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European Industrial Doctorate for enhancing upstream biopharmaceutical manufacturing process development through single cell analysis

Deliverables

Optimisation of the production process for CAR T cells dose-efficacy correlation

Optimisation of the production process for CAR T cells and understanding of the doseefficacy correlation

Effect of different protein product types on productivity and glycan heterogeneity in CHO cells

Understanding of the effect of different protein product types on productivity and glycan heterogeneity in CHO cells

Cell biology during extended HCDP culture

Understanding of the underlying cell biology during extended HCDP culture

Rhapsody scRNASeq, mtDNA and proteomics of cell therapies

Rhapsody scRNASeq mtDNA and proteomics of cell therapies complete

Manuscripts submitted to peer-reviewed journals (i.e. peer reviewed primary research papers to be published after publication by journal)

Papers on STACCATO research results will be submitted to open access peerreviewed journals For nonopen access publications articles will be deposited in an online repository to be made accessible

STACCATO Podcast Seminar Series

Biannual seminars to be broadcasted via FacebookLive Each seminar will be published via the STACCATO podcast on the project website

Conference presentations and posters

Participation of ESRs and PIs at relecant scientific conferences to disseminate the latest project results

STACCATO Website

The project website of STACCATO will have the main purpose of illustrating the application of single cell analysis for bioprocess development to the general public Additionally it will be the main platform for disseminating resarch project results and informing about the project in general

Publications

Proof-of-Concept of Continuous Transfection for Adeno-Associated Virus Production in Microcarrier-Based Culture

Author(s): Brian Ladd, Kevin Bowes, Mats Lundgren, Torbjörn Gräslund and Veronique Chotteau
Published in: Processes, Issue 2022, 10(3), 515, 2022, ISSN 2227-9717
Publisher: MDPI
DOI: 10.3390/pr10030515

Impact of dual baculovirus infection on the Sf9 insect cell transcriptome during AAV production using single-cell RNA-seq

Author(s): Virgolini N., Silvano M., Hagan R., Correia R., Alves P., Clarke C., Roldao A., Isidro I.
Published in: Biotechnology & Bioengineering, 2023, ISSN 1097-0290
Publisher: Wiley Online Library
DOI: 10.22541/au.167121909.92795915/v1

Dissecting insect cell heterogeneity during influenza VLP production using single-cell transcriptomics

Author(s): Marco Silvano, Nikolaus Virgolini, Ricardo Correia, Colin Clarke, Ines A. Isidro, Paula M. Alves, Antonio Roldao
Published in: Frontiers in Bioengineering and Biotechnology, Issue vol. 11, 2023, ISSN 2296-4185
Publisher: Frontiers
DOI: 10.3389/fbioe.2023.1143255

Comparison of Clinically Relevant Oncolytic Virus Platforms for Enhancing T Cell Therapy of Solid Tumors

Author(s): Cervera-Carrascon V., Quixabeira DCA., Havunen R., Santos JM., Kutvonen E., Clubb JHA., Siurala M., Heiniö C., Zafar S., Koivula T., Lumen D., Vaha M., Garcia-Horsman A., Airaksinen AJ., Sorsa S., Anttila M., Hukkanen V., Kanerva A., Hemminki A.
Published in: Molecular therapy oncolytics, Issue vol.17, 2020, ISSN 2372-7705
Publisher: CellPress
DOI: 10.1016/j.omto.2020.03.003

Development of a Syrian Hamster anti-PD-L1 monoclonal antibody enables adenoviral oncolytic immunotherapy modelling in an immunocompetent virus replication permissive setting.

Author(s): Clubb J., Kudling T.V., Quixabeira D., Santos J., Havunen R., Heiniö C., Cervera-Carrascon V., Pakola S., Basnet S., Grönberg-Vähä-Koskela s., Kanerva A., & Hemminki A.
Published in: Frontiers in Immunology, Issue vol.14, 2023, ISSN 1664-3224
Publisher: Frontiers
DOI: 10.3389/fimmu.2023.1060540

Monitoring CAR T cell generation with a CD8-targeted lentiviral vector by single-cell transcriptomics

Author(s): Charitidis F.T., Adabi E., Thalheimer F.B., Clarke C., Buchholz C.J.
Published in: Molecular Therapy – Methods & Clinical Development, Issue vol.23, 2022, ISSN 2329-0501
Publisher: CellPress
DOI: 10.1016/j.omtm.2021.09.019

