Adaptive modeling optimized by the data fusion strategy: Real-time dying cell percentage prediction using capacitance spectroscopy

The previous research showcased a partial least squares (PLS) regression model accurately predicting cell death percentages using in-line capacitance spectra. The current study advances the model accuracy through adaptive modeling employing a data fusion approach. This strategy enhances prediction performance by incorporating variables from the Cole-Cole model, conductivity and its derivatives over time, and Mahalanobis distance into the predictor matrix (X-matrix). Firstly, the Cole-Cole model, a mechanistic model with parameters linked to early cell death onset, was integrated to enhance prediction performance. Secondly, the inclusion of conductivity and its derivatives over time in the X-matrix mitigated prediction fluctuations resulting from abrupt conductivity changes during process operations. Thirdly, Mahalanobis distance, depicting spectral changes relative to a reference spectrum from a previous time point, improved model adaptability to independent test sets, thereby enhancing performance. The final data fusion model substantially decreased root-mean squared error of prediction (RMSEP) by around 50%, which is a significant boost in prediction accuracy compared to the prior PLS model. Robustness against reference spectrum selection was confirmed by consistent performance across various time points. In conclusion, this study illustrates that the data fusion strategy substantially enhances the model accuracy compared to the previous model relying solely on capacitance spectra.

Capacitance spectroscopy enables real-time monitoring of early cell death in mammalian cell culture

BACKGROUND/AIMS

Previous work developed a quantitative model using capacitance spectroscopy in an at-line setup to predict the dying cell percentage measured from a flow cytometer. This work aimed to transfer the at-line model to monitor lab-scale bioreactors in real-time, waiving the need for frequent sampling and enabling precise controls.

METHODS AND RESULTS

Due to the difference between the at-line and in-line capacitance probes, direct application of the at-line model resulted in poor accuracy and high prediction bias. A new model with a variable range and offering similar spectral shape across all probes was first constructed, improving prediction accuracy. Moreover, the global calibration method included the variance of different probes and scales in the model, reducing prediction bias. External parameter orthogonalization, a preprocessing method, also mitigated the interference from feeding, which further improved model performance. The root-mean-square error of prediction of the final model was 6.56% (8.42% of the prediction range) with an R² of 92.4%.

CONCLUSION

The culture evolution trajectory predicted by the in-line model captured the cell death and alarmed cell death onset earlier than the trypan blue exclusion test. Additionally, the incorporation of at-line spectra following orthogonal design into the calibration set was shown to generate calibration models that are more robust than the calibration models constructed using the in-line spectra only. This is advantageous, as at-line spectral collection is easier, faster, and more material-sparing than in-line spectra collection.

Rapid At-line Early Cell Death Quantification using Capacitance Spectroscopy

Cell death is one of the failure modes of mammalian cell culture. Apoptosis is a regulated cell death process mainly observed in cell culture. Timely detection of apoptosis onset allows opportunities for preventive controls that ensure high productivity and consistent product quality. Capacitance spectroscopy captures the apoptosis-related cellular properties changes and thus quantifies the percentage of dying cells. This work demonstrated a quantification model that measures the percentage of apoptotic cells using a capacitance spectrometer in an at-line setup. When predicting the independent test set collected from bench-scale bioreactors, the root-mean-squared error of prediction (RMSEP) was 8.8% (equivalent to 9.9% of the prediction range). The predicted culture evolution trajectory aligned with measured values from the flow cytometer. Furthermore, this method alarms cell death onset earlier than the traditional viability test, i.e., trypan blue exclusion test. Comparing to flow cytometry (the traditional early cell death detection method), this method is rapid, simple, and less labor-intensive. Additionally, this at-line setup can be easily transferred between scales (e.g., lab-scale for development to manufacturing-scale), which benefits process transfers between facilities, scale-up, and other process transitions. This article is protected by copyright. All rights reserved.

Abstract 2997: Dynarrestin, a novel dynein inhibitor that does not block ciliogenesis

Introduction: Aberrant hedgehog (Hh) pathway activation contributes to the pathogenesis of multiple cancers. Currently available Hh pathway inhibitors target Smoothened (Smo) which can acquire mutations causing drug resistance. Therefore, a major challenge is to identify compounds that inhibit Hh signaling downstream of Smoothened.

Methods: We conducted a high-throughput screening (HTS) campaign of 337,000 small molecules using a Hh-dependent differentiation assay of C3H10T1/2 cells into osteoclasts. Primary active screening hits were validated by a cell-based assay cascade including motor neuron differentiation from mouse embryonic stem cells, Gli reporter activation in ShhLight2 cells and proliferation of heterozygous Patched (PTCH+/-) medulloblastoma (MB) cells. Smo binding was monitored in membrane-based Cyclopamine competition assays. To identify the underlying target identification of promising hits, affinity chromatography was performed followed by label-free quantitative (LFQ) tandem mass spectrometry. Effects on cytoplasmic dynein were examined in Smo trafficking and in vitro microtubules motility assays as well as by live cell imaging of labeled endosome movement.

