Scholarly Publications - Molecular Biology and Genetics

Permanent URI for this collectionhttps://hdl.handle.net/11693/115514

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Open Access
Regulation of translation elongation and integrated stress response in heat-shocked neurons
(Cell Press, 2025-05-27) Seluzicki, Caitlin M.; Razavi-Mohseni, Milad; Türker, Fulya; Patel, Priyal; Hua, Boyang; Beer, Michael A.; Goff, Loyal; Margolis, Seth S.
Neurons deviate from a canonical heat shock response (HSR). Here, we revealed that neuronal adaptation to heat shock accompanies a brake on mRNA translation, slowed elongating ribosomes, phosphorylation of eukaryotic elongation factor-2 (p-eEF2), and suppressed the integrated stress response (ISR). Returning neurons to control temperature within 1 h of starting heat shock was necessary for survival and allowed for restored translation following dephosphorylation of eEF2. Subsequent to recovery, neurons briefly activated the ISR and were sensitive to the ISR inhibitor ISRIB, which enhanced protein synthesis and survival. Ribosome profiling and RNA sequencing (RNA-seq) identified newly synthesized and existing transcripts associated with ribosomes during heat shock. Preservation of these transcripts for translation during recovery was in part mediated by p-eEF2 and slowed ribosomes. Our work supports a neuronal heat shock model of a partially suspended state of translation poised for rapid reversal if recovery becomes an option and provides insight into regulation between the HSR and the ISR.
Open Access
Dual- signature role of INHBA and DDIT4 as biomarkers and therapeutic targets in colorectal cancer
(Wiley, 2025-07-29) Belder, N.; Demirkol Canlı, S.; Tamam, S.; Çulcu, S.; Göktuna, İsmail Serkan; Yılmaz, E.; Savaş, B.; Akbulut, H.; Özdağ Sevgili, H.
Colorectal cancer (CRC) ranks third in incidence and second in cancer deaths globally. Despite advancements in conventional diagnostic methods and therapies, CRC's molecular heterogeneity limits effective management and prevention, keeping it among the leading causes of cancer mortality. This study aimed to find prognostic/diagnostic biomarkers and therapeutic targets for CRC using bioinformatics, clinicopathological data, and experimental analyses. We analyzed three GEO CRC datasets, identifying 388 differentially expressed genes (DEGs) between tumor and normal samples (-log2FC- ≥ 1, adj p < 0.01), with 139 consistently upregulated. Enrichr pathway analysis revealed oncogenic pathways linked to these genes. We then performed Cox regression to identify key genes associated with CRC prognosis and found INHBA (HR = 2.240, p = 0.002) and DDIT4 (HR = 2.279, p = 0.001) to be significant independent prognostic markers. A positive correlation between INHBA and DDIT4 was observed, with high expression linked to shorter survival outcomes (p < 0.05), advanced stages (p < 0.05), and recurrence (p < 0.05). Expression rose from normal tissue to polyps to cancer across five cohorts (p < 0.001), aiding early diagnosis insights. GSEA analyses suggested these genes are involved in CRC carcinogenesis via hypoxia and epithelial-mesenchymal transition. A prognostic risk score model based on these two genes and cancer stage was developed and validated in external datasets, stratifying patients into high/low-risk groups with distinct survival (p < 0.001). Experimentally, INHBA and DDIT4 overexpression was confirmed in CRC tissues and cells; dual siRNA knockdown reduced proliferation and boosted apoptosis, proving their roles in progression. These findings highlight INHBA and DDIT4 as promising biomarkers and therapeutic targets, with the risk score model offering potential for CRC management. Dual inhibition of these genes presents a novel therapeutic strategy.
Open Access
Neuronal membrane proteasomes (NMP) and NMP-derived peptides modulate neuronal signaling through NMDA receptor activation
(WILEY, 2025-07-29) Türker, Fulya; Margolis, S
Open Access
Academia Europaea’s guidelines for the visualization of clinical outcomes
(Nature Research, 2025-10-14) Hegyi, Peter; Garami, Andras; Solymosi, Katalin; Morsanyi, Kinga; Kuppuswamy, Annapoorna; Wenning, Alexander S.; Vancsa, Szilard; Varga, Gabor; Teutsch, Brigitta; Rancz, Anett; Obeidat, Mahmoud; Nagy, Rita; Harnos, Andrea; Farkas, Richard; Engh, Marie Anne; Barna, Viktoria; Zumla, Alimuddin; Zaidi, Mone; Yu, Jun; Yazici, Hasan; Wong, John E. L.; Wensing, Michel; Vieth, Michael; Varro, Andras; Thompson, David R.; Thiery, Jean Paul; Szekanecz, Zoltan; Swash, Michael; Steyerberg, Ewout W.; Skakkebæk, Niels Erik; Shariat, Shahrokh; Sermeus, Walter; Schwab, Matthias; Schulz, Rainer; Saunders, Philippa; Sackley, Catherine; Rossor, Martin; Rogler, Gerhard; Reitsma, Pieter; Reiner, Zeljko; Qin, Ling; Poynard, Thierry; Piguet, Vincent; Petersen, Ole H.; Peters, Godefridus J.; Misrahi, Micheline; Megraud, Francis; McKenna, Hugh; McInnes, Iain; McCormack, Brendan; Mancia, Giuseppe; Kumar, M. N. V. Ravi; Lyu, Aiping; Lyons, Ronan A.; Levi-Schaffer, Francesca; Laurence, Jeffrey C.; Lau, C.S.; Langs, Georg; Kondorosi, Eva; Kaprio, Jaakko; Juhasz, Gabor; Joensuu, Heikki; Jakovljevic, Mihajlo; Hulshoff Pol, Hilleke; Holzer, Peter; Hogendoorn, Pancras C. W.; Gulyas, Balazs; Grzybowski, Andrzej; Glover, Vivette; Giamarellou, Helen; Ganser, Arnold; Gambari, Roberto; Fitzgerald, Rebecca; Filippatos, Gerasimos; Ferdinandy, Peter; Fauser, Bart; Esiri, Margaret; Dorobantu, Maria; Dobrev, Dobromir; Del Prato, Stefano; de Herder, Wouter W.; Dayan, Peter; Daly, Ann K.; Dalkara, Turgay; Cohen, Adam; Ceron, Jose Joaquin; Carvalho, Felix; Buitelaar, Jan; Brugha, Traolach Sean; Bennett, Derrick; Banach, Maciej; Balla, Jozsef; Anadon, Arturo; Agyemang, Charles; Agusti, Alvar
A working group of Academia Europaea proposes the addition of a ‘ring diagram’ in clinical publications for the quick evaluation of translational implications.
