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Hire Dr. Joseph N.

Finland

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Scientific Writing, Editing, Bioinformatics

Profile Summary

Bio-molecular research scientist with a keen interest in resolving the molecular basis of disease, and translating these into diagnostic, therapeutic or prognostic tools. Previous projects: 2007: Protein Engineering – directed evolution of bacterial LacI gene Scope 2011: Brain caffeine metabolism in healthy subjects. I was involved in setting up an in vitro assay to validate these findings at the molecular level, and shed more light on the mechanisms involved. 2012: Cardiovascular Disease risk markers. Set up invitro bioassay to elucidate the functional relevance of a novel cardiovascular risk factor - homoarginine 2008 - 2014: Thesis: Creatine Deficiency Syndromes: A Clinical, Molecular and Functional Approach. Vrije Universiteit Link: http://dare.ubvu.vu.nl/handle/1871/52196#accept 2013: Systemic Markers of Seasonal Allergic Rhinitis - Set up and carried out proteomic assessment of samples from allergic and non-allergic individuals 2014: Developing predicitive classifiers of carbon nanotube toxicity. Set up invitro exposure protocols for assessment of known toxicity endpoints, followed by comparative proteomic assessment of cells exposed to different forms of carbon nanotubes 2015: Evaluation of Systemic Post Translational Modification changes upon exposure to engineered nanomaterials 2016: Invivo molecular diagnostics (transcriptomics) of indoor moisture and mold damage exposure 2017: small RNAs as biomarkers of adverse exposure to nano silver

Subject Matter Expertise

• ★ Molecular Biology
• ★ Technical & Scientific Writing
• ☆ Nanotechnology & Nanomaterials
• ☆ Liquid Chromatography/HPLC
• ☆ Carbon Materials
• ☆ Biochemistry
• ☆ Biomarkers
• ☆ Transcriptomics
• ☆ Proteomics
• ☆ Data Analysis
• ☆ Bioinformatics
• ☆ Cardiovascular Disease
• ☆ Neuropathology
• ☆ Metabolism & Metabolic Disease

Services

• Writing
• Data & AI

Writing Technical Writing

Data & AI Statistical Analysis, Data Visualization, Big Data Analytics, Data Insights

Work Experience

University of Helsinki

- Present

Researcher

University of Helsinki - Human Microbiome Research Programme

January 2019 - Present

Researcher

University of Helsinki

2019 - Present

Postdoctoral Researcher

University of Helsinki - Medicum

November 2016 - January 2019

Postdoctoral Researcher

University of Helsinki

2016 - 2019

Researcher

Finnish Institute of Occupational Health

2013 - 2015

Researcher in Training

Vrije University Medical Center

September 2008 - August 2013

OIO

VU University Medical Center

September 2008 - February 2013

Intern

Institute of Atomic and Molecular Physics, Amsterdam

November 2007 - June 2008

Intern

Royal Tropical Institute, Amsterdam

March 2007 - August 2007

Education

PhD Molecular Genetics

Vrije University, University Medical Centre, Amsterdam, Netherlands

November 2008 - June 2014

PhD (Clinical Chemistry)

Vrije Universiteit Amsterdam

2008 - 2014

MSc - Molecular Cell Biology

Vrije University

September 2006 - October 2008

BSc - Biochemistry and Medical Laboratory Technology

University of Buea

September 2001 - October 2004

Certifications

• Certification details not provided.

Publications

JOURNAL ARTICLE

Joseph Dingbobga Tanyi Ndika, Piia Karisola, Pia Kinaret, Marit Ilves, Harri Alenius (2021). Profiling Non-Coding RNA Changes Associated with 16 Different Engineered Nanomaterials in a Mouse Airway Exposure Model . Cells.

Profiling Non-Coding RNA Changes Associated with 16 Different Engineered Nanomaterials in a Mouse Airway Exposure Model @article{7de2524a05c6419e8c00c58f8e17379f, title = "Profiling Non-Coding RNA Changes Associated with 16 Different Engineered Nanomaterials in a Mouse Airway Exposure Model", abstract = "Perturbations in cellular molecular events and their associated biological processes provide opportunities for hazard assessment based on toxicogenomic profiling. Long non-coding RNAs (lncRNAs) are transcribed from DNA but are typically not translated into full-length proteins. Via epigenetic regulation, they play important roles in organismal response to environmental stress. The effects of nanoparticles on this important part of the epigenome are understudied. In this study, we investigated changes in lncRNA associated with hazardous inhalatory exposure of mice to 16 engineered nanomaterials (ENM)-4 ENM (copper oxide, multi-walled carbon nanotubes, spherical titanium dioxide, and rod-like titanium dioxide particles) with 4 different surface chemistries (pristine, COOH, NH2, and PEG). Mice were exposed to 10 mu g of ENM by oropharyngeal aspiration for 4 consecutive days, followed by cytological analyses and transcriptomic characterization of whole lung tissues. The number of significantly altered non-coding RNA transcripts, suggestive of their degrees of toxicity, was different for each ENM type. Particle surface chemistry and shape also had varying effects on lncRNA expression. NH2 and PEG caused the strongest and weakest responses, respectively. Via correlational analyses to mRNA expression from the same samples, we could deduce that significantly altered lncRNAs are potential regulators of genes involved in mitotic cell division and DNA damage response. This study sheds more light on epigenetic mechanisms of ENM toxicity and also emphasizes the importance of the lncRNA superfamily as toxicogenomic markers of adverse ENM exposure.", keywords = "nanoparticles, toxicogenomics, long non-coding RNA, TITANIUM-DIOXIDE, TOXICITY, INDUCE, 1182 Biochemistry, cell and molecular biology", author = "Joseph Ndika and Piia Karisola and Pia Kinaret and Marit Ilves and Harri Alenius", year = "2021", month = may, doi = "10.3390/cells10051085", language = "English", volume = "10", journal = "Cells", issn = "2073-4409", publisher = "MDPI", number = "5", } . Cells.

Toxicogenomic Profiling of 28 Nanomaterials in Mouse Airways @article{6e520336614c4bde8ea58cf048d448db, title = "Toxicogenomic Profiling of 28 Nanomaterials in Mouse Airways", abstract = "Toxicogenomics opens novel opportunities for hazard assessment by utilizing computational methods to map molecular events and biological processes. In this study, the transcriptomic and immunopathological changes associated with airway exposure to a total of 28 engineered nanomaterials (ENM) are investigated. The ENM are selected to have different core (Ag, Au, TiO2, CuO, nanodiamond, and multiwalled carbon nanotubes) and surface chemistries (COOH, NH2, or polyethylene glycosylation (PEG)). Additionally, ENM with variations in either size (Au) or shape (TiO2) are included. Mice are exposed to 10 mu g of ENM by oropharyngeal aspiration for 4 consecutive days, followed by extensive histological/cytological analyses and transcriptomic characterization of lung tissue. The results demonstrate that transcriptomic alterations are correlated with the inflammatory cell infiltrate in the lungs. Surface modification has varying effects on the airways with amination rendering the strongest inflammatory response, while PEGylation suppresses toxicity. However, toxicological responses are also dependent on ENM core chemistry. In addition to ENM-specific transcriptional changes, a subset of 50 shared differentially expressed genes is also highlighted that cluster these ENM according to their toxicity. This study provides the largest in vivo data set currently available and as such provides valuable information to be utilized in developing predictive models for ENM toxicity.", keywords = "airway exposure, immunotoxicity, nanomaterials, nanoparticles, nanotoxicology, toxicogenomics, transcriptomics, 221 Nano-technology", author = "Kinaret, {Pia A. S.} and Joseph Ndika and Marit Ilves and Henrik Wolff and Gerard Vales and Hannu Norppa and Kai Savolainen and Tiina Skoog and Juha Kere and Sergio Moya and Handy, {Richard D.} and Piia Karisola and Bengt Fadeel and Dario Greco and Harri Alenius", year = "2021", month = may, doi = "10.1002/advs.202004588", language = "English", volume = "8", journal = "Advanced Science", issn = "2198-3844", publisher = "Wiley", number = "10", } . Advanced Science.