Results: We identified dynarrestin, a novel aminothiazole that potently blocks Hh signaling and the proliferation of Hh-dependent PTCH+/- MB tumor cells (IC50∼70nM). Dynarrestin does not bind to Smo and is able to suppress the Hh pathway in the presence of the Smo agonist SAG and following the knockdown of the Hh pathway suppressor SUFU indicating that dynarrestin inhibits Hh signaling downstream of both Smo and SUFU. Chemical LFQ proteomics identified cytoplasmic dynein as the target of dynarrestin. Dyneins convert energy from ATP hydrolysis into motor activity and are essential for many cellular processes, including Hh signaling. Unlike other dynein inhibitory molecules, e.g. Ciliobrevins, dynarrestin inhibits Smoothened trafficking but not ciliogenesis. We further demonstrate that dynarrestin reversibly interferes with endosome movement, proper mitotic spindle orientation, and dynein-based microtubule translocation in vitro without blocking ATP hydrolysis.

Conclusions: Dynarrestin provides a novel dynein inhibitor with distinct specificity that uniquely facilitates probing dynein function. Given its multiple contributions to Hh signaling, mitosis and other cellular events, dynein remains a highly attractive target for medicinal chemistry programs aimed at exploiting and modulating its complex, poorly understood chemical cycle to interfere with different aspects of activity and function. We believe that unraveling dynein-dependent cellular processes by dynarrestin has great potential for development into novel anti-cancer drugs controlling Hh signaling downstream of Smoothened.

Citation Format: Matthias Baumann, Susanne Höing, Ting-Yu Yeh, Nancy Martinez, Peter Habenberger, Lea Kremer, Hannes CA. Drexler, Philipp Küchler, Peter Reinhardt, Axel Choidas, Mia-Lisa Zischinsky, Gunther Zischinsky, Stephanie A. Ketcham, Lydia Wagner, Peter Nussbaumer, Slava Ziegler, Bert Klebl, Trina Schroer, Hans R. Schöler, Herbert Waldmann, Jared L. Sterneckert. Dynarrestin, a novel dynein inhibitor that does not block ciliogenesis. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 2997.

Mycalolide B dissociates dynactin and abolishes retrograde axonal transport of dense-core vesicles

Although dynactin was believed to be a bidirectional facilitator of axonal transport, here mycalolide B is identified as a dynactin dissociator and shown to selectively abolish retrograde axonal transport of dense-core vesicles in hippocampal and Drosophila neurons. Thus dynactin has a strict obligatory unidirectional role in axonal transport.

Axonal transport is critical for maintaining synaptic transmission. Of interest, anterograde and retrograde axonal transport appear to be interdependent, as perturbing one directional motor often impairs movement in the opposite direction. Here live imaging of Drosophila and hippocampal neuron dense-core vesicles (DCVs) containing a neuropeptide or brain-derived neurotrophic factor shows that the F-actin depolymerizing macrolide toxin mycalolide B (MB) rapidly and selectively abolishes retrograde, but not anterograde, transport in the axon and the nerve terminal. Latrunculin A does not mimic MB, demonstrating that F-actin depolymerization is not responsible for unidirectional transport inhibition. Given that dynactin initiates retrograde transport and that amino acid sequences implicated in macrolide toxin binding are found in the dynactin component actin-related protein 1, we examined dynactin integrity. Remarkably, cell extract and purified protein experiments show that MB induces disassembly of the dynactin complex. Thus imaging selective retrograde transport inhibition led to the discovery of a small-molecule dynactin disruptor. The rapid unidirectional inhibition by MB suggests that dynactin is absolutely required for retrograde DCV transport but does not directly facilitate ongoing anterograde DCV transport in the axon or nerve terminal. More generally, MB's effects bolster the conclusion that anterograde and retrograde axonal transport are not necessarily interdependent.

Nudel/NudE and Lis1 promote dynein and dynactin interaction in the context of spindle morphogenesis

Nudel/NudE facilitates the binding of Lis1 to dynein, which subsequently enhances the recruitment of dynactin to dynein, and dynactin antagonizes Lis1 to relieve Lis1-induced dynein stall on microtubules.

Lis1, Nudel/NudE, and dynactin are regulators of cytoplasmic dynein, a minus end–directed, microtubule (MT)-based motor required for proper spindle assembly and orientation. In vitro studies have shown that dynactin promotes processive movement of dynein on MTs, whereas Lis1 causes dynein to enter a persistent force-generating state (referred to here as dynein stall). Yet how the activities of Lis1, Nudel/NudE, and dynactin are coordinated to regulate dynein remains poorly understood in vivo. Working in Xenopus egg extracts, we show that Nudel/NudE facilitates the binding of Lis1 to dynein, which enhances the recruitment of dynactin to dynein. We further report a novel Lis1-dependent dynein–dynactin interaction that is essential for the organization of mitotic spindle poles. Finally, using assays for MT gliding and spindle assembly, we demonstrate an antagonistic relationship between Lis1 and dynactin that allows dynactin to relieve Lis1-induced dynein stall on MTs. Our findings suggest the interesting possibility that Lis1 and dynactin could alternately engage with dynein to allow the motor to promote spindle assembly.