Open Access
PI3K signaling at the crossroads of lipid metabolism and cancer
(Springer Cham, 2024-12-01) Yılmaz, Şevval; Çizmecioğlu, Onur; Türkşen, Kürşad
The proto-oncogenic PI3K pathway is crucial for the integration of growth factor signaling and metabolic pathways to facilitate the coordination for cell growth. Since transformed cells have the ability to upregulate their anabolic pathways and selectively modulate a subset of metabolites functioning as anti- or pro-tumorigenic signal mediators, the question of how the levels of these metabolites are regulated has also become the center of attention for cancer researchers. Apart from its well-defined roles in glucose metabolism and peptide anabolism, the PI3K pathway appears to be a significant regulator of lipid metabolism and a potentiator of proto-oncogenic bioactive lipid metabolite signaling. In this review, we aim to describe the crosstalk between the PI3K pathway and bioactive lipid species of the three main lipid classes.
Open Access
Biochemical and epigenomic dissection of TFIIE function reveals gene-selective requirement in human transcription
(Nature Research, 2026-01-20) Cevher, Murat Alper; Wijerathne, Pasindu N.; Yozgat, Yasemin; Cevher, Sevda; Ito, Keiichi; Cihan, Ali; Zaynullina, Gulnara; Pan, ShiQi; Karlic, Serena
The general transcription factor TFIIE is believed to be universally required for RNA polymerase II (Pol II)-mediated transcription initiation. However, our biochemical assays and ENCODE ChIP-seq data suggest a more gene-selective role. Using Mediator-depleted HeLa nuclear extracts, we show that TFIIE can be less critical for transcription in the presence of endogenous nuclear components, whereas purified systems of GTFs, Pol II, and Mediator reveal TFIIE to be required for transcription. This conditional requirement led us to hypothesize that TFIIE acts only at a subset of promoters in vivo. Analysis of ENCODE datasets from K562 cells identified transcription start sites (TSS) classified as TFIIE-only by peak calling, lacking annotated TBP, ZZZ3, or MED1, alongside promoters co-bound by all. When we inspected the bigWig signal tracks, they revealed additional co-enrichment not captured by peak calls, suggesting that TFIIE-only sites reflect classification thresholds and not strict exclusivity. Heatmap analyses of TFIIE-bound promoters revealed selective co-enrichment with TBP, ZZZ3 and weaker enrichment with MED1, supporting a non-canonical pre-initiation complex configuration. Gene ontology analysis of these TFIIE-enriched promoters shows strong correlation to chromatin-related processes, suggesting that TFIIE coordinates transcription initiation with chromatin organization and genome stability.
