Moleküler Biyoloji, Genetik ve Biyomühendislik
Tissue Engineering / in vitro human cell-based blood-brain barrier models
Organ Chip Devices are biomimetic microsystems lined with living cells that replicate key functional and microenvironmental features of whole organs, including tissue-tissue interfaces, mechanical forces, fluid flow, and relevant chemical gradients.
Mustafaoglu Lab is dedicated to developing novel microfluidic systems that accurately replicate the blood-brain barrier (BBB) under physiological conditions in both healthy and diseased states. Our research encompasses various aspects, including establishing new protocols for differentiating stem cells into neurons and brain endothelial cells. Additionally, we design and fabricate unique microfluidic devices featuring channels capable of exerting shear and tensile stresses on cells to simulate physiological vascular movements within the brain. Our in vitro BBB models successfully replicate the permeability barrier, the physiologically relevant expression of tight junction proteins, and the functionality of multiple drug transporters. Importantly, these physiologically relevant human cell-based models enable the development of novel drug delivery approaches for the treatment of brain diseases. To enhance our models, we are employing state-of-the-art engineering approaches to incorporate sensors into our microfluidic models. This integration allows us to develop novel, human-based, in vitro models of the BBB that faithfully mimic key features observed in vivo and monitor simultaneous changes in disease development. These advancements could be utilized for drug screening purposes as well.
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Nanobioengineering / Drug Design and Delivery
Drug delivery refers to processes, formulations, methods, and systems to safely distribute a nanoparticle-based pharmaceutical product in the body for as long as it is needed to achieve the desired therapeutic effect.
Our group focuses on two main areas: developing advanced drug delivery systems and innovative nanoparticle targeting strategies. Our primary aim is to improve the treatment of central nervous system (CNS) diseases and cancer, ultimately leading to better patient outcomes. To achieve this, we combine our expertise in state-of-the-art wet lab techniques and physiologically relevant functional organ models with collaborations for computational approaches. Within our research, a major emphasis lies in designing nano-shuttle systems capable of crossing the blood-brain barrier (BBB). This presents a significant challenge in the field of drug delivery because the BBB, while evolutionarily advantageous, poses obstacles for delivering drugs to the brain. In fact, over 99% of drugs cannot pass through the BBB. In our lab, we address this problem by developing novel nano-shuttle systems decorated with functional moieties to target proteins on brain endothelial cells. These systems enable transcytosis, facilitating the delivery of drugs to the brain for the treatment of CNS disorders.
Machine Learning for Biology and Medicine
Machine learning aims at developing computer systems that can perform tasks without explicit instructions and improve themselves with experience, where the experience is encoded as data.
Our research aims at using this data effectively to deepen our understanding of the molecular basis of the workings of the cell, diseases, and to translate this knowledge into clinics for improving patient care.
Machine Learning for Biology and Medicine
Molecular evolution is an area investigating the changes in DNA and protein molecules. Evolutionary events help us gain insights into the history and present of the biological events.
Our research aims to understand evolutionary history of proteins. The conservation profiles of proteins shed light into their function, potential partners and the evaluation of human variants in the disease context. We are specifically interested in eukaryotic signal transduction initiated by G protein-coupled receptors. Moreover, we develop novel approaches and tools in phylogenetics to increase the performance of amino acid substitution prediction. Our studies help identifying mutations causing rare diseases. For more information, please visit our lab website.
Our research aims to understand how cells maintain their genome integrity through DNA repair mechanisms. We are interested in identifying the genomic factors playing role in nucleotide excision repair. We specifically focus on the formation and removal of DNA bulky adducts caused by ultraviolet and chemicals found in cigarette smoke, car exhaust and air pollution. For more information please visit our
Post-transcriptional gene regulation / Translation Control / Protein synthesis
Cancer cells regulate gene expression at multiple levels. While transcription has been the main focus, post-transcriptional regulation is now recognized as a key driver of cancer progression and a source for potential therapeutic targets.
Our research focuses on understanding the previously unknown connections between translation machinery and different cellular pathways that serve as novel cancer-specific vulnerabilities. We also study post-transcriptional regulation of key oncogenes and their non-canonical functions, using advanced in vitro and in vivo methods that integrate biochemistry, molecular biology, RNA biology, and cancer biology to uncover novel therapeutic targets.
Mitochondrial Dysfunction, Cancer Research, Aging
The research interests of my lab focus on the role of mitochondria in pathological conditions. Mitochondria are amazing organelles that we inherited from prokaryotic cells about a couple billion years ago. Since then, they have lived in the great eukaryotic house, helping us breathe and paying for the accommodation with the universal biological currency, ATP. They are also a major source of generating reactive oxygen species (ROS), which play a regulatory role in the process of life and programmed cell death.
