Matthias Nees
PhD, Dr. rer. nat.

Adjunct Professor, Department of Biology (Department of Biology)
Senior Research Fellow, Institute of Biomedicine (Institute of Biomedicine)

matthias.nees@utu.fi
+358 45 606 6406

Itäinen Pitkäkatu 4
Turku
Medisiina D
Office: D5



Areas of expertise
Translational Oncology, Cell Culture Model Systems, Personalised Medicine, Organoids, Tumor Models

Biography

01/2015 – now:  Adjunct Professor, University of Turku, Dept. Biomedicine and Anatomy; Coordinator of the High Content Screening Laboratory (HCSLab) 

Physiologically relevant models for translational oncology and personalized medicine, advanced 3D cell & tissue-culture models for early stage drug discovery, functional drug target validation (siRNA, shRNA). Phenotypic & high content screening, automated image analyses, elucidation of MOA and functional validation of diagnostic biomarkers

09/2016 – 10/2018 Docent at SRH Fernhochschule „The Mobile University“: Bachelor Degree Program Pharmaceutical Management & Technologies

Preparation of teaching materials for eLearning platforms, text books, podcasts and ePubs, lectures, workshops, coaching of students – online and on-site 

03/2005 – 12/2014 Group Leader and Principal Investigator, VTT Technical Research Centre of Finland OY, Turku (Teams “Systems Biology” and “Cell Culture Model Systems”)

Cell- and tissue-based model systems (3D organoid and tissue cultures) for phenotypic high content screening, automated image analysis & machine learning. Team Leader, management of interdisciplinary research groups (incl. Programmers, Biologists, Medical Students, Technicians, PostDocs, Masters’ and PhD students). Public/private partnerships PPP with industry partners, mainly funded by European Community (IMI, FP7, EuroTransBio, Marie Curie Training Networks, etc.), or Business Finland (formerly Tekes). 

04/2002 – 02/2005: Staff Scientist - Molecular Medicine Partnership Unit – European Molecular Biology Laboratory EMBL & University Hospital Heidelberg

Laboratory operations and management: gene expression analyses (microarrays), personalized medicine (childhood leukaemia and sarcomas), biobanking, genetic analyses (DNA sequencing); Diagnostics

06/2000 – 03/2002 – Staff Scientist – Clinical Cooperation Unit German Cancer Research Center (DKFZ) and University Hospital Heidelberg, Germany 

Translational oncology and personalized medicine: characterization of patient virus load and virus typing (HPV); primary cell- and tissue cultures, in vitro models for organotypic assays; microarray studies. Diagnostics: functional and diagnostic evaluation of biomarkers, DNA cloning and sequencing 

06/1997 –05/2000: Postdoctoral Fellow – National Cancer Institute NCI, National Institutes of Health NIH – Bethesda, Maryland, USA

Personalized medicine: in vitro model systems for disease progression, based on primary patient tissues and cell cultures, immortalization of primary cells by viral vectors & oncogenes

11/1993-04/1997: PhD thesis at German Cancer Research Center (DKFZ) Heidelberg, Germany – Dept. Applied Tumour Virology/Prof. Harald zur Hausen

Translational oncology: primary cell culture models for cancer initiation and progression

08/1992 - 10/1993: Master’s Thesis at the University Hospital Heidelberg, Germany – Molecular Biology Laboratory of the Ear, Neck & Throat Clinics HNO 

Translational oncology: analysis of mutations in primary patient materials, DNA sequencing

08/1990 – 07/1992 Scientific Research Assistant University Hospital Heidelberg/Germany




Research

Drug Discovery:  Coordination of contract research projects with the pharmaceutical industry, custom
research organizations (CROs), small- and medium-size enterprises SMEs, and
non-profit research institutes/universities. Early stage, preclinical drug discovery and lead development studies. 

Model Systems for Cancer: Evaluation of in vitro in vivo models (e.g. Xenografts, patient-derived PDX, genetically engineered mouse models GEMMs; tissue slices and explant cultures)

Cell- and tissue-based model systems: Complex
organotypic or 3D model systems (organoids) to recapitulate the architecture of
solid cancer tissues. Methods for microscopic imaging, automated image analysis
(“machine vision”), phenotypic- or imaging-based high content screening (HCS).

Cancer Biomarker Research: Protein/biomarker
expression in cancers using tissue
microarrays TMA
, RNA- and antibody-based protein immune-fluorescence and
immune histochemistry methods on fresh & FFPE-tissues (IHC, ISH).

Clinical cooperation units with Department of Pathology and Dept. of Urology at Turku University
Hospital TYKS): Biobanking of primary,
patient-derived materials (“Turku
Prostate Cancer Consortium, TPCC
”). Novel methods to isolate and
successfully propagate primary cell cultures for personalized medicine and drug
sensitivity-testing.

Bioinformatics & systems biology: Genome-wide mRNA studies (DNA Microarrays, Next Generation Sequencing,NGS, quantitative and realtime PCR,
qRT-PCR).  Investigating alternative splicing, DNA
copy-number alterations and mutations (CGH & SNP arrays; Sanger & NG
Sequencing) in cancer and cancer progression.



Teaching

Professor, SRH Fernhochschule – “The Mobile University” 09/(2016 – 09 /
2018: 
Bachelor degree program in Pharma-Management
& Technology

  • Pre-clinical and clinical drug
    development
  • Drug formulation and pharmaceutical
    drug development
  • Quality control/quality management
    and instrumental analytics, GMP
  • Industrial biotechnology,
    biologicals/biosimilars, and fermentation technologies (Upstream- and Downstream Processing)
  • Organic chemistry and biochemistry; Biochemistry of Nutrition
  • Molecular and cell biology
  • Drug market registration (EMA and FDA)
  • Drug safety and pharmacovigilance

Adjunct Professor and Docent, University of Turku/Finland; Master’s degree programme in Biomedical imaging (BIMA), Turku Bioimaging:

  • “Fluorescence in Bioanalytical
    Research” (ANAT5105, lecturer) 2015
  • “Bioimaging and microscopy”,
    ÅA_0432, lecturer) 2013, 2014, 2015 

Masters’ Degree Program, University of Turku:

  • “Bioinformatics in Drug Discovery”
    (DRUG0007, lecturer) 2015
  • “Genetics and drug discovery in
    cancer research”, (FYGE3209, organizer and lecturer, 2013 -2014)
  •  “Drug development in the
    pharmaceutical industry” (FYGE3208, organizer & lecturer, 2012 -2013);
  • “Cancer Functional Genetics: From
    Mechanisms to Drug Discovery” (organizer & lecturer, 2008-11)
  •  “Cancer Genetics & Genomics”
    (organizer & lecturer, 2005 - 2007
  • FinPharma Doctoral Program Drug Discovery (FPDP-DD):
  • “Epigenetic Processes as Drug
    Targets in Prostate Cancer”, FinPharma Graduate School

Turku Centre for Biotechnology CBT - Turku Centre for Computer Science
(TUCS):

  •  Systems Biology at University of
    Turku (2012 – 2015)
  •  Computational Biology C, for
    students of Bioinformatics; March 2012 - 2015
  •  “TERBIO Functional Genomics,
    Proteomics & Bioinformatics Course”, 2006-2015
Karolinska Institutet, Stockholm/Sweden

  • Nanotoxicology MiniSymposium,
    Institute for Toxicology, August 16, 2012
  • Advanced Cell Culture Training
    Course, Institute for Toxicology, Sept. 10- 12, 2010



Publications
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Inhibition of histone methyltransferase DOT1L silences ER alpha gene and blocks proliferation of antiestrogen-resistant breast cancer cells (2019)
Science Advances
Nassa G., Salvati A., Tarallo R., Gigantino V., Alexandrova E., Memoli D., Sellitto A., Rizzo F., Malanga D., Mirante T., Morelli E., Nees M., Åkerfelt M., Kangaspeska S., Nyman T.A., Milanesi L., Giurato G., Weisz A.
(
A1 Journal article – refereed)

Factors affecting intracellular delivery and release of hydrophilic versus hydrophobic cargo from mesoporous silica nanoparticles on 2D and 3D cell cultures (2018)
Pharmaceutics
Desai D., Åkerfelt M., Prabhakar N., Toriseva M., Näreoja T., Zhang J., Nees M., Rosenholm J.
(
A1 Journal article – refereed)

Frizzled-8 integrates Wnt-11 and transforming growth factor-beta signaling in prostate cancer (2018)
Nature Communications
Murillo-Garzon V, Gorrono-Etxebarria I, Akerfelt M, Puustinen MC, Sistonen L, Nees M, Carton J, Waxman J, Kypta RM
(
A1 Journal article – refereed)

Increased HSF1 expression predicts shorter disease-specific survival of prostate cancer patients following radical prostatectomy (2018)
Oncotarget
Johanna K. Björk, Ilmari Ahonen, Tuomas Mirtti, Andrew Erickson, Antti Rannikko, Anna Bützow, Stig Nordling, Johan Lundin, Mikael Lundin, Lea Sistonen, Matthias Nees, Malin Åkerfelt
(
A1 Journal article – refereed)

A high-content image analysis approach for quantitative measurements of chemosensitivity in patient-derived tumor microtissues (2017)
Scientific Reports
Ahonen I, Akerfelt M, Toriseva M, Oswald E, Schuler J, Nees M
(
A1 Journal article – refereed)

Quantitative Phenotypic Image Analysis of Three-Dimensional Organotypic Cultures (2017) 3D Cell Culture Malin Åkerfelt, Mervi Toriseva, Matthias Nees
(
A3 Book chapter)

Heat-shock factor 2 is a suppressor of prostate cancer invasion (2016)
Oncogene
Björk JK, Åkerfelt M, Joutsen J, Puustinen MC, Cheng F, Sistonen L, Nees M.
(
A1 Journal article – refereed)