Open Access
FRI-146-YI Genetic polymorphisms associated with idiosyncratic drug-induced liver injury: a systematic review and bioinformatic analysis
(Elsevier BV, 2025-05) Matilla-Cabello, Gonzalo; Remesal-Doblado, Ángela; Çınar, Muazzez Çelebi; Bodoque-García, Ana; Metin Yılmaz, Fatma Betül; De los Santos Fernández, Romina; Alvarez-Alvarez, Ismael; Konu, Özlen; Andrade, Raul J.; Akdogan, Gülçin Cakan; Lucena, Maria Isabel; Villanueva, Marina
Open Access
Human LY9 governs CD4⁺ T cell IFN-γ immunity to Mycobacterium tuberculosis
(American Association for the Advancement of Science, 2025-05-30) Ogishi, Masato; Puchan, Julia; Yang, Rui; Arias, Andrés Augusto; Han, Ji Eun; Nguyen, Tina; Gutiérrez-Cózar, Rebeca; Conil, Clément; Seeleuthner, Yoann; Rinchai, Darawan; Zhang, Peng; Ponsin, Khoren; Chaldebas, Matthieu; Feng, Yi; Neehus, Anna-Lena; Delmonte, Ottavia M.; Khan, Taushif; Landegren, Nils; Eriksson, Daniel; Bohlen, Jonathan; Peel, Jessica N.; Fagniez, Iris; Pelham, Simon J.; Lei, Wei-Te; Chrabieh, Maya; Laine, Candice; Ouair, Hind; Benhsaien, Ibtihal; Abid, Ahmed; Abderrhamani Ghorfi, Ismail; Souhi, Hicham; Ouazzani, Hanane; Aniss, Rafik; Riminton, D. Sean; Kämpe, Olle; Turvey, Stuart E.; Marr, Nico; Notarangelo, Luigi D.; Hatipoglu, Nevin; Bousfiha, Aziz; Özçelik, Tayfun; El Baghdadi, Jamila; Cobat, Aurelie; Ma, Cindy S.; Abel, Laurent; Puel, Anne; Bustamante, Jacinta; Engel, Pablo; Gros, Philippe; Tangye, Stuart G.; Sallusto, Federica; Boisson-Dupuis, Stéphanie; Casanova, Jean-Laurent
CD4⁺ T cells are indispensable for optimal immunity to Mycobacterium tuberculosis (M.tb), a pathogen that triggers tuberculosis (TB) in humans. M.tb-specific human CD4⁺ T cells are known to polarize toward an interferon-γ (IFN-γ)–producing, CCR4−CCR6⁺CXCR3⁺T-bet⁺RORγT⁺ T helper 1* cell ($T_H1*$ cell) memory phenotype. We report that autosomal recessive deficiency of the human lymphocytic surface receptor LY9 (SLAMF3 and CD229), which is found in less than 10−5 individuals in the general population, underlies TB in three unrelated patients due to selective impairment in IFN-γ production by $T_H1*$ cells. $T_H1*$ cells express higher levels of LY9 than other CD4⁺ T cells. Mechanistically, LY9 polarizes naïve CD4⁺ T cells toward memory $T_H1*$ cells by inducing T-bet via signaling lymphocytic activation molecule (SLAM)–associated protein (SAP) and RORγT (thymus-specific retinoid-related orphan receptor γ) without SAP. LY9 costimulation enhances TCR-driven IFN-γ production of memory $T_H1*$, but not TH1, cells in a T cell–intrinsic manner via NFAT1 (nuclear factor of activated T cells 1) and RORγT. LY9 is likely to govern an optimal $T_H1*$ cell– and IFN-γ–dependent protective immunity to M.tb in humans.
Open Access
Genetic contribution to idiosyncratic drug-induced liver injury: a systematic review and bioinformatic analysis
(Springer, 2025-06-10) Matilla-Cabello, Gonzalo; Sanabria-Cabrera, Judith; Remesal-Doblado, Angela; Çelebi-Çınar, Muazzez; Bodoque-Garcia, Ana; Metin-Yılmaz, Fatma Betül; de Los Santos-Fernandez, R. L.; Alvarez-Alvarez, Ismael; Karakayalı, Özlen Konu; Andrade, Raul J.; Cakan-Akdogan, Gulcin; Lucena, M. Isabel; Villanueva-Paz, Marina
Background: Individual genetics plays a crucial role in idiosyncratic drug-induced liver injury (DILI). This study performs a comprehensive systematic review and analysis of DILI and genetics literature, focused on elucidating relevant genes, drugs and functional enrichments. Methods: Using PRISMA 2020 Guidelines, we identified eligible literature published up to June 30th, 2023, in four databases with a refined search strategy for DILI and genetic-related terms. Original articles on human patients with at least one control group, that reported statistically significant variants between groups and indicated validated DILI biochemical criteria were included. Data extraction and bioinformatic analyses were performed using R v4.4.1. Functional enrichment analyses were conducted using KEGG database. Results: A total of 25,874 records were screened. Ultimately, 139 original articles were included: 124 studies involving variants associated to DILI susceptibility (DILI-Risk set), 36 involving variants associated to DILI protection (DILI-Protective set), and 21 for both. In DILI-Risk set 83 genes were included, being NAT2, HLA-B, HLA-DRB1, HLA-A and HLA-DQB1 the most frequent, whilst DILI-Protective set comprised 25 genes. The most common culprit drugs for both sets were antimycobacterials, antineoplastics and direct acting antivirals. Hierarchical analysis performed with KEGG enrichment analysis revealed major pathway clusters in DILI-Risk set corresponding to i) regulation of the adaptive immune response and cytotoxicity mediated by T and NK cells (HLA family); ii) general inflammatory response (TNF, NFKB1, and RELA); iii) porphyrin, ascorbate and aldarate metabolism (UGT family); iv) drug metabolism pathways (CYP450 and GST families) and v) biliary secretion and hepatic cellular transport (ABC family and SLCO1B1). Conclusion: This work highlights the major role of the immune system and oxidative stress response in DILI, providing a solid basis for further studies focused on most reported genes, as well as on more uncommon genes with strong functional significance in hepatotoxicity. Funding: PI21/01248; PID2022-140169OB-C21; HORIZON-STAYHLTH-101095679; PT23/00137; PI24/01205
