Scholarly Publications - Molecular Biology and Genetics

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Open Access
Corrigendum to “model organisms for investigating the functional involvement of NRF2 in non-communicable diseases” [Redox Biol. 79 (2025) 103464] (Redox Biology (2025) 79, (S2213231724004427), (10.1016/j.redox.2024.103464))
(Elsevier BV, 2025-03) Rojo, Ana, I; Buttari, Brigitta; Cadenas, Susana; Carlos, Ana Rita; Cuadrado, Antonio; Falcao, Ana Sofia; Lopez, Manuela G.; Georgiev, Milen I.; Grochot-Przeczek, Anna; Gumeni, Sentiljana; Jimenez-Villegas, Jose; Horbanczuk, Jaroslaw Olav; Konu, Özlen; Lastres-Becker, Isabel; Levonen, Anna-Liisa; Maksimova, Viktorija; Michaeloudes, Charalambos; Mihaylova, Liliya, V; Mickael, Michel Edwar; Milisav, Irina; Miova, Biljana; Rada, Patricia; Santos, Marlene; Seabra, Miguel C.; Strac, Dubravka Svob; Tenreiro, Sandra; Trougakos, Ioannis P.; Dinkova-Kostova, Albena T.
The authors regret to inform that a duplicate figure was included in the original publication. The correct version of Figure 9 is available below. The authors would like to apologise for any inconvenience caused.[Figure presented] © 2025 The Author(s)
Open Access
Synthesis and structure of novel phenothiazine derivatives, and compound prioritization via in silico target search and screening for cytotoxic and cholinesterase modulatory activities in liver cancer cells and in vivo in zebrafish
(American Chemical Society, 2024-06-03) Kisla, Mehmet Murat; Yaman, Murat; Zengin Karadayi,Fikriye; Korkmaz, Büşra; Bayazeid, Ömer; Kumar, Amrish; Peravali, Ravindra; Güneş, Damla; Tiryaki, Rafed Said; Gelinci, Emine; Çakan Akdoğan, Gülçin; Ateş Alagöz, Zeynep; Konu, Özlen
Phenothiazines (PTZ) are antipsychotics known to modulate a variety of neurotransmitter activities that include dopaminergic and cholinergic signaling and have been identified as potential anticancer agents in vitro. However, it is important to also test whether a highly cytotoxic, repurposed, or novel PTZ has low toxicity and neuromodulatory activity in vivo using vertebrate model organisms, such as zebrafish. In this study, we synthesized novel phenothiazines and screened them in vitro in liver cancer and in vivo in zebrafish embryos/larvae. The syntheses of several intermediate PTZ 10-yl acyl chlorides were followed by elemental analysis and determination of 1H NMR and 13C NMR mass (ESI+) spectra of a large number of novel PTZ 10-carboxamides. Cytotoxicities of 28 PTZ derivatives (1–28) screened against Hep3B and SkHep1 liver cancer cell lines revealed five intermediate and five novel leads along with trifluoperazine (TFP), prochlorperazine (PCP), and perphenazine, which are relatively more cytotoxic than the basic PTZ core. Overall, the derivatives were more cytotoxic to Hep3B than SkHep1 cells. Moreover, in silico target screening identified cholinesterases as some of the commonest targets of the screened phenothiazines. Interestingly, molecular docking studies with acetylcholinesterase (AChE) and butyrylcholinesterase proteins showed that the most cytotoxic compounds 1, 3, PCP, and TFP behaved similar to Huprin W in their amino acid interactions with the AChE protein. The highly cytotoxic intermediate PTZ derivative 1 exhibited a relatively lower toxicity profile than those of 2 and 3 during the zebrafish development. It also modulated in vivo the cholinesterase activity in a dose-dependent manner while significantly increasing the total cholinesterase activity and/or ACHE mRNA levels, independent of the liver cancer cell type. Our screen also identified novel phenothiazines, i.e., 8 and 10, with significant cytotoxic and cholinesterase modulatory effects in liver cancer cells; yet both compounds had low levels of toxicity in zebrafish. Moreover, they modulated the cholinesterase activity or expression of ACHE in a cancer cell line-specific manner, and compound 10 significantly inhibited the cholinesterase activity in zebrafish. Accordingly, using a successful combination of in silico, in vitro, and in vivo approaches, we identified several lead anticancer and cholinesterase modulatory PTZ derivatives for future research.
