscopy; Oxford Nanoimager). DBSCAN algorithms for cluster analysis (Web-based programs developed by LumeVR) measured cluster size and number, nearest neighbor cluster distances, and protein co-localizations. Calcium sparks in live CMs loaded with Fluo-4 were captured by line-scanning laser microscopy (Zeiss 980) to assess spontaneous SR Ca 2+ leak. STORM imaging of normal CMs showed that ~60% of RyR clusters consisted of 10-50 RyR localizations (locs) with 100-200 Jph molecules co-localized within 210 nm radius of the cluster centroid. Although Jph locs per cluster increased proportionately with increased cluster size, PTU cells had markedly less Jph co-localized with RyR at all cluster sizes compared to EU and PTU+T3 cells. The reduction of associated Jph was most evident in super-clusters (>250 RyR locs). 3D image analysis showed nearest neighbor distances between RyR clusters that were significantly increased in the PTU CMs vs EU (749±146 nm vs 640±140 nm), which were normalized with T3-treatment (616±60 nm). Numbers of RyR clusters without associated Jph locs were significantly higher in PTU cells, and reduced with T3. RyR Ca 2+ leak as measured by spontaneous Ca 2+ sparks was increased in PTU CMs, but decreased significantly to control values in T3-treated cells. This study supports a regulatory role of T3 in maintaining TT-SR dyad structures, in part by increasing Jph co-localization with RyR clusters, thus promoting efficient interaction of RyR with LTCC channels for effective EC-coupling and cardiac output. Study funded by NIH R15HL15406 and by resources of the NYIT Imaging Center. This is the full abstract presented at the American Physiology Summit 2023 meeting and is only available in HTML format. There are no additional versions or additional content available for this abstract. Physiology was not involved in the peer review process.

Possible frequent multiple mitochondrial DNA copies in a single nucleoid in HeLa cells

Previously, a number of ~ 1.4 of mitochondrial DNA (mtDNA) molecules in a single nucleoid was reported, which would reflect a minimum nucleoid division. We applied 3D-double-color direct stochastic optical reconstruction microscopy (dSTORM), i.e. nanoscopy with ~ 25–40 nm x,y-resolution, together with our novel method of Delaunay segmentation of 3D data to identify unbiased 3D-overlaps. Noncoding D-loops were recognized in HeLa cells by mtDNA fluorescence in situ hybridization (mtFISH) 7S-DNA 250-bp probe, containing biotin, visualized by anti-biotin/Cy3B-conjugated antibodies. Other mtFISH probes with biotin or Alexa Fluor 647 (A647) against ATP6-COX3 gene overlaps (1,100 bp) were also used. Nucleoids were imaged by anti-DNA/(A647-)-Cy3B-conjugated antibodies. Resulting histograms counting mtFISH-loci/nucleoid overlaps demonstrated that 45% to 70% of visualized nucleoids contained two or more D-loops or ATP6-COX3-loci, indicating two or more mtDNA molecules per nucleoid. With increasing number of mtDNA per nucleoid, diameters were larger and their distribution histograms peaked at ~ 300 nm. A wide nucleoid diameter distribution was obtained also using 2D-STED for their imaging by anti-DNA/A647. At unchanged mtDNA copy number in osteosarcoma 143B cells, TFAM expression increased nucleoid spatial density 1.67-fold, indicating expansion of existing mtDNA and its redistribution into more nucleoids upon the higher TFAM/mtDNA stoichiometry. Validation of nucleoid imaging was also done with two TFAM mutants unable to bend or dimerize, respectively, which reduced both copy number and nucleoid spatial density by 80%. We conclude that frequently more than one mtDNA molecule exists within a single nucleoid in HeLa cells and that mitochondrial nucleoids do exist in a non-uniform size range.