Open Access
Escape from TGF-β-induced senescence promotes aggressive hallmarks in epithelial hepatocellular carcinoma cells
(John Wiley & Sons Ltd., 2025-03-14) Kalyoncu, Minenur; Demirci, Dilara; Eris, Sude; Dayanc, Bengisu; Cakiroglu, Ece; Basol, Merve; Uysal, Merve; Cakan-Akdogan, Gulcin; Liu, Fang; Öztürk, Mehmet; Karakülah, Gökhan; Şentürk, Şerif
Transforming growth factor-β (TGF-β) signaling and cellular senescence are key hallmarks of hepatocellular carcinoma (HCC) pathogenesis. Despite provoking senescence-associated growth arrest in epithelial HCC cells, elevated TGF-β activity paradoxically correlates with increased aggressiveness and poor prognosis in advanced tumors. Whether the transition between these dichotomous functions involves modulation of the senescence phenotype during disease progression remains elusive. Exploiting the epithelial HCC cell line Huh7 as a robust model, we demonstrate that chronic exposure to TGF-β prompts escape from Smad3-mediated senescence, leading to the development of TGF-β resistance. This altered state is characterized by an optimal proliferation rate and the acquisition of molecular and functional traits of less-differentiated mesenchymal cells, coinciding with differential growth capacity in 2D and 3D culture conditions, epithelial-to-mesenchymal transition (EMT), and increased invasiveness in vitro, and metastasis in vivo. Mechanistically, resistant cells exhibit defective activation and nuclear trafficking of Smad molecules, particularly Smad3, as ectopic activation of the TGF-β/Smad3 axis is able to reinstate TGF-β sensitivity. An integrated transcriptomic landscape reveals both shared and distinct gene signatures associated with senescent and TGF-β resistant states. Importantly, genetic ablation and molecular studies identify microtubule affinity regulating kinase 1 (MARK1) and glutamate metabotropic receptor 8 (GRM8) as critical modulators of the resistance phenomenon, potentially by impairing spatiotemporal signaling dynamics of Smad activity. Our findings unveil a novel phenomenon wherein epithelial HCC cells may exploit senescence plasticity as a mechanism to oppose TGF-β anti-tumor responses and progress towards more aggressive HCC phenotypes.
Open Access
Deleterious variants in the autophagy-related gene RB1CC1/FIP200 impair immunity to SARS-CoV-2
(Nature Research, 2025-11-27) Hu, Lili; van der Sluis, Renee M.; Castelino, Kennith Brian; Zhang, Bao-Cun; Ronit, Andreas; Zillinger, Thomas; Werner, Marvin; Jørgensen, Sofie Eg; Hansen, Anne Louise; Pedersen, Alice; Narita, Ryo; Reinert, Line S.; Bundgaard, Bettina; Helleberg, Marie; Benfield, Thomas; Storgaard, Merete; Hansen, Kristoffer Skaalum; Bodilsen, Jacob; Zhang, Shen-Ying; Zhang, Qian; Zatz, Mayana; Wauters, Joost; von Bernuth, Horst; Vinh, Donald C.; Vianna, Fernanda Sales Luiz; van de Beek, Diederik; Uddin, Mohammed J.; Uddin, K. M. Furkan; Turvey, Stuart E.; Trouillet-Assant, Sophie; Tiberghien, Pierre; Thorball, Christian; Temel, Şehime Gülsün; Tayoun, Ahmad Abou; Tangye, Stuart G.; Tancevski, Ivan; Su, Helen C.; Spaan, András N.; Soumelis, Vassili; Soler-Palacín, Pere; Snow, Andrew L.; Slaby, Ondrej; Shcherbina, Anna; Shahrooei, Mohammad; Seppänen, Mikko R. J.; Sediva, Anna; Sancho-Shimizu, Vanessa; Rodríguez-Gallego, Carlos; Resnick, Igor; Renia, Laurent; Ramaswamy, Sathishkumar; Quintana-Murci, Lluis; Puel, Anne; Pujol, Aurora; Prando, Carolina; Planas, Anna M.; Peter, Jonny; Perlin, David S.; Perez-Tur, Jordi; de Diego, Rebeca Perez; Pan-Hammarström, Qiang; Ozcelik, Firat; Ozcelik, Tayfun; Okamoto, Keisuke; Okada, Satoshi; O’Farrelly, Cliona; Novelli, Giuseppe; Novelli, Antonio; Notarangelo, Luigi D.; Ng, Lisa F. P.; Morio, Tomohiro; Mironska, Kristina; Milner, Joshua D.; Meyts, Isabelle; Mentré, France; Maródi, László; Mansouri, Davood; Mahévas, Matthieu; Lucas, Carrie L.; Ling, Yun; Lau, Yu-Lung; Ku, Cheng-Lung; Kisand, Kai; Karamitros, Timokratis; Kaja, Elżbieta; Jouanguy, Emmanuelle; Itan, Yuval; Imai, Kohsuke; Husebye, Eystein; Hsieh, Elena W. Y.; Heath, James R.; Hammarström, Lennart; Halwani, Rabih; Hagin, David; Haerynck, Filomeen; Gut, Marta; Gorochov, Guy; Froidure, Antoine; Franco, José Luis; Flores, Carlos; Fellay, Jacques; Espinosa-Padilla, Sara; Eloy, Philippine; El Baghdadi, Jamila; Duvlis, Sotirija; Duval, Xavier; Dündar, Munis; Drolet, Beth A.; Desai, Murkesh; Dalgard, Clifton L.; Cooper, Megan A.; Constantinescu, Stefan N.; Condino-Neto, Antonio; Colobran, Roger; Cobat, Aurélie; Christodoulou, John; Casari, Giorgio; Bryceson, Yenan; Brodin, Petter; Bousfiha, Ahmed A.; Borghesi, Alessandro; Bondarenko, Anastasiia; Bolze, Alexandre; Bogunovic, Dusan; Biggs, Catherine M.; Belot, Alexandre; Bastard, Paul; Feldman, Hagit Baris; Arkin, Lisa M.; Arias, Andrés A.; Andreakos, Evangelos; Anderson, Mark S.; Al-Mulla, Fahd; Al-Muhsen, Saleh; Aiuti, Alessandro; Abel, Laurent; Holm, Christian K.; Cobat, Aurelie; Casanova, Jean-Laurent; Reggiori, Fulvio; Mari, Muriel; Paludan, Søren R.; Mogensen, Trine H.