Embargo
A novel injectable nanotherapeutic platform increasing the bioavailability and anti-tumor efficacy of Arachidonylcyclopropylamide on an ectopic non-small cell lung cancer xenograft model: A randomized controlled trial
(Elsevier BV, 2024-12-31) Boyacıoğlu, Özge; Varan, Cem; Bilensoy, Erem; Aykut, Zaliha Gamze; Recber, Tuba; Nemutlu, Emirhan; Kılıç, Nedret; Korkusuz, Petek
Rapid progressing non-small cell lung adenocarcinoma (NSCLC) decreases treatment success. Cannabinoids emerge as drug candidates for NSCLC due to their anti-tumoral capabilities. We previously reported the controlled release of Arachidonylcyclopropylamide (ACPA) selectively targeting cannabinoid 1 (CB1) receptor in NSCLC cells in vitro. Hydrophobic polymers like polycaprolactone (PCL) offer prolonged circulation time and slower drug clearance which is suitable for hydrophobic molecules like ACPA. Thus, the extended circulation time with enhanced bioavailability and half-life of nanoparticular ACPA is crucial for its therapeutic performance in the tumor area. We assumed that a novel high technology-controlled release system increasing the bioavailability of ACPA compared to free ACPA could be transferred to the clinic when validated in vivo. Plasma profile of ACPA and ACPA-loaded PCL-based nanomedicine by LC-MS/MS and complete blood count (CBC) was assessed in wild-type Balb/c mice. Tumor growth in nanomedicine-applied NSCLC-induced athymic nude mice was assessed using bioluminescence imaging (BLI) and caliper measurements, histomorphometry,immunohistochemistry, TUNEL assay, and Western blot on days 7-21. Injectable NanoACPA increased its systemic exposure to tissues 5.5 times and maximum plasma concentration 6 times higher than free ACPA by substantially improving bioavailability. The potent effect of NanoACPA lasted for at least two days on ectopic NSCLC model through Akt/PI3K, Ras/MEK/Erk, and JNK pathways that diminished Ki-67 proliferative and promoted TUNEL apoptotic cell scores on days 7-21. The output reveals that NanoACPA platform could be a chemotherapeutic for NSCLC in the clinic following scale-up GLP/GMP-based phase trials, owing to therapeutic efficacy at a safe low dose window.
Open Access
Breast cancer plasticity after chemotherapy highlights the need for re-evaluation of subtyping in residual cancer and metastatic tissues
(MDPI AG, 2024-05-31) Padzinska-Pruszynska, Irena Barbara; Akbar, Muhammad Waqas; Isbilen, Murat; Gorka, Emilia; Küçükkaraduman, Barış; Canli, Secil Demirkol; Dedeoğlu, Ege; Azizolli, Shila; Cela, Isli; Akçay, Abbas Güven; Hakanoğlu, Haşim; Bodnar, Lubomir; Cierniak, Szczepan; Kozielec, Zygmunt; Pruszynski, Jacek Jerzy; Bittel, Martyna; Gure, Ali Osmay; Krol, Magdalena; Taciak, Bartlomiej
This research paper presents a novel approach to identifying biomarkers that can be used to prognosticate patients with triple-negative breast cancer (TNBC) eligible for neoadjuvant therapy. The study utilized survival and RNA sequencing data from a cohort of TNBC patients and identified 276 genes whose expression was related to survival in such patients. The gene expression data were then used to classify patients into two major groups based on the presence or absence of Wingless/Integrated-pathway (Wnt-pathway) and mesenchymal (Mes) markers (Wnt/Mes). Patients with a low expression of Wnt/Mes-related genes had a favorable outcome, with no deaths observed during follow-up, while patients with a high expression of Wnt/Mes genes had a higher mortality rate of 50% within 19 months. The identified gene list could be validated and potentially used to shape treatment options for TNBC patients eligible for neoadjuvant therapy providing valuable insights into the development of more effective treatments for TNBC. Our data also showed significant variation in gene expression profiles before and after chemotherapy, with most tumors switching to a more mesenchymal/stem cell-like profile. To verify this observation, we performed an in silico analysis to classify breast cancer tumors in Prediction Analysis of Microarray 50 (PAM50) molecular classes before treatment and after treatment using gene expression data. Our findings demonstrate that following drug intervention and metastasis, certain tumors undergo a transition to alternative subtypes, resulting in diminished therapeutic efficacy. This underscores the necessity for reevaluation of patients who have experienced relapse or metastasis post-chemotherapy, with a focus on molecular subtyping. Tailoring treatment strategies based on these refined subtypes is imperative to optimize therapeutic outcomes for affected individuals.
Open Access
Protocol to study neuronal membrane proteasome function in mouse peripheral sensory neurons
(Cell Press, 2025-03-21) Krueger, Emily R.; Church, Taylor R.; Brennan, Anna; Türker, Fulya; Villalón Landeros, Eric
Neuronal membrane proteasomes (NMPs) are expressed on a subset of somatosensory dorsal root ganglion (DRG) neurons and influence mechanical and pain sensitivity. Here, we present a protocol for studying NMP function in mouse peripheral sensory neurons. We describe steps for procuring and culturing primary DRG neurons. We then detail biochemical and antibody feeding approaches to analyze NMP expression and localization. Finally, we include Ca2+ imaging techniques for investigating NMP function in DRG neurons. For complete details on the use and execution of this protocol, please refer to Villalón Landeros et al.1 © 2024 The Author(s)
Open Access
Recent advances towards the understanding of secondary acute myeloid leukemia progression
(MDPI AG, 2024-02-27) Auerbach, Scott; Puka, Beana; Golla, Upendarrao; Chachoua, Ilyas
Secondary acute myeloid leukemia (sAML) is a heterogeneous malignant hematopoietic disease that arises either from an antecedent hematologic disorder (AHD) including myelodysplastic syndromes (MDS), myeloproliferative neoplasms (MPN), aplastic anemia (AA), or as a result of exposure to genotoxic chemotherapeutic agents or radiotherapy (therapy related AML, tAML). sAML is diagnosed when the number of blasts is ≥20% in the bone marrow or peripheral blood, and it is characterized by poor prognosis, resistance to therapy and low overall survival rate. With the recent advances in next generation sequencing technologies, our understanding of the molecular events associated with sAML evolution has significantly increased and opened new perspectives for the development of novel therapies. The genetic aberrations that are associated with sAML affect genes involved in processes such as splicing, chromatin modification and genome integrity. Moreover, non-coding RNAs’ emerged as an important contributing factor to leukemogenesis. For decades, the standard treatment for secondary AML has been the 7 + 3 regimen of cytarabine and daunorubicin which prolongs survival for several months, but modifications in either dosage or delivery has significantly extended that time. Apart from traditional chemotherapy, hematopoietic stem cell transplantation, CAR-T cell therapy and small molecule inhibitors have also emerged to treat sAML.