As we age, mitochondrial function declines, they gradually lose their respiratory activity, and damage accumulates in their mitochondrial genome. Similarly, our organs deteriorate differently over time, so for the same chronological age, the biological age of mitochondria in them is also different, which manifests itself in a different set of mitochondrial dysfunctions (MDF). MDF influence a wide range of human pathologies, including cancer, metabolic and cardiovascular diseases. Understanding how this puzzle works in the context of the living organism is an ongoing challenge of our research, conducted on several fronts:
1. Studying the effects of MDF-inducing drugs on a specific subpopulation of cancer resistant and cancer stem cells as part of anti-cancer therapy;
2. Studying the molecular mechanisms of MDF associated with aging of individual organs;
3. study of horizontal transfer of mitochondria from cell to cell via extracellular vesicles and tunnel nanotubes.
Models: primary and immortal cells, mice, Artemia salina
Collaborations:
Department of Epidemiology and Biostatistics, Schulich School of Medicine and Dentistry, Western University, London, Canada
Department of Biological Sciences, University of Illinois at Chicago, Chicago, USA
Department of Chemical Sciences, Federico II Naples University, Naples, Italy
Plant Molecular Biology and Genetics
Research in plant molecular biology and genetics is attracting increasing attention within the scientific community, because biotechnology research is extensively involved in product development for many agricultural, chemical, and pharmaceutical companies. Through application of molecular biology techniques, new plant varieties are being developed which are resistant to broad spectrum herbicides, insects, viral pathogens and extreme environmental conditions. Testing and analysis of genetically modified organisms (GMO) is also carried out in our laboratories.
Investigation of genetic and molecular basis of biotic (diseases and insects) and abiotic (drought, cold, salt, heat, mineral deficiency.) stress response mechanisms, and herbicide resistance with identification and tagging of related genes in plants are main interests. The scientific knowledge generated in the light of those studies are used in genetic improvement of cultivated wheats by exploiting wild wheat, production of stress tolerant crop plants via genetic transformation and pathogen free plant materials by in vitro propagation.
Biodiversity in plants is explored at the genic and genomic level with DNA-RNA fingerprinting and comparative genome analysis. Gene transmission and silencing in plants are also investigated.
Machine Learning for Biology and Medicine
Understanding of fundamental and applied aspects of plant mineral nutrition and plant nutritional physiology is the main research area. Role of plant nutrition in i) mitigating abiotic stress (such as heat and drought), ii) climate change-linked stress and iii) improving nutritional value of food crops are the high priority research tasks.
Crop plants are often exposed to diverse environmental stress conditions which are becoming more frequent with the global warming. Our on-going research activities are focused on characterization of the role of adequate plant mineral nutrition in mitigating stress-related decreases in plant growth, and identify major physiological mechanisms involved in protection of plants from stress conditions. In these studies, a particular attention is paid to the contribution of mineral nutrition to the antioxidative defense mechanisms of plants. Second major research topic of the group is related to Hidden Hunger problem in human populations (i.e., deficiencies of micronutrients including zinc, iron, iodine and selenium). Hidden Hunger affects health of about two billion people worldwide and associated with reduced dietary intake of micronutrients. An extensive research program is ongoing investigating i) the role of agronomic and genetic approaches for improving concentrations of micronutrients in food crops and ii) understanding physiological and molecular mechanisms affecting the root uptake, shoot transport and seed deposition of micronutrients.
Post-translational Protein Modifications by SUMO & Ubiquitin
Our dynamic team is dedicated to uncovering the intricate roles of SUMOylation in health and pathogenesis, with a strong focus on advancing cell and disease biology and drug discovery. We conduct curiosity-driven fundamental research to dissect the functions of SUMOylation in key cellular processes and pathogenesis. To achieve this, we employ multidisciplinary approaches, including cell biology, biochemistry, high-resolution imaging, proteomics, and transgenic animal models of disease.
Our lab is particularly interested in neurodegeneration and the development of novel therapeutics for neurodegenerative diseases, specifically Amyotrophic Lateral Sclerosis (ALS). ALS is a devastating neurodegenerative disease characterized by the degeneration of motor neurons in the brainstem and spinal cord, typically leading to death within 3 to 4 years of symptom onset. It is the most common motor neuron disease in humans and the third most prevalent neurodegenerative disorder after Alzheimer’s and Parkinson’s diseases, with very limited treatment options available.
At the basic science level, we investigate the role of sumoylation in ALS pathogenesis to gain insights into the mechanisms of neurodegeneration in ALS patients. At the translational level, our long-term goal is to enhance the clearance of toxic proteins from the motor neurons of ALS patients. To this end, we are currently exploring the potential of targeting sumoylation as a therapeutic strategy.
