The year 2024 has been a remarkable chapter for the İTÜ Molecular Biology and Genetics Department, highlighted by outstanding achievements and dynamic collaborations. Through groundbreaking research published in prestigious journals, our faculty and students have continued to enhance the department’s reputation for academic and scientific excellence. These accomplishments underscore our steadfast commitment to advancing the field of molecular biology and genetics while nurturing an engaging and innovative academic environment. As we look toward 2025, we remain inspired to reach even greater heights.

Prof. Dr. Ceren Çıracı and her team published “Utilization of photoacoustic spectral analysis for immune cell size Characterization”

Assist. Prof. Dr. Abdülhalim Kılıç  and his team published “High throughput microparticle production using microfabricated nozzle array”

Researchers have developed an innovative Microparticle Production System (MPS) using a piezoelectric transducer and microfabricated nozzle array. This system efficiently produces highly uniform PLGA microparticles for controlled drug delivery. The resulting particles demonstrated sustained release of an antibiotic and effectively inhibited bacterial growth, highlighting the technology’s potential for scalable, industrial-grade pharmaceutical manufacturing.

A team of researchers has developed a Microparticle Production System (MPS) that overcomes critical barriers in manufacturing advanced drug delivery technologies. While polymeric microparticles are ideal for delivering medication in a stable, controlled manner, traditional production methods often suffer from inconsistent particle sizes, low yield, and processes that can damage sensitive drugs, limiting their industrial-scale application.

This new MPS integrates a precision-engineered spray head, featuring a microfabricated nozzle array, with a piezoelectric transducer. When activated, the transducer vibrates at a high frequency, atomizing a polymer-drug solution into a fine mist of exceptionally uniform micro-droplets. These droplets are then rapidly dried into solid microparticles. This innovative approach allows for high-throughput production at room temperature, preserving the integrity of heat-sensitive pharmaceuticals.

In proof-of-concept experiments, the system successfully produced PLGA microparticles with a consistent average diameter of 8.9 µm. When loaded with the model antibiotic Chloramphenicol, the particles achieved a 38.7% encapsulation efficiency and demonstrated a sustained, triphasic drug release over 100 hours. Furthermore, these drug-loaded microparticles showed significant antibacterial activity against E. coli, confirming their therapeutic efficacy.

By offering a scalable, precise, and gentle fabrication method, this system bridges the gap between laboratory research and industrial pharmaceutical production. It paves the way for the mass manufacturing of advanced drug delivery platforms, holding the promise of creating safer and more effective treatments for a wide range of medical conditions.

DOI: https://doi.org/10.1039/d4ra09032b

Prof. Dr. Murat Kaya  and his team published “Role of Invertebrate Biological Origin in Chitin Nanocrystal’s Morphology, Chirality, and Self-Assembly”

This study explores the unique chitin structure in Bryozoa, revealing a novel spiderweb-like nanoarchitecture distinct from the Bouligand pattern in arthropods. The findings highlight significant structural diversity in invertebrate exoskeletons and suggest that chiral organization in chitin arises from tissue architecture, offering new possibilities for biomaterial innovation from marine sources

Chitin is a naturally abundant biopolymer that reinforces the exoskeletons of many invertebrates. It is best known for its role in the Bouligand structure found in arthropods—a twisted, layered fiber arrangement that offers strength, iridescence, and impact resistance. This structure has long inspired biomimetic material design, but prior studies have primarily focused on arthropods.

In a recent international study, researchers led by Dr. Murat Kaya from Istanbul Technical University (Türkiye) explored chitin architecture in Bryozoa, a lesser-studied invertebrate phylum. The multidisciplinary team included Dr. Kui Yu (University of Cambridge, UK, and Delft University of Technology, Netherlands), who conducted nanostructural analysis; Dr. Kine Østnes Hansen (UiT – The Arctic University of Norway), who provided marine biology insights; Dr. Martin Vinther Sørensen (Natural History Museum of Denmark, University of Copenhagen), who offered taxonomic expertise; and Dr. Muhammad Mujtaba (VTT Technical Research Centre of Finland), who investigated nanocrystal self-assembly.

