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NAD + exerts its stabilizing effects on microtubules through SIRT3. (A) SIRT3 overexpression inhibits vinblastine-mediated microtubule depolymerization. To determine if a sirtuin mediates the effects of NAD + on microtubules, we tested each sirtuin for its effects on microtubule stability. In these experiments, MCF-7 cells were transfected with C-terminal GFP-tagged versions of SIRT1-7, and microtubule depolymerization was elicited by treatment of cells with vinblastine (VB; 100 nM) for 2 h. Microtubules were visualized by anti-Tyr-tubulin immunostaining (green). In control-transfected cells, minimal microtubule polymer mass remained after vinblastine treatment. However, cells expressing SIRT3-GFP exhibited marked protection of microtubules from vinblastine treatment. (Scale bar, 10 μm.) (B) Quantification of results in A. To quantify microtubule polymer mass in MCF-7 cells, polymerized microtubules were identified and binarized using the Tubeness plugin in Fiji, which identifies linear structures. The total area of the cell was calculated, and the graph represents the ratio of microtubule polymers to cell area, which we refer to as the polymerization index. We measured ∼100 cells from n = 3 replicates. Bar graph represents mean ± SEM; **P < 0.01 (one-way ANOVA with Tukey's post hoc test). (C) SIRT3 is necessary for the effects of NAD + on microtubule depolymerization. To determine if the effects of NAD + on microtubule stability are mediated through SIRT3, we monitored the effects of SIRT3 knockdown on NAD +-induced stabilization of microtubules. MCF-7 cells were treated with 100 nM vinblastine for 2 h, which results in both loss of the microtubule cytoskeleton and subsequent cell shrinkage. Microtubules were visualized by anti-Tyr-tubulin immunostaining (green). Treatment of these cells with 1 mM NAD + prevents the loss of the microtubule cytoskeleton and plasma membrane collapse. However, this effect of NAD + is lost in cells expressing either of two SIRT3specific shRNA. These cells also display more membrane collapse than control cells, suggesting that the loss of SIRT3 may make the cells more sensitive to vinblastine. These data indicate that SIRT3 is required for the protective effects of NAD + on the microtubule cytoskeleton. (Scale bar, 10 μm.) (D) Quantification of results in C. Quantification was performed as described in B. We measured ∼100 cells from n = 3 replicates. Bar graph represents mean ± SEM; **P < 0.01, ***P < 0.001 (one-way ANOVA with Tukey's post hoc test). 

NAD + exerts its stabilizing effects on microtubules through SIRT3. (A) SIRT3 overexpression inhibits vinblastine-mediated microtubule depolymerization. To determine if a sirtuin mediates the effects of NAD + on microtubules, we tested each sirtuin for its effects on microtubule stability. In these experiments, MCF-7 cells were transfected with C-terminal GFP-tagged versions of SIRT1-7, and microtubule depolymerization was elicited by treatment of cells with vinblastine (VB; 100 nM) for 2 h. Microtubules were visualized by anti-Tyr-tubulin immunostaining (green). In control-transfected cells, minimal microtubule polymer mass remained after vinblastine treatment. However, cells expressing SIRT3-GFP exhibited marked protection of microtubules from vinblastine treatment. (Scale bar, 10 μm.) (B) Quantification of results in A. To quantify microtubule polymer mass in MCF-7 cells, polymerized microtubules were identified and binarized using the Tubeness plugin in Fiji, which identifies linear structures. The total area of the cell was calculated, and the graph represents the ratio of microtubule polymers to cell area, which we refer to as the polymerization index. We measured ∼100 cells from n = 3 replicates. Bar graph represents mean ± SEM; **P < 0.01 (one-way ANOVA with Tukey's post hoc test). (C) SIRT3 is necessary for the effects of NAD + on microtubule depolymerization. To determine if the effects of NAD + on microtubule stability are mediated through SIRT3, we monitored the effects of SIRT3 knockdown on NAD +-induced stabilization of microtubules. MCF-7 cells were treated with 100 nM vinblastine for 2 h, which results in both loss of the microtubule cytoskeleton and subsequent cell shrinkage. Microtubules were visualized by anti-Tyr-tubulin immunostaining (green). Treatment of these cells with 1 mM NAD + prevents the loss of the microtubule cytoskeleton and plasma membrane collapse. However, this effect of NAD + is lost in cells expressing either of two SIRT3specific shRNA. These cells also display more membrane collapse than control cells, suggesting that the loss of SIRT3 may make the cells more sensitive to vinblastine. These data indicate that SIRT3 is required for the protective effects of NAD + on the microtubule cytoskeleton. (Scale bar, 10 μm.) (D) Quantification of results in C. Quantification was performed as described in B. We measured ∼100 cells from n = 3 replicates. Bar graph represents mean ± SEM; **P < 0.01, ***P < 0.001 (one-way ANOVA with Tukey's post hoc test). 