For more information, please visit the website of our research group.
Signaling and metal-binding proteins
The ultimate goal in biomolecular structural studies is to understand how conformational changes in the 3D structure contribute to the function of the molecule and what happens when the molecule cannot perform its function for example in case of mutations in the gene for a protein or under disease conditions.
We focus on two problems: (1) Mechanisms of G protein signaling in plants, (2) How are metal binding and release regulated in metal transfer proteins, metallothioneins in plants and ferric binding protein in H. influenzae. We are experimentalists, working at different levels starting with recombinant protein production in E. coli. We conduct biochemical and biophysical characterization of proteins using standard wet-lab techniques, as well as chromatography, absorption spectroscopy, circular dichroism and light scattering. For determination 3D structural properties of the target proteins we perform X-ray solution scattering measurements at a European synchrotron radiation facility (e.g. Petra III at DESY, Hamburg). Our work has therapeutic as well as biosensor applications.
Machine Learning for Biology and Medicine
Structural and Computational Biology
We work on the structure-function relationship of plant metallothioneins, structural analysis of plant TOLL-interleukin I like resistance genes and TALE protein derived from the plant pathogen Xanthomonas. We study plant G-proteins involved in signal transduction using modeling and synchrotron X-ray diffraction and scattering methods. We perform protein structure prediction using molecular modeling, homology modeling and various other computational tools. A circular dichroism (CD), FPLC and HPLC equipment are routinely used for structure prediction and protein purification.
The group working on proteins is interested in factors affecting the biological activity, viscoelastic properties of proteins, conformational multiplicity, conformational search on loop regions in proteins and tolerance of protein function to sequence variation.
Understanding Protein Function through Structure and Dynamics
We seek to design conditions under which proteins are encouraged to sample conformations that serve a specific purpose. This includes pH and ionic strength modulation, as well as point mutations introduced at locations that are prone to inducing mechanical effects. We utilize atomistic and coarse-grained simulations supplemented by theoretical developments to cover the pico-millisecond time scales, and nano-micrometer length scales. We have developed network-based models to study the basic features contributing to structure/function relationships in these systems. These include:
Elastic network models in 1-D (GNM) and 3-D (ANM). (ANM server is located at http://midst.sabanciuniv.edu/anm)
Optimal paths along the networks to identify key locations participating in their proper functioning. (available as a server under Services link at http://midst.sabanciuniv.edu)
System identification based on perturbation/response scanning (PRS) to study the near-equilibrium dynamics. (PRS server is located at http://midst.sabanciuniv.edu/prs)
Prediction of relaxation times contributing to equilibrium fluctuations.
Some problems of interest are, iron piracy from humans by bacteria, molecular mechanisms that lead to mutants conferring resistance to bacteria in competitive inhibition, DNA binding properties of TALE proteins to design better TALENs, tetramerization of proteins with key roles in human cancer.
Structural Proteomics and Data driven Modeling
New developments in mass spectrometry have opened up the possibility to infer structural information of proteins and large protein complexes on a proteome-wide scale. We are developing methods and web-services that use chemical cross-link data to drive different molecular modeling simulations. Furthermore, proteomics data from limited proteolysis coupled to targeted mass-spectrometry experiments provides us information on subtle and global conformational changes on proteins. We use the data to establish the activity of enzymes, identify targets for small molecules or determine protein stabilities; all on a proteome-wide scale.
Further Information
Pictured: Molecular dynamics studies on TALE DNA binding proteins from plant pathogenic Xanthomonas bacteria. Information derived from naturally occurring TALE proteins is used to design TALEN proteins which are biotechnological tools that mutate desired gene loci in complex genomes such as the human genome. We are investigating the DNA binding properties of TALE proteins to design better TALENs.
Synthesis and Molecular Effects of Nanoantioxidants
Antioxidants are greatly used to prevent oxidative stress and related disorders. Our research focuses on understanding oxidative stress-related cellular and molecular events and combating it through a variety of antioxidants. For this purpose, nano antioxidants can be synthesized, offering great promise to overcome solubility and stability problems.
Currently, our lab focuses on characterizing the biological effects of drug-loaded nanoparticles in several cell lines. In one of our projects, we are trying to increase the antioxidant defense capacity of cells by using a nano-antioxidant system. For this purpose, a nanosystem has been developed and is being tested in the 3T3 fibroblast cell line. More recently, we are seeking to design and implement a nanoparticle-porphyrin-based theranostic agent to be used in targeted photodynamic therapy.
Our specific aims regarding theranostics are: