Browsing by Subject "PLATFORM"

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  • Ritchie, Alexandra; Laitinen, Suvi; Katajisto, Pekka; Englund, Johanna I. (2022)
    Techniques to acquire and analyze biological images are central to life science. However, the workflow downstream of imaging can be complex and involve several tools, leading to creation of very specialized scripts and pipelines that are difficult to reproduce by other users. Although many commercial and open-source software are available, non-expert users are often challenged by a knowledge gap in setting up analysis pipelines and selecting correct tools for extracting data from images. Moreover, a significant share of everyday image analysis requires simple tools, such as precise segmentation, cell counting, and recording of fluorescent intensities. Hence, there is a need for user-friendly platforms for everyday image analysis that do not require extensive prior knowledge on bioimage analysis or coding. We set out to create a bioimage analysis software that has a straightforward interface and covers common analysis tasks such as object segmentation and analysis, in a practical, reproducible, and modular fashion. We envision our software being useful for analysis of cultured cells, histological sections, and high-content data.
  • Izzo, Massimiliano; Mortola, Francesco; Arnulfo, Gabriele; Fato, Marco M.; Varesio, Luigi (2014)
    Motivation: Molecular biology laboratories require extensive metadata to improve data collection and analysis. The heterogeneity of the collected metadata grows as research is evolving in to international multi-disciplinary collaborations and increasing data sharing among institutions. Single standardization is not feasible and it becomes crucial to develop digital repositories with flexible and extensible data models, as in the case of modern integrated biobanks management. Results: We developed a novel data model in JSON format to describe heterogeneous data in a generic biomedical science scenario. The model is built on two hierarchical entities: processes and events, roughly corresponding to research studies and analysis steps within a single study. A number of sequential events can be grouped in a process building up a hierarchical structure to track patient and sample history. Each event can produce new data. Data is described by a set of user-defined metadata, and may have one or more associated files. We integrated the model in a web based digital repository with a data grid storage to manage large data sets located in geographically distinct areas. We built a graphical interface that allows authorized users to define new data types dynamically, according to their requirements. Operators compose queries on metadata fields using a flexible search interface and run them on the database and on the grid. We applied the digital repository to the integrated management of samples, patients and medical history in the BIT-Gaslini biobank. The platform currently manages 1800 samples of over 900 patients. Microarray data from 150 analyses are stored on the grid storage and replicated on two physical resources for preservation. The system is equipped with data integration capabilities with other biobanks for worldwide information sharing. Conclusions: Our data model enables users to continuously define flexible, ad hoc, and loosely structured metadata, for information sharing in specific research projects and purposes. This approach can improve sensitively interdisciplinary research collaboration and allows to track patients' clinical records, sample management information, and genomic data. The web interface allows the operators to easily manage, query, and annotate the files, without dealing with the technicalities of the data grid.
  • Barmaki, Samineh; Obermaier, Daniela; Kankuri, Esko; Vuola, Jyrki; Franssila, Sami; jokinen, Ville (2020)
    A hypoxic (low oxygen level) microenvironment and nitric oxide paracrine signaling play important roles in the control of both biological and pathological cell responses. In this study, we present a microfluidic chip architecture for nitric oxide delivery under a hypoxic microenvironment in human embryonic kidney cells (HEK-293). The chip utilizes two separate, but interdigitated microfluidic channels. The hypoxic microenvironment was created by sodium sulfite as the oxygen scavenger in one of the channels. The nitric oxide microenvironment was created by sodium nitroprusside as the light-activated nitric oxide donor in the other channel. The solutions are separated from the cell culture by a 30 µm thick gas-permeable, but liquid-impermeable polydimethylsiloxane membrane. We show that the architecture is preliminarily feasible to define the gaseous microenvironment of a cell culture in the 100 µm and 1 mm length scales.
  • Barmaki, Samineh; Jokinen, Ville; Obermaier, Daniela; Blokhina, Daria; Korhonen, Matti; Ras, Robin H. A.; Vuola, Jyrki; Franssila, Sami; Kankuri, Esko (2018)
    Physiological oxygen levels within the tissue microenvironment are usually lower than 14%, in stem cell niches these levels can be as low as 0-1%. In cell cultures, such low oxygen levels are usually mimicked by altering the global culture environment either by O-2 removal (vacuum or oxygen absorption) or by N-2 supplementation for O-2 replacement. To generate a targeted cellular hypoxic microenvironment under ambient atmospheric conditions, we characterised the ability of the dissolved oxygen-depleting sodium sulfite to generate an in-liquid oxygen sink. We utilised a microfluidic design to place the cultured cells in the vertical oxygen gradient and to physically separate the cells from the liquid. We demonstrate generation of a chemical in-liquid oxygen sink that modifies the surrounding O-2 concentrations. O-2 level control in the sink-generated hypoxia gradient is achievable by varying the thickness of the polydimethylsiloxane membrane. We show that intracellular hypoxia and hypoxia response element-dependent signalling is instigated in cells exposed to the microfluidic in-liquid O-2 sink-generated hypoxia gradient. Moreover, we show that microfluidic flow controls site-specific microenvironmental kinetics of the chemical O-2 sink reaction, which enables generation of intermittent hypoxia/re-oxygenation cycles. The microfluidic O-2 sink chip targets hypoxia to the cell culture microenvironment exposed to the microfluidic channel architecture solely by depleting O-2 while other sites in the same culture well remain unaffected. Thus, responses of both hypoxic and bystander cells can be characterised. Moreover, control of microfluidic flow enables generation of intermittent hypoxia or hypoxia/re-oxygenation cycles. (C) 2018 Published by Elsevier Ltd on behalf of Acta Materialia Inc.
  • Fraser, James P.; Postnikov, Pavel; Miliutina, Elena; Kolska, Zdenka; Valiev, Rashid; Svorcik, Vaclav; Lyutakov, Oleksiy; Ganin, Alexey Y.; Guselnikova, Olga (2020)
    Two-dimensional (2D) transition-metal dichalcogenides have become promising candidates for surface-enhanced Raman spectroscopy (SERS), but currently very few examples of detection of relevant molecules are available. Herein, we show the detection of the lipophilic disease marker beta-sitosterol on few-layered MoTe2 films. The chemical vapor deposition (CVD)-grown films are capable of nanomolar detection, exceeding the performance of alternative noble-metal surfaces. We confirm that the enhancement occurs through the chemical enhancement (CE) mechanism via formation of a surface-analyte complex, which leads to an enhancement factor of approximate to 10(4), as confirmed by Fourier transform infrared (FTIR), UV-vis, and cyclic voltammetry (CV) analyses and density functional theory (DFT) calculations. Low values of signal deviation over a seven-layered MoTe2 film confirms the homogeneity and reproducibility of the results in comparison to noble-metal substrate analogues. Furthermore, beta-sitosterol detection within cell culture media, a minimal loss of signal over 50 days, and the opportunity for sensor regeneration suggest that MoTe2 can become a promising new SERS platform for biosensing.
  • Tähkä, Sari M.; Bonabi, Ashkan; Jokinen, Ville P.; Sikanen, Tiina M. (2017)
    This work describes aqueous and non-aqueous capillary electrophoresis on thiol-ene-based microfluidic separation devices that feature fully integrated and sharp electrospray ionization (ESI) emitters. The chip fabrication is based on simple and low-cost replica-molding of thiol-ene polymers under standard laboratory conditions. The mechanical rigidity and the stability of the materials against organic solvents, acids and bases could be tuned by adjusting the respective stoichiometric ratio of the thiol and allyl ("ene") monomers, which allowed us to carry out electrophoresis separation in both aqueous and non-aqueous (methanol- and ethanol-based) background electrolytes. The stability of the ESI signal was generally
  • Skurnik, Mikael; Jaakkola, Salla; Mattinen, Laura; von Ossowski, Lotta; Nawaz, Ayesha; Pajunen, Maria; Happonen, Lotta J. (2021)
    Bacteriophages vB_YpeM_fEV-1 (fEV-1) and vB_YpeM_fD1 (fD1) were isolated from incoming sewage water samples in Turku, Finland, using Yersinia pestis strains EV76 and KIM D27 as enrichment hosts, respectively. Genomic analysis and transmission electron microscopy established that fEV-1 is a novel type of dwarf myovirus, while fD1 is a T4-like myovirus. The genome sizes are 38 and 167 kb, respectively. To date, the morphology and genome sequences of some dwarf myoviruses have been described; however, a proteome characterization such as the one presented here, has currently been lacking for this group of viruses. Notably, fEV-1 is the first dwarf myovirus described for Y. pestis. The host range of fEV-1 was restricted strictly to Y. pestis strains, while that of fD1 also included other members of Enterobacterales such as Escherichia coli and Yersinia pseudotuberculosis. In this study, we present the life cycles, genomes, and proteomes of two Yersinia myoviruses, fEV-1 and fD1.
  • Korpelainen, Helena; Pietiläinen, Maria (2017)
    We conducted DNA metabarcoding (based on the nuclear ITS2 region) to characterize indoor pollen samples (possibly accompanied by other plant fragments) and to discover whether there are seasonal changes in their taxonomic diversity. It was shown that DNA metabarcoding has potential to allow a good discovery of taxonomic diversity. The number of spermatophyte families and genera varied greatly among sampling sites (pooled results per building) and times, between 9-40 and 10-66, respectively. Comparable Shannon's diversity indices equaled 0.33-2.76 and 0.94-3.16. The total number of spermatophyte genera found during the study was 187, of which 43.9, 39.6, 7.5 and 9.1% represented wild, garden/crop and indoor house plants, and non-domestic fruit or other plant material, respectively. Comparable proportions of individual sequences equaled 77.4, 18.8, 2.7 and 1.1%, respectively. When comparing plant diversities and taxonomic composition among buildings or between seasons, no obvious pattern was detected, except for the second summer, when pollen coming from outdoors was highly dominant and the proportions of likely allergens, birch, grass, alder and mugwort pollen, were very high. The average pairwise values of SOrensen(Chao) indices that were used to compare similarities for taxon composition between samples among the samples from the two university buildings, two nurseries and farmhouse equaled 0.514, 0.109, 0.564, 0.865 and 0.867, respectively, while the mean similarity index for all samples was 0.524. Cleaning frequency may strongly contribute to the observed diversity. The discovery of considerable diversities, including pollen coming from outside, in both winter and summer shows that substantial amounts of pollen produced in summer enter buildings and stay there throughout the year.
  • Hlushchenko, Iryna; Hotulainen, Pirta (2019)
    Synaptic plasticity underlies central brain functions, such as learning. Ca2+ signaling is involved in both strengthening and weakening of synapses, but it is still unclear how one signal molecule can induce two opposite outcomes. By identifying molecules, which can distinguish between signaling leading to weakening or strengthening, we can improve our understanding of how synaptic plasticity is regulated. Here, we tested gelsolin's response to the induction of chemical long-term potentiation (cLTP) or long-term depression (cLTD) in cultured rat hippocampal neurons. We show that gelsolin relocates from the dendritic shaft to dendritic spines upon cLTD induction while it did not show any relocalization upon cLTP induction. Dendritic spines are small actin-rich protrusions on dendrites, where LTD/LTP-responsive excitatory synapses are located. We propose that the LTD-induced modest - but relatively long-lasting - elevation of Ca2+ concentration increases the affinity of gelsolin to F-actin. As F-actin is enriched in dendritic spines, it is probable that increased affinity to F-actin induces the relocalization of gelsolin.
  • Minnema, Jordi; Wolff, Jan; Koivisto, Juha; Lucka, Felix; Batenburg, Kees Joost; Forouzanfar, Tymour; van Eijnatten, Maureen (2021)
    Background and objective: Over the past decade, convolutional neural networks (CNNs) have revolutionized the field of medical image segmentation. Prompted by the developments in computational resources and the availability of large datasets, a wide variety of different two-dimensional (2D) and threedimensional (3D) CNN training strategies have been proposed. However, a systematic comparison of the impact of these strategies on the image segmentation performance is still lacking. Therefore, this study aimed to compare eight different CNN training strategies, namely 2D (axial, sagittal and coronal slices), 2.5D (3 and 5 adjacent slices), majority voting, randomly oriented 2D cross-sections and 3D patches. Methods: These eight strategies were used to train a U-Net and an MS-D network for the segmentation of simulated cone-beam computed tomography (CBCT) images comprising randomly-placed non-overlapping cylinders and experimental CBCT images of anthropomorphic phantom heads. The resulting segmentation performances were quantitatively compared by calculating Dice similarity coefficients. In addition, all segmented and gold standard experimental CBCT images were converted into virtual 3D models and compared using orientation-based surface comparisons. Results: The CNN training strategy that generally resulted in the best performances on both simulated and experimental CBCT images was majority voting. When employing 2D training strategies, the segmentation performance can be optimized by training on image slices that are perpendicular to the predominant orientation of the anatomical structure of interest. Such spatial features should be taken into account when choosing or developing novel CNN training strategies for medical image segmentation. Conclusions: The results of this study will help clinicians and engineers to choose the most-suited CNN training strategy for CBCT image segmentation. (c) 2021 The Authors. Published by Elsevier B.V. This is an open access article under the CC BY license ( http://creativecommons.org/licenses/by/4.0/ )
  • Hokkinen, Lasse; Mäkelä, Teemu; Savolainen, Sauli; Kangasniemi, Marko (2021)
    Background: Computed tomography perfusion (CTP) is the mainstay to determine possible eligibility for endovascular thrombectomy (EVT), but there is still a need for alternative methods in patient triage. Purpose: To study the ability of a computed tomography angiography (CTA)-based convolutional neural network (CNN) method in predicting final infarct volume in patients with large vessel occlusion successfully treated with endovascular therapy. Materials and Methods: The accuracy of the CTA source image-based CNN in final infarct volume prediction was evaluated against follow-up CT or MR imaging in 89 patients with anterior circulation ischemic stroke successfully treated with EVT as defined by Thrombolysis in Cerebral Infarction category 2b or 3 using Pearson correlation coefficients and intraclass correlation coefficients. Convolutional neural network performance was also compared to a commercially available CTP-based software (RAPID, iSchemaView). Results: A correlation with final infarct volumes was found for both CNN and CTP-RAPID in patients presenting 6-24 h from symptom onset or last known well, with r = 0.67 (p < 0.001) and r = 0.82 (p < 0.001), respectively. Correlations with final infarct volumes in the early time window (0-6 h) were r = 0.43 (p = 0.002) for the CNN and r = 0.58 (p < 0.001) for CTP-RAPID. Compared to CTP-RAPID predictions, CNN estimated eligibility for thrombectomy according to ischemic core size in the late time window with a sensitivity of 0.38 and specificity of 0.89. Conclusion: A CTA-based CNN method had moderate correlation with final infarct volumes in the late time window in patients successfully treated with EVT.
  • Sathyanarayanan, Gowtham; Haapala, Markus; Kiiski, Iiro; Sikanen, Tiina (2018)
    We report the development and characterization of digital microfluidic (DMF) immobilized enzyme reactors (IMERs) for studying cytochrome P450 (CYP)-mediated drug metabolism on droplet scale. The on-chip IMERs consist of porous polymer (thiol-ene) monolith plugs prepared in situ by photopolymerization and functionalized with recombinant CYP1A1 isoforms (an important detoxification route for many drugs and other xenobiotics). The DMF devices also incorporate inexpensive, inkjet-printed microheaters for on-demand regio-specific heating of the IMERs to physiological temperature, which is crucial for maintaining the activity of the temperature-sensitive CYP reaction. For on-chip monitoring of the CYP activity, the DMF devices were combined with a commercial well-plate reader, and a custom fluorescence quantification method was developed for detection of the chosen CYP1A1 model activity (ethoxyresorufin-O-deethylation). The reproducibility of the developed assay was examined with the help of ten parallel CYP-IMERs. All CYP-IMERs provided statistically significant difference (in fluorescence response) compared to any of the negative controls (including room-temperature reactions). The average (n = 10) turnover rate was 20.3 +/- 9.0 fmol resorufin per minute. Via parallelization, the concept of the droplet-based CYP-IMER developed in this study provides a viable approach to rapid and low-cost prediction of the metabolic clearance of new chemical entities in vitro.
  • Bjorninen, Miina; Gilmore, Kerry; Pelto, Jani; Seppänen-Kaijansinkko, Riitta; Kellomaki, Minna; Miettinen, Susanna; Wallace, Gordon; Grijpma, Dirk; Haimi, Suvi (2017)
    We investigated the use of polypyrrole (PPy)-coated polymer scaffolds and electrical stimulation (ES) to differentiate adipose stem cells (ASCs) towards smooth muscle cells (SMCs). Since tissue engineering lacks robust and reusable 3D ES devices we developed a device that can deliver ES in a reliable, repeatable, and cost-efficient way in a 3D environment. Long pulse (1 ms) or short pulse (0.25 ms) biphasic electric current at a frequency of 10 Hz was applied to ASCs to study the effects of ES on ASC viability and differentiation towards SMCs on the PPy-coated scaffolds. PPy-coated scaffolds promoted proliferation and induced stronger calponin, myosin heavy chain (MHC) and smooth muscle actin (SMA) expression in ASCs compared to uncoated scaffolds. ES with 1 ms pulse width increased the number of viable cells by day 7 compared to controls and remained at similar levels to controls by day 14, whereas shorter pulses significantly decreased viability compared to the other groups. Both ES protocols supported smooth muscle expression markers. Our results indicate that electrical stimulation on PPy-coated scaffolds applied through the novel 3D ES device is a valid approach for vascular smooth muscle tissue engineering.
  • Hokkinen, Lasse M I; Mäkelä, Teemu Olavi; Savolainen, Sauli; Kangasniemi, Marko Matti (2021)
    Background Computed tomography angiography (CTA) imaging is needed in current guideline-based stroke diagnosis, and infarct core size is one factor in guiding treatment decisions. We studied the efficacy of a convolutional neural network (CNN) in final infarct volume prediction from CTA and compared the results to a CT perfusion (CTP)-based commercially available software (RAPID, iSchemaView). Methods We retrospectively selected 83 consecutive stroke cases treated with thrombolytic therapy or receiving supportive care that presented to Helsinki University Hospital between January 2018 and July 2019. We compared CNN-derived ischaemic lesion volumes to final infarct volumes that were manually segmented from follow-up CT and to CTP-RAPID ischaemic core volumes. Results An overall correlation of r = 0.83 was found between CNN outputs and final infarct volumes. The strongest correlation was found in a subgroup of patients that presented more than 9 h of symptom onset (r = 0.90). A good correlation was found between the CNN outputs and CTP-RAPID ischaemic core volumes (r = 0.89) and the CNN was able to classify patients for thrombolytic therapy or supportive care with a 1.00 sensitivity and 0.94 specificity. Conclusions A CTA-based CNN software can provide good infarct core volume estimates as observed in follow-up imaging studies. CNN-derived infarct volumes had a good correlation to CTP-RAPID ischaemic core volumes.
  • Freitag, Tobias L.; Podojil, Joseph R.; Pearson, Ryan M.; Fokta, Frank J.; Sahl, Cecilia; Messing, Marcel; Andersson, Leif C.; Leskinen, Katarzyna; Saavalainen, Päivi; Hoover, Lisa I.; Huang, Kelly; Phippard, Deborah; Maleki, Sanaz; King, Nicholas J. C.; Shea, Lonnie D.; Miller, Stephen D.; Meri, Seppo K.; Getts, Daniel R. (2020)
  • Zhang, Hongbo; Zhu, Yueqi; Qu, Liangliang; Wu, Huayin; Kong, Haixin; Yang, Zhou; Chen, Dong; Mäkilä, Ermei; Salonen, Jarno; Santos, Helder A.; Hai, Mingtan; Weitz, David A. (2018)
    Porous silicon nanoparticles (PSiNPs) and gold nanorods (AuNRs) can be used as biocompatible nanocarriers for delivery of therapeutics but undesired leakage makes them inefficient. By encapsulating the PSiNPs and AuNRs in a hydrogel shell, we create a biocompatible functional nano carrier that enables sustained release of therapeutics. Here, we report the fabrication of AuNRs-conjugated PSi nanoparticles (AuNRsPSiNPs) through two-step chemical reaction for high capacity loading of hydrophobic and hydrophilic therapeutics with photothermal property. Furthermore, using water-in-oil microemulsion templates, we encapsulate the AuNRsPSiNPs within a calcium alginate hydrogel nanoshell, creating a versatile biocompatible nanocarrier to codeliver therapeutics for biomedical applications. We find that the functionalized nanohydrogel effectively controls the release rate of the therapeutics while maintaining a high loading efficiency and tunable loading ratios. Notably, combinations of therapeutics coloaded in the functionalized nanohydrogels significantly enhance inhibition of multidrug resistance through synergism and promote faster cancer cell death when combined with photothermal therapy. Moreover, the AuNRs can mediate the conversion of near-infrared laser radiation into heat, increasing the release of therapeutics as well as thermally inducing cell damage to promote faster cancer cell death. Our AuNRsPSiNPs functionalized calcium alginate nanohydrogel holds great promise for photothermal combination therapy and other advanced biomedical applications.
  • Manrique, Pilar; Bolduc, Benjamin; Walk, Seth T.; van der Oost, John; de Vos, Willem M.; Young, Mark J. (2016)
    The role of bacteriophages in influencing the structure and function of the healthy human gut microbiome is unknown. With few exceptions, previous studies have found a high level of heterogeneity in bacteriophages from healthy individuals. To better estimate and identify the shared phageome of humans, we analyzed a deep DNA sequence dataset of active bacteriophages and available metagenomic datasets of the gut bacteriophage community from healthy individuals. We found 23 shared bacteriophages in more than one-half of 64 healthy individuals from around the world. These shared bacteriophages were found in a significantly smaller percentage of individuals with gastrointestinal/irritable bowel disease. A network analysis identified 44 bacteriophage groups of which 9 (20%) were shared in more than one-half of all 64 individuals. These results provide strong evidence of a healthy gut phageome (HGP) in humans. The bacteriophage community in the human gut is a mixture of three classes: a set of core bacteriophages shared among more than one-half of all people, a common set of bacteriophages found in 20-50% of individuals, and a set of bacteriophages that are either rarely shared or unique to a person. We propose that the core and common bacteriophage communities are globally distributed and comprise the HGP, which plays an important role in maintaining gut microbiome structure/function and thereby contributes significantly to human health.
  • Badawy, Shimaa; Pajunen, Maria I.; Haiko, Johanna; Baka, Zakaria A. M.; Abou-Dobara, Mohamed; El-Sayed, Ahmed K. A.; Skurnik, Mikael (2020)
    Acinetobacter baumanniiis an opportunistic pathogen that presents a serious clinical challenge due to its increasing resistance to all available antibiotics. Phage therapy has been introduced recently to treat antibiotic-incurableA. baumanniiinfections. In search for newA. baumanniispecific bacteriophages, 20 clinicalA. baumanniistrains were used in two pools in an attempt to enrich phages from sewage. The enrichment resulted in induction of resident prophage(s) and three temperate bacteriophages, named vB_AbaS_fEg-Aba01, vB_AbaS_fLi-Aba02 and vB_AbaS_fLi-Aba03, all able to infect only one strain (#6597) of the 20 clinical strains, were isolated. Morphological characteristics obtained by transmission electron microscopy together with the genomic information revealed that the phages belong to the familySiphoviridae. The ca. 35 kb genomic sequences of the phages were >99% identical to each other. The linear ds DNA genomes of the phages contained 10 nt cohesive end termini, 52-54 predicted genes, anattPsite and one tRNA gene each. A database search revealed an >99% identical prophage in the genome ofA. baumanniistrain AbPK1 (acc. no. CP024576.1). Over 99% identical prophages were also identified from two of the original 20 clinical strains (#5707 and #5920) and both were shown to be spontaneously inducible, thus very likely being the origins of the isolated phages. The phage vB_AbaS_fEg-Aba01 was also able to lysogenize the susceptible strain #6597 demonstrating that it was fully functional. The phages showed a very narrow host range infecting only twoA. baumanniistrains. In conclusion, we have isolated and characterized three novel temperateSiphoviridaephages that infectA.baumannii.
  • Pekkonen, Pirita; Alve, Sanni; Balistreri, Giuseppe; Gramolelli, Silvia; Tatti-Bugaeva, Olga; Paatero, Ilkka; Niiranen, Otso; Tuohinto, Krista; Perala, Nina; Taiwo, Adewale; Zinovkina, Nadezhda; Repo, Pauliina; Icay, Katherine; Ivaska, Joanna; Saharinen, Pipsa; Hautaniemi, Sampsa; Lehti, Kaisa; Ojala, Paivi M. (2018)
    Lymphatic invasion and lymph node metastasis correlate with poor clinical outcome in melanoma. However, the mechanisms of lymphatic dissemination in distant metastasis remain incompletely understood. We show here that exposure of expansively growing human WM852 melanoma cells, but not singly invasive Bowes cells, to lymphatic endothelial cells (LEC) in 3D co-culture facilitates melanoma distant organ metastasis in mice. To dissect the underlying molecular mechanisms, we established LEC co-cultures with different melanoma cells originating from primary tumors or metastases. Notably, the expansively growing metastatic melanoma cells adopted an invasively sprouting phenotype in 3D matrix that was dependent on MMP14, Notch3 and beta 1-integrin. Unexpectedly, MMP14 was necessary for LEC-induced Notch3 induction and coincident beta 1-integrin activation. Moreover, MMP14 and Notch3 were required for LEC-mediated metastasis of zebrafish xenografts. This study uncovers a unique mechanism whereby LEC contact promotes melanoma metastasis by inducing a reversible switch from 3D growth to invasively sprouting cell phenotype.
  • Cenev, Zoran; Zhang, Hongbo; Sariola, Veikko; Rahikkala, Antti Tuomas Antero; Almeida Santos, Helder; Liu, Dongfei; Zhou, Quan (2018)
    Selective, precise, and high-throughput manipulation of individual superparamagnetic microparticles has profound applications in performing location-tailored in vitro biomedical studies. The current techniques for manipulation of microparticles allow only a single particle in the manipulation workspace, or simultaneous transportation of multiple microparticles in batches. In this work, a method based on a robotized electromagnetic needle for manipulation of individual superparamagnetic microparticles within a microparticle population is introduced. By automatically controlling the highly localized magnetic field of the needle, a single microparticle is selectively picked when its neighboring particle is few micrometers away. Supported by the nanometer resolution of the robotic positioner, particles are placed at sub-micrometer precision. This manipulation technique allows the creating of arbitrary patterns, sorting of microparticles based on size and morphology, and transporting of individual microparticles in 3D space. Therefore, this approach has the potential to enable more deterministic and quantitative microanalysis and microsynthesis using superparamagnetic microparticles.