Open Access
Leishmania extracellular vesicles mediate protection against cutaneous leishmaniasis
(Wiley, 2024-09) Tokmak, İbrahim; Yılmaz, İsmail Cem; Giirse, Muzaffer Mayda; Yazar, Volkan; Salih, Bekir; Güler, Ülkü; Gürsel, İhsan; Gürsel, Mayda
Open Access
Molecular mechanisms of PI3K isoform dependence in embryonic growth
(Galenos Yayınevi, 2024-08-29) Atıcı, Sena; Çizmecioğlu, Onur
Objective The phosphoinositide 3-kinase (PI3K) pathway is an important signaling mechanism for cell proliferation and metabolism. Mutations that activate PIK3CA may make cells p110a dependent, but when phosphatase tensin homolog (PTEN) is lost, the p110b isoform of PI3Ks becomes more important. However, the exact mechanism underlying the prevalence of p110s remains unclear. In this study, our aim was to elucidate the processes behind PI3K isoform dependency in a cellular model of embryonic development. Material and Methods In order to understand PI3K isoform prevalence, mouse embryonic fibroblasts (MEFs) were used and p110b, PTEN and Rac1 activity was modulated using retroviral plasmids. Expression levels and cellular growth were assessed by performing immunoblots and crystal violet assays. Results The levels of PTEN had only a partial effect on the prevalence of PI3K isoforms in MEFs. The dependency on p110a diminished when PTEN was depleted. Of note, when PTEN expression was repressed, there was no full transition in dependency from one PI3K isoform to the other. Interestingly, the viability of PTEN-depleted MEFs became less dependent on p110a and more dependent on p110b when p110b was overexpressed. Nevertheless, the overexpression of p110b in conjunction with PTEN knock-downs did not result in a complete shift of isoforms in PI3Ks. Finally, we investigated Rac1 activation with a mutant allele and determined a more potent increase in p110b prominence in MEFs. Conclusion These findings suggest that multiple cellular parameters, including PTEN status, PI3K isoform levels, and Rac1 activity, combine to influence PI3K isoform prevalence, rather than a single determinant.
Open Access
Immunogenicity and protective capacity of a CpG ODN adjuvanted alum adsorbed bivalent meningococcal outer membrane vesicle vaccine
(Oxford University Press, 2024-03-27) Yıldırım, Tuğçe Canavar; Özsürekçi, Yasemin; Yıldırım, Muzaffer; Evcili, İrem; Yazar, Volkan; Aykaç, Kübra; Güler, Ülkü; Salih, Bekir; Gürsel, Mayda; Gürsel, İhsan
Invasive meningococcal disease (IMD) is caused by Neisseria meningitidis, with the main serogroups responsible for the disease being A, B, C, W, X, and Y. To date, several vaccines targeting N. meningitidis have been developed albeit with a short-lived protection. Given that MenW and MenB are the most common causes of IMD in Europe, Turkey, and the Middle East, we aimed to develop an outer membrane vesicle (OMV) based bivalent vaccine as the heterologous antigen source. Herein, we compared the immunogenicity, and breadth of serum bactericidal activity (SBA) assay-based protective coverage of OMV vaccine to the X serotype with existing commercial meningococcal conjugate and polysaccharide (PS) vaccines in a murine model. BALB/c mice were immunized with preclinical batches of the W + B OMV vaccine, either adjuvanted with Alum, CpG ODN, or their combinations, and compared with a MenACYW conjugate vaccine (Nimenrix^TM, Pfizer), and a MenB OMV-based vaccine (Bexsero®, GSK), The immune responses were assessed through enzyme-linked immunosorbent assay (ELISA) and SBA assay. Antibody responses and SBA titers were significantly higher in the W + B OMV vaccine when adjuvanted with Alum or CpG ODN, as compared to the control groups. Moreover, the SBA titers were not only significantly higher than those achieved with available conjugated ACYW vaccines but also on par with the 4CMenB vaccines. In conclusion, the W + B OMV vaccine demonstrated the capacity to elicit robust antibody responses, surpassing or matching the levels induced by licensed meningococcal vaccines. Consequently, the W + B OMV vaccine could potentially serve as a viable alternative or supplement to existing meningococcal vaccines.
Open Access
A common form of dominant human IFNAR1 deficiency impairs IFN-α and -ω but not IFN-β-dependent immunity
(Rockefeller University Press, 2024-12-16) Qureshah, Fahd Al; Pen, Jérémie Le; Weerd, Nicole A. de; Moncada-Velez, Marcela; Materna, Marie; Lin, Daniel C.; Milisavljevic, Baptiste; Vianna, Fernanda; Bizien, Lucy; Lorenzo, Lazaro; Lecuit, Marc; Pommier, Jean-David; Keles, Sevgi; Özçelik, Tayfun; Pedraza-Sanchez, Sigifredo; Prost, Nicolas de; Zein, Loubna El; Hammoud, Hassan; Ng, Lisa F.P.; Halwani, Rabih; Sharif-Askari, Narjes Saheb; Lau, Yu Lung; Tam, Anthony R.; Singh, Neha; Bhattad, Sagar; Berkun, Yackov; Chantratita, Wasun; Aguilar-López, Raúl; Shahrooei, Mohammad; Abel, Laurent; Bastard, Paul; Jouanguy, Emmanuelle; Béziat, Vivien; Zhang, Peng; Rice, Charles M.; Cobat, Aurélie; Zhang, Shen-Ying; Hertzog, Paul J.; Casanova, Jean-Laurent; Zhang, Qian
Autosomal recessive deficiency of the IFNAR1 or IFNAR2 chain of the human type I IFN receptor abolishes cellular responses to IFN-α, -β, and -ω, underlies severe viral diseases, and is globally very rare, except for IFNAR1 and IFNAR2 deficiency in Western Polynesia and the Arctic, respectively. We report 11 human IFNAR1 alleles, the products of which impair but do not abolish responses to IFN-α and -ω without affecting responses to IFN-β. Ten of these alleles are rare in all populations studied, but the remaining allele (P335del) is common in Southern China (minor allele frequency ≈2%). Cells heterozygous for these variants display a dominant phenotype in vitro with impaired responses to IFN-α and -ω, but not -β, and viral susceptibility. Negative dominance, rather than haploinsufficiency, accounts for this dominance. Patients heterozygous for these variants are prone to viral diseases, attesting to both the dominance of these variants clinically and the importance of IFN-α and -ω for protective immunity against some viruses.
Open Access
Heterozygous BTNL8 variants in individuals with multisystem inflammatory syndrome in children (MIS-C)
(Rockefeller University Press, 2024-11-22) Bellos, Evangelos; Santillo, Dilys; Vantourout, Pierre; Jackson, Heather R.; Duret, Amedine; Hearn, Henry; Seeleuthner, Yoann; Talouarn, Estelle; Hodeib, Stephanie; Patel, Harsita; Powell, Oliver; Yeoh, Sophya; Mustafa, Sobia; Habgood-coote, Dominic; Nichols, Samuel; Elorrieta, Leire Estramiana; D’souza, Giselle; Wright, Victoria J.; Estrada-rivadeneyra, Diego; Tremoulet, Adriana H.; Dummer, Kirsten B.; Netea, Stejara A.; Condino-neto, Antonio; Lau, Yu Lung; Cuadros, Esmeralda Núñez; Toubiana, Julie; Pena, Marisol Holanda; Rieux-laucat, Frédéric; Luyt, Charles-edouard; Haerynck, Filomeen; Mège, Jean Louis; Chakravorty, Samya; Haddad, Elie; Morin, Marie-paule; Akcan, Özge Metin; Keles, Sevgi; Emiroglu, Melike; Alkan, Gulsum; Öz, Sadiye Kübra Tüter; Bozdemir, Sefika Elmas; Morelle, Guillaume; Volokha, Alla; Kendir-demirkol, Yasemin; Sözeri, Betul; Coskuner, Taner; Gulhan, Aysun Yahsi, Belgin; Kanik-yuksek, Saliha; Bayhan, Gulsum Iclal; Ozkaya-parlakay, Aslinur; Yesilbas, Osman; Hatipoglu, Nevin; Özçelik, Tayfun; Belot, Alexandre; Chopin, Emilie; Barlogis, Vincent; Sevketoglu, Esra; Menentoglu, Emin; Aydin, Zeynep Gokce Gayretli; Bloomfield, Marketa; Alkhater, Suzan A.; Cyrus, Cyril; Stepanovskiy, Yuriy; Bondarenko, Anastasiia; Öz, Fatma Nur; Polat, Meltem; Fremuth, Jiří; Lebl, Jan; Geraldo, Amyrath; Jouanguy, Emmanuelle; Carter, Michael J.; Wellman, Paul; Peters, Mark; Diego, Rebeca Pérez De; Edwards, Lindsey Ann; Chiu, Christopher; Noursadeghi, Mahdad; Bolze, Alexandre; Shimizu, Chisato; Kaforou, Myrsini; Hamilton, Melissa Shea; Herberg, Jethro A.; Schmitt, Erica G.; Rodriguez-palmero, Agusti; Pujol, Aurora; Kim, Jihoon; Cobat, Aurélie; Abel, Laurent; Zhang, Shen-ying; Casanova, Jean-laurent; Kuijpers, Taco W.; Burns, Jane C.; Levin, Michael; Hayday, Adrian C.; Sancho-shimizu, Vanessa
Multisystem inflammatory syndrome in children (MIS-C) is a rare condition following SARS-CoV-2 infection associated with intestinal manifestations. Genetic predisposition, including inborn errors of the OAS-RNAseL pathway, has been reported. We sequenced 154 MIS-C patients and utilized a novel statistical framework of gene burden analysis, “burdenMC,” which identified an enrichment for rare predicted-deleterious variants in BTNL8 (OR = 4.2, 95% CI: 3.5-5.3, P < 10-6). BTNL8 encodes an intestinal epithelial regulator of Vγ4+γδ T cells implicated in regulating gut homeostasis. Enrichment was exclusive to MIS-C, being absent in patients with COVID-19 or bacterial disease. Using an available functional test for BTNL8, rare variants from a larger cohort of MIS-C patients (n = 835) were tested which identified eight variants in 18 patients (2.2%) with impaired engagement of Vγ4+γδ T cells. Most of these variants were in the B30.2 domain of BTNL8 implicated in sensing epithelial cell status. These findings were associated with altered intestinal permeability, suggesting a possible link between disrupted gut homeostasis and MIS-C-associated enteropathy triggered by SARS-CoV-2.