Shirin Tavakoli, Otto Kalevi Kari, Tiina Turunen, Tatu Eero Anton Lajunen, Mechthild Schmitt, Julia Lehtinen, Fumitaka Tasaka, Petteri Parkkila, Joseph Dingbobga Tanyi Ndika, Tapani Juhani Samuel Viitala, et al.(2021). Diffusion and Protein Corona Formation of Lipid-Based Nanoparticles in the Vitreous Humor . Molecular Pharmaceutics. 18. (2). p. 699--713. American Chemical Society

ORP2, a cholesterol transporter, regulates angiogenic signaling in endothelial cells @article{4d5725404ce14583857d656ca66bc968, title = "ORP2, a cholesterol transporter, regulates angiogenic signaling in endothelial cells", abstract = "Oxysterol-binding protein-related protein 2 (ORP2), a cholesterol-PI(4,5)P(2)countercurrent transporter, was recently identified as a novel regulator of plasma membrane (PM) cholesterol and PI(4,5)P(2)content in HeLa cells. Here, we investigate the role of ORP2 in endothelial cell (EC) cholesterol and PI(4,5)P(2)distribution, angiogenic signaling, and angiogenesis. We show that ORP2 knock-down modifies the distribution of cholesterol accessible to a D4H probe, between late endosomes and the PM. Depletion of ORP2 from ECs inhibits their angiogenic tube formation capacity, alters the gene expression of angiogenic signaling pathways such as VEGFR2, Akt, mTOR, eNOS, and Notch, and reduces EC migration, proliferation, and cell viability. We show that ORP2 regulates the integrity of VEGFR2 at the PM in a cholesterol-dependent manner, the depletion of ORP2 resulting in proteolytic cleavage by matrix metalloproteinases, and reduced activity of VEGFR2 and its downstream signaling. We demonstrate that ORP2 depletion increases the PM PI(4,5)P(2)coincident with altered F-actin morphology, and reduces both VEGFR2 and cholesterol in buoyant raft membranes. Moreover, ORP2 knock-down suppresses the expression of the lipid raft-associated proteins VE-cadherin and caveolin-1. Analysis of the retinal microvasculature in ORP2 knock-out mice generated during this study demonstrates the subtle alterations of morphology characterized by reduced vessel length and increased density of tip cells and perpendicular sprouts. Gene expression changes in the retina suggest disturbance of sterol homeostasis, downregulation of VE-cadherin, and a putative disturbance of Notch signaling. Our data identifies ORP2 as a novel regulator of EC cholesterol and PI(4,5)P(2)homeostasis and cholesterol-dependent angiogenic signaling.", keywords = "angiogenesis, cholesterol trafficking, Osbpl2, VEGF receptor, OXYSTEROL-BINDING-PROTEIN, GROWTH-FACTOR, VE-CADHERIN, SUPPRESSES ANGIOGENESIS, MAMMALIAN TARGET, UP-REGULATION, LIPID RAFTS, MEMBRANE, RECEPTOR, TRAFFICKING, 3111 Biomedicine, 1182 Biochemistry, cell and molecular biology", author = "Annika Koponen and Guoping Pan and Kivel{\"a}, {Annukka M.} and Arthur Ralko and Taskinen, {Juuso H.} and Amita Arora and Riikka Kosonen and Kari, {Otto K.} and Joseph Ndika and Elina Ikonen and Wonhwa Cho and Daoguang Yan and Olkkonen, {Vesa M.}", year = "2020", month = nov, doi = "10.1096/fj.202000202R", language = "English", volume = "34", pages = "14671--14694", journal = "FASEB Journal", issn = "0892-6638", publisher = "Federation of American Societies for Experimental Biology", number = "11", } . FASEB Journal.

Immune-microbiota interaction in Finnish and Russian Karelia young people with high and low allergy prevalence @article{8c230a173a664fb8bfd794d920fb84b1, title = "Immune-microbiota interaction in Finnish and Russian Karelia young people with high and low allergy prevalence", abstract = "Background After the Second World War, the population living in the Karelian region was strictly divided by the {"}iron curtain{"} between Finland and Russia. This resulted in different lifestyle, standard of living, and exposure to the environment. Allergic manifestations and sensitization to common allergens have been much more common on the Finnish compared to the Russian side. Objective The remarkable allergy disparity in the Finnish and Russian Karelia calls for immunological explanations. Methods Young people, aged 15-20 years, in the Finnish (n = 69) and Russian (n = 75) Karelia were studied. The impact of genetic variation on the phenotype was studied by a genome-wide association analysis. Differences in gene expression (transcriptome) were explored from the blood mononuclear cells (PBMC) and related to skin and nasal epithelium microbiota and sensitization. Results The genotype differences between the Finnish and Russian populations did not explain the allergy gap. The network of gene expression and skin and nasal microbiota was richer and more diverse in the Russian subjects. When the function of 261 differentially expressed genes was explored, innate immunity pathways were suppressed among Russians compared to Finns. Differences in the gene expression paralleled the microbiota disparity. High Acinetobacter abundance in Russians correlated with suppression of innate immune response. High-total IgE was associated with enhanced anti-viral response in the Finnish but not in the Russian subjects. Conclusions and clinical relevance Young populations living in the Finnish and Russian Karelia show marked differences in genome-wide gene expression and host contrasting skin and nasal epithelium microbiota. The rich gene-microbe network in Russians seems to result in a better-balanced innate immunity and associates with low allergy prevalence.", keywords = "environment and hygiene hypothesis, epidemiology, omics- and systems biology, LONG NONCODING RNAS, ASTHMA RISK, HOUSE-DUST, DISEASES, EXPOSURE, 3121 General medicine, internal medicine and other clinical medicine", author = "Lasse Ruokolainen and Nanna Fyhrquist and Tiina Laatikainen and Petri Auvinen and Vittorio Fortino and Giovanni Scala and Pekka Jousilahti and Piia Karisola and Johanna Vendelin and Antti Karkman and Olga Markelova and M{\"a}kel{\"a}, {Mika J.} and Sari Lehtim{\"a}ki and Joseph Ndika and Noora Ottman and Laura Paalanen and Lars Paulin and Erkki Vartiainen and {von Hertzen}, Leena and Dario Greco and Tari Haahtela and Harri Alenius", year = "2020", month = oct, doi = "10.1111/cea.13728", language = "English", volume = "50", pages = "1148--1158", journal = "Clinical and Experimental Allergy", issn = "0954-7894", publisher = "Wiley", number = "10", } . Clinical and Experimental Allergy.

Influence of Cell Membrane Wrapping on the Cell-Porous Silicon Nanoparticle Interactions @article{b6821899c1084dbbb28f55b266679f6f, title = "Influence of Cell Membrane Wrapping on the Cell-Porous Silicon Nanoparticle Interactions", abstract = "Biohybrid nanosystems represent the cutting‐edge research in biofunctionalization of micro‐ and nano‐systems. Their physicochemical properties bring along advantages in the circulation time, camouflaging from the phagocytes, and novel antigens. This is partially a result of the qualitative differences in the protein corona, and the preferential targeting and uptake in homologous cells. However, the effect of the cell membrane on the cellular endocytosis mechanisms and time has not been fully evaluated yet. Here, the effect is assessed by quantitative flow cytometry analysis on the endocytosis of hydrophilic, negatively charged porous silicon nanoparticles and on their membrane‐coated counterparts, in the presence of chemical inhibitors of different uptake pathways. Principal component analysis is used to analyze all the data and extrapolate patterns to highlight the cell‐specific differences in the endocytosis mechanisms. Furthermore, the differences in the composition of static protein corona between naked and coated particles are investigated together with how these differences affect the interaction with human macrophages. Overall, the presence of the cell membrane only influences the speed and the entity of nanoparticles association with the cells, while there is no direct effect on the endocytosis pathways, composition of protein corona, or any reduction in macrophage‐mediated uptake.", keywords = "COATED NANOPARTICLES, DRUG-DELIVERY, IMPACT, VIVO PROTEIN CORONA, biohybrids, cancer cell membranes, nanoparticle uptake, nanoparticles, protein corona, 3111 Biomedicine, 318 Medical biotechnology, 221 Nano-technology", author = "Flavia Fontana and Hanna Lindstedt and Alexandra Correia and Jacopo Chiaro and Otto Kari and Joseph Ndika and Harri Alenius and Jonas Buck and Sandro Sieber and Ermei M{\"a}kil{\"a} and Jarno Salonen and Arto Urtti and Vincenzo Cerullo and Jouni Hirvonen and Santos, {H{\'e}lder A.}", year = "2020", month = sep, day = "9", doi = "10.1002/adhm.202000529", language = "English", volume = "9", journal = "Advanced Healthcare Materials", issn = "2192-2640", publisher = "Wiley", number = "17", } . Advanced Healthcare Materials.