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Significance Nicotinamide adenine dinucleotide (NAD ⁺ ) is an endogenous small molecule that has effects on diverse processes, including obesity, lifespan, and cancer. A major goal is to identify the NAD ⁺ -regulated cellular pathways that may mediate these effects. In this study, we demonstrate that NAD ⁺ regulates the microtubule cytoskeleton. We...

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... These large datasets increase the sensitivity of our measurements, allowing us to detect minimal yet significant changes in MT dynamic signatures. Our computational approach has revealed novel organizational and regulatory patterns in MT homeostasis, initially in renal cell carcinoma 5 , and has begun to impact studies on a wide range of topics in cell and cancer biology [43][44][45][46][47][48][49][50][51][52][53][54][55] . ...
... We can now start identifying the proteins/pathways that regulate them and investigate their relative expression in patient-derived PCa organoids 56 , as cultures with high clinical relevance. In addition, we recently published our computational results on the analysis of the effects of one of the components of the organoid media, Nicotinamide, on MT dynamics 47 . ...
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(See also the 8 PDF files appended below) The treatment of prostate cancer (PCa) has been impeded by the lack of clinically relevant disease models. There are only three PCa cell lines as available models of this heterogeneous disease out of the over 1,000 publicly available cancer cell lines; patient-derived xenografts (PDX) have proven rarely possible to establish thus far. My previous work in PCa cell lines has demonstrated that we can associate the alterations in a particular parameter of microtubule (MT) dynamics to taxane resistance in ERG overexpressing cells. MT regulating genes such as chTOG, CLIP170, MAP4, MCAK, TPX2 and Op18 to name a few are implicated in the process of conferring drug resistance and susceptibility. Because these genes are also involved in the regulation of MT dynamics, my central hypothesis is that computational analysis of MT dynamics (MT signature) can serve as a real-time readout of cell susceptibility to drug action, which will allow to discover mechanisms of resistance. Therefore, to test my hypotheses in patient-derived cells, I propose to perform two specific aims in patient-derived PCa organoids: Specific Aim 1: Define and validate cancer-specific MT dynamics signatures of MT-targeting agents (MTA) resistance. I will image and measure endogenous and drug-induced signatures (consisting of 12 descriptive parameters) of MT dynamics alterations in patient- derived cancer organoids using ClusterTrack. For each organoid type, I will measure populations of cells before and after treatment with MTAs, and will perform statistical analysis. I will use, as a starting point, samples with known patient treatment outcome for specific MTAs (Docetaxel, Cabazitaxel, Eribulin, etc.), which will allow me to validate the MT signatures and classify them into sensitive and resistant groups using clustering. Specific Aim 2: Define cancer-specific molecular mechanisms of MTA resistance to elucidate targeting strategies. I will extract RNA and will perform differential expression analysis of MT regulators in patient-derived cancer organoids as well as pathway analysis using iPAGE. I will correlate the RNA-seq MT signatures to the validated MT dynamics signatures obtained in Aim 1 using pattern matching. Correlated signatures will contain multiple up- or down-regulated MT regulator genes. I will test the proteins in these lists as candidates for personalized targets in knockdown and overexpression experiments. This approach could identify novel candidates for effective targeted therapies in metastatic disease within the MT-interacting transcriptome. I will further test these novel organoids into PDX models of PCa to confirm sensitization and therapeutic susceptibility in vivo. Further validation, of both prognostic and predictive markers, will be done by comparing ex vivo tumor growth kinetics and treatment predictions to outcomes of patients with similar genetic profiles, after drug treatment, enrolled in clinical trials. See: github.com/amatov/SegmentationBiomarkerCTC, github.com/amatov/AntibodyTextureMorphology, github.com/amatov/DataSetTracker