Open Access
Higher COVID-19 pneumonia risk associated with anti-IFN-α than with anti-IFN-ω auto-Abs in children
(Rockefeller University Press, 2024-01-04) Bastard, Paul; Gervais, Adrian; Taniguchi, Maki; Saare, Liisa; Särekannu, Karita; Voyer, Tom le; Philippot, Quentin; Rosain, Jeremie; Bizien, Lucy; Asano, Takaki; Garcia-Prat, Marina; Parra-Martínez, Alba; Migaud, Mélanie; Tsumura, Miyuki; Conti, Francesca; Belot, Alexandre; Rivière, Jacques G.; Morio, Tomohiro; Tanaka, Junko; Javouhey, Etienne; Haerynck, Filomeen; Duvlis, Sotirija; Özçelik, Tayfun; Keles, Sevgi; Redondo, yacine tandjaoui-lambiotte; Escoda, Simon; Husain, Maya; Pan-Hammarström, Qiang; Hammarström, Lennart; Gloria, Ahlijah; Haidar, Anthony ABI; Soudee, Camille; Abolhassani, Hassan; Sahanic, Sabina; Tancevski, Ivan; Nukui, Yoko; Hayakawa, Seiichi; Chrousos, George P.; Michos, Athanasios; Tatsi, Elizabeth; Filippatos, Filippos; Rodriguez-Palmero, Agusti; García, Jesús Troya; Tipu, Imran; Meyts, Isabelle; Roussel, Lucie; Ostrowski, Sisse Rye; Schidlowski, Laire; Prando, Carolina; Condino-Neto, Antonio; Cheikh, Nathalie; Bousfiha, Ahmed Aziz; Bakkouri, Jalila EL; Peterson, Pärt; Pujol, Aurora; Lévy, Romain; Quartier, Pierre; Vinh, Donald C.; Boisson, Bertrand; Béziat, Vivien; Zhang, Shen-Ying; Borghesi, Alessandro; Pession, Andrea; Andreakos, Evangelos; Marr, Nico; Mentis, Alexios-Fotios; Mogensen, Trine Hyrup; Rodríguez-Gallego, Carlos; Soler-Palacín, Pere; Colobran, Roger; Tillmann, Vallo; Neven, Benedicte; Trouillet-Assant, Sophie; Brodin, Petter; Abel, Laurent; Jouanguy, Emmanuelle; Zhang, Qian; Martinon-Torres, Federico; Salas, Antonio; Gómez-Carballa, Alberto; Gonzalez-Granado, Luis Ignacio; Kisand, Kai; Okada, Satoshi; Puel, Anne; Cobat, Aurélie; Casanova, Jean-Laurent
We found that 19 (10.4%) of 183 unvaccinated children hospitalized for COVID-19 pneumonia had autoantibodies (auto-Abs) neutralizing type I IFNs (IFN-alpha 2 in 10 patients: IFN-alpha 2 only in three, IFN-alpha 2 plus IFN-omega in five, and IFN-alpha 2, IFN-omega plus IFN-beta in two; IFN-omega only in nine patients). Seven children (3.8%) had Abs neutralizing at least 10 ng/ml of one IFN, whereas the other 12 (6.6%) had Abs neutralizing only 100 pg/ml. The auto-Abs neutralized both unglycosylated and glycosylated IFNs. We also detected auto-Abs neutralizing 100 pg/ml IFN-alpha 2 in 4 of 2,267 uninfected children (0.2%) and auto-Abs neutralizing IFN-omega in 45 children (2%). The odds ratios (ORs) for life-threatening COVID-19 pneumonia were, therefore, higher for auto-Abs neutralizing IFN-alpha 2 only (OR [95% CI] = 67.6 [5.7-9,196.6]) than for auto-Abs neutralizing IFN-. only (OR [95% CI] = 2.6 [1.2-5.3]). ORs were also higher for auto-Abs neutralizing high concentrations (OR [95% CI] = 12.9 [4.6-35.9]) than for those neutralizing low concentrations (OR [95% CI] = 5.5 [3.1-9.6]) of IFN-omega and/or IFN-alpha 2.
Open Access
SARS-CoV-2 brainstem encephalitis in human inherited DBR1 deficiency
(Rockefeller University Press, 2024-07-18) Yi-Hao Chan; Lundberg, Vanja; Pen, Jérémie Le; Yuan, Jiayi; Lee, Danyel; Pinci, Francesca; Volpi, Stefano; Nakajima, Koji; Bondet, Vincent; Linnéa Åkesson, Sanna Emmy; Khobrekar, Noopur; Bodansky, Aaron; Du, Likun; Melander, Tina; Mariaggi, Alice-Andrée; Seeleuthner, Yoann; Saleh, Tariq Shikh; Chakravarty, Debanjana; Marits, Per; Dobbs, Kerry; Vonlanthen, Sofie; Hennings, Viktoria; Thörn, Karolina; Rinchai, Darawan; Bizien, Lucy; Chaldebas, Matthieu; Sobh, Ali; Özçelik, Tayfun; Keles, Sevgi; AlKhater, Suzan; Prando, Carolina; Meyts, Isabelle; Wilson, Michael; Rosain, Jeremie; Jouanguy, Emmanuelle; Aubart, Melodie; Abel, Laurent; Mogensen, Trine Hyrup; Pan-Hammarström, Qiang; Gao, Daxing; Duffy, Darragh; Cobat, Aurélie; Berg, Stefan; Notarangelo, Luigi; Harschnitz, Oliver; Rice, Charles M.; Studer, Lorenz; Casanova, Jean-Laurent; Ekwall, Olov; Zhang, Shen-Ying
Inherited deficiency of the RNA lariat–debranching enzyme 1 (DBR1) is a rare etiology of brainstem viral encephalitis. The cellular basis of disease and the range of viral predisposition are unclear. We report inherited DBR1 deficiency in a 14-year-old boy who suffered from isolated SARS-CoV-2 brainstem encephalitis. The patient is homozygous for a previously reported hypomorphic and pathogenic DBR1 variant (I120T). Consistently, DBR1 I120T/I120T fibroblasts from affected individuals from this and another unrelated kindred have similarly low levels of DBR1 protein and high levels of RNA lariats. DBR1 I120T/I120T human pluripotent stem cell (hPSC)–derived hindbrain neurons are highly susceptible to SARS-CoV-2 infection. Exogenous WT DBR1 expression in DBR1 I120T/I120T fibroblasts and hindbrain neurons rescued the RNA lariat accumulation phenotype. Moreover, expression of exogenous RNA lariats, mimicking DBR1 deficiency, increased the susceptibility of WT hindbrain neurons to SARS-CoV-2 infection. Inborn errors of DBR1 impair hindbrain neuron–intrinsic antiviral immunity, predisposing to viral infections of the brainstem, including that by SARS-CoV-2.
Open Access
Bone marrow mesenchymal stromal cells supportregeneration of intestinal damage in a colitis mouse model,independent of their CXCR4 expression
(Wiley-Blackwell Publishing, Inc., 2024-05-14) Pervin, B.; Gizer, M.; Seker, M.E.; Erol, Ö.D.; Gür, S.N.; Polat, E.G.; Değirmenci Uzun, Bahar; Korkusuz, P.; Aerts-Kaya, F.
Inflammatory bowel disease (IBD) is characterized by a chronically dysregulated immune response in the gastrointestinal tract. Bone marrow multipotent mesenchymal stromal cells have an important immunomodulatory function and support regeneration of inflamed tissue by secretion of soluble factors as well as through direct local differentiation. CXCR4 is the receptor for CXCL12 (SDF-1, stromal-derived factor-1) and has been shown to be the main chemokine receptor, required for homing of MSCs. Increased expression of CXCL12 by inflamed intestinal tissue causes constitutive inflammation by attracting lymphocytes but can also be used to direct MSCs to sites of injury/inflammation. Trypsin is typically used to dissociate MSCs into single-cell suspensions but has also been shown to digest surface CXCR4. Here, we assessed the regenerative effects of $CXCR4^{high}$ and $CXCR4^{low}$ MSCs in an immune-deficient mouse model of DSS-induced colitis. We found that transplantation of MSCs resulted in clinical improvement and histological recovery of intestinal epithelium. In contrary to our expectations, the levels of CXCR4 on transplanted MSCs did not affect their regenerative supporting potential, indicating that paracrine effects of MSCs may be largely responsible for their regenerative/protective effects.
Open Access
Whole-exome sequencing for genetic diagnosis of idiopathic liver injury in children
(Wiley-Blackwell Publishing Ltd., 2024-06) Lülecioğlu, Ayşima Atılgan; Yazıcı, Yılmaz Yücehan; Baran, Alperen; Warasnhe, Khaled; Beyaz, Şengül; Aytekin, Caner; Özcay, Figen; Aydemir, Yusuf; Barış, Zeren; Belkaya, Serkan
Genome-wide approaches, such as whole-exome sequencing (WES), are widely used to decipher the genetic mechanisms underlying inter-individual variability in disease susceptibility. We aimed to dissect inborn monogenic determinants of idiopathic liver injury in otherwise healthy children. We thus performed WES for 20 patients presented with paediatric-onset recurrent elevated transaminases (rELT) or acute liver failure (ALF) of unknown aetiology. A stringent variant screening was undertaken on a manually-curated panel of 380 genes predisposing to inherited human diseases with hepatobiliary involvement in the OMIM database. We identified rare nonsynonymous variants in nine genes in six patients (five rELT and one ALF). We next performed a case-level evaluation to assess the causal concordance between the gene mutated and clinical symptoms of the affected patient. A genetic diagnosis was confirmed in four rELT patients (40%), among whom two carried novel mutations in ACOX2 or PYGL, and two had previously-reported morbid variants in ABCB4 or PHKA2. We also detected rare variants with uncertain clinical significance in CDAN1, JAG1, PCK2, SLC27A5 or VPS33B in rELT or ALF patients. In conclusion, implementation of WES improves diagnostic yield and enables precision management in paediatric cases of liver injury with unknown aetiology, in particular recurrent hypertransaminasemia.
Embargo
Enhancing preventive and therapeutic cancer vaccine efficacy through biotherapeutic ligand-associated extracellular vesicles
(Elsevier Ltd, 2024-12) Kahraman, Tamer; Akpınar, Gözde Güçlüler; Yıldırım, Muzaffer; Larssen, Pia; Bayyurt-Kocabaş, Banu; Yağcı, Fuat Cem; Gürsel, Arda; Horuluoğlu, Begüm Han; Yazar, Volkan; Ayanoğlu, İhsan Cihan; Yıldırım, Tuğce Canavar; Evcili, İrem; Yılmaz, İsmail Cem; Eldh, Maria; Gabrielsson, Susanne; Güler, Ülkü; Salih, Bekir; Gursel, Mayda; Gürsel, İhsan
Extracellular vesicles (EVs), secreted by almost all living cells, have gained significant attention for their role in intercellular communication and their potential as versatile carriers for biotherapeutics. However, the clinical translation of EV-based therapies faces significant challenges, primarily due to the lack of efficient methods for loading biotherapeutic agents into EVs. This study introduces a simple, reproducible strategy for the simultaneous incorporation of various biotherapeutics within EVs. The process is gentle and preserves the essential physicochemical and biological characteristics of EVs, thereby protecting labile ligands from premature degradation and elimination. The binding and uptake efficiency of EVs by target cells reached approximately 97 % within 24 h of incubation. Administration of EVs loaded with oligodeoxynucleotides (ODN) resulted in a 4-fold increase in $IFNy^{+}$ $CD4^{+}$ T cells and a 5-fold increase in $IFNy^{+}$ $CD8^{+}$ T cells in the spleens and lymph nodes. Additionally, the co-administration of EVs with ODN and ovalbumin (OVA) induced elevated Th1-biased antibody responses and antigen-specific cytotoxic T-cell responses, providing long-lasting complete protection in 60 % of mice against T-cell thymoma challenge. Furthermore, EVs associated with three different ligands (OVA, CpG-ODN, and α-GalCer) effectively regressed established murine melanoma and significantly improved survival rates in mice. This study presents a powerful and promising approach to overcoming the limitations of EV-based cancer vaccines, advancing the development of effective cancer immunotherapies.
Embargo
Ultrasensitive electrochemical immunosensor system for determination of autologous SOX2 antibody
(Elsevier BV, 2024-01-20) Özçelikay-Akyıldız, Göksu; Ünal, Mehmet Altay; Atakan, Şükrü; Gülden, Seçil; Kızılelma, Bilal; Aydın, Safa; Özkan, Sibel A.
Lung cancer is mainly seen as the cancer type in the world. Lung cancer causes the death of many people. It is classified as large -cell neuroendocrine carcinoma (LCNEC), small -cell lung cancer (SCLC), and adenocarcinoma by the World Health Organization (WHO) in 2015. Small cell lung cancer (SCLC) is a highly aggressive type of cancer, accounting for approximately 20% of all cases. By performing the serological analysis of expression cDNA libraries (SEREX), the humoral immune response of SCLC patients is determined. SEREX of SCLC cell lines using pooled sera of SCLC patients led to the isolation of SOX2 genes. The between SOX2 antigen expression intensity and autologous antibody presence has a significant correlation because SOX2 is the main antigen eliciting antiSOX responses. Electrochemical biosensors take much attention because of their simplicity, selectivity, and sensitivity in clinical analysis. Antibody -based surface recognizes antibody -specific antigens. This work aims to fabricate an immunosensor for determining autologous SOX2 antibodies using a multi -walled carbon nanotubemodified screen -printed electrode (DRP-MWCNT). All immobilization processes were evaluated with cyclic voltammetry (CV) and electrochemical impedance spectroscopy (EIS). The critical parameters were optimized, such as EDC/NHS concentration and time, SOX2 protein concentration and incubation time, BSA ratio, BSA blocking time, and anti-SOX2 antibody incubation time. The developed immunosensor, under optimal conditions, shows a linear response of autologous SOX2 antibody between 0.005 ng.mL-1 and 0.1 ng.mL-1. The limit of detection and quantification were 0.001 and 0.004 ng.mL-1, respectively. The electrode morphologies were examined with a scanning electron microscope (SEM). Lastly, the developed immunosensor was applied to a synthetic serum sample, and the linear range was compared with enzyme -linked immunosorbent assay (ELISA).
