Enhanced OTUD6B Expression in Triple-Negative Breast Carcinoma (TNBC) Correlates Inversely with Patient Outcomes
To elucidate the expression magnitude and clinical ramifications of OTUD6B in triple-negative breast carcinoma (TNBC), an inaugural bioinformatics scrutiny was undertaken leveraging the breast carcinoma dataset from the TCGA repository. Utilizing the data analytics platform available at http://gepia.cancer-pku.cn/, we discerned a pronounced augmentation in the OTUD6B expression within TNBC neoplastic specimens when juxtaposed with their cognate peri-tumoral normal tissues, a trend observed pervasively across all breast carcinoma subcategories (Fig. 1A). Moreover, when TNBC neoplastic specimens were benchmarked against their respective paracancerous tissues, the OTUD6B expression levels were conspicuously amplified (Fig. 1B). The ensuing Kaplan-Meier survival trajectory analysis unveiled a correlation: elevated OTUD6B expression presaged diminished overall survival (OS) metrics in the TNBC cohort (Fig. 1C). This data nexus intimates a presumable instrumental role of OTUD6B in accentuating TNBC pathogenesis and modulating patient outcomes. To lend empirical weight to our bioinformatics revelations, we procured neoplastic and paracancerous specimens from TNBC-afflicted patients under our institutional care. Subsequent evaluations, employing immunohistochemical and Western blot methodologies, evinced markedly augmented OTUD6B protein concentrations within TNBC neoplastic specimens relative to their adjacent normative counterparts (Fig. 1D, E). This empirical data dovetails seamlessly with our bioinformatics inferences, reinforcing the proposition of heightened OTUD6B expression in TNBC and its correlation with a suboptimal prognosis.
siRNA-Mediated Knockdown of OTUD6B Attenuates Proliferative, Invasive, and Migratory Phenotypes of Triple-Negative Breast Carcinoma (TNBC) Cells and Augments Their DOX Receptivity
In our quest to decipher the functional implications of OTUD6B within the biological milieu of triple-negative breast carcinoma (TNBC) cells, we embarked on an analysis of its expression within TNBC cellular lines, specifically MDA-MB-231 and MDA-MB-453. EdU incorporation assays unambiguously illuminated the pronounced inhibitory impact of OTUD6B siRNA on the proliferative dynamics of TNBC cells (Fig. 2A-B). Complementarily, employing Transwell migration and scratch wound-healing assays, we ascertained that the OTUD6B siRNA engendered a substantive curtailment in the migratory and invasive capacities of TNBC cells (Fig. 2C-H). Collectively, this suite of observations postulates a facilitative role for OTUD6B in the proliferative, migratory, and invasive orchestrations of TNBC cells. Delving deeper into the nexus between OTUD6B and chemosensitivity in TNBC, we employed the CCK8 viability assay. Our findings elucidate that siRNA-mediated OTUD6B abrogation amplifies the cytotoxic response of TNBC cells to DOX, as manifested by a substantial diminution in their half maximal inhibitory concentration (IC50) vis-à-vis the control cohort (Fig. 2I-J).
Efficacious Incorporation of OTUD6B siRNA and DOX within an Engineered DNA Tetrahedral Framework
For the fabrication and conveyance of the OTUD6B siRNA and DOX using DNA tetrahedron nanoparticles, we harnessed a DNA self-assemblage technique. This methodology capitalizes on four singularly stranded DNAs (ssDNAs), founded on the axioms of nucleobase complementarity, to engineer a robust tetrahedral configuration (Td)[22]. Of the quartet, three ssDNAs spanned 63 nucleotides (nt) in length, whilst the fourth extended to 87 nt. Following the engenderment of Td siOTUD6B via nucleobase complementarity, a concoction of DOX and siOTUD6B @ Td was forged, culminating in the resultant compound siOTUD6B/DOX @ Td, illustratively represented in Fig. 3A.
By meticulously refining synthesis parameters – encompassing temperature, chronological duration, ionic concentration, and auxiliary variables – we discerned the quintessential blueprint for crafting DNA tetrahedral nanoparticles. In particular, DNA tetrahedra were engineered under varying magnesium (Mg2+) ionic concentrations: 12.5 mM, 25 mM, and 50 mM. The derivatives from each synthetic phase were profiled via 8% polyacrylamide gel electrophoresis. Observations underscored that the electrophoretic band intensity, indicative of residual unreacted entities, was at its nadir, and synthetic yield peaked when Mg2 + concentrations oscillated between 12.5 mM and 25 mM (Fig. 3B). Balancing efficiency vis-à-vis economic considerations, a Mg2 + concentration of 12.5 mM was earmarked for ensuing synthetic endeavors. Atomic Force Microscopy (AFM) elucidations unveiled a distinctive tetrahedral morphology accompanied by homogeneous dimensions for the fabricated DNA tetrahedral nanoparticles (Fig. 3C). Such revelations authenticate the triumphant synthesis of our envisaged DNA tetrahedra.
Employing a UV spectrophotometric modality, we quantified the encapsulation prowess and the DOX assimilation rates. Data delineated a direct proportionality between drug assimilation and its increasing concentration, with a concomitant inverse relationship for encapsulation efficiency (Fig. 5D-E). These empirical outcomes fortify the successful integration of OTUD6B siRNA and DOX within DNA tetrahedral nanoparticles.