The clinical outcome of SARS-CoV-2 infection spans from asymptomatic viral elimination to lethal COVID-19 pneumonia, which is due to type I interferon (IFN) deficiency in at least 15–20% of cases. We report two unrelated male patients with critical COVID-19 who are heterozygous for rare deleterious variants in RB1CC1, encoding the autophagy-related FIP200 protein. Airway epithelial cells genetically deprived of FIP200 or cell lines expressing the RB1CC1/FIP200 patient variants exhibit elevated SARS-CoV-2 replication and impaired autophagic flux. The antiviral function of FIP200 is independent of canonical autophagy and type I IFN, but involves the selective autophagy receptor NDP52. We identify a non-canonical function of FIP200 in a novel lysosomal degradation pathway, in which SARS-CoV-2 virions are targeted to single-membrane compartments for degradation of viral RNA in LC3B-positive acidified vesicles. This pathway is impaired in FIP200-deficient cells and in cells expressing FIP200 patient haplotypes. Collectively, we describe a cell-autonomous anti-SARS-CoV-2 restriction pathway, dependent on FIP200 and NDP52, and independent of canonical autophagy and type I IFN, which can underlie critical COVID-19 pneumonia.
Open Access
Purinergic ecto-enzyme CD73 is a context-dependent tumor suppressor in colorectal cancer
(American Society for Biochemistry and Molecular Biology Inc., 2025-10-27) Chau, Tieu Lan; Borucu, Ümran; Uygur, Beste; Özkurt, Ahmet Göktuğ; Kılıç, Eylül; Işık, Aynur; Gemalmayan, Ayşe Dila; Çekiç, Çağlar; Akyol, Aytekin; Demirkol Canlı, Seçil; Göktuna, Serkan İsmail
Inhibition of purinergic signaling in cancer has recently received great attention. The purinergic ecto-enzyme CD73 represents a prominent candidate; however its intrinsic role in colorectal cancer (CRC) cells has not been fully investigated. Stable depletion of CD73 expression by using CRISPR/Cas9 in CRC cell lines led to increased cell proliferation, enhanced cell motility and the formation of larger xenograft tumors in mice. These observations may be explained by an exacerbation of the EMT process. In addition, acquired resistance to gefitinib, an EGFR inhibitor, in various CRC models is associated with the loss of CD73 expression. Overexpression of CD73 in CRC cells can revert some of these phenotypes, resulting in slower cell migration, forming smaller xenograft tumors, sensitizing gefitinib response and enhanced apoptosis. Further supporting the tumor suppressive roles of CD73, its overexpression in CRC cells increased vulnerability to cell death induced by multiple agents while its depletion provided protection. Moreover, our bioinformatic analyses with human patient samples supported our in vitro and in vivo results, indicating that the tumor suppressor function of CD73 depends on stromal content and infiltrating immune cell. Collectively, our data strongly reveal that CD73 can function as a tumor suppressor in CRC cells. Therefore, inhibition of CD73 in general may not bring the expected outcome in patient subgroups with poor immune cell infiltration highlighting the need for careful evaluation and personalized treatment based on histopathological features of tumors.
Open Access
The magnetic beads-based sandwich-shaped immune complexes for rapid and sensitive amperometric detection of SOX2 protein
(TUBITAK, 2025-02-17) Özçeli̇kay Akyildiz, Göksu; Ünal, Mehmet Altay; Gülden, Seçil; Özkan, Sibel A.