Increased expression of fibroblast growth factor 13 in prostate cancer is associated with shortened time to biochemical recurrence after radical prostatectomy (2016)
International Journal of Cancer
Yu L, Toriseva M, Tuomala M, Seikkula H, Elo T, Tuomela J, Kallajoki M, Mirtti T, Taimen P, Bostrom PJ, Alanen K, Nurmi M, Nees M, Harkonen P
(
A1 Journal article – refereed)

Morphological Clustering of Cell Cultures Based on Size, Shape, and Texture Features (2016)
Statistics in Biopharmaceutical Research
Ilmari Ahonen, Ville Härmä, Hannu-Pekka Schukov, Matthias Nees, Jaakko Nevalainen
(
A1 Journal article – refereed)

Revisiting the expression and function of follicle-stimulation hormone receptor in human umbilical vein endothelial cells (2016)
Scientific Reports
Stelmaszewska J, Chrusciel M, Doroszko M, Åkerfelt M, Ponikwicka-Tyszko D, Nees M, Frentsch M, Li X, Kero J, Huhtaniemi I, Wolczynski S, Rahman NA.
(
A1 Journal article – refereed)

Stratification of aggressive prostate cancer from indolent disease-Prospective controlled trial utilizing expression of 11 genes in apparently benign tissue (2016)
Urologic Oncology: Seminars and Original Investigations
Alinezhad S, Vaananen RM, Tallgren T, Perez IM, Jambor I, Aronen H, Kahkonen E, Ettala O, Syvanen K, Nees M, Kallajoki M, Taimen P, Bostrom PJ, Pettersson K
(
A1 Journal article – refereed)

Validation of Novel Biomarkers for Prostate Cancer Progression by the Combination of Bioinformatics, Clinical and Functional Studies (2016)
PLoS ONE
Alinezhad S, Väänänen RM, Mattsson J, Li YF, Tallgren T, Ochoa NT, Bjartell A, Åkerfelt M, Taimen P, Boström PJ, Pettersson K, Nees M
(
A1 Journal article – refereed)

Automated tracking of tumor-stroma morphology in microtissues identifies targets within the tumor microenvironment for therapeutic intervention (2015)
Oncotarget
Malin Åkerfelt, Neslihan Bayramoglu, Sean Robinson, Mervi Toriseva, Hannu-Pekka Schukov, Ville Härmä, Johannes Virtanen, Raija Sormunen, Mika Kaakinen, Juho Kannala, Lauri Eklund, Janne Heikkilä, Matthias Nees
(
A1 Journal article – refereed)

Optimization of Invasion-Specific Effects of Betulin Derivatives on Prostate Cancer Cells through Lead Development (2015)
PLoS ONE
Harma V, Haavikko R, Virtanen J, Ahonen I, Schukov HP, Alakurtti S, Purev E, Rischer H, Yli-Kauhaluoma J, Moreira VM, Nees M, Oksman-Caldentey KM
(
A1 Journal article – refereed)

Segmentation of Image Data from Complex Organotypic 3D Models of Cancer Tissues with Markov Random Fields (2015)
PLoS ONE
Robinson S, Guyon L, Nevalainen J, Toriseva M, Åkerfelt M, Nees M
(
A1 Journal article – refereed)

Quantification of Dynamic Morphological Drug Responses in 3D Organotypic Cell Cultures by Automated Image Analysis (2014)
PLoS ONE
Härmä V, Schukov HP, Happonen A, Ahonen I, Virtanen J, Siitari H, Åkerfelt M, Lötjönen J, Nees M
(
A1 Journal article – refereed)

Validation of proposed prostate cancer biomarkers with gene expression data: a long road to travel (2014)
Cancer and Metastasis Reviews
Adriana Amaro, Alessia Isabella Esposito, Anna Gallina, Matthias Nees, Giovanna Angelini, Adriana Albini, Ulrich Pfeffer
(
A1 Journal article – refereed)

Enhanced serine production by bone metastatic breast cancer cells stimulates osteoclastogenesis (vol 125, pg 421, 2011) (2012)
Breast Cancer Research and Treatment
Pollari S, Kakonen SM, EDGREN H, WOLF M, Kohonen P, SARA H, GUISE T, NEES M, KALLIONIEMI O
(
B1 Journal article)

Systematic knockdown of epigenetic enzymes identifies a novel histone demethylase PHF8 overexpressed in prostate cancer with an impact on cell proliferation, migration and invasion. (2012)
Oncogene
Björkman M, Östling P, Härmä V, Virtanen J, Mpindi JP, Rantala J, Mirtti T, Vesterinen T, Lundin M, Sankila A, Rannikko A, Kaivanto E, Kohonen P, Kallioniemi O, Nees M
(
A1 Journal article – refereed)

Enhanced serine production by bone metastatic breast cancer cells stimulates osteoclastogenesis (2011)
Breast Cancer Research and Treatment
Pollari Sirkku, Käkönen Sanna-Maria, Edgren Henrik, Wolf Maija, Kohonen Pekka, Sara Henri, Guise Theresa, Nees Matthias, Kallioniemi Olli
(
A1 Journal article – refereed)


Last updated on 2019-17-08 at 02:18