Effects of culture media and suspension expansion technologies in mesenchymal stem cell manufacturing - A computational bioprocess and bioeconomics study

Mesenchymal stem cell (MSC) based therapies are promising for a large spectrum of unmet medical needs. Despite this promise, the scaling-up of production of clinical grade MSCs is hindered by the use of planar technologies that require intensive labor and are not enough to meet market demands, as well as due to high product and process variability introduced by the use of xenogeneic materials. This work presents a new bioprocess and bioeconomics model of stem cell expansion to support informed decisions for stem cells process scaling up at reduced annual costs. The intrinsic equations and parameters that capture the cell biological features, according with their source and media used, are embedded in the model. A target number of cells per dose of 140 million and a GMP facility of 400 sq mt with 4 BSCs and 8 incubators will be used as the baseline for expansion of both bone marrow MSCs (BM-MSCs) and adipose stem cells (ASCs) using planar expansion technologies. The current standard medium for MSC culture containing fetal bovine serum (FBS) will be compared with the xeno-free alternative of human platelet lysate (hPL). The use of hPL for both cell sources results in an increase of the number of doses produced and a decrease of the cost of goods (CoG) per dose (Table 1). In order to improve the production capacity, 8 bioreactors with capacity up to 50L were input in the model, using xeno-free plastic microcarriers for cell adhesion and hPL as the culture medium. The model results indicate that the investment in the use of suspension cultures is valuable due to a considerable increase in the production and a decrease of CoG/dose. As the number of doses produced per year increases, the reagent costs dominate relatively to the facility costs (Fig. 1). Sensitivity analysis was performed by varying 11 model variables by +/- 33%. The main factors that influence annual capacity and CoGs are related to harvesting density and yield, growth rates and microcarrier area and concentration (Table 2). These findings may be used to improve the design of expansion methods with fully xeno-free materials and highlight the relevance of the optimization of harvesting and downstream processing protocols. Please click Additional Files below to see the full abstract

Scalable generation of cerebellar neurons from pluripotent stem cells

Human induced pluripotent stem cells (iPSCs) have great potential for disease modeling and provide a valuable source for regenerative approaches. However, generating iPSC-derived models to study brain diseases remains a challenge. In particular, our ability to differentiate cerebellar neurons from pluripotent stem cells is still limited. Recently, we described the long-term culture of cerebellar neuroepithelium formed from human iPSCs, recapitulating the early developmental events of the cerebellum. Additionally, an efficient maturation of replated cerebellar progenitors into distinct types of functional cerebellar neurons was also achieved under defined and feeder-free conditions. However, developing a scalable protocol that allows to produce large numbers of organoids and high yields of mature neurons in a 3D bioreactor culture systems is still a difficult challenge. In this work, we present a new approach for the reproducible and scalable generation of mid-hindbrain organoids under chemically defined conditions by using the novel PBS 0.1 (100 mL) Vertical-Wheel single-use bioreactor. In this system, an efficient cell aggregation with shape and size-controlled aggregates can be obtained, which is important for homogeneous and efficient differentiation. Moreover, a larger amount of iPSC-derived aggregates can be generated without being excessively labour-intensive, achieving 431 ± 53.6 aggregates/mL at 24 hours after seeding. After differentiation, distinct types of cerebellar neurons were generated, including Purkinje cells (Calbindin+), Granule cells (BARHL1+ and Pax6+), Golgi cells (Neurogranin+ and GAD65+), Deep cerebellar nuclei projection neurons (TBR1+) and Non-Golgi-type interneurons (Parvalbumin+ and Calbindin-). These cells show signs of efficient maturation, staining positive for MAP2, and are able to change intracellular Ca2+ concentration following KCl stimulation. In this system, human iPSC-derived organoids are able to mature into different mature cerebellar neurons and to survive for up to 3 months, without replating and co-culture with feeder layers

Development of a scale-down approach to the scalable culture of induced Pluripotent Stem Cells on microcarriers using single-use Vertical-Wheel™ bioreactors under xeno-free conditions