Sex-Determining Region Y-box 2 (SOX2) is a transcription factor protein. SOX2 expression is related to lymph node metastasis and distant metastasis in colorectal carcinomas. SOX2 was determined with the first magnetic disposable immunoplatform. The designed sandwich-shaped immune complexes were formed by a capture antibody, SOX2 protein, and biotinylated secondary antibodies (dAb/HRP). The sandwich-shaped immune complex was linked to carboxylic acid functionalized magnetic beads (HOOCMBs). This magnetic bioconjugate was dropped on the surface of the screen-printed carbon electrode (SPCE). The amperometric measurement was performed at –0.20 V in the presence of hydroquinone (HQ) and H2O2 against a silver pseudo-reference electrode. The optimization parameters affecting the immunoassay response were evaluated. The analytical evaluation of the magnetic disposable immunoplatform for the amperometric detection of SOX2 standards was done. The developed immunosensor shows high sensitivity (LOD of 1.37 ng mL−1) and a short analysis time (15 min). Potential interfering compounds found in serum samples were tested. The storage stability of magnetic disposable immunoplatform was evaluated. The developed immunosensor was compared with the ELISA method. © TÜBİTAK.
Open Access
Randomization based evaluation of distinct topological and cancer expression characteristics of mutually acting gene pairs
(Oxford University Press, 2025-04-21) Dalgıç, Ertuğrul; Çelebi-Çınar, Muazzez; Vural-Özdeniz, Merve; Konu, Özlen
Small scale molecular network patterns and motifs are crucial for systems level understanding of cellular information transduction. Using randomizations, we statistically explored, previously overlooked basic patterns of mutually acting pairs, i.e. mutually positive (PP) or negative (NN) and positive-negative (PN) pairs, in two comprehensive and distinct large-scale molecular networks from literature; the human protein signaling network (PSN) and the human gene regulatory network (GRN). Only the positive and negative signs of all interacting pairs were randomized, while the gene pairs and the number of positive and negative signs in the original network were kept constant. While the numbers of NN and PN pairs were significantly higher, the number of PP pairs was significantly lower than randomly expected values. Genes participating in mutual pairs were more connected than other genes. NN genes were more connected than PP and PN in GRN for all types of degree values, including in, out, positive or negative connections, but less connected for in-degree and more connected for out-degree values in PSN. They also had significantly high number of intersections with each other and PN pairs than randomly expected values, indicating potential cooperative mechanisms. The three mutual interaction designs we examined had distinct RNA and protein expression correlation characteristics. NN protein pairs were uniquely over-represented across normal tissue samples, whose negative correlations were lost across cancer tissue samples. PP and PN pairs showed non-random positive RNA or protein expression correlation across normal or cancer tissue samples. Moreover, we developed an online tool, i.e. MGPNet, for further user specific analysis of mutual gene pairs. We identified SNCA with significantly enriched negatively correlated NN pairs. Unique non-random characteristics of mutual gene pairs identified in two different comprehensive molecular networks could provide valuable information for a better comparative understanding of molecular design principles between normal and cancer states. Insight Box/Paragraph Statement: This study provides a systems-level perspective on cellular information transduction by analyzing mutually acting pairs of genes. By examining mutually positive (PP), mutually negative (NN), and positive-negative (PN) pairs in the human protein signaling network (PSN) and the human gene regulatory network (GRN), we uncover significant variations in their connectivity and expression correlation. Our findings highlight the unique features of NN pairs across normal and cancer tissues and offer insights into molecular design principles. The development of the MGPNet tool further enhances user-specific analyses, enabling a deeper understanding of gene pair mechanisms and their potential cooperative roles in cellular processes.
Open Access
Sex, stress, and the heart: long-term cardiovascular effects of embryonic metabolic disruption
(American Physiological Society, 2026-01-01) Lees, John J.; Biçici, Betül; Berglund, Stina; Smith, Kerri L. M.; Galli, Gina; Altimiras, Jordi; Guerrero-Bosagna, Carlos
Adverse conditions within the embryonic environment can alter embryogenesis, programing systemic physiological changes that may manifest as disease states in adult life. The process of developmental programing represents an important factor underlying cardiometabolic diseases, many of which are leading causes of death globally. Importantly, there is evidence that males are less tolerant to certain environmental perturbations during embryogenesis, mirrored by sex differences in the incidence of certain cardiometabolic diseases. Understanding sex differences in programed responses in mammalian models is complicated by maternal compensation and placental factors. Avian models offer a valuable comparable system in which such effects are not present. Here, we investigate the influence of developmental hypoxia and hypothermia in programing cardiovascular structure and function in the domestic chicken (Gallus gallus domesticus). In agreement with mammalian studies, adult males but not females show pathological mitochondrial morphology and respiratory capacity, ventricular hypertrophy, and reduced body weight programed by embryonic hypothermia and hypoxia. Notably, adult males but not females incubated under combined hypoxia and hypothermia display reduced left ventricle size, more spherical mitochondria, and a reduction in mitochondrial complex IV activity in cardiomyocytes. Adult females incubated under hypothermic conditions show higher protein levels of mitochondrial complex V and do not display the same level of telomere shortening in comparison with males incubated under identical conditions. These data not only represent novel findings in birds but also demonstrate the utility of the avian model for understanding sex differences in developmental stress responses, revealing common responses among endothermic amniotes. NEW & NOTEWORTHY How does stress before birth shape lifelong heart health? We show that chickens exposed to low oxygen or cold during development grow into adults with long-lasting, sex-specific heart changes. Males developed smaller bodies, altered heart structure, mitochondrial dysfunction, and faster telomere shortening, whereas females showed enlarged hearts but preserved mitochondrial function. Our findings reveal how early environmental stress programs cardiovascular health differently in males and females, with broad relevance for understanding heart disease risk.