Abstract 4253: Pan-cancer analysis of XPO1 R749Q mutations across 217,570 patients reveals association with high tumor mutational burden and therapy resistance

Abstract Background: XPO1 is a nuclear export receptor responsible for exporting >200 proteins out of the nucleus, including many cancer-related proteins. We previously reported recurrent hotspot mutations occurring in XPO1 in cancer and identified XPO1 R749Q variant only in solid tumors. To determine the prevalence of XPO1 mutations across cancer types, we performed a large-scale genomic analysis of 217,570 patients with cancer to identify and characterize XPO1 variants from real-world patient tumors. Methods: Solid tumor samples representing 14 cancer types were submitted to Caris Life Sciences (Phoenix, AZ) for Next-generation sequencing of DNA (592 genes or WES). TMB-High (defined as >10 mt/MB) and dMMR/MSI-H was tested by IHC/NGS. We engineered CRISPR knock-in HCT116 and LS-174T colon cancer isogenic cell lines bearing XPO1 R749Q mutations and Stochastic Optical Reconstruction Microscopy (STORM) analysis was performed. Structural modeling was performed with published XPO1 structures by mapping XPO1 mutations from the MSKCC-IMPACT dataset. Results: A total of 96 patients with XPO1 R749Q mutations were identified (50% occurred in endometrial cancer and 23% occurred in colorectal cancer). TMB-H was observed in 92% of XPO1 R749Q mt tumors (9% were dMMR/MSI-H), while 86% of XPO1 R749Q mt tumors were POLE-mutated within the endonuclease domain. Median variant allele frequency for XPO1 R749Q mt and POLE mt were 25% and 29%, respectively. STORM imaging revealed that XPO1 R749Q mutant cells had significant localization of XPO1 in the cytoplasm compared to XPO1 WT cells, especially at the outside edge of the nuclear pores. Structural modeling predicted that XPO1 R749Q mt affected the regulatory H9-loop of XPO1 favoring increased shuttling and retention in the cytoplasm. Mass spectrometry analysis of nuclear and cytoplasmic fractionated proteomes confirmed that XPO1 R749Q mt cells had increased export of proteins compared to XPO1 WT cells. A library screen of >200 FDA-approved drugs revealed a strong therapeutic resistance of XPO1 R749Q cells, especially to chemotherapies used in the treatment of colon cancer. XPO1 inhibition with selinexor synergized with chemotherapy in XPO1 R749Q mt cells in vitro and overcame resistance to irinotecan in vivo in xenograft mice models. Conclusion: This study sheds novel insights into the role of nuclear export in cancers. Specifically, XPO1 R749Q mutations are enriched in TMB-H endometrial and colon cancers and increase nuclear export of key proteins that confer resistance to therapies using DNA-damaging agents. Our current work aims to identify novel therapies that can overcome resistance to DNA-damaging therapies seen in XPO1 mutant cells, such as immune checkpoint inhibitor (ICI) therapy given the co-occurrence with POLE mutations and recent reports of high level of response to ICI therapy in TMB-H and POLE mt colorectal cancers. Citation Format: Tulasigeri M. Totiger, Yasmine Baca, Wannasiri Chiraphapphaiboon, Sana Chaudhry, Skye Montoya, Monika Chojnacka, Gabriel Gaidosh, Jumana Afaghani, Maurizio Affer, Christopher D. Armstrong, Ryan Notti, Jenna Zabroski, Jacob Jahn, Vindhya Nawaratne, Ramiro Verdun, Hai Dang Nguyen, Chadi Nabhan, Thomas J. Herzog, Phil Walker, Andrew Elliott, Emil Lou, Wafik S. El-Deiry, Edith Mitchell, Jose Antonio Rodriguez, Justin Taylor. Pan-cancer analysis of XPO1 R749Q mutations across 217,570 patients reveals association with high tumor mutational burden and therapy resistance. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4253.

Abstract 459: Targeting the non-junctional tumorigenic function of connexin43 in cancer cell plasticity

Abstract Tumors are highly heterogeneous and dynamic, with both cancer cells and cancer stem cells (CSCs) displaying a high degree of plasticity contributing to metastasis and tumor recurrence following treatment. Epithelial-mesenchymal transition (EMT) enables cancer cells to acquire migratory and invasive characteristics, access the circulatory system, and metastasize. Moreover, EMT is associated with therapeutic resistance and CSC generation. Our previous research demonstrated a redistribution of the gap junction protein connexin43 (Cx43) from the plasma membrane to the cytosol during EMT. Using super-resolution STochastic Optical Reconstruction Microscopy (STORM), we have recently identified increased interaction of such intracellular Cx43 with microtubules during EMT and in primary glioblastoma (GBM) CSCs (GSCs). We further report a tumorigenic function for cytosolic Cx43/microtubule complexing in cancer cell and CSC proliferation, migration, and survival. Cx43 localization and activity is regulated by multiple sites for protein-protein interaction within the Cx43 carboxy-terminus (CT), including a tubulin binding domain. We employed a Cx43 mimetic peptide named JM2 (juxtamembrane 2) encompassing the microtubule binding sequence of the Cx43 CT. Following administration, JM2 efficiently and specifically disrupts the interaction of Cx43 with microtubules, inhibits GSC-derived neurosphere formation in vitro, and patient GBM-derived organoid growth ex vivo. Using an orthotopic GBM patient derived xenograft mouse model, we demonstrate in vivo that JM2 significantly decreases the number of GSCs within brain tumors, inhibits the formation of highly invasive GBM tumors, and increases mouse survival in combination with the chemotherapy alkylating agent temozolomide. Further examining the role of Cx43/microtubule complexing in the context of metastatic disease, we observed JM2 also decreases mesenchymal marker expression and inhibits cell migration and invasion in EMT models. Using an in vivo orthotopic breast cancer mouse model we find that intratumoral administration of JM2 prevents metastasis, significantly decreasing cancer cell lung colonization. Our findings validate targeting Cx43 complexing with microtubules, with JM2, as a novel therapeutic approach for cancer treatment through inhibition of EMT-associated increases in invasion and metastasis, and elimination of CSCs. Modulation of non-junctional Cx43 functions therefore represents a viable therapeutic approach to target cellular plasticity with broad therapeutic implications for many cancers. Citation Format: Samy Lamouille, Christina E. Wheeler, Stacie E. Deaver, Michael J. Zeitz, Zhi Sheng, Robert G. Gourdie, James W. Smyth. Targeting the non-junctional tumorigenic function of connexin43 in cancer cell plasticity [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 459.

Abstract 886: Fine-tuned CAIX targeted CAR-T cells exhibit superior efficacy and mitigate on-target off-tumor side effects

Abstract Chimeric Antigen Receptor (CAR) T cell therapy is a new type of “living drug” that has proven to be a powerful immunotherapy for hematologic malignancies. To date, there are six CAR-T products approved by the FDA for hematologic malignancies, four targeting CD19, and two targeting B-cell maturation antigen (BCMA). However, this success has not yet been transferred to solid tumors. A major hurdle is the on-target off-tumor toxicities due to the shared expression of target antigen on normal tissues. Carbonic anhydrase IX (CAIX) is highly expressed in clear cell renal cell carcinoma (ccRCC); however, it is also expressed on bile duct at a lower physiological level leading to off-tumor toxicity of CAIX targeted therapies. The first anti-CAIX CAR-T studies, using the 1st generation G250 CAR-T cells plus IL-2 to treat patients with metastatic ccRCC, caused severe liver enzyme abnormalities in the treated patients after CAR-T cell infusions. To understand CAIX expression on tumor and normal tissues, we quantified CAIX expression on ccRCC patient samples and healthy bile duct tissues using direct stochastic optical reconstruction microscopy (dSTORM) which provides single-molecule resolution. Tet-On inducible CAIX expressing cell lines were established to mimic various CAIX densities on normal tissue and tumor samples. Using biolayer interferometry (BLI) and avidity analyzer, we identified a low-affinity, high-avidity anti-CAIX CAR G9. G9 CAR-T cells only kill CAIX high ccRCC tumor cells but not CAIX low normal cholangiocytes, and exhibited a CAIX density dependent response to Tet-On inducible CAIX expressing cell lines. Compared to high-affinity G250 CAR-T cells, G9 showed a better safety profile and a wider therapeutic window. G9 demonstrated a superior ex vivo efficacy on ccRCC patient derived organotypic tumor spheroids (PDOTS) 3D cultures which recapitulate ccRCC patient tumor microenvironment (TME), as well as low toxicity on cholangiocyte derived organotypic spheroids (CDOS). In summary, affinity/avidity fine-tuned CAIX targeted CAR-T cell therapy holds promise to achieve cures of ccRCC by efficaciously killing tumor cells and mitigating on-target off-tumor toxicity on normal tissues. Citation Format: Yufei Wang, Alicia Buck, Gabriella Kastrunes, Rabia Abbas, Michael Lynch, Zhou Zhong, Song-My Hoang, Andras Miklosi, Kun Huang, Jae-Won Cho, Marion Grimaud, Cecile Razimbaud, Matthew Chang, Atef Fayed, Audrey Apollon, Nithyassree Murugan, Ze-Hua Li, Tran Thai, Luann Zerefa, Brandon Piel, Elena Ivanova, Amy Cameron, Quang-De Nguyen, Zhu Zhu, Kevin Wei, Yasmin Nabil Laimon, Aseman Bagheri Sheshdeh, Sabina Signoretti, David A. Braun, Catherine J. Wu, Toni K. Choueiri, Jon Wee, Cloud P. Paweletz, Martin Hemberg, Aedin C. Culhane, David A. Barbie, Gordon J. Freeman, Wayne A. Marasco. Fine-tuned CAIX targeted CAR-T cells exhibit superior efficacy and mitigate on-target off-tumor side effects [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 886.

Abstract 777: Super-resolution imaging of heterochromatin structure detects early events in lung cancer

Abstract Early detection of lung cancer is essential to reduce lung cancer-related morbidity and mortality. Despite significant efforts, current approaches suffer from high false-positive rates or limited sensitivity. There is a critical need for non-invasive, cost-effective technologies that detect the early changes in lung carcinogenesis with high sensitivity and specificity. Abnormal chromatin structure is one of the hallmarks of cancer cells and is independent of molecular pathways making it an attractive target for early cancer detection. In this study, we assessed the use of super-resolution stochastic optical reconstruction microscopy (STORM) to detect abnormal heterochromatin disruption in lung carcinogenesis. First, utilizing a mouse model of tobacco carcinogen (NNK)-induced lung adenocarcinoma, we analyzed heterochromatin structure in the lungs of NNK-treated mice at 8, 15 and 20 weeks post-NNK exposure together with non-treated control mice at the same time points. Super-resolution images of NNK-induced lung lesions at all time points showed significant disruption of condensed heterochromatin nanodomains compared to normal alveolar epithelial cells from the control mice, consistent with our data from other tumor types. Importantly, the normal-appearing bronchial epithelial cell nuclei from NNK-treated mice also showed significant heterochromatin disruption in NNK-treated mice at 15 and 20 weeks (P< 0.0001), demonstrating that this method can detect early changes. Next, we sought to confirm this in humans. Super-resolution imaging showed that, compared to normal alveolar and bronchial epithelial cells from control subjects without cancer, the heterochromatin structure was more disrupted in tumor cells from patients with lung adenocarcinoma (LUAD) and squamous cell carcinoma (LUSC). We also observed significant disrupted heterochromatin structure in tumor-adjacent normal tissue at the tumor margin. Lastly, we performed a pilot study on bronchial epithelial cells isolated from sputum samples from 11 cigarette smokers with or without lung cancer. The heterochromatin structure in the bronchial epithelial cells collected from lung cancer patients at the time of diagnosis was significantly more disrupted than those from smokers without lung cancer (P= 0.004). Our results support disrupted heterochromatin structure as an early event in lung carcinogenesis and demonstrate the feasibility of utilizing super-resolution imaging of heterochromatin structure for early detection of lung cancer using sputum samples. Citation Format: Laura P. Stabile, Xuejiao Sun, Jianquan Xu, Beatriz Kanterewicz, David O. Wilson, Sanja Dacic, Lora H. Rigatti, Brenda Diergaarde, Yang Liu. Super-resolution imaging of heterochromatin structure detects early events in lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 777.

Purification Analysis, Intracellular Tracking, and Colocalization of Extracellular Vesicles Using Atomic Force and 3D Single-Molecule Localization Microscopy.

Extracellular vesicles (EVs) play a key role in cell-cell communication and thus have great potential to be utilized as therapeutic agents and diagnostic tools. In this study, we implemented single-molecule microscopy techniques as a toolbox for a comprehensive characterization as well as measurement of the cellular uptake of HEK293T cell-derived EVs (eGFP-labeled) in HeLa cells. A combination of fluorescence and atomic force microscopy revealed a fraction of 68% fluorescently labeled EVs with an average size of ∼45 nm. Two-color single-molecule fluorescence microscopy analysis elucidated the 3D dynamics of EVs entering HeLa cells. 3D colocalization analysis of two-color direct stochastic optical reconstruction microscopy (dSTORM) images revealed that 25% of EVs that experienced uptake colocalized with transferrin, which has been linked to early recycling of endosomes and clathrin-mediated endocytosis. The localization analysis was combined with stepwise photobleaching, providing a comparison of protein aggregation outside and inside the cells.

Disruption of Phosphodiesterase 3A Binding to SERCA2 Increases SERCA2 Activity and Reduces Mortality in Mice With Chronic Heart Failure.

Increasing SERCA2 (sarco[endo]-plasmic reticulum Ca2+ ATPase 2) activity is suggested to be beneficial in chronic heart failure, but no selective SERCA2-activating drugs are available. PDE3A (phosphodiesterase 3A) is proposed to be present in the SERCA2 interactome and limit SERCA2 activity. Disruption of PDE3A from SERCA2 might thus be a strategy to develop SERCA2 activators. Confocal microscopy, 2-color direct stochastic optical reconstruction microscopy, proximity ligation assays, immunoprecipitations, peptide arrays, and surface plasmon resonance were used to investigate colocalization between SERCA2 and PDE3A in cardiomyocytes, map the SERCA2/PDE3A interaction sites, and optimize disruptor peptides that release PDE3A from SERCA2. Functional experiments assessing the effect of PDE3A-binding to SERCA2 were performed in cardiomyocytes and HEK293 vesicles. The effect of SERCA2/PDE3A disruption by the disruptor peptide OptF (optimized peptide F) on cardiac mortality and function was evaluated during 20 weeks in 2 consecutive randomized, blinded, and controlled preclinical trials in a total of 148 mice injected with recombinant adeno-associated virus 9 (rAAV9)-OptF, rAAV9-control (Ctrl), or PBS, before undergoing aortic banding (AB) or sham surgery and subsequent phenotyping with serial echocardiography, cardiac magnetic resonance imaging, histology, and functional and molecular assays. PDE3A colocalized with SERCA2 in human nonfailing, human failing, and rodent myocardium. Amino acids 277-402 of PDE3A bound directly to amino acids 169-216 within the actuator domain of SERCA2. Disruption of PDE3A from SERCA2 increased SERCA2 activity in normal and failing cardiomyocytes. SERCA2/PDE3A disruptor peptides increased SERCA2 activity also in the presence of protein kinase A inhibitors and in phospholamban-deficient mice, and had no effect in mice with cardiomyocyte-specific inactivation of SERCA2. Cotransfection of PDE3A reduced SERCA2 activity in HEK293 vesicles. Treatment with rAAV9-OptF reduced cardiac mortality compared with rAAV9-Ctrl (hazard ratio, 0.26 [95% CI, 0.11 to 0.63]) and PBS (hazard ratio, 0.28 [95% CI, 0.09 to 0.90]) 20 weeks after AB. Mice injected with rAAV9-OptF had improved contractility and no difference in cardiac remodeling compared with rAAV9-Ctrl after aortic banding. Our results suggest that PDE3A regulates SERCA2 activity through direct binding, independently of the catalytic activity of PDE3A. Targeting the SERCA2/PDE3A interaction prevented cardiac mortality after AB, most likely by improving cardiac contractility.

Super-Resolution Imaging of Bacterial Secreted Proteins Using Genetic Code Expansion.

Type three secretion systems (T3SSs) enable gram-negative bacteria to inject a battery of effector proteins directly into the cytosol of eukaryotic host cells. Upon entry, the injected effector proteins cooperatively modulate eukaryotic signaling pathways and reprogram cellular functions, enabling bacterial entry and survival. Monitoring and localizing these secreted effector proteins in the context of infections provides a footprint for defining the dynamic interface of host-pathogen interactions. However, labeling and imaging bacterial proteins in host cells without disrupting their structure/function is technically challenging. Constructing fluorescent fusion proteins does not resolve this problem, because the fusion proteins jam the secretory apparatus and thus are not secreted. To overcome these obstacles, we recently employed a method for site-specific fluorescent labeling of bacterial secreted effectors, as well as other difficult-to-label proteins, using genetic code expansion (GCE). This paper provides a complete step-by-step protocol to label Salmonella secreted effectors using GCE site-specifically, followed by directions for imaging the subcellular localization of secreted proteins in HeLa cells using direct stochastic optical reconstruction microscopy (dSTORM) Recent findings suggest that the incorporation of non-canonical amino acids (ncAAs) via GCE, followed by bio-orthogonal labeling with tetrazine-containing dyes, is a viable technique for selective labeling and visualization of bacterial secreted proteins and subsequent image analysis in the host. The goal of this article is to provide a straightforward and clear protocol that can be employed by investigators interested in conducting super-resolution imaging using GCE to study various biological processes in bacteria and viruses, as well as host-pathogen interactions.

