Biology subjects

Aitken, C.

Publications and source records attributed to Aitken, C..

6 recordsLinked to original sources

bioRxiv2024

The mitochondrial-targeted antioxidant SkQ1 prevents mitochondrial-linked apoptosis but not necroptosis or skeletal muscle atrophy in ovarian cancer

The degree to which mitochondrial-linked cell death pathways contribute to skeletal muscle atrophy during cancer remain unknown. Here, we combined a novel and robust mouse model of metastatic ovarian cancer with chronic administration of the mitochondrial-targeted antioxidant SkQ1 to determine the time-dependent and muscle-specific relationships of mitochondrial-linked apoptosis and necroptosis to the development of muscle atrophy in the type II B-rich gastrocnemius. Early-stage ovarian cancer reduced type II B fibre cross-sectional area in the gastrocnemius but did not alter mitochondrial H2O2 emission despite increased activities of mitochondrial-linked caspase-9 and-3 regulators of apoptosis. During late-stage ovarian cancer, sustained atrophy was associated with increased mitochondrial H2O2 emission potential in vitro, a greater probability of calcium-triggered mitochondrial permeability transition and increases in downstream caspase-9 and -3 activity. SkQ1 attenuated mitochondrial H2O2 emission and caspase-9 and -3 activity in late-stage ovarian cancer but did not prevent atrophy. Necroptosis markers were heterogeneous across time with total RIPK1 increasing during early-stage cancer which reverted to normal levels by late-stages while phosphorylated RIPK3 decreased below control levels. These discoveries indicate that preventing increases in mitochondrial-linked apoptotic caspase-9 and -3 activity during late-stage ovarian cancer with SkQ1 does not prevent atrophy of type II B fibres. Furthermore, necroptotic markers are inconclusive during cancer in this muscle type but are not modified by SkQ1. These results do not support a causal relationship between mitochondrial H2O2-linked apoptosis or necroptosis and atrophy in type II B fibres during ovarian cancer but do not rule out potential relationships in other muscle types. Key PointsO_LICancer increases mitochondrial reactive oxygen species (ROS) in skeletal muscle during atrophy, but the role of ROS in regulating cell death remains unknown. C_LIO_LIWe show that attenuating gastrocnemius mitochondrial ROS with the mitochondrial-targeted antioxidant SkQ1 prevented mitochondrial-linked pro-apoptotic caspase 9- and 3-activities but did not affect markers of necroptosis in a mouse model of ovarian cancer. C_LIO_LIReductions in gastrocnemius muscle fibre cross-sectional areas and the wet weights of several muscles were not prevented by SkQ1. C_LIO_LIThese findings demonstrate that mitochondrial ROS regulate apoptotic caspases but not necroptosis, and neither pathway is linked to gastrocnemius atrophy in mice with ovarian cancer. C_LIO_LIThe degree to which mitochondrial ROS-linked cell death pathways regulate muscle mass in other muscle types and cancer models requires further investigation. C_LI

physiology↗

bioRxiv2024

Mitochondrial-targeted plastoquinone therapy ameliorates early onset muscle weakness that precedes ovarian cancer cachexia in mice

Cancer cachexia, and the related loss of muscle and strength, worsens quality of life and lowers overall survival. Recently, a novel pre-atrophy muscle weakness was identified during early-stage cancer. While mitochondrial stress responses are associated with early-stage pre-atrophy weakness, a causal relationship has not been established. Using a robust mouse model of metastatic epithelial ovarian cancer (EOC)-induced cachexia, we found the well-established mitochondrial-targeted plastoquinone SkQ1 partially prevents pre-atrophy weakness in the diaphragm. Furthermore, SkQ1 improved force production during atrophy without preventing atrophy itself in the tibialis anterior and diaphragm. EOC reduced flexor digitorum brevis (FDB) force production and myoplasmic free calcium ([Ca2+]i) during contraction in single muscle fibers, both of which were prevented by SkQ1. Remarkably, changes in mitochondrial reactive oxygen species and pyruvate metabolism were heterogeneous across time and between muscle types which highlights a considerable complexity in the relationships between mitochondria and muscle remodeling throughout EOC. These discoveries identify that muscle weakness can occur independent of atrophy throughout EOC in a manner that is linked to improved calcium handling. The findings also demonstrate that mitochondrial-targeted therapies exert a robust effect in preserving muscle force during the early pre-atrophy period and in late-stage EOC once cachexia has become severe.

physiology↗

bioRxiv2023

Specific genomic targeting of the RNF12/RLIM E3 ubiquitin ligase selectively programmes developmental transcription