... These large datasets increase the sensitivity of the assay, allowing us to detect very small yet significant changes in MT dynamic signatures. Our computational approach has revealed novel organizational and regulatory patterns in MT homeostasis (initially in renal cell carcinoma 40 ) and has begun to impact studies on a wide range of topics in cell and cancer biology [41][42][43][44][45][46][47][48][49][50][51][52][53] . Our main objective in this proposal is to elucidate the various mechanisms of resistance by (i) classifying these signatures based on patient treatment outcome to investigate individual mechanisms of resistance to MT chemotherapy. ...
... It is conceivable that PCa which is different histologically would require different concentration of Y-27632 ROCK inhibitor; we will test this and will continue to systematically explore media compositions. We recently published our computational results on the analysis of the effects of another component of the organoid media, Nicotinamide, on MT dynamics 45 . There are two types of prostate organoids in our nomenclature: PR1-7 (primary) and PCa1 (metastatic). ...
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See: github.com/amatov/InstantaneousFlowTracker, github.com/amatov/ClusterTrackTubuline, github.com/amatov/DyneinFunctionAnalysis, github.com/amatov/SegmentationBiomarkerCTC, github.com/amatov/AutomatedBlotQuantification, github.com/amatov/DataSetTracker
... When NMNAT2, a ratelimiting enzyme in NAD+ production was diminished, abnormal spindle assembly increased (Wu et al., 2019). Also, NAD+ and SIRT3, a mitochondrial NAD+ dependent sirtuin, have been shown to control microtubule dynamics and reduce susceptibility to antimicrotubule agents such as vinblastine and colchicine (Harkcom et al., 2014). Additionally, SIRT4, another mitochondrial NAD+ dependent sirtuin, acts as a novel centrosomal/ microtubule-associated protein in the regulation of cell cycle progression (Bergmann et al., 2020). ...
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... Hence, our results indicated that α-Ac-Tub restored axonal transport of mitochondria and energy failure after ICH. These results were consistent with previous findings, which demonstrated that restoring cellular energetics prevented microtubule disassembly and axonal degeneration and promoted axonal regeneration (Han et al., 2020;Harkcom et al., 2014;Park et al., 2013). ...
... Recent studies demonstrated that energy failure occurred within 24 h after axotomy and triggered microtubule disassembly and axonal degeneration (Harkcom et al., 2014;Ruschel et al., 2015). Similarly, live imaging results revealed that mPTP was immediately activated in dendrites after stroke, which led to mitochondrial transmembrane potential collapse, Ca 2+ overload, and energy failure (Liu & Murphy, 2009). ...
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... Therefore, we asked whether CD38-cADPR signaling stimulated ryanodine receptors in our astrocyte mitochondrial release model. Based on previous studies [44][45][46][47], NAD (5 mM) was added to rat cortical astrocytes to stimulate CD38 pathway. Immunocytochemistry showed that an hour after NAD treatment in astrocytes, the braintype ryanodine receptor 3 (RyR3) appeared to be coexpressed with the ER; no co-localization was detected with the Golgi (Fig. 1a). ...
... Second, physiological concentrations of NAD + and NADH in vivo may be in the micromolar range, but our study used 5 mM of NAD to stimulate cultured astrocytes in vitro. It has been reported that the millimolar range of NAD was sufficient for signaling experiments in vitro [44,45]. Moreover, NAD has a short half-life of about 1 h [46]. ...