A systematic study on the use of multifunctional nanodiamonds for neuritogenesis and super-resolution imaging

BackgroundRegeneration of defective neurons in central nervous system is a highlighted issue for neurodegenerative disease treatment. Various tissue engineering approaches have focused on neuritogenesis to achieve the regeneration of damaged neuronal cells because damaged neurons often fail to achieve spontaneous restoration of neonatal neurites. Meanwhile, owing to the demand for a better diagnosis, studies of super-resolution imaging techniques in fluorescence microscopy have triggered the technological development to surpass the classical resolution dictated by the optical diffraction limit for precise observations of neuronal behaviors. Herein, the multifunctional nanodiamonds (NDs) as neuritogenesis promoters and super-resolution imaging probes were studied.MethodsTo investigate the neuritogenesis-inducing capability of NDs, ND-containing growing medium and differentiation medium were added to the HT-22 hippocampal neuronal cells and incubated for 10 d. In vitro and ex vivo images were visualized through custom-built two-photon microscopy using NDs as imaging probes and the direct stochastic optical reconstruction microscopy (dSTORM) process was performed for the super-resolution reconstruction owing to the photoblinking properties of NDs. Moreover, ex vivo imaging of the mouse brain was performed 24 h after the intravenous injection of NDs.ResultsNDs were endocytosed by the cells and promoted spontaneous neuritogenesis without any differentiation factors, where NDs exhibited no significant toxicity with their outstanding biocompatibility. The images of ND-endocytosed cells were reconstructed into super-resolution images through dSTORM, thereby addressing the problem of image distortion due to nano-sized particles, including size expansion and the challenge in distinguishing the nearby located particles. Furthermore, the ex vivo images of NDs in mouse brain confirmed that NDs could penetrate the blood–brain barrier (BBB) and retain their photoblinking property for dSTORM application.ConclusionsIt was demonstrated that the NDs are capable of dSTORM super-resolution imaging, neuritogenic facilitation, and BBB penetration, suggesting their remarkable potential in biological applications.Graphical

STORM-based multi-functional carbon dots for investigating HS- interaction with mitochondria in living cells

By investigating the interaction between subcellular components using visualization techniques, pathological processes can be intuitively analyzed to reveal the origins of associated disorders more efficiently. Based on the Stochastic optical reconstruction microscopy (STORM) imaging nanoscopy, this study is the first to achieve a higher resolution and high signal-to-background ratio image of living cells by employing photoblinking carbon dots (P-CDs). Accordingly, this example can be used to explore the interaction between subcellular structures more precisely and clearly. Thus, the current study provides a potent method for visualizing the etiology of associated disorders.

5P Physiologically relevant treatment models to investigate epigenetic mechanisms driving platinum resistance in ovarian high grade serous carcinoma

The prognosis for patients with platinum-resistant ovarian High Grade Serous Carcinoma (HGSC) remains poor. BriTROC-1 data indicate that genomic alterations alone cannot explain acquired platinum resistance. We investigate epigenetic changes that may drive platinum resistance in HGSC. Using in an in vitro two-dimensional model, we recreated multiple cycles of chemotherapy. We utilised both established cell lines and primary cultures derived from HGSC ascites. Following cell characterisation (p53, PAX8 IHC), carboplatin sensitivity was assessed (sulforhodamine B assay). Cells were then pulsed with four cycles of carboplatin (50μM for 6 hours) with a week of recovery between each cycle. Methylation (Illumina 850k array), transcriptomic (RNAseq) and chromatin accessibility (ATACseq) assays were performed. Cells were also imaged using Stochastic Optical Reconstruction Microscopy. Firstly, we focused on RNAseq analysis to evaluate genes (and related biological processes) that are consistently enriched following carboplatin cycles and the unique genes that are conversely enriched at cycle level. We attempted to identify uniformly up-/down-regulated pathways across the different cultures. These data were compared with the same results obtained from the OvCar4, an established HGSC cell line and IVR01, an in-vivo resistant OvCar4 derivative. The ATACseq and methylation analyses are still ongoing, aiming to identify possible concordant changes in the chromatin accessibility and the methylation patterns that will allow us to clarify the changes observed in transcriptomic. The preliminary data obtained from the RNAseq analysis show that the highest number of enriched genes seems to occur after the first Carboplatin cycle, with a lower number of progressively enriched genes across all other ones. No constant biological processes were identified for the moment, across the different primary cell cultures. Further comparisons will be certainly needed. Understanding the epigenetic landscape of HGSC using physiologically relevant models will allow us to identify possible therapeutic targets that could eventually prevent platinum resistance.