Their findings revealed that bryozoan chitin features a previously undocumented spiderweb-like nanostructure—distinct from the well-known Bouligand pattern. This represents the first comprehensive structural analysis of chitin in Bryozoa and underscores the surprising diversity of exoskeletal architectures among invertebrates.

When comparing chitin nanocrystals, the team found bryozoan-derived crystals to be significantly smaller and thinner than those from arthropods, yet chemically similar. Unlike arthropod nanocrystals, however, they did not self-assemble into the typical chiral nematic (Bouligand) structures. This suggests that such chiral organization is likely influenced more by tissue-level architecture than by chitin’s intrinsic molecular properties.

This discovery broadens the understanding of chitin’s structural variability and introduces a novel, biologically sourced nanomaterial with unique physical characteristics. The distinct properties of bryozoan chitin nanocrystals could inspire the design of advanced biomaterials for use in biomedicine, pharmaceuticals, food technology, agriculture, and cosmetics, highlighting the untapped potential of marine biodiversity.

DOI: https://doi.org/10.1021/acs.langmuir.5c01167

Prof. Dr. Zeynep Petek Çakar and her team published “Molecular Characterization of Propolis-Resistant Saccharomyces cerevisiae Obtained by Evolutionary Engineering”

In their recent study published by the international journal Fermentation (Volume 11, Issue 2, 2025, Q2 in Scopus rankings) entitled “Molecular Characterization of Propolis-Resistant Saccharomyces cerevisiae Obtained by Evolutionary Engineering”, Prof. Dr. Zeynep Petek Çakar’s research group at ITU Department of Molecular Biology and Genetics applied adaptive laboratory evolution to improve yeast's tolerance to propolis, which is known for its strong antimicrobial activity and growing potential in food and pharmaceutical applications. The publication resulted from the Ph.D. thesis of Dr. Filiz Demir-Yılmaz, ITU Graduate School, Dept. of Molecular Biology-Genetics and Biotechnology.

Propolis, a complex resinous substance collected by honeybees, has strong antimicrobial properties and is increasingly considered for use in industrial fermentations. However, its potential inhibitory effect on production yeast strains has posed a challenge. In this study, the evolved strain exhibited significantly improved growth under propolis stress, reduced reactive oxygen species, enhanced cell wall integrity, and even cross-resistance to caffeine. Through whole-genome resequencing and transcriptomic analyses, the researchers identified key molecular changes associated with propolis resistance, including upregulation of genes related to oxidoreductase activity, transmembrane transport, protein folding, and pleiotropic drug resistance. Notably, mutations were observed in the PDR1 gene, which encodes a major transcription factor regulating multidrug resistance. This study highlights the crucial role of pleiotropic drug response pathways and cell wall robustness in overcoming natural antimicrobial stress. The evolved yeast strain FD11 also shows promise for ethanol fermentation applications, where propolis could serve as a selective agent against microbial contamination.

DOI: https://doi.org/10.3390/fermentation11020047

Prof. Dr. Gizem Dinler Doğanay and her team published “A BAG-1-inhibitory peptide, GO-Pep, suppresses c-Raf activity in cancer” in the journal Communications Biology.

The present study presents a novel approach to target cancer cell survival pathways by interfering with the BAG-1 and c-Raf interaction. BAG-1 (Bcl-2-associated athanogene-1) is a multifunctional co-chaperone that enhances the stability and activity of c-Raf, a key kinase in the MAPK/ERK signaling pathway. Overactivation of this pathway is frequently associated with cancer cell proliferation, survival, and resistance to therapy.