The E3 ubiquitin ligase RNF12/RLIM controls developmental gene expression and is mutated in the X-linked intellectual disability disorder Tonne-Kalscheuer syndrome (TOKAS). However, the mechanisms by which RNF12 E3 ubiquitin ligase activity controls specific gene expression signatures are not known. Here, we show that chromatin forms a regulatory platform for RNF12 substrate ubiquitylation and transcriptional patterning. RNF12 is recruited to specific genomic regions via a distinct consensus sequence motif, which enables targeting to key transcription factor substrate REX1. Mechanistically, RNF12 chromatin recruitment is largely REX1 independent, but is achieved via the conserved basic region (BR) adjacent to the RING domain. This region is critical for REX1 ubiquitylation on chromatin and downstream RNF12-dependent gene regulation. Furthermore, we find that RNF12 N-terminal sequences suppress chromatin recruitment and substrate ubiquitylation, uncovering a previously unappreciated autoinhibitory mechanism that governs genome targeting. Taken together, our results provide insight into mechanisms by which selective substrate targeting of an E3 ubiquitin ligase enables specific programming of gene expression.

cell biology↗

bioRxiv2020

Analysis of coagulation factor IX in bioreactor cell culture medium predicts yield and quality of the purified product

Coagulation factor IX (FIX) is a highly complex post-translationally modified human serum glycoprotein and a high-value biopharmaceutical. The quality of recombinant FIX (rFIX), especially complete {gamma}-carboxylation, is critical for rFIX clinical efficacy. Changes in bioreactor operating conditions can impact rFIX production and occupancy and structure of rFIX post-translational modifications (PTMs). We hypothesized that monitoring the bioreactor cell culture supernatant with Data Independent Acquisition Mass Spectrometry (DIA-MS) proteomics would allow us to predict product yield and quality after purification. With the goal of optimizing rFIX production, we developed a suite of MS proteomics analytical methods and used these to investigate changes in rFIX yield, {gamma}-carboxylation, other PTMs, and host cell proteins during bioreactor culture and after purification. Our methods provided a detailed overview of the dynamics of site-specific PTM occupancy and abundance on rFIX during production, which accurately predicted the efficiency of purification and the quality of the purified product from different culture conditions. In addition, we identified new PTMs in rFIX, some of which were near the GLA domain and could impact rFIX GLA-dependent purification efficiency and protein function. The workflows presented here are applicable to other biologics and expression systems, and should aid in the optimization and quality control of upstream and downstream bioprocesses.

biochemistry↗

bioRxiv2020

S-Trap eliminates cell culture media polymeric surfactants for effective proteomic analysis of mammalian cell bioreactor supernatants

Proteomic analysis of bioreactor supernatants can inform on cellular metabolic status, viability, and productivity, as well as product quality, which can in turn help optimize bioreactor operation. Incubating mammalian cells in bioreactors requires the addition of polymeric surfactants such as Pluronic F68, which reduce the sheer stress caused by agitation. However, these surfactants are incompatible with mass spectrometry proteomics and must be eliminated during sample preparation. Here, we compared four different sample preparation methods to eliminate polymeric surfactants from filtered bioreactor supernatant samples: organic solvent precipitation; filter-assisted sample preparation (FASP); S-Trap; and single-pot, solid-phase, sample preparation (SP3). We found that SP3 and S-Trap substantially reduced or eliminated the polymer(s), but S-Trap provided the most robust clean-up and highest quality data. Additionally, we observed that SP3 sample preparation of our samples and in other published datasets was associated with partial alkylation of cysteines, which could impact the confidence and robustness of protein identification and quantification. Finally, we observed that several commercial mammalian cell culture media and media supplements also contained polymers with similar mass spectrometry profiles, and we suggest that proteomic analyses in these media will also benefit from the use of S-Trap sample preparation.

biochemistry↗

bioRxiv2017

Rps3/uS3 promotes mRNA binding at the 40S ribosome entry channel and stabilizes preinitiation complexes at start codons

The eukaryotic 43S pre-initiation complex (PIC) bearing Met-tRNA[Formula] in a ternary complex (TC) with eIF2-GTP scans the mRNA leader for an AUG codon in favorable \"Kozak\" context. AUG recognition provokes rearrangement from an open PIC conformation with TC bound in a state not fully engaged with the P site (\"POUT\") to a closed, arrested conformation with TC tightly bound in the \"PIN\" state. Yeast ribosomal protein Rps3/uS3 resides in the mRNA entry channel of the 40S subunit and contacts mRNA via conserved residues whose functional importance was unknown. We show that substitutions of these residues reduce bulk translation initiation and diminish initiation at near-cognate UUG start codons in yeast mutants in which UUG selection is abnormally high (Sui-), conferring the Ssu- phenotype. Two such Ssu- substitutions--R116D and R117D--also increase discrimination against an AUG codon in suboptimal Kozak context. Consistently, the Arg116 and Arg117 substitutions destabilize TC binding to 48S PICs reconstituted in vitro with mRNA harboring a UUG start codon, indicating destabilization of the closed PIN state with a UUG:anticodon mismatch. Using model mRNAs lacking contacts with either the mRNA entry or exit channels of the 40S subunit, we demonstrate that Arg116/Arg117 are crucial for stabilizing PIC:mRNA contacts at the entry channel, complementing the function of eIF3 at both entry and exit channels. The corresponding residues in bacterial uS3 promote the helicase activity of the elongating ribosome, suggesting that uS3 contacts with mRNA enhance multiple phases of translation across different domains of life.

genetics↗