Alignstein: Optimal transport for improved LC-MS retention time alignment

Background

Reproducibility of liquid chromatography separation is limited by retention time drift. As a result, measured signals lack correspondence over replicates of the liquid chromatography–mass spectrometry (LC-MS) experiments. Correction of these errors is named retention time alignment and needs to be performed before further quantitative analysis. Despite the availability of numerous alignment algorithms, their accuracy is limited (e.g., for retention time drift that swaps analytes’ elution order).

Results

We present the Alignstein, an algorithm for LC-MS retention time alignment. It correctly finds correspondence even for swapped signals. To achieve this, we implemented the generalization of the Wasserstein distance to compare multidimensional features without any reduction of the information or dimension of the analyzed data. Moreover, Alignstein by design requires neither a reference sample nor prior signal identification. We validate the algorithm on publicly available benchmark datasets obtaining competitive results. Finally, we show that it can detect the information contained in the tandem mass spectrum by the spatial properties of chromatograms.

Conclusions

We show that the use of optimal transport effectively overcomes the limitations of existing algorithms for statistical analysis of mass spectrometry datasets. The algorithm’s source code is available at https://github.com/grzsko/Alignstein.

OUP accepted manuscript

Mesenchymal progenitor cells (MPCs) have shown promise initiating articular cartilage repair, with benefits largely attributed to the trophic factors they secrete. These factors can be found in the conditioned medium (CM) collected from cell cultures, and it is believed that extracellular vesicles (EVs) within this CM are at least partially responsible for MPC therapeutic efficacy. This study aimed to examine the functionality of the EV fraction of CM compared to whole CM obtained from human adipose-derived MPCs in an in vivo murine cartilage defect model. Mice treated with whole CM or the EV fraction demonstrated an enhanced cartilage repair score and type II collagen deposition at the injury site compared to saline controls. We then developed a scalable bioprocess using stirred suspension bioreactors (SSBs) to generate clinically relevant quantities of MPC-EVs. Whereas static monolayer culture systems are simple to use and readily accessible, SSBs offer increased scalability and a more homogenous environment due to constant mixing. This study evaluated the biochemical and functional properties of MPCs and their EV fractions generated in static culture versus SSBs. Functionality was assessed using in vitro MPC chondrogenesis as an outcome measure. SSBs supported increased MPC expression of cartilage-specific genes, and EV fractions derived from both static and SSB culture systems upregulated type II collagen production by MPCs. These results suggest that SSBs are an effective platform for the generation of MPC-derived EVs with the potential to induce cartilage repair.

Hypoxia-induced downregulation of cyclooxygenase 2 leads to the loss of immunoprivilege of allogeneic mesenchymal stem cells

Allogeneic mesenchymal stem cells (MSCs) from young and healthy donors are reported to hold the potential to treat several immunological and degenerative disorders. However, recent data from animal studies and clinical trials demonstrate that immunogenicity and poor survival of transplanted MSCs impaired the efficacy of cells for regenerative applications. It is reported that initially immunoprivileged under in vitro conditions, MSCs are targeted by the host immune system after transplantation in the ischemic tissues in vivo. We performed in vitro (in MSCs) and in vivo (in the rat model of myocardial infarction [MI]) studies to elucidate the mechanisms responsible for the change in the immunophenotype of MSCs from immunoprivileged to immunogenic under ischemic conditions. We have recently reported that a soluble factor prostaglandin E2 (PGE2) preserves the immunoprivilege of allogeneic MSCs. In the current study, we found that PGE2 levels, which were elevated during normoxia, decreased in MSCs following exposure to hypoxia. Further, we found that proteasome-mediated degradation of cyclooxygenase-2 (COX2, rate-limiting enzyme in PGE2 biosynthesis) in hypoxic MSCs is responsible for PGE2 decrease and loss of immunoprivilege of MSCs. While investigating the mechanisms of COX2 degradation in hypoxic MSCs, we found that in normoxic MSCs, COP9 signalosome subunit 5 (CSN5) binds to COX2 and prevents its degradation by the proteasome. However, exposure to hypoxia leads to a decrease in CSN5 levels and its binding to COX2, rendering COX2 protein susceptible to proteasome-mediated degradation. This subsequently causes PGE2 downregulation and loss of immunoprivilege of MSCs. Maintaining COX2 levels in MSCs preserves immunoprivilege in vitro and improves the survival of transplanted MSCs in a rat model of MI. These data provide novel mechanistic evidence that PGE2 is downregulated in hypoxic MSCs which is responsible for the post-transplantation rejection of allogeneic MSCs. Therefore, our data suggest that the new strategies that target CSN5-COX2 signaling may improve survival and utility of transplanted allogeneic MSCs in the ischemic heart.

Cross talk between 26S proteasome and mitochondria in human mesenchymal stem cells' ability to survive under hypoxia stress

Mesenchymal stem cells (MSCs) are regarded as unique cells which play an imperative role in the field of regenerative medicine. They are characterized by the self-renewal capacity, multi-lineage differentiation abilities and immunomodulation properties which render them perfectly ideal cell type for treating a wide range of chronic diseases. Despite these enchanted features, there are many hurdles that need to be circumvented to ensure their long-term survival and viability after transplantation. Recently, hypoxia has been indicated as one of the most baffling stress conditions that can affect the survival rate of MSCs either positively or negatively depending on the level of hypoxia. MSCs can survive well under moderate hypoxia, but die shortly if they were exposed to severe hypoxia without clearly convincing explanation for this enigma. The current study reveals a novel mechanism of 26S proteasome in controlling the ability of BM-MSCs to withstand hypoxic stress by maintaining proper mitochondrial function. The results indicated that 26S proteasome remains functioning once BM- MSCs are exposed to moderate hypoxia (2.5%O2) and preserves their survival and proliferation mediated by intact mitochondrial performance, whereas 26S proteasome becomes inactive when BM-MSCs faces severe hypoxia that lead to poor mitochondrial function and less chance to survive longer. The outcomes of this study demonstrated the importance of 26S proteasome machinery in enhancing the resistance of BM-MSCs to hypoxic stress condition which may help in better planning future studies that target this system. Schematic representation summarizing the findings of the current study. 26S proteasome function preservation in normoxia and moderate hypoxia leads to maintain appropriate proliferation and mitochondrial activity in human BM-MSCs and promote their survival. On the opposite side, severe hypoxia disrupts the 26S proteasome function leading to significant reduction in the proliferation, survival and mitochondrial dynamics in human BM-MSCs causing their death.

Antagonistic Interactions between Benzo[a]pyrene and Fullerene (C60) in Toxicological Response of Marine Mussels

This study aimed to assess the ecotoxicological effects of the interaction of fullerene (C60) and benzo[a]pyrene (B[a]P) on the marine mussel, Mytilus galloprovincialis. The uptake of nC60, B[a]P and mixtures of nC60 and B[a]P into tissues was confirmed by Gas Chromatography-Mass Spectrometry (GC-MS), Liquid Chromatography-High Resolution Mass Spectrometry (LC-HRMS) and Inductively Coupled Plasma Mass Spectrometer (ICP-MS). Biomarkers of DNA damage as well as proteomics analysis were applied to unravel the interactive effect of B[a]P and C60. Antagonistic responses were observed at the genotoxic and proteomic level. Differentially expressed proteins (DEPs) were only identified in the B[a]P single exposure and the B[a]P mixture exposure groups containing 1 mg/L of C60, the majority of which were downregulated (~52%). No DEPs were identified at any of the concentrations of nC60 (p < 0.05, 1% FDR). Using DEPs identified at a threshold of (p < 0.05; B[a]P and B[a]P mixture with nC60), gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) pathway analysis indicated that these proteins were enriched with a broad spectrum of biological processes and pathways, including those broadly associated with protein processing, cellular processes and environmental information processing. Among those significantly enriched pathways, the ribosome was consistently the top enriched term irrespective of treatment or concentration and plays an important role as the site of biological protein synthesis and translation. Our results demonstrate the complex multi-modal response to environmental stressors in M. galloprovincialis.