Subphysiological temperature induces pervasive alternative splicing in Chinese hamster ovary cells

Author(s): Ioanna Tzani, Craig Monger, Krishna Motheramgari, Clair Gallagher, Ryan Hagan, Paul Kelly, Alan Costello, Justine Meiller, Patrick Floris, Lin Zhang, Martin Clynes, Jonathan Bones, Niall Barron, Colin Clarke
Published in: Biotechnology and Bioengineering, Issue 117/8, 2020, Page(s) 2489-2503, ISSN 0006-3592
Publisher: Wiley - V C H Verlag GmbbH & Co.
DOI: 10.1002/bit.27365

Systemic Delivery of Oncolytic Adenovirus to Tumors Using Tumor-Infiltrating Lymphocytes as Carriers

Author(s): Santos J, Heiniö C, Quixabeira D, Zafar S, Clubb J, Pakola S, Cervera-Carrascon V, Havunen R, Kanerva A, Hemminki A.
Published in: Cells, Issue vol. 10 issue 5, 2022, ISSN 2073-4409
Publisher: MDPI
DOI: 10.3390/cells10050978

Adenovirus Encoding Tumor Necrosis Factor Alpha and Interleukin 2 Induces a Tertiary Lymphoid Structure Signature in Immune Checkpoint Inhibitor Refractory Head and Neck Cancer

Author(s): Clubb J.H.A., Kudling T.V., Heiniö C., Basnet S., Pakola S., Cervera Carrascón V., Santos J.M., Quixabeira D.C.A., Havunen R., Sorsa S., Zheng V., Salo T., Bäck L., Aro K., Tulokas S., Loimu V., Hemminki A.
Published in: Frontiers in Immunology, Issue vol. 13, 2022, ISSN 1664-3224
Publisher: Frontiers
DOI: 10.3389/fimmu.2022.794251

Transcriptome analysis of Sf9 insect cells during production of recombinant Adeno‐associated virus

Author(s): Nikolaus Virgolini; Ryan Hagan; Ricardo Correia; Marco Silvano; Sofia Fernandes; Paula M. Alves; Colin Clarke; António Roldão; Inês A. Isidro
Published in: Biotechnology Journal, 2022, ISSN 1860-7314
Publisher: Wiley Online Library
DOI: 10.1002/biot.202200466

Expression of Extracellular Vesicle PIWI-interacting RNAs over hiPSC-cardiomyocyte differentiation

Author(s): Louro A.F., Virgolini N., Paiva M.A., Isidro I.A., Alves P.M., Gomes-Alves P., Serra M.
Published in: Frontiers in Physiology, Issue Vol 13, 2022, ISSN 1664-042X
Publisher: Frontiers Research Foundation
DOI: 10.3389/fphys.2022.926528

Local delivery of interleukin 7 with an oncolytic adenovirus activates tumor-infiltrating lymphocytes and causes tumor regression

Author(s): Kudling T.V., Clubb J.H.A., Quixabeira D.C.A., Santos J.M., Havunen R., Kononov A., Heiniö C., Cervera-Carrascon V., Pakola S., Basnet S., Grönberg-Vähä-Koskela S., Arias V., Gladwyn-Ng I., Aro K., Bäck L., Räsänen J., Ilonen I., Borenius K., Räsänen M., Hemminki O., Rannikko A., Kanerva A., Tapper J., Hemminki A.
Published in: OncoImmunology, Issue vol. 11, issue 1, 2022, ISSN 2162-4011
Publisher: Landes Bioscience
DOI: 10.1080/2162402x.2022.2096572

Gene expression analysis of adapted insect cells during influenza VLP production using RNA-sequencing

Author(s): Silvano, M., Correia, R., Virgolini, N., Clarke, C., Alves, P.M., Isidro, I.A., Roldão, A.
Published in: Viruses, Issue vol- 14 issue 10, 2022, ISSN 1999-4915
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/v14102238

Tracing production instability in a clonally derived CHO cell line using single‐cell transcriptomics

Author(s): Ioanna Tzani, Nicolas Herrmann, Sara Carillo, Cathy A. Spargo, Ryan Hagan, Niall Barron, Jonathan Bones, W. Shannon Dillmore, Colin Clarke
Published in: Biotechnology and Bioengineering, 2021, ISSN 0006-3592
Publisher: Wiley - V C H Verlag GmbbH & Co.
DOI: 10.1002/bit.27715

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