Efficient Intracellular Uptake of DNA Tetrahedra by TNBC Cells Facilitates Concurrent OTUD6B Gene Suppression and DOX Liberation
To ascertain the targeted proficiency of the DNA tetrahedral nanoparticles towards TNBC cells and the concomitant discharge of siOTUD6B and DOX for therapeutic intervention, TNBC cells were exposed to free siOTUD6B and siOTUD6B@Td. Laser confocal microscopy was subsequently deployed to monitor the intracellular assimilation of these nanoparticles. Observational data illuminated a pronounced augmentation in the fluorescence intensity within MDA-MB-231 and MDA-MB-453 cellular substrates post-treatment with siOTUD6B@Td vis-à-vis the isolated siRNA, underscoring the efficacious cellular endocytosis of siOTUD6B@Td complexes (Fig. 4a). A subsequent proteomic assessment via Western blotting unveiled a marked diminution in the OTUD6B protein abundance within the TNBC cells subjected to the siOTUD6B@Td regimen, in contrast to the control siRNA or the Td matrix incorporated with a scrambled siRNA. This ascertains the potent gene suppression effectuated by the siOTUD6B@Td amalgamation (Fig. 6b).
Pivoting towards the evaluation of DOX’s potentiating effects on TNBC post its integration within DNA tetrahedra, we orchestrated CCK8 experiments juxtaposing various nanoparticle concoctions. The empirical findings elucidated that cellular viability in MDA-MD-231 and MDA-MD-453 strains underwent significant curtailment upon therapeutic intervention using the siOTUD6/DOX@Td composite, as juxtaposed to solitary DOX@Td administration (Fig. 4D-E). Collectively, these revelations substantiate the premise that DNA tetrahedral nanoparticles adeptly permeate TNBC cells, orchestrating a dually therapeutic paradigm: silencing the OTUBD6 gene whilst concurrently liberating DOX, culminating in the amplified inhibition of TNBC cellular operations.
The Delivery via DNA Tetrahedral Vectors Markedly Attenuates Tumoral Proliferation in an In Vivo TNBC Cell Transplant Paradigm
To elucidate the in vivo antineoplastic potential of the DNA tetrahedral nanoparticles, we instituted a TNBC cell-transplanted tumorigenesis model as an experimental platform for drug conveyance assessment. Given the innate vulnerability of free siRNA to nuclease-mediated degradation in vivo, thereby compromising its therapeutic integrity, we juxtaposed the therapeutic outcomes among a Td vector-encapsulated scramble siRNA control cohort, the Td vector-incorporated siOTUD6B group, and the siOTUD6B/DOX@Td composite within the TNBC tumor framework. Upon culmination of the experimental period, tumoral evolution was chronicled, and associated tissues—both tumoral and organ-specific—were harvested for multifaceted analyses. The accrued tissues underwent procedural evaluations encompassing mass determination, photographic documentation, hematoxylin and eosin (HE) staining, Terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL) staining, and proteomic profiling via Western blotting. Empirical observations underscored the pronounced anti-tumoral efficacy of the siOTUD6B/DOX@Td amalgamation, surpassing that of the scramble siRNA@Td and the isolated siOTUD6B@Td (Fig. 5A-B). This was further substantiated by a salient decrement in the tumoral mass (Fig. 5c). Histopathological examinations via HE staining unveiled that the siOTUD6B/DOX@Td composite potently diminished oncogenic cellular abundance whilst amplifying necrotic zones (Fig. 5D). Concurrently, TUNEL staining manifested a notable augmentation in apoptotic cellular prevalence upon administration of the siOTUD6B/DOX@Td composite (Fig. 5D). Proteomic analyses, as deduced from Western blotting, elucidated a tangible suppression in the OTUD6B protein abundance in tumors subjected to the siOTUD6B/DOX@Td regimen (Fig. 5E). Importantly, a thorough histopathological survey, via HE staining, failed to detect any discernible adverse effects on critical organ systems, including the spleen, pulmonary, and renal tissues (Fig. 5f). Cumulatively, these revelations bolster the premise that DNA tetrahedral vectors exhibit potent anti-tumoral capacities while preserving a commendable biosafety profile within in vivo TNBC transplantation constructs.
Seeking to delineate the molecular underpinnings associated with OTUD6B, we discerned its putative role as a suppressor of FOXO3. Exogenous augmentation of OTUD6B within MDA-MB-231 cells notably mitigated intracellular quotas of FOXO3 protein, whilst siRNA-mediated OTUD6B abrogation reciprocated with elevated FOXO3 expression (Fig. 7A). Given its deubiquitinating enzyme characterization, elevated OTUD6B was observed to amplify the ubiquitin-modification profile of FOXO3 (Fig. 7B). Ancillary literature has implicated OTUD6B-mediated regulation of the MDM2 ubiquitin ligase. Ergo, we ventured to probe the ramifications of OTUD6B on MDM2’s ubiquitination status and expression via immunoprecipitation assays (Fig. 7C). Empirical outputs from MDA-MB-231 cells corroborated an interactive alliance between OTUD6B and MDM2, modulating the latter’s ubiquitination dynamics (Fig. 7D). In both the overexpression and silencing paradigms pertaining to OTUD6B within MDA-MB-231 cellular systems, perturbations were observed at both transcriptional and translational echelons for OTUD6B, MDM2, and FOXO3 (Figs. 7E-G). Intriguingly, OTUD6B’s modulatory effect on FOXO3 appeared antithetical to its influence on MDM2 dynamics within MDA-MB-231 cells. These revelations underscore the potential of siRNA-mediated OTUD6B targeting to incapacitate TNBC cellular activities via curbing MDM2 deubiquitination and orchestrating the amplification of FOXO3 expression (Fig. 7H). Extending these molecular insights, cellular assays employing our synthesized siOTUD6B@Td nanoparticles corroborated that siOTUDB@Td treatment culminated in a marked abatement of OTUD6B expression while reciprocally elevating FOXO3 levels (Figures I-J), thus reinforcing the molecular mechanism wherein OTUD6B potentially stabilizes MDM2 entities and facilitates the catabolism of FOXO3 proteins, thereby modulating the trajectory of TNBC evolution.