A peptide was designed and characterized, GO-Pep, that selectively binds to BAG-1 and blocks its interaction with c-Raf. In vitro and in vivo experiments demonstrated that GO-Pep effectively reduces c-Raf phosphorylation and downstream ERK activation in cancer cells. This disruption leads to impaired signaling, decreased cell proliferation, and increased apoptosis in multiple cancer models, including those with elevated BAG-1 expression.

Importantly, GO-Pep showed specificity towards cancer cells with minimal toxicity in normal cells, suggesting a promising therapeutic window. The peptide’s inhibitory mechanism also provides valuable insights into the regulation of oncogenic kinases via molecular chaperones.

Overall, this study highlights the therapeutic potential of targeting protein-protein interactions in cancer signaling networks. GO-Pep represents a first-in-class peptide that antagonizes BAG-1 function and suppresses oncogenic c-Raf activity. These findings open new avenues for developing peptide-based inhibitors that can modulate critical protein interactions involved in tumor progression and treatment resistance.

Prof. Dr. Gizem Dinler Doğanay and her team published “X-ray crystallographic and hydrogen deuterium exchange studies confirm alternate kinetic models for homolog insulin monomers”

This study explores the structural and dynamic properties of homologous insulin monomers using a combination of X-ray crystallography and hydrogen-deuterium exchange mass spectrometry (HDX-MS). Insulin, a critical hormone for glucose metabolism, exhibits complex conformational behavior that influences its biological activity and stability. Understanding the kinetic models underlying these conformations is essential for improved therapeutic design.

X-ray crystallography provided high-resolution structural snapshots of insulin monomers, revealing subtle but significant differences in their conformational states. These static images, while informative, capture only discrete states along the protein’s dynamic landscape. To complement this, hydrogen-deuterium exchange experiments were employed to monitor the exchange rates of backbone amide hydrogens, which reflect protein flexibility and solvent accessibility over time.

The integration of these two techniques confirmed the presence of alternate kinetic models for the homologous insulin monomers. Specifically, the HDX-MS data demonstrated variable exchange rates consistent with multiple conformational ensembles that interconvert on different timescales. These findings support the hypothesis that insulin monomers do not exist in a single, static structure but rather sample a dynamic range of conformations that impact their functional behavior.

This research advances the understanding of insulin’s molecular dynamics by linking structural snapshots with solution-phase flexibility. The insights gained have implications for the design of insulin analogs with improved stability and activity profiles. Moreover, the methodological approach combining crystallography and HDX-MS can be applied broadly to study other proteins with complex kinetic behaviors, providing a powerful platform for dissecting protein dynamics and function.

DOI: https://doi.org/10.1371/journal.pone.0319282

A research team led by Prof. Dr. Nevin Gül Karagüler from the Department of Molecular Biology and Genetics at Istanbul Technical University, in collaboration with Dr. Merve Öztuğ Kılınç from TÜBİTAK UME, has made significant strides in developing a metrologically traceable method for the quantification of cardiac troponin I (cTnI)—a crucial protein biomarker for diagnosing acute myocardial infarction (AMI).

The study, published in the peer-reviewed journal Clinical Chemistry and Laboratory Medicine (CCLM), is part of the PhD thesis of Meltem Aşıcıoğlu Küçük and presents a comparative evaluation of peptide-based versus protein-based calibration strategies for the quantification of cTnI using isotope dilution liquid chromatography-tandem mass spectrometry (ID-LC-MS/MS).

Cardiac troponin I (cTnI) is a clinically relevant protein biomarker for acute myocardial infarction and it is released into the bloodstream when the heart muscle is damaged. Because it circulates at extremely low concentrations, its accurate quantification is both clinically and analytically challenging. Ensuring SI-traceability—the ability to link measurement results to the International System of Units—is critical for obtaining reliable and comparable test results across different clinical laboratories and diagnostic systems.

The researchers initially focused on developing a peptide-based calibration method, where synthetic peptides corresponding to specific sequences of the target protein are used as reference materials. This method was designed to be compatible with existing LC-MS/MS instrumentation and aimed to overcome some of the limitations associated with full protein calibrators, such as structural heterogeneity and stability concerns.