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... Hence, our results indicated that α-Ac-Tub restored axonal transport of mitochondria and energy failure after ICH. These results were consistent with previous findings, which demonstrated that restoring cellular energetics prevented microtubule disassembly and axonal degeneration and promoted axonal regeneration (Han et al., 2020;Harkcom et al., 2014;Park et al., 2013). ...
... Recent studies demonstrated that energy failure occurred within 24 h after axotomy and triggered microtubule disassembly and axonal degeneration (Harkcom et al., 2014;Ruschel et al., 2015). Similarly, live imaging results revealed that mPTP was immediately activated in dendrites after stroke, which led to mitochondrial transmembrane potential collapse, Ca 2+ overload, and energy failure (Liu & Murphy, 2009). ...
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Full-text available
Injury to long axonal projections is a central pathological feature at the early phase of intracerebral hemorrhage (ICH). It has been reported to contribute to persistent functional disability following ICH. However, the molecular mechanisms that drive axonal degeneration remain unclear. Autologous blood was injected into the striatum to mimic the pathology of ICH. Observed significant swollen axons with characteristic retraction bulbs were found around the striatal hematoma at 24 h after ICH. Electronic microscopic examination revealed highly disorganized microtubule and swollen mitochondria in the retraction bulbs. MEC17 is a specific α‐tubulin acetyltransferase, ablation of acetylated α‐tubulin in MEC17−/− mice aggravated axonal injury, axonal transport mitochondria dysfunction, and motor dysfunction. In contrast, treatment with tubastatin A (TubA), which promotes microtubule acetylation, significantly alleviated axonal injury and protected the integrity of the corticospinal tract and fine motor function after ICH. Moreover, results showed that 41% mitochondria were preferentially bundled to the acetylated α‐tubulin in identifiable axons and dendrites in primary neurons. This impaired axonal transport of mitochondria in primary neurons of MEC17−/− mice. Given that opening of mitochondrial permeability transition pore (mPTP) induces mitochondrial dysfunction and impairs ATP supply thereby promoting axonal injury, we enhanced the availability of acetylated α‐tubulin using TubA and inhibited mPTP opening with cyclosporin A. The results indicated that this combined treatment synergistically protected corticospinal tract integrity and promoted fine motor control recovery. These findings reveal key intracellular mechanisms that drive axonal degeneration after ICH and highlight the need to target multiple factors and respective regulatory mechanisms as an effective approach to prevent axonal degeneration and motor dysfunction after ICH. image
... Furthermore, NAD + also plays a role in controlling the actin cytoskeleton (Venter et al. 2014). However, it is unclear how BtpA depletion of NAD + would help to stabilize microtubules, a proposed role for this effector based on transfection experiments (Felix et al. 2014), given that microtubule depolymerization is blocked by increasing intracellular NAD + levels (Harkcom et al. 2014). ...
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... MT hyperstabilization plays a direct role in paclitaxel neurotoxicity (10), and a single nucleotide polymorphism in TUBB2a, a gene encoding a tubulin isoform, is associated with an enhanced risk of CIPN (11). Moreover, MT dynamics and stability are influenced by nicotinamide adenine dinucleotide (NAD+) levels through sirtuin modulation (12), suggesting a tubulin-mediated mechanism also for the NAD+-consuming activity of Sterile Alpha and Tir Motifs-containing protein 1 (SARM1) in driving axonal degeneration in CIPN models (13). ...
... Further work is necessary to provide insight into this regulation and the cross-talk between D2 and other tubulin PTMs, such as polyglutamylation and acetylation in the control of mitochondria energetics and dynamics. It will be equally crucial to investigate whether D2 accumulation affects responses to pro-survival and pro-death signals that could play a role in CIPN axon degeneration, including regulation of TRPV and Ca 2+ channels (12,13,21,23,61,62). ...