DNA nanostructures as a tool for targeted antimicrobial delivery

Antibiotic resistance is a growing worldwide human health issue that is now threatening to render us vulnerable once again to infections that have been treatable for decades. Various approaches have been proposed in the effort to overcome this threat and effectively treat bacterial infections. We report the use of DNA origami nanostructures [1], functionalized with aptamers, as a vehicle for delivering the antimicrobials in a specific and efficient manner. We test the system against Gram positive (Bacillus subtilis) and Gram negative (Escherichia coli) targets. We use direct stochastic optical reconstruction microscopy (dSTORM) and atomic force microscopy (AFM) to characterize the DNA origami nanostructures and structured illumination microscopy (SIM) to assess the binding of the origami to the bacteria. We show that treatment with lysozyme-functionalized origami slows bacterial growth more effectively than treatment with free lysozyme. Our study introduces DNA origami as a tool in the fight against antibiotic resistance, and our results demonstrate the specificity and efficiency of the nanostructure as a drug delivery vehicle. [1] I. Mela, P. P. Vallejo-Ramirez, S. Makarchuk, G. Christie, D. Bailey, R. M. Henderson, H. Sugiyama, M. Endo, C. F. Kaminski, Angew. Chem. Int. Ed. 2020, 59, 12698, https://doi.org/10.1002/anie.202002740.

Three-dimensional single-molecule super-resolution imaging of proteins involved in primary cilia formation.

Primary cilia are organelles that protrude from the cell membrane of most human cells where they perform critical sensory and signaling functions. Defects and mutations in proteins in the primary cilium cause a range of diseases and syndromes collectively termed ciliopathies. Intracellular primary cilium formation begins with the recruitment of Golgi-derived pre-ciliary vesicles to the distal appendages of the mother centriole, but the molecular mechanisms behind the recruitment of the distal appendage proteins are not fully understood. The proteins Rab34 and MyosinVa were found through structured illumination microscopy (SIM) to be closely associated with these pre-ciliary vesicles during this step. However, because of the sub-diffraction size and three-dimensional (3D) structures of the centriole and of the involved proteins, higher resolution multi-target 3D microscopy is required to resolve their organization. To address this limitation, 3D two-color direct stochastic optical reconstruction microscopy (dSTORM) was implemented, providing a single-molecule localization precision of roughly 20 nm in all dimensions. A two-channel 4f emissions system was constructed using a 2-μm axial range double helix phase mask for single-molecule localization in 3D through point spread function engineering. This system allowed for 3D single-molecule super-resolution imaging of Rab34 and MyosinVa in two different color-channels together with imaging of the centriolar protein FOP in both color-channels for context and precise channel registration. The resulting 3D super-resolved reconstructions revealed the nanoscale structures formed by these proteins at the pre-ciliary vesicles, the structural relation between Rab34 and MyosinVa, and their position in relation to the mother centriole.

Three-dimensional single-molecule localization microscopy with metal-induced energy transfer.

Over the past two decades, super-resolution microscopy has seen a tremendous development in speed and resolution, but for most of its methods, there exists a remarkable gap between lateral and axial resolution, which is by a factor of 2 to 3 worse. One recently developed method to close this gap is metal-induced energy transfer (MIET) imaging, which achieves an axial resolution down to nanometers. It exploits the distance-dependent quenching of fluorescence when a fluorescent molecule is brought close to a metal surface. We combine the extreme axial resolution of MIET imaging with the extraordinary lateral resolution of single-molecule localization microscopy, in particular with direct stochastic optical reconstruction microscopy (dSTORM). This combination allows us to achieve isotropic three-dimensional super-resolution imaging of subcellular structures. Moreover, we used spectral demixing for implementing dual-color MIET-dSTORM that allows us to image and colocalize, in three dimensions, two different cellular structures simultaneously.

Antibody Functionalization of Ultrasmall Fluorescent Core–Shell Aluminosilicate Nanoparticle Probes for Advanced Intracellular Labeling and Optical Super Resolution Microscopy

Fluorescent labeling of cellular substructures is commonly performed using antibody–organic dye conjugates. Organic dyes do not exhibit ideal optical properties in terms of brightness and photostability, however, in particular when it comes to advanced optical super-resolution microscopy (SRM) applications. Here, we demonstrate the efficient conjugation of widely available secondary antibodies and cationic species to ultrasmall (sub-10 nm) fluorescent silica core─poly(ethylene glycol) shell (core–shell) aluminosilicate nanoparticles (aC′ dots) encapsulating different color dyes for specific targeting and high-quality fluorescence imaging of structures of the cytoskeleton (tubulin and actin) and nucleus, respectively. We show that the different color aC′ dots provide enhanced brightness and photostability relative to their parent dyes. As recently discovered, we further demonstrate that they exhibit photo-induced blinking with low ON–OFF duty cycles enabling optical SRM, for example, in the form of stochastic optical reconstruction microscopy (STORM), without the need for complex imaging setups or cocktails. After carefully optimizing Ab–aC′ dot conjugation as well as cell structure labeling protocols in fixed and permeabilized HeLa and MDA-MB-231 cells, we demonstrate three-color STORM and exemplify improved resolution compared to standard antibody–dye conjugates. This work paves the way to next-generation multifunctional optical probes based on ultrasmall silica nanoparticle platforms for advanced applications in bioimaging, nanomedicine, and beyond.

DSTORM-Based Single-Cell Protein Quantitative Analysis Can Effectively Evaluate the Degradation Ability of PROTACs.

As an emerging therapeutic strategy, proteolysis-targeting chimeras (PROTACs) have been proven to be superior to traditional drugs in many aspects. However, due to their unique mechanism of action, existing methods for evaluating the degradation still have many limitations, which seriously restricts the development of PROTACs. In this methodological study, using direct stochastic optical reconstruction microscopy (dSTORM)-based single-cell protein quantitative analysis, we systematically investigated the dynamic degradation characteristics of FLT3 protein during PROTACs treatment. We found that the distribution of FLT3 varies between FLT3-ITD mutation and FLT3-WT cells. PROTACs had an obvious time-course effect on protein degradation and present two distinct phases; this provided a basis for deciding when to evaluate protein degradation. High concentrations of PROTACs were more effective than long-time administration because a higher Dmax was achieved. Two-color dSTORM-based colocalization analysis efficiently detected the proportion of ternary complexes, making it very useful in screening PROTACs. Taken together, our findings show that the dSTORM method is an ideal tool for evaluating PROTACs and will accelerate the development of new PROTACs.

Switching of Organic Fluorophores by Glycerol‐sulfite Interactions for Single‐Molecule Super‐Resolution Microscopy**

AbstractPhotoinduced off‐switching of organic fluorophores is used in super‐resolution microscopy to separate and localize single fluorescent molecules. However, this method typically relies on the use of complex imaging buffers that make use of enzymatic oxygen scavengers to remove oxygen and primary thiols to reversibly reduce excited fluorophores to a non‐fluorescent state. Here, we show that the interactions between sodium sulfite and glycerol can also be used for efficient switching of common organic fluorophores. The addition of glycerol to the imaging buffer allows us to tune the dye switching from intermittent fluorescence to the off‐state. We additionally show that sodium sulfite‐glycerol‐based buffers are especially useful for imaging at low laser illumination intensities in high‐refractive index solutions and samples embedded in agarose gel. This significantly simplifies the implementation of different super‐resolution microscopy modalities such as direct STochastic Optical Reconstruction Microscopy (dSTORM) and Super‐resolution Optical Fluctuation Imaging (SOFI).