Subsequently, the team performed a comprehensive comparison between this newly developed method and their previously published protein-based calibration approach. By evaluating parameters such as accuracy, reproducibility, and robustness, the researchers provided critical insights into the advantages and limitations of both calibration strategies. Their findings support the continued development of tailored primary standards—either peptide-based or protein-based—depending on the specific clinical and analytical context.

This work not only advances the field of clinical mass spectrometry but also contributes to global metrological efforts to standardize protein biomarker measurements. The study sets a solid foundation for future projects focused on improving diagnostic reliability and inter-laboratory harmonization for cardiac biomarkers.

Reference:
 Aşıcıoğlu, M., Swart, C., Saban, E., Yürek, E., Karagüler, N., & Öztuğ, M. (2025). Comparative evaluation of peptide vs. protein-based calibration for quantification of cardiac troponin I using ID-LC-MS/MS. Clinical Chemistry and Laboratory Medicine, 63(5), 1016–1030.
https://doi.org/10.1515/cclm-2024-09997

Transcriptional Regulation Shaped by Nuclear Factor I Family: A Study Led by Assoc. Prof. Dr. Aslı Kumbasar and Her Colleagues

The research was conducted by Dr. Dicle Malaymar Pınar, a former PhD student of Assoc. Prof. Dr. Aslı Kumbasar at Istanbul Technical University, within the scope of her doctoral dissertation. In collaboration with Dr. Markku Varjosalo from the University of Helsinki, they published the article entitled “Nuclear Factor I Family Members are Key Transcription Factors Regulating Gene Expression” in the prestigious journal Molecular and Cellular Proteomics, which is indexed as a Q1 journal in Scopus.

The Nuclear Factor I (NFI) family, as pioneering transcription factors, navigates the DNA landscape, guiding and regulating other transcription factors such as SOX2 to their “home” promoters. This study reveals the critical role of NFI proteins in orchestrating chromatin dynamics and gene regulation, ultimately influencing essential cellular processes through complex interaction networks.

This study identifies members of the NFI family as central transcription factors involved in transcriptional regulation, chromatin organization, and cellular signaling. Through comprehensive omics-based approaches, the researchers discovered unique and dynamic interactions among NFI proteins, including an alternative splicing isoform, NFIB4, which notably lacks DNA-binding ability. Although the NFI proteins show some redundancy, the study demonstrated that each family member possesses distinct high-confidence interactors and gene targets, suggesting distinct roles within the transcriptional regulatory networks. Notably, time-dependent proximity labeling unveiled a highly dynamic nature of NFI protein-protein interaction networks and hinted at the temporal modulation of NFI interactions. NFIB4 engages with proteins associated with mRNA regulation, which suggests that NFIs have roles beyond traditional DNA binding and transcriptional modulation. Kumbasar and her colleagues' findings highlight NFIs as master regulators, orchestrating gene expression and influencing key cellular processes, with significant implications for understanding transcriptional regulation and potential roles in cancer.

YÖK-YUDAB Fellow Ilgın Işıltan Co-Authors Study on Axonal Microtubule Polarity in FASEB Journal

As part of the YÖK-YUDAB scholarship program, Research Assistant Ilgın Işıltan Sividya conducted a portion of her PhD research at Prof. Dr. Peter Baas’s laboratory at Drexel University. During her time there, she contributed to a collaborative study which resulted in the publication of the article titled “Regulation of Axonal Microtubule Polarity Orientation in Different Kinds of Neurons” in the prestigious journal FASEB Journal (Q1 in Scopus ranking).

Axonal microtubules (MTs) are nearly all oriented with their plus-ends out, and this polarity is critical for the regulation of axonal morphology, cytoplasmic content distribution, and the directed transport of cargo along the axon. Understanding how this polarity is established and maintained is essential for gaining insights into normal neuronal development and function, as well as the mechanisms underlying various neurodegenerative disorders.