Front cover - Cell Membrane Wrapping: Influence of Cell Membrane Wrapping on the Cell−Porous Silicon Nanoparticle Interactions (Adv. Healthcare Mater. 17/2020) @article{f7ea7fbb8f594f0e9ca71bea1fc2f649, title = "Front cover - Cell Membrane Wrapping: Influence of Cell Membrane Wrapping on the Cell−Porous Silicon Nanoparticle Interactions (Adv. Healthcare Mater. 17/2020)", abstract = "Biohybrid nanosystems represent the cutting‐edge research in biofunctionalization of micro‐ and nano‐systems. Their physicochemical properties bring along advantages in the circulation time, camouflaging from the phagocytes, and novel antigens. This is partially a result of the qualitative differences in the protein corona, and the preferential targeting and uptake in homologous cells. However, the effect of the cell membrane on the cellular endocytosis mechanisms and time has not been fully evaluated yet. Here, the effect is assessed by quantitative flow cytometry analysis on the endocytosis of hydrophilic, negatively charged porous silicon nanoparticles and on their membrane‐coated counterparts, in the presence of chemical inhibitors of different uptake pathways. Principal component analysis is used to analyze all the data and extrapolate patterns to highlight the cell‐specific differences in the endocytosis mechanisms. Furthermore, the differences in the composition of static protein corona between naked and coated particles are investigated together with how these differences affect the interaction with human macrophages. Overall, the presence of the cell membrane only influences the speed and the entity of nanoparticles association with the cells, while there is no direct effect on the endocytosis pathways, composition of protein corona, or any reduction in macrophage‐mediated uptake.", keywords = "COATED NANOPARTICLES, DRUG-DELIVERY, IMPACT, VIVO PROTEIN CORONA, biohybrids, cancer cell membranes, nanoparticle uptake, nanoparticles, protein corona, 3111 Biomedicine, 318 Medical biotechnology, 221 Nano-technology", author = "Flavia Fontana and Hanna Lindstedt and Alexandra Correia and Jacopo Chiaro and Otto Kari and Joseph Ndika and Harri Alenius and Jonas Buck and Sandro Sieber and Ermei M{\"a}kil{\"a} and Jarno Salonen and Arto Urtti and Vincenzo Cerullo and Jouni Hirvonen and Santos, {H{\'e}lder A.}", year = "2020", month = sep, day = "9", doi = "10.1002/adhm.202070056", language = "English", volume = "9", journal = "Advanced Healthcare Materials", issn = "2192-2640", publisher = "Wiley", number = "17", } . Advanced Healthcare Materials.

Mechanistic Similarities between 3D Human Bronchial Epithelium and Mice Lung, Exposed to Copper Oxide Nanoparticles, Support Non-Animal Methods for Hazard Assessment @article{aeb5372075574a159d5b84ea0aad19aa, title = "Mechanistic Similarities between 3D Human Bronchial Epithelium and Mice Lung, Exposed to Copper Oxide Nanoparticles, Support Non-Animal Methods for Hazard Assessment", abstract = "The diversity and increasing prevalence of products derived from engineered nanomaterials (ENM), warrants implementation of non-animal approaches to health hazard assessment for ethical and practical reasons. Although non-animal approaches are becoming increasingly popular, there are almost no studies of side-by-side comparisons with traditional in vivo assays. Here, transcriptomics is used to investigate mechanistic similarities between healthy/asthmatic models of 3D air-liquid interface (ALI) cultures of donor-derived human bronchial epithelia cells, and mouse lung tissue, following exposure to copper oxide ENM. Only 19% of mouse lung genes with human orthologues are not expressed in the human 3D ALI model. Despite differences in taxonomy and cellular complexity between the systems, a core subset of matching genes cluster mouse and human samples strictly based on ENM dose (exposure severity). Overlapping gene orthologue pairs are highly enriched for innate immune functions, suggesting an important and maybe underestimated role of epithelial cells. In conclusion, 3D ALI models based on epithelial cells, are primed to bridge the gap between traditional 2D in vitro assays and animal models of airway exposure, and transcriptomics appears to be a unifying dose metric that links in vivo and in vitro test systems.", keywords = "air-liquid interface, copper oxide nanoparticles, mouse versus human, nanosafety, non-animal, transcriptomics, GENE-EXPRESSION, QUANTUM DOTS, TOXICITY, CELLS, RESPONSES, PATHWAYS, INNATE, 1182 Biochemistry, cell and molecular biology, 221 Nano-technology, 1184 Genetics, developmental biology, physiology", author = "Joseph Ndika and Marit Ilves and Kooter, {Ingeborg M.} and Mariska Gr{\"o}llers-Mulderij and Evert Duistermaat and Tromp, {Peter C.} and Frieke Kuper and Pia Kinaret and Dario Greco and Piia Karisola and Harri Alenius", year = "2020", month = sep, doi = "10.1002/smll.202000527", language = "English", volume = "16", journal = "Small", issn = "1613-6810", publisher = "Wiley-VCH", number = "36", } . Small.

Light-Activated Liposomes Coated with Hyaluronic Acid as a Potential Drug Delivery System @article{8a18d148c7c7413d86ec181151a5c8a6, title = "Light-Activated Liposomes Coated with Hyaluronic Acid as a Potential Drug Delivery System", abstract = "Light-activated liposomes permit site and time-specific drug delivery to ocular and systemic targets. We combined a light activation technology based on indocyanine green with a hyaluronic acid (HA) coating by synthesizing HA-lipid conjugates. HA is an endogenous vitreal polysaccharide and a potential targeting moiety to cluster of differentiation 44 (CD44)-expressing cells. Light-activated drug release from 100 nm HA-coated liposomes was functional in buffer, plasma, and vitreous samples. The HA-coating improved stability in plasma compared to polyethylene glycol (PEG)-coated liposomes. Liposomal protein coronas on HA- and PEG-coated liposomes after dynamic exposure to undiluted human plasma and porcine vitreous samples were hydrophilic and negatively charged, thicker in plasma (similar to 5 nm hard, similar to 10 nm soft coronas) than in vitreous (similar to 2 nm hard, similar to 3 nm soft coronas) samples. Their compositions were dependent on liposome formulation and surface charge in plasma but not in vitreous samples. Compared to the PEG coating, the HA-coated liposomes bound more proteins in vitreous samples and enriched proteins related to collagen interactions, possibly explaining their slightly reduced vitreal mobility. The properties of the most abundant proteins did not correlate with liposome size or charge, but included proteins with surfactant and immune system functions in plasma and vitreous samples. The HA-coated light-activated liposomes are a functional and promising alternative for intravenous and ocular drug delivery.", keywords = "317 Pharmacy, hyaluronic acid, liposome, drug release, light activation, stability, mobility, biocorona, INDOCYANINE GREEN, BIOMOLECULAR CORONA, BIOLOGICAL IDENTITY, PROTEIN CORONA, PEG, NANOPARTICLES, DIFFUSION, HYDROGELS, KINETICS, BINDING, hyaluronic acid, liposome, drug release, light activation, stability, mobility, biocorona, INDOCYANINE GREEN, BIOMOLECULAR CORONA, BIOLOGICAL IDENTITY, PROTEIN CORONA, PEG, NANOPARTICLES, DIFFUSION, HYDROGELS, KINETICS, BINDING", author = "Kari, {Otto K.} and Shirin Tavakoli and Petteri Parkkila and Simone Baan and Roosa Savolainen and Teemu Ruoslahti and Johansson, {Niklas G.} and Joseph Ndika and Harri Alenius and Tapani Viitala and Arto Urtti and Tatu Lajunen", year = "2020", month = aug, day = "12", doi = "10.3390/pharmaceutics12080763", language = "English", volume = "12", journal = "Pharmaceutics", issn = "1999-4923", publisher = "MDPI", number = "8", } . Pharmaceutics.

Otto Kalevi Kari, Shirin Tavakoli, Petteri Parkkila, Simone Baan, Roosa Savolainen, Teemu Ruoslahti, Niklas G Johansson, Joseph Dingbobga Tanyi Ndika, Harri Alenius, Tapani Juhani Samuel Viitala, et al. (2020). Light-Activated Liposomes Coated with Hyaluronic Acid as a Potential Drug Delivery System . Pharmaceutics.

In situ analysis of liposome hard and soft protein corona structure and composition in a single label-free workflow @article{fb56b432a8714803a74d1e63fb5a311e, title = "In situ analysis of liposome hard and soft protein corona structure and composition in a single label-free workflow", abstract = "Methodological constraints have limited our ability to study protein corona formation, slowing nanomedicine development and their successful translation into the clinic. We determined hard and soft corona structural properties along with the corresponding proteomic compositions on liposomes in a label-free workflow: surface plasmon resonance and a custom biosensor for in situ structure determination on liposomes and corona separation, and proteomics using sensitive nanoliquid chromatography tandem mass spectrometry with open-source bioinformatics platforms. Undiluted human plasma under dynamic flow conditions was used for in vivo relevance. Proof-of-concept is presented with a regular liposome formulation and two light-triggered indocyanine green (ICG) liposome formulations in preclinical development. We observed formulation-dependent differences in corona structure (thickness, protein-to-lipid ratio, and surface mass density) and protein enrichment. Liposomal lipids induced the enrichment of stealth-mediating apolipoproteins in the hard coronas regardless of pegylation, and their preferential enrichment in the soft corona of the pegylated liposome formulation with ICG was observed. This suggests that the soft corona of loosely interacting proteins contributes to the stealth properties as a component of the biological identity modulated by nanomaterial surface properties. The workflow addresses significant methodological gaps in biocorona research by providing truly complementary hard and soft corona compositions with corresponding in situ structural parameters for the first time. It has been designed into a convenient and easily reproducible single-experiment format suited for preclinical development of lipid nanomedicines.", keywords = "318 Medical biotechnology, PLASMON RESONANCE SENSORS, PEG CHAIN-LENGTH, BIOMOLECULAR CORONA, COMPLEMENT ACTIVATION, BIOLOGICAL IDENTITY, TIME-EVOLUTION, NANOPARTICLES, SURFACE, VIVO, ADSORPTION, PLASMON RESONANCE SENSORS, PEG CHAIN-LENGTH, BIOMOLECULAR CORONA, COMPLEMENT ACTIVATION, BIOLOGICAL IDENTITY, TIME-EVOLUTION, NANOPARTICLES, SURFACE, VIVO, ADSORPTION", author = "Kari, {Otto K.} and Joseph Ndika and Petteri Parkkila and Antti Louna and Tatu Lajunen and Anne Puustinen and Tapani Viitala and Harri Alenius and Arto Urtti", year = "2020", month = jan, day = "21", doi = "10.1039/C9NR08186K", language = "English", volume = "12", pages = "1728--1741", journal = "Nanoscale", issn = "2040-3364", publisher = "Royal Society of Chemistry", number = "3", } . Nanoscale.

Artificially Cloaked Viral Nanovaccine for Cancer Immunotherapy @article{a47d935604ba48d3bc82680520378026, title = "Artificially Cloaked Viral Nanovaccine for Cancer Immunotherapy", abstract = "Virus-based cancer vaccines are nowadays considered an interesting approach in the field of cancer immunotherapy, despite the observation that the majority of the immune responses they elicit are against the virus and not against the tumor. In contrast, targeting tumor associated antigens is effective, however the identification of these antigens remains challenging. Here, we describe ExtraCRAd, a multi-vaccination strategy focused on an oncolytic virus artificially wrapped with tumor cancer membranes carrying tumor antigens. We demonstrate that ExtraCRAd displays increased infectivity and oncolytic effect in vitro and in vivo. We show that this nanoparticle platform controls the growth of aggressive melanoma and lung tumors in vivo both in preventive and therapeutic setting, creating a highly specific anti-cancer immune response. In conclusion, ExtraCRAd might serve as the next generation of personalized cancer vaccines with enhanced features over standard vaccination regimens, representing an alternative way to target cancer.", keywords = "ADENOVIRUS, ANTIGEN, CO-DELIVERY, GENE-TRANSFER, IN-VIVO, NANOPARTICLES, OVARIAN-CANCER, SOLID TUMORS, T-CELL THERAPY, VACCINATION, immunotherapy, biohybrid nanoparticles, oncolytic vaccines, oncolytic virus, oncoimmunology, 317 Pharmacy, 318 Medical biotechnology", author = "Manlio Fusciello and Flavia Fontana and Siri T{\"a}htinen and Cristian Capasso and Sara Feola and {da Silva Lopes Martins}, Beatriz and Jacopo Chiaro and Karita Peltonen and Leena Yl{\"o}sm{\"a}ki and Erkko Yl{\"o}sm{\"a}ki and {Hamdan Hissaoui}, Firas and Kari, {Otto K.} and Joseph Ndika and Harri Alenius and Arto Urtti and Hirvonen, {Jouni T.} and Santos, {H{\'e}lder A.} and Vincenzo Cerullo", year = "2019", month = dec, day = "17", doi = "10.1038/s41467-019-13744-8", language = "English", volume = "10", journal = "Nature Communications", issn = "2041-1723", publisher = "Nature Publishing Group", } . Nature Communications.

Silver, titanium dioxide, and zinc oxide nanoparticles trigger miRNA/isomiR expression changes in THP-1 cells that are proportional to their health hazard potential @article{e2389b856139479f969710f0dd44575f, title = "Silver, titanium dioxide, and zinc oxide nanoparticles trigger miRNA/isomiR expression changes in THP-1 cells that are proportional to their health hazard potential", abstract = "After over a decade of nanosafety research, it is indisputable that the vast majority of nano-sized particles induce a plethora of adverse cellular responses - the severity of which is linked to the material's physicochemical properties. Differentiated THP-1 cells were previously exposed for 6 h and 24 h to silver, titanium dioxide, and zinc oxide nanoparticles at the maximum molar concentration at which no more than 15% cellular cytotoxicity was observed. All three nanoparticles differed in extent of induction of biological pathways corresponding to immune response signaling and metal ion homeostasis. In this study, we integrated gene and miRNA expression profiles from the same cells to propose miRNA biomarkers of adverse exposure to metal-based nanoparticles. We employed RNA sequencing together with a quantitative strategy that also enables analysis of the overlooked repertoire of length and sequence miRNA variants called isomiRs. Whilst only modest changes in expression were observed within the first 6 h of exposure, the miRNA/isomiR (miR) profiles of each nanoparticle were unique. Via canonical correlation and pathway enrichment analyses, we identified a co-regulated miR-mRNA cluster, predicted to be highly relevant for cellular response to metal ion homeostasis. These miRs were annotated to be canonical or variant isoforms of hsa-miR-142-5p, -342-3p, -5100, -6087, -6894-3p, and -7704. Hsa-miR-5100 was differentially expressed in response to each nanoparticle in both the 6 h and 24 h exposures. Taken together, this co-regulated miR-mRNA cluster could represent potential biomarkers of sub-toxic metal-based nanoparticle exposure.", keywords = "Metal-based nanoparticle, bio-nano reactivity, miRNA, isomiR, MIR-142-3P FUNCTIONS, TUMOR-SUPPRESSOR, RISK-ASSESSMENT, MICRORNAS, NANOMATERIALS, MECHANISM, PATHWAYS, TOOLS, 3111 Biomedicine, 1182 Biochemistry, cell and molecular biology", author = "Joseph Ndika and Umair Seemab and Wing-Lam Poon and Vittorio Fortino and Hani El-Nezami and Piia Karisola and Harri Alenius", year = "2019", month = nov, day = "26", doi = "10.1080/17435390.2019.1661040", language = "English", volume = "13", pages = "1380--1395", journal = "Nanotoxicology", issn = "1743-5390", publisher = "Taylor & Francis", number = "10", } . Nanotoxicology.

Surface PEGylation suppresses pulmonary effects of CuO in allergen-induced lung inflammation @article{65729ed2067f4daba877f419b40ca454, title = "Surface PEGylation suppresses pulmonary effects of CuO in allergen-induced lung inflammation", abstract = "BackgroundCopper oxide (CuO) nanomaterials are used in a wide range of industrial and commercial applications. These materials can be hazardous, especially if they are inhaled. As a result, the pulmonary effects of CuO nanomaterials have been studied in healthy subjects but limited knowledge exists today about their effects on lungs with allergic airway inflammation (AAI). The objective of this study was to investigate how pristine CuO modulates allergic lung inflammation and whether surface modifications can influence its reactivity.CuO and its carboxylated (CuO COOH), methylaminated (CuO NH3) and PEGylated (CuO PEG) derivatives were administered here on four consecutive days via oropharyngeal aspiration in a mouse model of AAI. Standard genome-wide gene expression profiling as well as conventional histopathological and immunological methods were used to investigate the modulatory effects of the nanomaterials on both healthy and compromised immune system.ResultsOur data demonstrates that although CuO materials did not considerably influence hallmarks of allergic airway inflammation, the materials exacerbated the existing lung inflammation by eliciting dramatic pulmonary neutrophilia. Transcriptomic analysis showed that CuO, CuO COOH and CuO NH3 commonly enriched neutrophil-related biological processes, especially in healthy mice. In sharp contrast, CuO PEG had a significantly lower potential in triggering changes in lungs of healthy and allergic mice revealing that surface PEGylation suppresses the effects triggered by the pristine material.ConclusionsCuO as well as its functionalized forms worsen allergic airway inflammation by causing neutrophilia in the lungs, however, our results also show that surface PEGylation can be a promising approach for inhibiting the effects of pristine CuO. Our study provides information for health and safety assessment of modified CuO materials, and it can be useful in the development of nanomedical applications.", keywords = "CuO, Engineered nanomaterial, Health effects, Inflammation, Asthma, Allergic airway inflammation, Risk assessment, COPPER-OXIDE NANOPARTICLES, WALLED CARBON NANOTUBES, EPITHELIAL-CELLS, AIRWAY INFLAMMATION, INHALATION EXPOSURE, GENE-EXPRESSION, TOXICITY, ASTHMA, NANOMATERIALS, PARTICLES, 3111 Biomedicine", author = "Marit Ilves and Kinaret, {Pia Anneli Sofia} and Joseph Ndika and Piia Karisola and Veer Marwah and Vittorio Fortino and Yuri Fedutik and Manuel Correia and Nicky Ehrlich and Katrin Loeschner and Alexandros Besinis and Joanne Vassallo and Handy, {Richard D.} and Henrik Wolff and Kai Savolainen and Dario Greco and Harri Alenius", year = "2019", month = jul, day = "5", doi = "10.1186/s12989-019-0309-1", language = "English", volume = "16", journal = "Particle and Fibre Toxicology", issn = "1743-8977", publisher = "BMC", } . Particle and Fibre Toxicology.

Ilves M, Kinaret PAS, Ndika J, Karisola P, Marwah V, Fortino V, Fedutik Y, Correia M, Ehrlich N, Loeschner K, et al.(2019). Surface PEGylation suppresses pulmonary effects of CuO in allergen-induced lung inflammation . Particle and fibre toxicology.

(2019). Molecular Signature of Asthma-Enhanced Sensitivity to CuO Nanoparticle Aerosols from 3D Cell Model . ACS Nano.

Molecular Signature of Asthma-Enhanced Sensitivity to CuO Nanoparticle Aerosols from 3D Cell Model @article{f27278380a694b90bf53090f0053cd89, title = "Molecular Signature of Asthma-Enhanced Sensitivity to CuO Nanoparticle Aerosols from 3D Cell Model", abstract = "More than 5% of any population suffers from asthma, and there are indications that these individuals are more sensitive to nanoparticle aerosols than the healthy population. We used an air-liquid interface model of inhalation exposure to investigate global transcriptomic responses in reconstituted three-dimensional airway epithelia of healthy and asthmatic subjects exposed to pristine (nCuO) and carboxylated (nCuO(COOH)) copper oxide nanoparticle aerosols. A dose-dependent increase in cytotoxicity (highest in asthmatic donor cells) and pro-inflammatory signaling within 24 h confirmed the reliability and sensitivity of the system to detect acute inhalation toxicity. Gene expression changes between nanoparticle-exposed versus air-exposed cells were investigated. Hierarchical clustering based on the expression profiles of all differentially expressed genes (DEGs), cell-death-associated DEGs (567 genes), or a subset of 48 highly overlapping DEGs categorized all samples according to {"}exposure severity{"}, wherein nanoparticle surface chemistry and asthma are incorporated into the dose-response axis. For example, asthmatics exposed to low and medium dose nCuO clustered with healthy donor cells exposed to medium and high dose nCuO, respectively. Of note, a set of genes with high relevance to mucociliary clearance were observed to distinctly differentiate asthmatic and healthy donor cells. These genes also responded differently to nCuO and nCuO(COOH) nanoparticles. Additionally, because response to transition-metal nanoparticles was a highly enriched Gene Ontology term (FDR 8 X 10(-13)) from the subset of 48 highly overlapping DEGs, these genes may represent biomarkers to a potentially large variety of metal/metal oxide nanoparticles.", keywords = "copper(II) oxide, nanoparticles, asthma, 3d human bronchial epithelial cells, air-liquid interface and transcriptomics, AIR-LIQUID INTERFACE, THYMIC STROMAL LYMPHOPOIETIN, OXIDE NANOPARTICLES, EPITHELIAL-CELLS, MUCOCILIARY CLEARANCE, OXIDATIVE STRESS, GENE-EXPRESSION, QUANTUM DOTS, ZINC-OXIDE, DEPOSITION, 1182 Biochemistry, cell and molecular biology", author = "Ingeborg Kooter and Marit Ilves and Mariska Grollers-Mulderij and Evert Duistermaat and Tromp, {Peter C.} and Frieke Kuper and Pia Kinaret and Kai Savolainen and Dario Greco and Piia Karisola and Joseph Ndika and Harri Alenius", year = "2019", month = jun, doi = "10.1021/acsnano.9b01823", language = "English", volume = "13", pages = "6932--6946", journal = "ACS Nano", issn = "1936-0851", publisher = "American Chemical Society", number = "6", } . ACS Nano.

Nasal mucosa and blood cell transcriptome profiles do not reflect respiratory symptoms associated with moisture damage @article{d399bf4e11ce47fdb94a34fd7ec36c4f, title = "Nasal mucosa and blood cell transcriptome profiles do not reflect respiratory symptoms associated with moisture damage", abstract = "Upper and lower respiratory symptoms and asthma are adverse health effects associated with moisture-damaged buildings. Quantitative measures to detect adverse health effects related to exposure to dampness and mold are needed. Here, we investigate differences in gene expression between occupants of moisture-damaged and reference buildings. Moisture-damaged (N=11) and control (N=5) buildings were evaluated for dampness and mold by trained inspectors. The transcriptomics cohort consisted of nasal brushings and peripheral blood mononuclear cells (PBMCs) from 86 teachers, with/without self-perceived respiratory symptoms. Subject categories comprised reference (R) and damaged (D) buildings with (S) or without (NS) symptoms, that is, R-S, R-NS, DS, and D-NS. Component analyses and k-means clustering of transcriptome profiles did not distinguish building status (R/D) or presence of respiratory symptoms (S/NS). Only one nasal mucosa gene (YBX3P1) exhibited a significant change in expression between D-S and D-NS. Nine other nasal mucosa genes were differentially expressed between R-S and D-S teachers. No differentially expressed genes were identified in PBMCs. We conclude that the observed mRNA differences provide very weak biological evidence for adverse health effects associated with subject occupancy of the specified moisture-damaged buildings. This emphasizes the need to evaluate all potential factors (including those not related to toxicity) influencing perceived/self-reported ill health in moisture-damaged buildings.", keywords = "exposure biomarkers, moisture-damaged buildings, respiratory symptoms, transcriptomics, ALLERGIC RHINITIS, DEFENSE, 3142 Public health care science, environmental and occupational health", author = "J. Ndika and H. Suojalehto and M. Taubel and M. Lehto and K. Karvala and P. Pallasaho and J. Sund and P. Auvinen and K. J{\"a}rvi and J. Pekkanen and P. Kinaret and D. Greco and A. Hyv{\"a}rinen and H. Alenius", year = "2018", month = sep, doi = "10.1111/ina.12472", language = "English", volume = "28", pages = "721--731", journal = "Indoor Air", issn = "0905-6947", publisher = "Wiley", number = "5", } . Indoor Air.

Elucidating differential nano-bio interactions of multi-walled andsingle-walled carbon nanotubes using subcellular proteomics @article{abb2a194c8884120962967e0c8c01cd9, title = "Elucidating differential nano-bio interactions of multi-walled andsingle-walled carbon nanotubes using subcellular proteomics", abstract = "Understanding the relationship between adverse exposure events and specific material properties will facilitate predictive classification of carbon nanotubes (CNTs) according to their mechanisms of action, and a safe-by-design approach for the next generation of CNTs. Mass-spectrometry-based proteomics is a reliable tool to uncover the molecular dynamics of hazardous exposures, yet challenges persist with regards to its limited dynamic range when sampling whole organisms, tissues or cell lysates. Here, the simplicity of the sub-cellular proteome was harnessed to unravel distinctive adverse exposure outcomes at the molecular level, between two CNT subtypes. A549, MRC9 and human macrophage cells, were exposed for 24h to non-cytotoxic doses of single-walled or multi-walled CNTs (swCNTs or mwCNTs). Label-free proteomics on enriched cytoplasmic fractions was complemented with analyses of reactive oxygen species (ROS) production and mitochondrial integrity. The extent/number of modulated proteoforms indicated the single-walled variant was more bioactive. Greater enrichment of pathways corresponding to oxido-reductive activity was consistent with greater intracellular ROS induction and mitochondrial dysfunction capacities of swCNTs. Other compromised cellular functions, as revealed by pathway analysis were; ribosome, spliceosome and DNA repair. Highly upregulated proteins (fold change in abundance >6) such as, APOC3, RBP4 and INS are also highlighted as potential markers of hazardous CNT exposure. We conclude that, changes in cytosolic proteome abundance resulting from nano-bio interactions, elucidate adverse response pathways and their distinctive molecular components. Our results indicate that CNT-protein interactions might have a thus far unappreciated significance for protein trafficking, and this warrants further investigation.", keywords = "3111 Biomedicine", author = "Ndika, {Joseph Dingbobga Tanyi} and Jukka Sund and Harri Alenius and Anne Puustinen", year = "2018", month = apr, day = "24", doi = "10.1080/17435390.2018.1465141", language = "English", volume = "12", pages = "554--570", journal = "Nanotoxicology", issn = "1743-5390", publisher = "Taylor & Francis", number = "6", } . Nanotoxicology.

Joseph D. T. Ndika and Jukka Sund and Harri Alenius and Anne Puustinen(2018). Elucidating differential nano-bio interactions of multi-walled andsingle-walled carbon nanotubes using subcellular proteomics . Nanotoxicology. 0. (0). p. 1-17. Taylor & Francis

Epithelial proteome profiling suggests the essential role of interferon-inducible proteins in patients with allergic rhinitis @article{4dd1950e16c54eb9b4be4292c45fd863, title = "Epithelial proteome profiling suggests the essential role of interferon-inducible proteins in patients with allergic rhinitis", abstract = "Background: Seasonal allergic rhinitis (SAR) caused by intermittent exposure to seasonal pollen causes itching, nasal congestion, and repeated sneezing, with profound effects on quality of life, work productivity, and school performance. Although both the genotype and environmental factors can contribute to the immunologic basis of allergic reactions, the molecular underpinnings associated with the pathogenesis of allergic rhinitis are not entirely clear.Methods: To address these questions, nasal epithelial brushings were collected from 29 patients with SAR and 31 control subjects during and after the pollen season. We then implemented an orbitrap-based, bottom-up, label-free quantitative proteomics approach, followed by multivariate analyses to identify differentially abundant (DA) proteins among the 4 sample groups.Results: We identified a total of 133 DA proteins for which the most significantly overrepresented functional category was found to be interferon 1 signaling. Two proteins, cystatin 1 and myeloblastin, the former of which protects against protease activity of allergens and the latter with a role in epithelial barrier function, were DA in patients with SAR and control subjects, irrespective of season. Moreover, interferon-inducible protein with tetratricopeptide repeats 1, cystatin 1, and interferon-inducible protein with tetratricopeptide repeats 3 were found to be differentially regulated between patients with SAR and control subjects, with inverse abundance dynamics during the transition from fall to spring.Conclusion: We identified type 1 interferon-regulated proteins as biomarkers in patients with SAR, potentially playing an important role in its pathogenesis. Moreover, when compared with patients with SAR, healthy subjects exhibit an antagonistic proteomic response across seasons, which might prove to be a therapeutic target for disease prevention.", keywords = "Seasonal allergic rhinitis, nasal epithelia, proteomics, interferon 1 signaling, biomarkers, NASAL MUCUS, BARRIER FUNCTION, ASTHMA, IMPACT, QUANTIFICATION, SENSITIZATION, GENETICS, DISEASES, 3121 General medicine, internal medicine and other clinical medicine", author = "Joseph Ndika and Liisa Airaksinen and Hille Suojalehto and Piia Karisola and Nanna Fyhrquist and Anne Puustinen and Harri Alenius", year = "2017", month = nov, doi = "10.1016/j.jaci.2017.05.040", language = "English", volume = "140", pages = "1288--1298", journal = "Journal of Allergy and Clinical Immunology", issn = "0091-6749", publisher = "Mosby Elsevier", number = "5", } . Journal of Allergy and Clinical Immunology.

et al.(2017). Nano-sized zinc oxide and silver, but not titanium dioxide, induce innate and adaptive immunity and antiviral response in differentiated THP-1 cells . Nanotoxicology.

(2017). Epithelial proteome profiling suggests the essential role of interferon-inducible proteins in patients with allergic rhinitis . The Journal of allergy and clinical immunology.

W. L. Poon, Harri Alenius, Joseph Dingbobga Tanyi Ndika, Vittorio Fortino, Vesa Kolhinen, Arunas Mesceriakovas, Mingfu Wang, Dario Greco, Anna Lähde, Jorma Jokiniemi, et al.(2017). Nano-sized zinc oxide and silver, but not titanium dioxide, induce innate and adaptive immunity and antiviral response in differentiated THP-1 cells . Nanotoxicology. 11. (7). p. 936--951. Taylor & Francis

(2014). RNA sequencing of creatine transporter (SLC6A8) deficient fibroblasts reveals impairment of the extracellular matrix . Human mutation.

RNA Sequencing of Creatine Transporter (SLC6A8) Deficient Fibroblasts Reveals Impairment of the Extracellular Matrix @article{706724d2eb1143d69d88ead0f1c31f23, title = "RNA Sequencing of Creatine Transporter (SLC6A8) Deficient Fibroblasts Reveals Impairment of the Extracellular Matrix", abstract = "Creatine transporter (SLC6A8) deficiency is the most common cause of cerebral creatine syndromes, and is characterized by depletion of creatine in the brain. Manifestations of this X-linked disorder include intellectual disability, speech/language impairment, behavior abnormalities, and seizures. At the moment, no effective treatment is available. In order to investigate the molecular pathophysiology of this disorder, we performed RNA sequencing on fibroblasts derived from patients. The transcriptomes of fibroblast cells from eight unrelated individuals with SLC6A8 deficiency and three wild-type controls were sequenced. SLC6A8 mutations with different effects on the protein product resulted in different gene expression profiles. Differential gene expression analysis followed by gene ontology term enrichment analysis revealed that especially the expression of genes encoding components of the extracellular matrix and cytoskeleton are altered in SLC6A8 deficiency, such as collagens, keratins, integrins, and cadherins. This suggests an important novel role for creatine in the structural development and maintenance of cells. It is likely that the (extracellular) structure of brain cells is also impaired in SLC6A8-deficient patients, and future studies are necessary to confirm this and to reveal the true functions of creatine in the brain. (C) 2014 Wiley Periodicals, Inc.", keywords = "creatine, extracellular matrix, RNA-seq, epilepsy, SLC6A8, GUANIDINOACETATE METHYLTRANSFERASE DEFICIENCY, GENE-EXPRESSION DATA, INBORN ERROR, SYNAPTIC PLASTICITY, MENTAL-RETARDATION, SEQ, METABOLISM, ONTOLOGY, SYSTEM, CELLS, 3111 Biomedicine", author = "Benjamin Nota and Ndika, {Joseph D. T.} and {van de Kamp}, {Jiddeke M.} and Kanhai, {Warsha A.} and {van Dooren}, {Silvy J. M.} and {van de Wiel}, {Mark A.} and Gerard Pals and Salomons, {Gajja S.}", year = "2014", month = sep, doi = "10.1002/humu.22609", language = "English", volume = "35", pages = "1128--1135", journal = "Human Mutation", issn = "1059-7794", publisher = "John Wiley & Sons, Ltd", number = "9", } . Human Mutation.

Post-transcriptional regulation of the creatine transporter gene @article{fe540dad1a7443b2b59eb3a2e38c6a1b, title = "Post-transcriptional regulation of the creatine transporter gene: Functional relevance of alternative splicing", abstract = "Background: Aberrations in about 10-15% of X-chromosome genes account for intellectual disability (ID); with a prevalence of 1-3% (Gecz et al., 2009 [1]). The SLC6A8 gene, mapped to Xq28, encodes the creatine transporter (CTR1). Mutations in SLC6A8, and the ensuing decrease in brain creatine, lead to co-occurrence of speech/language delay, autism-like behaviors and epilepsy with ID. A splice variant of SLC6A8-SLC6A8C, containing intron 4 and exons 5-13, was identified. Herein, we report the identification of a novel variant SLC6A8D, and functional relevance of these isoforms.Methods: Via (quantitative) RT-PCR, uptake assays, and confocal microscopy, we investigated their expression and function vis-a-vis creatine transport.Results: SLC6A8D is homologous to SLC6A8C except for a deletion of exon 9 (without occurrence of a frame shift). Both contain an open reading frame encoding a truncated protein but otherwise identical to CTR1. Like SLC6A8, both variants are predominantly expressed in tissues with high energy requirement. Our experiments reveal that these truncated isoforms do not transport creatine. However, in SLC6A8 (CTR1)-overexpressing cells, a subsequent infection (transduction) with viral constructs encoding either the SLC6A8C (CTR4) or SLC6A8D (CfR5) isoform resulted in a significant increase in creatine accumulation compared to C1'R1 cells re-infected with viral constructs containing the empty vector. Moreover, transient transfection of CTR4 or C1'R5 into HEK293 cells resulted in significantly higher creatine uptake.Conclusions: CTR4 and CTR5 are possible regulators of the creatine transporter since their overexpression results in upregulated CTR1 protein and creatine uptake.General significance: Provides added insight into the mechanism(s) of creatine transport regulation. (c) 2014 Elsevier B.V. All rights reserved.", keywords = "Na+ /Cl- cotransporter, Creatine transporter, Alternative splicing, Creatine uptake upregulation, Intellectual disability, UBIQUITIN LIGASE NEDD4-2, EPITHELIAL NA+ CHANNEL, NEUROTRANSMITTER TRANSPORTERS, MESSENGER-RNA, INBORN ERROR, KINASES SGK1, SERUM, RAT, SUPPLEMENTATION, DEFICIENCY", author = "Ndika, {Joseph D. T.} and Cristina Martinez-Munoz and Nandaja Anand and {van Dooren}, {Silvy J. M.} and Warsha Kanhai and Smith, {Desiree E. C.} and Cornelis Jakobs and Salomons, {Gajja S.}", year = "2014", month = jun, doi = "10.1016/j.bbagen.2014.02.012", language = "English", volume = "1840", pages = "2070--2079", journal = "Biochimica et Biophysica Acta. General Subjects", issn = "0304-4165", publisher = "Elsevier Scientific Publ. Co", number = "6", } . Biochimica et Biophysica Acta. General Subjects.

(2014). Post-transcriptional regulation of the creatine transporter gene: functional relevance of alternative splicing . Biochimica et biophysica acta.

et al.(2014). Thirteen new patients with guanidinoacetate methyltransferase deficiency and functional characterization of nineteen novel missense variants in the GAMT gene . Human mutation.

Thirteen New Patients with Guanidinoacetate Methyltransferase Deficiency and Functional Characterization of Nineteen Novel Missense Variants in the GAMT Gene @article{2d319d1d5e564e14a0b02616f230749d, title = "Thirteen New Patients with Guanidinoacetate Methyltransferase Deficiency and Functional Characterization of Nineteen Novel Missense Variants in the GAMT Gene", abstract = "Guanidinoacetate methyltransferase deficiency (GAMT-D) is an autosomal recessively inherited disorder of creatine biosynthesis. Creatine deficiency on cranial proton magnetic resonance spectroscopy, and elevated guanidinoacetate levels in body fluids are the biomarkers of GAMT-D. In 74 patients, 50 different mutations in the GAMT gene have been identified with missense variants being the most common. Clinical and biochemical features of the patients with missense variants were obtained from their physicians using a questionnaire. In 20 patients, 17 missense variants, 25% had a severe, 55% a moderate, and 20% a mild phenotype. The effect of these variants on GAMT enzyme activity was overexpressed using primary GAMT-D fibroblasts: 17 variants retained no significant activity and are therefore considered pathogenic. Two additional variants, c.22C>A (p.Pro8Thr) and c.79T>C (p.Tyr27His) (the latter detected in control cohorts) are in fact not pathogenic as these alleles restored GAMT enzyme activity, although both were predicted to be possibly damaging by in silico analysis. We report 13 new patients with GAMT-D, six novel mutations and functional analysis of 19 missense variants, all being included in our public LOVD database. Our functional assay is important for the confirmation of the pathogenicity of identified missense variants in the GAMT gene.", keywords = "GAMT, GAMT-D, site-directed mutagenesis, missense variants, INBORN ERROR, MENTAL-RETARDATION, RAT-LIVER, CREATINE, METABOLISM, FEATURES, IMPACT, ENZYME, BRAIN", author = "Saadet Mercimek-Mahmutoglu and Joseph Ndika and Warsha Kanhai and {de Villemeur}, {Thierry Billette} and David Cheillan and Ernst Christensen and Nathalie Dorison and Vickie Hannig and Yvonne Hendriks and Hofstede, {Floris C.} and Laurence Lion-Francois and Lund, {Allan M.} and Helen Mundy and Gaele Pitelet and Miquel Raspall-Chaure and Scott-Schwoerer, {Jessica A.} and Katalin Szakszon and Vassili Valayannopoulos and Monique Williams and Salomons, {Gajja S.}", year = "2014", month = apr, doi = "10.1002/humu.22511", language = "English", volume = "35", pages = "462--469", journal = "Human Mutation", issn = "1059-7794", publisher = "John Wiley & Sons, Ltd", number = "4", } . Human Mutation.

Cloning and characterization of the promoter regions from the parent and paralogous creatine transporter genes @article{48cad7888be74b66b83ba8218ca8fc9f, title = "Cloning and characterization of the promoter regions from the parent and paralogous creatine transporter genes", abstract = "Interconversion between phosphocreatine and creatine, catalyzed by creatine kinase is crucial in the supply of ATP to tissues with high energy demand. Creatine's importance has been established by its use as an ergogenic aid in sport, as well as the development of intellectual disability in patients with congenital creatine deficiency. Creatine biosynthesis is complemented by dietary creatine uptake. Intracellular transport of creatine is carried out by a creatine transporter protein (CT1/CRT/CRTR) encoded by the SLC6A8 gene. Most tissues express this gene, with highest levels detected in skeletal muscle and kidney. There are lower levels of the gene detected in colon, brain, heart, testis and prostate. The mechanism(s) by which this regulation occurs is still poorly understood. A duplicated unprocessed pseudogene of SLC6A8-SLC6A10P has been mapped to chromosome 16p11.2 (contains the entire SLC6A8 gene, plus 2293 bp of 5'flanking sequence and its entire 3'UTR). Expression of SLC6A10P has so far only been shown in human testis and brain. It is still unclear as to what is the function of SLC6A10P. In a patient with autism, a chromosomal breakpoint that intersects the 5'flanking region of SLC6A10P was identified; suggesting that SLC6A10P is a non-coding RNA involved in autism. Our aim was to investigate the presence of cis-acting factor(s) that regulate expression of the creatine transporter, as well as to determine if these factors are functionally conserved upstream of the creatine transporter pseudogene.Via gene-specific PCR, cloning and functional luciferase assays we identified a 1104 bp sequence proximal to the mRNA start site of the SLC6A8 gene with promoter activity in five cell types. The corresponding 5'flanking sequence (1050 bp) on the pseudogene also had promoter activity in all 5 cell lines. Surprisingly the pseudogene promoter was stronger than that of its parent gene in 4 of the cell lines tested. To the best of our knowledge, this is the first experimental evidence of a pseudogene with stronger promoter activity than its parental gene. (C) 2013 Elsevier B.V. All rights reserved.", keywords = "Creatine transport, Transcriptional regulation, Promoter, Pseudogene, LINKED MENTAL-RETARDATION, HUMAN GENOME, DEFICIENCY, 16P11.2, SLC6A8, XQ28, IDENTIFICATION, ASSIGNMENT, AUTISM, LEVEL", author = "Ndika, {Joseph D. T.} and Vera Lusink and Claudine Beaubrun and Warsha Kanhai and Cristina Martinez-Munoz and Cornelis Jakobs and Salomons, {Gajja S.}", year = "2014", month = jan, day = "10", doi = "10.1016/j.gene.2013.10.008", language = "English", volume = "533", pages = "488--493", journal = "Gene", issn = "0378-1119", publisher = "Elsevier Scientific Publ. Co", number = "2", } . Gene.

(2014). Cloning and characterization of the promoter regions from the parent and paralogous creatine transporter genes . Gene.

Ndika, Joseph Dingbobga Tanyi(2014). Creatine Deficiency Syndromes: A Clinical, Molecular and Functional Approach. Amsterdam: Vrije Universiteit

(2013). Environmental dependence of genetic constraint . PLoS genetics.

Environmental Dependence of Genetic Constraint @article{91f189571828494d86ce75aebd365ca2, title = "Environmental Dependence of Genetic Constraint", abstract = "The epistatic interactions that underlie evolutionary constraint have mainly been studied for constant external conditions. However, environmental changes may modulate epistasis and hence affect genetic constraints. Here we investigate genetic constraints in the adaptive evolution of a novel regulatory function in variable environments, using the lac repressor, LacI, as a model system. We have systematically reconstructed mutational trajectories from wild type LacI to three different variants that each exhibit an inverse response to the inducing ligand IPTG, and analyzed the higher-order interactions between genetic and environmental changes. We find epistasis to depend strongly on the environment. As a result, mutational steps essential to inversion but inaccessible by positive selection in one environment, become accessible in another. We present a graphical method to analyze the observed complex higher-order interactions between multiple mutations and environmental change, and show how the interactions can be explained by a combination of mutational effects on allostery and thermodynamic stability. This dependency of genetic constraint on the environment should fundamentally affect evolutionary dynamics and affects the interpretation of phylogenetic data.", keywords = "EMPIRICAL FITNESS LANDSCAPES, ESCHERICHIA-COLI, MOLECULAR EVOLUTION, CRYSTAL-STRUCTURE, SIGN EPISTASIS, PROTEIN, REPRESSOR, PHYLOGENETICS, HETEROTACHY, ADAPTATION", author = "{de Vos}, {Marjon G. J.} and Poelwijk, {Frank J.} and Nico Battich and Ndika, {Joseph D. T.} and Tans, {Sander J.}", year = "2013", month = jun, doi = "10.1371/journal.pgen.1003580", language = "English", volume = "9", journal = "PLoS Genetics", issn = "1553-7390", publisher = "PUBLIC LIBRARY OF SCIENCE", number = "6", } . PLoS Genetics.

Promiscuous activity of arginine @article{16acda395af046da8a548cdd519ac518, title = "Promiscuous activity of arginine: glycine amidinotransferase is responsible for the synthesis of the novel cardiovascular risk factor homoarginine", abstract = "Low plasma homoarginine has emerged as a risk marker for cardiovascular disease. We exploited cells of a patient with a rare inborn error of metabolism to explore potential pathways of homoarginine synthesis, using stable isotopes and mass spectrometry. Control lymphoblasts, as opposed to lymphoblasts from an arginine:glycine amidinotransferase (AGAT)-deficient patient, were able to synthesize homoarginine from arginine and lysine. In contrast, in a patient with a deficiency of the urea cycle enzyme argininosuccinate synthase, plasma homoarginine was not decreased. We conclude that promiscuous activity of AGAT, a key enzyme in creatine synthesis, plays a pivotal role in homoarginine synthesis. (C) 2012 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.", keywords = "Homoarginine, Arginine:glycine amidinotransferase (AGAT), Argininosuccinate synthase (ASS), Cardiovascular disease, ASYMMETRIC DIMETHYLARGININE, SYMMETRIC DIMETHYLARGININE, CREATINE SUPPLEMENTATION, SUBSTRATE-SPECIFICITY, LIQUID-CHROMATOGRAPHY, GUANIDINO COMPOUNDS, BIOLOGICAL SAMPLES, AMINO-ACIDS, HOMOCITRULLINE, DEFICIENCY", author = "Mariska Davids and Ndika, {Joseph D. T.} and Salomons, {Gajja S.} and Blom, {Henk J.} and Tom Teerlink", year = "2012", month = oct, day = "19", doi = "10.1016/j.febslet.2012.08.020", language = "English", volume = "586", pages = "3653--3657", journal = "FEBS Letters", issn = "0014-5793", publisher = "Elsevier Scientific Publ. Co", number = "20", } . FEBS Letters.

(2012). Promiscuous activity of arginine:glycine amidinotransferase is responsible for the synthesis of the novel cardiovascular risk factor homoarginine . FEBS letters.

(2012). Developmental progress and creatine restoration upon long-term creatine supplementation of a patient with arginine:glycine amidinotransferase deficiency . Molecular genetics and metabolism.

Developmental progress and creatine restoration upon long-term creatine supplementation of a patient with arginine @article{7d1c0d3eee104dd3aad7673f9adbe2b1, title = "Developmental progress and creatine restoration upon long-term creatine supplementation of a patient with arginine: glycine amidinotransferase deficiency", abstract = "Background: Arginine:glycineamidinotransferase (AGAT/GATM) deficiency has been described in 9 patients across 4 families. Here we describe the clinical outcome and response to creatine supplementation in a patient of the second family affected with AGAT deficiency a 9-year-old girl.Patient and methods: Delayed motor milestones were noticed from 4 months of age and at 14 months moderate hypotonia, developmental delay and failure to thrive. Laboratory studies revealed low plasma creatine as well as extremely low levels of guanidinoacetic acid in urine and plasma. Proton magnetic resonance spectroscopy (MRS) of the brain showed absence of creatine. DNA sequence analysis revealed a homozygous mutation (c.484+1G>T) in the AGAT/GATM gene. AGAT activity was not detectable in lymphoblasts and RNA analysis revealed a truncated mRNA (r.289_484del196) that is degraded via Nonsense Mediated Decay. At 16 months, Bayley's Infant Development Scale (BIDS) showed functioning at 43% of chronologic age. Oral creatine supplementation (up to 800 mg/kg/day) was begun.Results: At age 9 years she demonstrated advanced academic performance. Partial recovery of cerebral creatine levels was demonstrated on MRS at 25 months of age. Brain MRS at 40 months of age revealed a creatine/NAA ratio of about 80% of that in age-matched controls.Conclusions: 8 years post initiation of oral creatine supplementation, patient demonstrates superior nonverbal and academic abilities, with average verbal skills. We emphasize that early diagnosis combined with early treatment onset of AGAT deficiency may lead to improvement of developmental outcome. (C) 2012 Elsevier Inc. All rights reserved.", keywords = "AGAT, Creatine deficiency, Developmental delay, Creatine supplementation, GUANIDINOACETATE METHYLTRANSFERASE DEFICIENCY, AGAT DEFICIENCY, INBORN ERROR, METABOLISM, DISEASE", author = "Ndika, {Joseph D. T.} and Kathreen Johnston and Barkovich, {James A.} and Wirt, {Michael D.} and Patricia O'Neill and Betsalel, {Ofir T.} and Cornelis Jakobs and Salomons, {Gajja S.}", year = "2012", month = may, doi = "10.1016/j.ymgme.2012.01.017", language = "English", volume = "106", pages = "48--54", journal = "Molecular Genetics and Metabolism", issn = "1096-7192", publisher = "ACADEMIC PRESS INC ELSEVIER SCIENCE", number = "1", } . Molecular Genetics and Metabolism.

Nasal mucosa and blood cell transcriptome profiles do not reflect respiratory symptoms associated with moisture‐damage @article{doi:10.1111/ina.12472, author= {Ndika Joseph and Suojalehto Hille and Täubel Martin and Lehto Maili and Karvala Kirsi and Pallasaho Paula and Sund Jukka and Auvinen Petri and Järvi Kati and Pekkanen Juha and Kinaret Pia and Greco Dario and Hyvärinen Anne and Alenius Harri}, title= {Nasal mucosa and blood cell transcriptome profiles do not reflect respiratory symptoms associated with moisture‐damage}, journal= {Indoor Air}, volume= {0}, number= {ja}, pages= {}, keywords= {Moisture‐damaged buildings, respiratory symptoms, transcriptomics, exposure biomarkers}, doi= {10.1111/ina.12472}, url= {https://onlinelibrary.wiley.com/doi/abs/10.1111/ina.12472}, eprint= {https://onlinelibrary.wiley.com/doi/pdf/10.1111/ina.12472}, abstract= {Abstract Upper and lower respiratory symptoms and asthma are adverse health effects associated with moisture‐damaged buildings. Quantitative measures to detect adverse health effects related to exposure to dampness and mold are needed. Here, we investigate differences in gene expression between occupants of moisture‐damaged and reference buildings. Moisture‐damaged (N=11) and control (N=5) buildings were evaluated for dampness and mold by trained inspectors. The transcriptomics cohort consisted of nasal brushings and peripheral blood mononuclear cells (PBMCs) from 86 teachers, with/without self‐perceived respiratory symptoms. Subject categories comprised reference (R) and damaged (D) buildings with (S) or without (NS) symptoms; i.e. R‐S, R‐NS, DS and D‐NS. Component analyses and k‐means clustering of transcriptome profiles did not distinguish building status (R/D) or presence of respiratory symptoms (S/NS). Only one nasal mucosa gene (YBX3P1) exhibited a significant change in expression between D‐S and D‐NS. Nine other nasal mucosa genes were differentially expressed between R‐S and D‐S teachers. No differentially expressed genes were identified in PBMCs. We conclude that the observed mRNA differences provide very weak biological evidence for adverse health effects associated with subject occupancy of the specified moisture‐damaged buildings. This emphasizes the need to evaluate all potential factors (including those not related to toxicity) influencing perceived/self‐reported ill‐health in moisture‐damaged buildings. This article is protected by copyright. All rights reserved.}} . Indoor Air.