Open Access
A novel heterozygous NFKB2 variant in a multiplex family with common variable immune deficiency and autoantibodies against type I IFNs
(Springer New York LLC, 2024-11-23) Baran, Alperen; Lülecioğlu, Aysima Atılgan; Gao, Liwei; Yazıcı, Yılmaz Yücehan; Demirel, Fevzi; Metin, Ayşe; Casanova, Jean-Laurent; Pue, Anne; Le Voyer, Tom; Beyaz, Şengül; Belkaya, Serkan
We studied a family with three male individuals across two generations affected by common variable immune deficiency (CVID). We identified a novel missense heterozygous variant (c.2602T>A:p.Y868N) of NFKB2 in all patients and not in healthy relatives. Functional studies of the mutant allele in an overexpression system and of the patients’ cells confirmed the deleteriousness of the NFKB2 variant and genotype, respectively, on the activation of the non-canonical NF-κB signaling pathway. Impaired processing of p100 into p52 underlies p100 accumulation, which results in gain-of-function (GOF) of IκBδ inhibitory activity and loss-of-function (LOF) of p52 transcriptional activity. The three patients’ plasma contained autoantibodies that neutralized IFN-α2 and/or IFN-ω, accounting for the severe or recurrent viral diseases of the patients, including influenza pneumonia in one sibling, and severe COVID-19 and recurrent herpes labialis in another. Our results confirm that NFKB2 alleles that are IκBδ GOF and p52 LOF can underlie CVID and drive the production of autoantibodies neutralizing type I IFNs, thereby predisposing to severe viral diseases.
Open Access
The aesthetic experience of interior spaces with curvilinear boundaries and various space properties in immersive and desktop-based virtual environments
(American Psychological Association, 2024-12-05) Elver Boz, Tuğce; Demirkan, Halime; Ürgen, Burcu Ayşen
The study aims to investigate participants' aesthetic experience in response to environments with curvilinear boundaries that are presented in two different virtual environments (VEs), namely immersive (IVE) and desktop-based virtual environments (DTVE). To this end, 60 participants were presented with 360 degrees 32 VE visualizations that had either horizontal or vertical curvilinear boundaries and possessed various architectural properties (size/light/texture/color) using a head-mounted display and a desktop computer. The aesthetic experience in response to these visualizations was measured in terms of the three key dimensions identified in a previous study (Elver Boz et al., 2022): familiarity, excitement, and fascination. In addition, participants' sense of presence in the two different environments was measured. The results show that familiarity and excitement dimensions were significantly higher in IVE than in DTVE, whereas the two environments did not significantly differ from each other in terms of the fascination dimension. As for the boundary types, the familiarity dimension was significantly higher in horizontal curvilinear boundaries than in vertical ones. In contrast, excitement and fascination dimensions were significantly higher in vertical curvilinear boundaries than in horizontal ones. The only dimension that showed an interaction between boundary types and the type of VE was excitement. Finally, IVE induced a higher presence feeling than DTVE. Overall, results suggest that people's aesthetic experiences toward built environments change as a function of the boundary types and the medium they are presented with these environments and that different dimensions of the aesthetic experience are affected differently by these variables.
Embargo
Computational modeling of the anti-inflammatory complexes of IL37
(Elsevier Inc., 2025-01-18) Şardağ, İnci; Düvenci, Zeynep Şevval; Belkaya, Serkan; Timuçin, Emel
Interleukin (IL) 37 is an anti-inflammatory cytokine belonging to the IL1 protein family. Owing to its pivotal role in modulating immune responses, elucidating the IL37 complex structures holds substantial therapeutic promise for various autoimmune disorders and cancers. However, none of the structures of IL37 complexes have been experimentally characterized. This computational study aims to address this gap through molecular modeling and classical molecular dynamics simulations. We modeled all protein–protein complexes of IL37 using a range of methods from homology modeling to AlphaFold2 multimer predictions. Models that successfully recapitulated experimental features underwent further analysis through molecular dynamics simulations. As positive controls, binary and ternary complexes of IL18 from PDB were included for comparison. Several key findings emerged from the comparative analysis of IL37 and IL18 complexes. IL37 complexes exhibited higher mobility than the IL18 complexes. Simulations of the IL37-IL18Rα complex revealed altered receptor conformations capable of accommodating a dimeric IL37, with the N-terminal loop of IL37 contributing significantly to complex mobility. Additionally, the glycosyl chain on N297 of IL18Rα, which contours one edge of the cytokine binding surface, acted as a steric block against the N-terminal loop of IL37. Further, investigations into interactions between IL37 and IL18BP suggested that a binding mode homologous to IL18 was unstable for IL37, indicating an alternative binding mechanism. