LIVIVO - The Search Portal for Life Sciences

zur deutschen Oberfläche wechseln
Advanced search

Search results

Result 1 - 10 of total 29

Search options

  1. Article ; Online: Comparison of two supporting matrices for patient-derived cancer cells in 3D drug sensitivity and resistance testing assay (3D-DSRT).

    Feodoroff, Michaela / Mikkonen, Piia / Turunen, Laura / Hassinen, Antti / Paasonen, Lauri / Paavolainen, Lassi / Potdar, Swapnil / Murumägi, Astrid / Kallioniemi, Olli / Pietiäinen, Vilja

    SLAS discovery : advancing life sciences R & D

    2023  Volume 28, Issue 4, Page(s) 138–148

    Abstract: Central to the success of functional precision medicine of solid tumors is to perform drug testing of patient-derived cancer cells (PDCs) in tumor-mimicking ex vivo conditions. While high throughput (HT) drug screening methods have been well-established ... ...

    Abstract Central to the success of functional precision medicine of solid tumors is to perform drug testing of patient-derived cancer cells (PDCs) in tumor-mimicking ex vivo conditions. While high throughput (HT) drug screening methods have been well-established for cells cultured in two-dimensional (2D) format, this approach may have limited value in predicting clinical responses. Here, we describe the results of the optimization of drug sensitivity and resistance testing (DSRT) in three-dimensional (3D) growth supporting matrices in a HT mode (3D-DSRT) using the hepatocyte cell line (HepG2) as an example. Supporting matrices included widely used animal-derived Matrigel and cellulose-based hydrogel, GrowDex, which has earlier been shown to support 3D growth of cell lines and stem cells. Further, the sensitivity of ovarian cancer PDCs, from two patients included in the functional precision medicine study, was tested for 52 drugs in 5 different concentrations using 3D-DSRT. Shortly, in the optimized protocol, the PDCs are embedded with matrices and seeded to 384-well plates to allow the formation of the spheroids prior to the addition of drugs in nanoliter volumes with acoustic dispenser. The sensitivity of spheroids to drug treatments is measured with cell viability readout (here, 72 h after addition of drugs). The quality control and data analysis are performed with openly available Breeze software. We show the usability of both matrices in established 3D-DSRT, and report 2D vs 3D growth condition dependent differences in sensitivities of ovarian cancer PDCs to MEK-inhibitors and cytotoxic drugs. This study provides a proof-of-concept for robust and fast screening of drug sensitivities of PDCs in 3D-DSRT, which is important not only for drug discovery but also for personalized ex vivo drug testing in functional precision medicine studies. These findings suggest that comparing results of 2D- and 3D-DSRT is essential for understanding drug mechanisms and for selecting the most effective treatment for the patient.
    MeSH term(s) Humans ; Female ; Animals ; Cell Line, Tumor ; Antineoplastic Agents/pharmacology ; High-Throughput Screening Assays/methods ; Drug Discovery ; Ovarian Neoplasms
    Chemical Substances Antineoplastic Agents
    Language English
    Publishing date 2023-03-20
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2885123-7
    ISSN 2472-5560 ; 2472-5552
    ISSN (online) 2472-5560
    ISSN 2472-5552
    DOI 10.1016/j.slasd.2023.03.002
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  2. Article ; Online: Protocol for 3D drug sensitivity and resistance testing of patient-derived cancer cells in 384-well plates.

    Feodoroff, Michaela / Mikkonen, Piia / Arjama, Mariliina / Murumägi, Astrid / Kallioniemi, Olli / Potdar, Swapnil / Turunen, Laura / Pietiäinen, Vilja

    SLAS discovery : advancing life sciences R & D

    2022  Volume 28, Issue 2, Page(s) 36–41

    Abstract: Establishment of drug testing of patient-derived cancer cells (PDCs) in physiologically relevant 3-dimensional (3D) culture is central for drug discovery and cancer research, as well as for functional precision medicine. Here, we describe the detailed ... ...

    Abstract Establishment of drug testing of patient-derived cancer cells (PDCs) in physiologically relevant 3-dimensional (3D) culture is central for drug discovery and cancer research, as well as for functional precision medicine. Here, we describe the detailed protocol allowing the 3D drug testing of PDCs - or any type of cells of interest - in Matrigel in 384-well plate format using automation. We also provide an alternative protocol, which does not require supporting matrices. The cancer tissue is obtained directly from clinics (after surgery or biopsy) and processed into single cell suspension. Systematic drug sensitivity and resistance testing (DSRT) is carried out on the PDCs directly after cancer cell isolation from tissue or on cells expanded for a few passages. In the 3D-DSRT assay, the PDCs are plated in 384-well plates in Matrigel, grown as spheroids, and treated with compounds of interest for 72 h. The cell viability is directly measured using a luminescence-based assay. Alternatively, prior to the cell viability measurement, drug-treated cells can be directly subjected to automated high-content bright field imaging or stained for fluorescence (live) cell microscopy for further image analysis. This is followed by the quality control and data analysis. The 3D-DSRT can be performed within a 1-3-week timeframe of the clinical sampling of cancer tissue, depending on the amount of the obtained tissue, growth rate of cancer cells, and the number of drugs being tested. The 3D-DSRT method can be flexibly modified, e.g., to be carried out with or without supporting matrices with U-bottom 384-well plates when appropriate for the PDCs or other cell models used.
    MeSH term(s) Humans ; Drug Screening Assays, Antitumor ; Drug Discovery/methods ; Neoplasms/drug therapy ; Collagen/pharmacology
    Chemical Substances Collagen (9007-34-5)
    Language English
    Publishing date 2022-12-01
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2885123-7
    ISSN 2472-5560 ; 2472-5552
    ISSN (online) 2472-5560
    ISSN 2472-5552
    DOI 10.1016/j.slasd.2022.11.003
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  3. Article ; Online: Drug repurposing platform for deciphering the druggable SARS-CoV-2 interactome.

    Bogacheva, Mariia S / Kuivanen, Suvi / Potdar, Swapnil / Hassinen, Antti / Huuskonen, Sini / Pöhner, Ina / Luck, Tamara J / Turunen, Laura / Feodoroff, Michaela / Szirovicza, Leonora / Savijoki, Kirsi / Saarela, Jani / Tammela, Päivi / Paavolainen, Lassi / Poso, Antti / Varjosalo, Markku / Kallioniemi, Olli / Pietiäinen, Vilja / Vapalahti, Olli

    Antiviral research

    2024  Volume 223, Page(s) 105813

    Abstract: The coronavirus disease 2019 (COVID-19) pandemic has heavily challenged the global healthcare system. Despite the vaccination programs, the new virus variants are circulating. Further research is required for understanding of the biology of severe acute ... ...

    Abstract The coronavirus disease 2019 (COVID-19) pandemic has heavily challenged the global healthcare system. Despite the vaccination programs, the new virus variants are circulating. Further research is required for understanding of the biology of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and for discovery of therapeutic agents against the virus. Here, we took advantage of drug repurposing to identify if existing drugs could inhibit SARS-CoV-2 infection. We established an open high throughput platform for in vitro screening of drugs against SARS-CoV-2 infection. We screened ∼1000 drugs for their ability to inhibit SARS-CoV-2-induced cell death in the African green monkey kidney cell line (Vero-E6), analyzed how the hit compounds affect the viral N (nucleocapsid) protein expression in human cell lines using high-content microscopic imaging and analysis, determined the hit drug targets in silico, and assessed their ability to cause phospholipidosis, which can interfere with the viral replication. Duvelisib was found by in silico interaction assay as a potential drug targeting virus-host protein interactions. The predicted interaction between PARP1 and S protein, affected by Duvelisib, was further validated by immunoprecipitation. Our results represent a rapidly applicable platform for drug repurposing and evaluation of the new emerging viruses' responses to the drugs. Further in silico studies help us to discover the druggable host pathways involved in the infectious cycle of SARS-CoV-2.
    MeSH term(s) Humans ; Animals ; Chlorocebus aethiops ; SARS-CoV-2 ; COVID-19 ; Drug Repositioning ; Biological Assay ; Cell Death ; Nucleocapsid Proteins
    Chemical Substances Nucleocapsid Proteins
    Language English
    Publishing date 2024-01-24
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 306628-9
    ISSN 1872-9096 ; 0166-3542
    ISSN (online) 1872-9096
    ISSN 0166-3542
    DOI 10.1016/j.antiviral.2024.105813
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  4. Article ; Online: High-Content Imaging to Phenotype Human Primary and iPSC-Derived Cells.