Open Access
Functional analysis of antipsychotics in Human iPSC-based neural progenitor 2D and 3D schizophrenia models
(MDPI AG, 2026-05-07) Farkas, Kiara Gitta; Vincze, Katalin; Tordai, Csongor; Özgen, Ece İlay; Gürler, Derin; Deli, Vera; Lilienberg, Julianna; Erdei, Zsuzsa; Sarkadi, Balázs; Réthelyi, János Miklós; Apáti, Ágota
Schizophrenia is a complex psychiatric disorder of complex etiology. Despite decades of antipsychotic drug development and treatment, the mechanisms underlying cellular drug effects remain incompletely understood. Induced pluripotent stem cell (iPSC)-based disease and pharmacological modelling offer new avenues for drug development. In this study, we explored the development of two- and three-dimensional neural progenitor cultures and the impact of different antipsychotics in a schizophrenia model. Four human iPSC lines, including two carrying a de novo ZMYND11 gene mutation associated with schizophrenia, were differentiated into hippocampal neural progenitor cells (NPCs), cultured either in monolayers or as 3D spheroids. While in monolayers the proliferation of the NPCs was similar, spheroids showed significant differences in scattered cell number and outgrowth size between schizophrenia mutant and wild-type NPCs. Since there is only limited information about the effects of antipsychotic agents on neural progenitor cell proliferation and differentiation, we investigated the effects of three molecules, representing three subgroups of antipsychotics, in the 2D and 3D NPC models. Our findings suggest that cell adhesion may play a crucial role in the molecular disease pathways of schizophrenia, highlighting the value of spheroid models for mechanistic and drug development studies. These studies may significantly help our understanding of the effects of schizophrenia on neural development and the response of progenitors to antipsychotic medications.
Open Access
Spreading depolarization triggers pro- and anti-inflammatory signalling: a potential link to headache
(Oxford University Press, 2025-01-17) Kaya, Zeynep; Belder, Nevin; Sever-Bahcekapili, Melike; Erdener, Şefik Evren; Dönmez-Demir, Buket; Baǧcı, Canan; Köroǧlu, Merve Nur; Bilguvar, Kaya; Dalkara, Turgay
Cortical spreading depolarization (CSD), the neurophysiological event believed to underlie aura, might trigger migraine headaches through inflammatory signalling that originates in neurons and spreads to the meninges via astrocytes. Increasing evidence from studies on rodents and migraine patients supports this hypothesis. The transition from pro-inflammatory to anti-inflammatory mechanisms is crucial for resolving inflammation. However, the resolution of inflammation in the context of CSD and migraine headaches remains poorly understood. This study aims to elucidate the progression of post-CSD inflammatory signalling and its resolution in neurons, astrocytes and microglia in mouse brains. CSD was triggered optogenetically or by pinprick. High mobility group box 1 release, caspase-1 activation and cell-specific activation of nuclear factor kappa B (NF-κB) pairs, along with ensuing transcriptomic changes, were evaluated using immunofluorescence, western blotting, co-immunoprecipitation, fluorescence resonance energy transfer analysis and cell-specific transcriptomics. Our findings indicate that after the initial burst, high mobility group box 1 release from neurons ceased, and caspase-1 activation, which peaked 1 h post-CSD, diminished within 3-5 h. This suggests that pro-inflammatory stimuli driving inflammatory signalling decreased within hours after CSD. Pro-inflammatory NF-κB p65:p50 pairs, along with anti-inflammatory cRel:p65 pairs, were detected in astrocyte nuclei shortly after CSD. However, 24 h post-CSD, the former had disappeared whereas the latter persisted, indicating a shift from pro- to anti-inflammatory activity in astrocytes. Pathway analysis of cell-specific transcriptomic data confirmed NF-κB-related pro-inflammatory transcription in astrocytes 1 h post-CSD, whereas no such activity was observed in neurons. Detailed transcriptomic analysis with Bayesian cell proportion reconstruction revealed that microglia exhibited transcriptional changes trending towards an anti-inflammatory profile, along with upregulation of several chemokines and cytokines (e.g. tumour necrosis factor). This suggests that microglia might play a role in supporting the inflammatory responses in astrocytes through the release of these mediators. The upregulation of genes involved in chemotaxis (e.g. Ccl3) and spine pruning (e.g. C1q) in microglia implies that microglia might contribute to synaptic repair, while inflammatory signalling in astrocytes could potentially modulate meningeal nociceptor activity through an extensive astrocyte endfeet syncytium abutting subarachnoid and perivascular spaces, although direct evidence remains incomplete. This nuanced understanding of the inflammatory response in CNS cell types highlights the intricate cellular interactions and responses to CSD. Following a single CSD, distinct transcriptomic responses occur in neurons, astrocytes and microglia, driving inflammatory and anti-inflammatory responses, potentially contributing to headache initiation and resolution.
Open Access
Sahara Desert sand “Chitligsan”: characterisation and assessment of antibacterial activity and cytotoxicity
(Royal Society of Chemistry, 2026) Ertunç, Gamze; Yılmaz, Ebru; Çelebi-Birand, Dilan; Kılıç, Büşra; Nigiz, Şeyma; Çubukcu, Evren; Özkul, Ceren; Aydın, Halil Murat; Duman, Memed
Antimicrobial resistance presents a significant global health concern, rendering antimicrobial therapies less effective and complicating the management of infectious diseases. To address this challenge, the utilisation of natural alternatives, particularly metal oxide-based nanomaterials, has emerged as a promising strategy due to their antimicrobial activity and favourable physicochemical properties, without inducing antimicrobial resistance. In this study, Chitligsan, a naturally occurring hybrid compound extracted from the sand of the Sahara Desert, was characterised and evaluated in terms of its antimicrobial activity and biocompatibility. The elemental and mineral composition of Chitligsan was investigated using FTIR, SEM-EDS, XRF, XRD, and Py-GC-MS analyses. The results indicated the presence of diverse metal oxide compounds, including $Fe_2O_3$, CaO, and $SiO_2$. Additionally, the antimicrobial efficacy of Chitligsan against several pathogenic bacteria, namely Pseudomonas aeruginosa, Escherichia coli, and Staphylococcus aureus, was evaluated. The cytotoxic potential of Chitligsan was assessed in the L929 fibroblast cell line using a scratch assay. Chitligsan exhibited antimicrobial activity against all tested bacterial species, as demonstrated by growth inhibition in the agar well diffusion assay. Furthermore, Chitligsan showed a high level of cytocompatibility, with cell viability exceeding 90%, as confirmed by the MTT assay. In conclusion, owing to its unique hybrid composition, low-cost availability, and dual antibacterial–biocompatible profile, Chitligsan may offer a novel platform for the development of sustainable antimicrobial systems.
Open Access
N-terminal half of MED14 is critical for mediator-RNA polymerase II interaction and the resulting transcription
(American Society for Biochemistry and Molecular Biology Inc., 2025-10-17) Barış, Yasemin; Jabbar, Javaid; Yozgat, Yasemin; Dinccelik-Aslan, Melike; Cigirgan, Ege; Erden, Merve; Bay, Sadik; Aslan, Volkan; Cevher, Murat Alper
Mediator is a large and evolutionarily conserved coactivator complex essential for RNA polymerase II (Pol II)-mediated gene regulation at multiple steps of the transcription process, including preinitiation complex assembly and function. Here, we used the MultiBac baculovirus expression system to generate recombinant human core Mediator subcomplexes and subsequent biochemical approaches to dissect the mechanism by which Mediator facilitates recruitment of Pol II to core promoters. Our results highlight a pivotal role in this process for the N-terminal half of the MED14 (MED14-NTD) subunit. We show that a reconstituted 15-subunit human core Mediator complex that contains only the MED14- NTD is fully functional in facilitating both basal and activated (p53) transcription. This complex directly interacts with the RPB1 subunit of Pol II and is required for recruiting Pol II to core promoters. LC-MS/MS analysis of Mediator-bound RPB1 indicates that the CTD is predominantly hypophosphorylated (≤1% detectable Ser5-P), consistent with recruitment-stage engagement. Moreover, recombinant RPB1 can completely reverse the human core Mediator-Pol II interaction. Notably, the human MED14-NTD region has secondary structure conservation with Schizosaccharomyces pombe. In addition, reanalysis of published cryo-EM structures of yeast Mediator-Pol II complexes strongly supports our conclusion. Thus, our analyses provide critical new insights into how Mediator binds to Pol II and recruits it to the promoters to facilitate transcription.
Open Access
Pan-cancer analysis of pyrimidine metabolism reveals signaling pathways connections with chemoresistance role
(Nature Publishing Group, 2025-12-24) Ramesh, Vignesh; Demirdizen, Mert; Pinna, Luisa; Doktor, Thomas Koed; Benso, Federica; Siddiqui, Mohammad Aarif; Ceppi, Paolo
Background: Deregulated pyrimidine metabolism (PyMet) contributes to various tumorigenic features of cancer, including chemoresistance and epithelial-to-mesenchymal transition. However, cancer often encompasses complex signalling and metabolic pathway cascades for its progression and understanding of these molecular regulatory processes in PyMet is quite limited. Methods: A comprehensive pan-cancer analysis of around 10,000 gene expression profiles of 32 cancer types was employed using a pathway-based approach utilising gene-sets of signalling and metabolic pathways. The findings were validated using in vitro inhibitor treatments, genetic perturbations and mouse-derived lung tumour organoids. Results: Pan-cancer analysis identified several top connections with PyMet, including TERT, MTOR, DAX1, HOXA1, TP53 and TNC, implying an interdependency of regulations, which in turn was linked to the chemoresistance mechanisms. Further, these PyMet-signalling interactions were validated in vitro by inhibiting thymidylate synthase (TS) activity using knockdown approach and by brequinar (BRQ), a DHODH inhibitor. Strikingly, the BRQ treatment profile showed a strong inverse association pattern with doxorubicin chemoresistance in multiple cancer types. Indeed, BRQ synergistically sensitises cells to doxorubicin in both lung cancer cell lines and mouse-derived Kras$^{G12D}$ p53$^{Δ/Δ}$ (KP) lung tumour organoids. Conclusions: The study highlights the PyMet-pathway interactions and its role in chemoresistance, providing a strategy for targeting PyMet in cancer.