This study investigates the distinct molecular mechanisms that regulate MT polarity patterns in hippocampal and sympathetic neurons, two major neuron types in vertebrates. Although both exhibit plus-end-out MT polarity, the proteins and pathways that establish and maintain this orientation differ between cell types. The researchers aimed to investigate and compare the regulatory mechanisms underlying MT polarity patterns in different types of cultured rat neurons.

Key findings in the study indicate that the cytoplasmic dynein-mediated mechanism is essential not only for sympathetic neurons from superior cervical ganglia but also for the regulation of MT polarity in hippocampal neurons. However, sympathetic neurons do not require either TRIM46, a microtubule crosslinker, or augmin, which is involved in microtubule nucleation, for their MT polarity pattern, unlike hippocampal neurons. Furthermore, the pharmacological shift of Kinesin-1 from organelle transport to microtubule sliding results in disruption of MT polarity only in hippocampal neurons but not in sympathetic neurons.

This study highlights that even within the same animal, the mechanisms regulating MT polarity patterns differ among distinct neuron types, likely due to their unique characteristics and requirements. The findings also advance our comprehension of cytoskeletal organization in neuronal development and maintenance, with implications for neurodegenerative disorders characterized by defects in microtubule organization and transport. Therefore, understanding how axons maintain MT polarity could lead to the development of therapies that improve this process, potentially restoring axonal transport impaired by MT polarity flaws and protecting neurons from degeneration.

DOI: 10.1096/fj.202500675RR

Title 1: ITU Research Assistant Ceyhun Toruntay Publishes Study on Nanoparticle-Based Gene Therapy for Breast Cancer

Ceyhun Toruntay, a research assistant from the Department of Molecular Biology and Genetics at Istanbul Technical University, has recently published a significant research article in the Journal of Cellular and Molecular Medicine. The study, titled "Anticancer Effects of MAPK6 siRNA-Loaded PLGA Nanoparticles in the Treatment of Breast Cancer," stems from his previous research conducted under the supervision of Prof. Dr. Banu Mansuroğlu at Yıldız Technical University.

Breast cancer (BC) remains the most frequently diagnosed cancer and one of the leading causes of cancer-related mortality in women worldwide. The MAPK6 gene, which encodes an atypical mitogen-activated protein kinase, has been found to be upregulated in breast cancer and is associated with key processes such as cell proliferation, differentiation, and survival. Consequently, silencing MAPK6 presents an attractive strategy for targeted therapy.

In this study, Ceyhun Toruntay and his colleagues aimed to investigate the anticancer potential of MAPK6 siRNA-loaded poly(lactic-co-glycolic acid) (PLGA) nanoparticles in MCF-7 breast cancer cells. The nanoparticles were successfully synthesized and characterized for their ability to deliver MAPK6-targeted siRNA effectively.

The results demonstrated that these nanoparticles effectively silenced MAPK6 expression, which led to a marked reduction in cell proliferation, migration, and colony formation, alongside a significant increase in apoptotic activity in MCF-7 cells. These in vitro findings confirm the efficacy of the formulation in suppressing aggressive cancer cell behavior.

The key findings of the study suggest that MAPK6 siRNA-loaded PLGA nanoparticles exhibit strong anticancer activity by directly inhibiting tumor-promoting mechanisms in breast cancer cells. Furthermore, the study provides compelling evidence that MAPK6 may serve as a potential therapeutic target in the treatment of breast cancer, paving the way for more effective and targeted nanoparticle-based gene therapy strategies.

This research contributes to the growing body of knowledge supporting nanoparticle-mediated siRNA delivery systems as promising alternatives in cancer treatment. It also reflects the successful outcomes of cross-institutional collaboration and the high-caliber research being conducted by young scientists within Turkish academic institutions.

DOI: 10.1111/jcmm.70309