    Veschini, Lorenzo / Sailem, Heba / Malani, Disha / Pietiäinen, Vilja / Stojiljkovic, Ana / Wiseman, Erika / Danovi, Davide

    Methods in molecular biology (Clifton, N.J.)

    2020  Volume 2185, Page(s) 423–445

    Abstract: Increasingly powerful microscopy, liquid handling, and computational techniques have enabled cell imaging in high throughput. Microscopy images are quantified using high-content analysis platforms linking object features to cell behavior. This can be ... ...

    Abstract Increasingly powerful microscopy, liquid handling, and computational techniques have enabled cell imaging in high throughput. Microscopy images are quantified using high-content analysis platforms linking object features to cell behavior. This can be attempted on physiologically relevant cell models, including stem cells and primary cells, in complex environments, and conceivably in the presence of perturbations. Recently, substantial focus has been devoted to cell profiling for cell therapy, assays for drug discovery or biomarker identification for clinical decision-making protocols, bringing this wealth of information into translational applications. In this chapter, we focus on two protocols enabling to (1) benchmark human cells, in particular human endothelial cells as a case study and (2) extract cells from blood for follow-up experiments including image-based drug testing. We also present concepts of high-content imaging and discuss the benefits and challenges, with the aim of enabling readers to tailor existing pipelines and bring such approaches closer to translational research and the clinic.
    MeSH term(s) Cellular Reprogramming Techniques ; Diagnostic Imaging ; High-Throughput Screening Assays ; Humans ; Induced Pluripotent Stem Cells/cytology ; Induced Pluripotent Stem Cells/metabolism ; Translational Medical Research
    Language English
    Publishing date 2020-11-08
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-0716-0810-4_27
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  5. Article ; Online: Ex Vivo Drug Testing in Patient-derived Papillary Renal Cancer Cells Reveals EGFR and the BCL2 Family as Therapeutic Targets.

    Angori, Silvia / Banaei-Esfahani, Amir / Mühlbauer, Katharina / Bolck, Hella A / Kahraman, Abdullah / Karakulak, Tülay / Poyet, Cédric / Feodoroff, Michaela / Potdar, Swapnil / Kallioniemi, Olli / Pietiäinen, Vilja / Schraml, Peter / Moch, Holger

    European urology focus

    2023  Volume 9, Issue 5, Page(s) 751–759

    Abstract: Background: Immune checkpoint inhibitors and antiangiogenic agents are used for first-line treatment of advanced papillary renal cell carcinoma (pRCC) but pRCC response rates to these therapies are low.: Objective: To generate and characterise a ... ...

    Abstract Background: Immune checkpoint inhibitors and antiangiogenic agents are used for first-line treatment of advanced papillary renal cell carcinoma (pRCC) but pRCC response rates to these therapies are low.
    Objective: To generate and characterise a functional ex vivo model to identify novel treatment options in advanced pRCC.
    Design, setting, and participants: We established patient-derived cell cultures (PDCs) from seven pRCC samples from patients and characterised them via genomic analysis and drug profiling.
    Outcome measurements and statistical analysis: Comprehensive molecular characterisation in terms of copy number analysis and whole-exome sequencing confirmed the concordance of pRCC PDCs with the original tumours. We evaluated their sensitivity to novel drugs by generating drug scores for each PDC.
    Results and limitations: PDCs confirmed pRCC-specific copy number variations such as gains in chromosomes 7, 16, and 17. Whole-exome sequencing revealed that PDCs retained mutations in pRCC-specific driver genes. We performed drug screening with 526 novel and oncological compounds. Whereas exposure to conventional drugs showed low efficacy, the results highlighted EGFR and BCL2 family inhibition as the most effective targets in our pRCC PDCs.
    Conclusions: High-throughput drug testing on newly established pRCC PDCs revealed that inhibition of EGFR and BCL2 family members could be a therapeutic strategy in pRCC.
    Patient summary: We used a new approach to generate patient-derived cells from a specific type of kidney cancer. We showed that these cells have the same genetic background as the original tumour and can be used as models to study novel treatment options for this type of kidney cancer.
    MeSH term(s) Humans ; Carcinoma, Renal Cell/drug therapy ; Carcinoma, Renal Cell/genetics ; Carcinoma, Renal Cell/pathology ; DNA Copy Number Variations ; ErbB Receptors/genetics ; Kidney Neoplasms/drug therapy ; Kidney Neoplasms/genetics ; Kidney Neoplasms/pathology ; Proto-Oncogene Proteins c-bcl-2/genetics
    Chemical Substances BCL2 protein, human ; EGFR protein, human (EC 2.7.10.1) ; ErbB Receptors (EC 2.7.10.1) ; Proto-Oncogene Proteins c-bcl-2
    Language English
    Publishing date 2023-03-16
    Publishing country Netherlands
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 2405-4569
    ISSN (online) 2405-4569
    DOI 10.1016/j.euf.2023.03.005
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  6. Article ; Online: SpheroidPicker for automated 3D cell culture manipulation using deep learning.

    Grexa, Istvan / Diosdi, Akos / Harmati, Maria / Kriston, Andras / Moshkov, Nikita / Buzas, Krisztina / Pietiäinen, Vilja / Koos, Krisztian / Horvath, Peter

    Scientific reports

    2021  Volume 11, Issue 1, Page(s) 14813

    Abstract: Recent statistics report that more than 3.7 million new cases of cancer occur in Europe yearly, and the disease accounts for approximately 20% of all deaths. High-throughput screening of cancer cell cultures has dominated the search for novel, effective ... ...

    Abstract Recent statistics report that more than 3.7 million new cases of cancer occur in Europe yearly, and the disease accounts for approximately 20% of all deaths. High-throughput screening of cancer cell cultures has dominated the search for novel, effective anticancer therapies in the past decades. Recently, functional assays with patient-derived ex vivo 3D cell culture have gained importance for drug discovery and precision medicine. We recently evaluated the major advancements and needs for the 3D cell culture screening, and concluded that strictly standardized and robust sample preparation is the most desired development. Here we propose an artificial intelligence-guided low-cost 3D cell culture delivery system. It consists of a light microscope, a micromanipulator, a syringe pump, and a controller computer. The system performs morphology-based feature analysis on spheroids and can select uniform sized or shaped spheroids to transfer them between various sample holders. It can select the samples from standard sample holders, including Petri dishes and microwell plates, and then transfer them to a variety of holders up to 384 well plates. The device performs reliable semi- and fully automated spheroid transfer. This results in highly controlled experimental conditions and eliminates non-trivial side effects of sample variability that is a key aspect towards next-generation precision medicine.
    MeSH term(s) Artificial Intelligence ; Cell Culture Techniques/instrumentation ; Cell Line, Tumor ; Deep Learning ; Drug Screening Assays, Antitumor ; High-Throughput Screening Assays ; Humans ; Neoplasms/drug therapy ; Neoplasms/pathology ; Precision Medicine ; Spheroids, Cellular/cytology ; Spheroids, Cellular/drug effects ; Spheroids, Cellular/pathology
    Language English
    Publishing date 2021-07-20
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/s41598-021-94217-1
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  7. Article ; Online: Genetics and molecular biology: identifying adipocytes and their origin.

    Pietiäinen, Vilja M / Ikonen, Elina

    Current opinion in lipidology

    2009  Volume 20, Issue 1, Page(s) 75–76

    MeSH term(s) Adipocytes/cytology ; Adipocytes/metabolism ; Adipocytes, White/cytology ; Adipocytes, White/metabolism ; Cell Differentiation/genetics ; Cell Lineage/genetics ; GTP-Binding Protein gamma Subunits/genetics ; GTP-Binding Protein gamma Subunits/metabolism ; Humans
    Chemical Substances BSCL2 protein, human ; GTP-Binding Protein gamma Subunits
    Language English
    Publishing date 2009-02
    Publishing country England
    Document type Editorial ; Research Support, Non-U.S. Gov't
    ZDB-ID 1045394-5
    ISSN 1473-6535 ; 0957-9672
    ISSN (online) 1473-6535
    ISSN 0957-9672
    DOI 10.1097/MOL.0b013e32832210c6
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  8. Article ; Online: iTReX: Interactive exploration of mono- and combination therapy dose response profiling data.

    ElHarouni, Dina / Berker, Yannick / Peterziel, Heike / Gopisetty, Apurva / Turunen, Laura / Kreth, Sina / Stainczyk, Sabine A / Oehme, Ina / Pietiäinen, Vilja / Jäger, Natalie / Witt, Olaf / Schlesner, Matthias / Oppermann, Sina

    Pharmacological research

    2021  Volume 175, Page(s) 105996

    Abstract: High throughput screening methods, measuring the sensitivity and resistance of tumor cells to drug treatments have been rapidly evolving. Not only do these screens allow correlating response profiles to tumor genomic features for developing novel ... ...

    Abstract High throughput screening methods, measuring the sensitivity and resistance of tumor cells to drug treatments have been rapidly evolving. Not only do these screens allow correlating response profiles to tumor genomic features for developing novel predictors of treatment response, but they can also add evidence for therapy decision making in precision oncology. Recent analysis methods developed for either assessing single agents or combination drug efficacies enable quantification of dose-response curves with restricted symmetric fit settings. Here, we introduce iTReX, a user-friendly and interactive Shiny/R application, for both the analysis of mono- and combination therapy responses. The application features an extended version of the drug sensitivity score (DSS) based on the integral of an advanced five-parameter dose-response curve model and a differential DSS for combination therapy profiling. Additionally, iTReX includes modules that visualize drug target interaction networks and support the detection of matches between top therapy hits and the sample omics features to enable the identification of druggable targets and biomarkers. iTReX enables the analysis of various quantitative drug or therapy response readouts (e.g. luminescence, fluorescence microscopy) and multiple treatment strategies (drug treatments, radiation). Using iTReX we validate a cost-effective drug combination screening approach and reveal the application's ability to identify potential sample-specific biomarkers based on drug target interaction networks. The iTReX web application is accessible at https://itrex.kitz-heidelberg.de.
    MeSH term(s) Antineoplastic Agents/administration & dosage ; Antineoplastic Combined Chemotherapy Protocols ; Cell Line, Tumor ; Dose-Response Relationship, Drug ; Drug Synergism ; Drug Therapy, Combination ; High-Throughput Screening Assays ; Humans ; Software
    Chemical Substances Antineoplastic Agents
    Language English
    Publishing date 2021-11-27
    Publishing country Netherlands
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1003347-6
    ISSN 1096-1186 ; 0031-6989 ; 1043-6618
    ISSN (online) 1096-1186
    ISSN 0031-6989 ; 1043-6618
    DOI 10.1016/j.phrs.2021.105996
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  9. Article ; Online: Association of tamoxifen resistance and lipid reprogramming in breast cancer.

    Hultsch, Susanne / Kankainen, Matti / Paavolainen, Lassi / Kovanen, Ruusu-Maaria / Ikonen, Elina / Kangaspeska, Sara / Pietiäinen, Vilja / Kallioniemi, Olli

    BMC cancer

    2018  Volume 18, Issue 1, Page(s) 850

    Abstract: Background: Tamoxifen treatment of estrogen receptor (ER)-positive breast cancer reduces mortality by 31%. However, over half of advanced ER-positive breast cancers are intrinsically resistant to tamoxifen and about 40% will acquire the resistance ... ...

    Abstract Background: Tamoxifen treatment of estrogen receptor (ER)-positive breast cancer reduces mortality by 31%. However, over half of advanced ER-positive breast cancers are intrinsically resistant to tamoxifen and about 40% will acquire the resistance during the treatment.
    Methods: In order to explore mechanisms underlying endocrine therapy resistance in breast cancer and to identify new therapeutic opportunities, we created tamoxifen-resistant breast cancer cell lines that represent the luminal A or the luminal B. Gene expression patterns revealed by RNA-sequencing in seven tamoxifen-resistant variants were compared with their isogenic parental cells. We further examined those transcriptomic alterations in a publicly available patient cohort.
    Results: We show that tamoxifen resistance cannot simply be explained by altered expression of individual genes, common mechanism across all resistant variants, or the appearance of new fusion genes. Instead, the resistant cell lines shared altered gene expression patterns associated with cell cycle, protein modification and metabolism, especially with the cholesterol pathway. In the tamoxifen-resistant T-47D cell variants we observed a striking increase of neutral lipids in lipid droplets as well as an accumulation of free cholesterol in the lysosomes. Tamoxifen-resistant cells were also less prone to lysosomal membrane permeabilization (LMP) and not vulnerable to compounds targeting the lipid metabolism. However, the cells were sensitive to disulfiram, LCS-1, and dasatinib.
    Conclusion: Altogether, our findings highlight a major role of LMP prevention in tamoxifen resistance, and suggest novel drug vulnerabilities associated with this phenotype.
    MeSH term(s) Antineoplastic Agents, Hormonal/pharmacology ; Breast Neoplasms/drug therapy ; Breast Neoplasms/genetics ; Breast Neoplasms/pathology ; Cellular Reprogramming/genetics ; Cholesterol/metabolism ; Drug Resistance, Neoplasm/genetics ; Estrogen Receptor alpha/genetics ; Female ; Gene Expression Regulation, Neoplastic/drug effects ; Humans ; Lipid Metabolism/genetics ; Lipids/biosynthesis ; Lipids/genetics ; Lysosomes/genetics ; MCF-7 Cells ; Tamoxifen/pharmacology ; Transcriptome/genetics ; Triglycerides/metabolism
    Chemical Substances Antineoplastic Agents, Hormonal ; Estrogen Receptor alpha ; Lipids ; Triglycerides ; Tamoxifen (094ZI81Y45) ; Cholesterol (97C5T2UQ7J)
    Language English
    Publishing date 2018-08-24
    Publishing country England
    Document type Journal Article
    ISSN 1471-2407
    ISSN (online) 1471-2407
    DOI 10.1186/s12885-018-4757-z
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  10. Article ; Online: SARS-CoV-2-host proteome interactions for antiviral drug discovery.

    Liu, Xiaonan / Huuskonen, Sini / Laitinen, Tuomo / Redchuk, Taras / Bogacheva, Mariia / Salokas, Kari / Pöhner, Ina / Öhman, Tiina / Tonduru, Arun Kumar / Hassinen, Antti / Gawriyski, Lisa / Keskitalo, Salla / Vartiainen, Maria K / Pietiäinen, Vilja / Poso, Antti / Varjosalo, Markku

    Molecular systems biology

    2021  Volume 17, Issue 11, Page(s) e10396

    Abstract: Treatment options for COVID-19, caused by SARS-CoV-2, remain limited. Understanding viral pathogenesis at the molecular level is critical to develop effective therapy. Some recent studies have explored SARS-CoV-2-host interactomes and provided great ... ...

    Abstract Treatment options for COVID-19, caused by SARS-CoV-2, remain limited. Understanding viral pathogenesis at the molecular level is critical to develop effective therapy. Some recent studies have explored SARS-CoV-2-host interactomes and provided great resources for understanding viral replication. However, host proteins that functionally associate with SARS-CoV-2 are localized in the corresponding subnetwork within the comprehensive human interactome. Therefore, constructing a downstream network including all potential viral receptors, host cell proteases, and cofactors is necessary and should be used as an additional criterion for the validation of critical host machineries used for viral processing. This study applied both affinity purification mass spectrometry (AP-MS) and the complementary proximity-based labeling MS method (BioID-MS) on 29 viral ORFs and 18 host proteins with potential roles in viral replication to map the interactions relevant to viral processing. The analysis yields a list of 693 hub proteins sharing interactions with both viral baits and host baits and revealed their biological significance for SARS-CoV-2. Those hub proteins then served as a rational resource for drug repurposing via a virtual screening approach. The overall process resulted in the suggested repurposing of 59 compounds for 15 protein targets. Furthermore, antiviral effects of some candidate drugs were observed in vitro validation using image-based drug screen with infectious SARS-CoV-2. In addition, our results suggest that the antiviral activity of methotrexate could be associated with its inhibitory effect on specific protein-protein interactions.
    MeSH term(s) Antiviral Agents/pharmacology ; COVID-19/virology ; Drug Discovery ; Drug Repositioning ; Host-Pathogen Interactions/drug effects ; Humans ; Mass Spectrometry ; Methotrexate/pharmacology ; Proteome/drug effects ; Proteomics ; SARS-CoV-2/physiology ; Virus Replication/drug effects ; COVID-19 Drug Treatment
    Chemical Substances Antiviral Agents ; Proteome ; Methotrexate (YL5FZ2Y5U1)
    Language English
    Publishing date 2021-10-28
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2193510-5
    ISSN 1744-4292 ; 1744-4292
    ISSN (online) 1744-4292
    ISSN 1744-4292
    DOI 10.15252/msb.202110396
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

To top