Induced Pluripotent Stem Cells (iPSC) are capable of extensive self-renewal while retaining the ability to differentiate into virtually all cell types of the body. These cells are the subject of much research and development activity aimed at the development of cell-based tools, which may speed drug discovery, and cell-based medical therapies that are being developed to address unmet medical needs. However, development of these therapies is hampered by manufacturing bottlenecks including production scale up to meet the anticipated demand. PBS Biotech, Inc. has developed a single use bioreactor with an innovative Vertical-Wheel™ design that promotes more homogenous and gentle particle suspension, under lower hydrodynamic shear environment than traditional bioreactor vessel design. Vertical-Wheel bioreactors are available from lab-scale vessels (PBS MINI) to larger production units (up to 500L). This study describes the culture of human iPSCs on microcarriers under xeno-free conditions using Vertical-Wheel bioreactors. Human iPSCs were cultured on microcarriers to provide surface for cell attachment using the chemically defined Essential 8 culture medium, a xeno-free, feeder-free culture medium. The culture conditions were optimized in terms of 1) initial cell/microcarrier ratio, 2) inoculation method and 3) agitation rate, in the PBS-0.1 vessel using 80 mL working volume. The cells were successfully expanded, up to a 7-fold increase in cell number, after 6 days in the bioreactor. Glucose consumption and lactate production were analyzed to prevent glucose starvation or excessive lactate accumulation. These optimized culture conditions were successfully repeated in a larger vessel, the PBS-0.5 using 300 mL working volume, demonstrating the scalability of the Vertical-Wheel system. With this PBS-0.5 bioreactor, 3 x 108 cells were produced after 6 days of operation, and the specific growth rate (0.72 day-1) was similar to the one observed with the PBS-0.1 (0.68 day-1). The applications of iPSC cells and their progeny, especially in clinical settings, will require a guarantee of cell quality. After PBS-MINI bioreactor culture, the expression of pluripotency markers, such as Oct4, Nanog, and SSEA4 was assessed by immunocytochemistry and flow cytometry. The directed differentiation into the neural lineage of the expanded cells was performed and the pluripotency of the cells was further tested after embryoid body formation. The robustness of this process method was evaluated by cultivating another iPSC cell line under the same process conditions, resulting in identical growth kinetics in the PBS MINI-0.1. The methodology developed herein, which grows human iPSC on microcarriers in single-use bioreactors using chemically defined xeno-free cultivation reagents provides a foundation upon which further refinement and scale-up of processes can be built for large scale production of iPSCs

Scalable production of human mesenchymal stromal cell-derived extracellular vesicles under serum-/xeno-free conditions in a microcarrier-based bioreactor culture system

Copyright © 2020 de Almeida Fuzeta, Bernardes, Oliveira, Costa, Fernandes-Platzgummer, Farinha, Rodrigues, Jung, Tseng, Milligan, Lee, Castanho, Gaspar, Cabral and da Silva. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.Mesenchymal stromal cells (MSC) hold great promise for tissue engineering and cell-based therapies due to their multilineage differentiation potential and intrinsic immunomodulatory and trophic activities. Over the past years, increasing evidence has proposed extracellular vesicles (EVs) as mediators of many of the MSC-associated therapeutic features. EVs have emerged as mediators of intercellular communication, being associated with multiple physiological processes, but also in the pathogenesis of several diseases. EVs are derived from cell membranes, allowing high biocompatibility to target cells, while their small size makes them ideal candidates to cross biological barriers. Despite the promising potential of EVs for therapeutic applications, robust manufacturing processes that would increase the consistency and scalability of EV production are still lacking. In this work, EVs were produced by MSC isolated from different human tissue sources [bone marrow (BM), adipose tissue (AT), and umbilical cord matrix (UCM)]. A serum-/xeno-free microcarrier-based culture system was implemented in a Vertical-WheelTM bioreactor (VWBR), employing a human platelet lysate culture supplement (UltraGROTM-PURE), toward the scalable production of MSC-derived EVs (MSC-EVs). The morphology and structure of the manufactured EVs were assessed by atomic force microscopy, while EV protein markers were successfully identified in EVs by Western blot, and EV surface charge was maintained relatively constant (between −15.5 ± 1.6 mV and −19.4 ± 1.4 mV), as determined by zeta potential measurements. When compared to traditional culture systems under static conditions (T-flasks), the VWBR system allowed the production of EVs at higher concentration (i.e., EV concentration in the conditioned medium) (5.7-fold increase overall) and productivity (i.e., amount of EVs generated per cell) (3-fold increase overall). BM, AT and UCM MSC cultured in the VWBR system yielded an average of 2.8 ± 0.1 × 1011, 3.1 ± 1.3 × 1011, and 4.1 ± 1.7 × 1011 EV particles (n = 3), respectively, in a 60 mL final volume. This bioreactor system also allowed to obtain a more robust MSC-EV production, regarding their purity, compared to static culture. Overall, we demonstrate that this scalable culture system can robustly manufacture EVs from MSC derived from different tissue sources, toward the development of novel therapeutic products.unding received by iBB-Institute for Bioengineering and Biosciences from the Portuguese Foundation for Science and Technology (FCT) (UID/BIO/04565/2020) and through the projects PTDC/EQU-EQU/31651/2017, PTDC/BBB-BQB/1693/2014, and PTDC/BTM-SAL/31057/2017 is acknowledged. Funding received from POR de Lisboa 2020 through the project PRECISE – Accelerating progress toward the new era of precision medicine (Project N. 16394) is also acknowledged. MAF (PD/BD/128328/2017) and FO (PD/BD/135046/2017) acknowledge FCT for the Ph.D. fellowships and DG (SFRH/BPD/109010/2015) for the Post-Doctoral fellowship.info:eu-repo/semantics/publishedVersio

A reference time scale for Site U1385 (Shackleton Site) on the SW Iberian Margin

We produced a composite depth scale and chronology for Site U1385 on the SW Iberian Margin. Using log(Ca/Ti) measured by core scanning XRF at 1-cm resolution in all holes, a composite section was constructed to 166.5 meters composite depth (mcd) that corrects for stretching and squeezing in each core. Oxygen isotopes of benthic foraminifera were correlated to a stacked δ^18O reference signal (LR04) to produce an oxygen isotope stratigraphy and age model. Variations in sediment color contain very strong precession signals at Site U1385, and the amplitude modulation of these cycles provides a powerful tool for developing an orbitally-tuned age model. We tuned the U1385 record by correlating peaks in L* to the local summer insolation maxima at 37^oN. The benthic δ^18O record of Site U1385, when placed on the tuned age model, generally agrees with other time scales within their respective chronologic uncertainties. The age model is transferred to down-core data to produce a continuous time series of log(Ca/Ti) that reflect relative changes of biogenic carbonate and detrital sediment. Biogenic carbonate increases during interglacial and interstadial climate states and decreases during glacial and stadial periods. Much of the variance in the log(Ca/Ti) is explained by a linear combination of orbital frequencies (precession, tilt and eccentricity), whereas the residual signal reflects suborbital climate variability. The strong correlation between suborbital log(Ca/Ti) variability and Greenland temperature over the last glacial cycle at Site U1385 suggests that this signal can be used as a proxy for millennial-scale climate variability over the past 1.5 Ma. Millennial climate variability, as expressed by log(Ca/Ti) at Site U1385, was a persistent feature of glacial climates over the past 1.5 Ma, including glacial periods of the early Pleistocene (‘41-kyr world’) when boundary conditions differed significantly from those of the late Pleistocene (‘100-kyr world’). Suborbital variability was suppressed during interglacial stages and enhanced during glacial periods, especially when benthic δ^18O surpassed ~ 3.3-3.5‰. Each glacial inception was marked by appearance of strong millennial variability and each deglaciation was preceded by a terminal stadial event. Suborbital variability may be a symptomatic feature of glacial climate or, alternatively, may play a more active role in the inception and/or termination of glacial cycles.This research was supported by the Natural Environmental Research Council Grant NE/K005804/1 to DH and LS and NE/J017922/1 to DH.This is the final version of the article. It first appeared from Elsevier via http://dx.doi.org/10.1016/j.gloplacha.2015.07.00

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

Single-Use Bioreactors for Human Pluripotent and Adult Stem Cells: Towards Regenerative Medicine Applications

Research on human stem cells, such as pluripotent stem cells and mesenchymal stromal cells, has shown much promise in their use for regenerative medicine approaches. However, their use in patients requires large-scale expansion systems while maintaining the quality of the cells. Due to their characteristics, bioreactors have been regarded as ideal platforms to harbour stem cell biomanufacturing at a large scale. Specifically, single-use bioreactors have been recommended by regulatory agencies due to reducing the risk of product contamination, and many different systems have already been developed. This review describes single-use bioreactor platforms which have been used for human stem cell expansion and differentiation, along with their comparison with reusable systems in the development of a stem cell bioprocess for clinical applications

Length-weight relationships for freshwater fish species from humid forest enclaves at the Brazilian semiarid

We report the length-weight relationships (LWR) for 11 fish species inhabiting headwater streams in the Araripe and Ibiapaba plateaus, Brazilian semiarid. Values of r2, a and b ranged respectively from.953 to.998, 0.010 to 0.043 and 2.81 to 3.69. Our reports on LWR are pioneer in humid forest enclaves at the Caatinga biome. Such enclaves of forest can be a checkpoint to climate change, but are under strong human pressure and remain under low investigation. © 2017 Blackwell Verlag GmbH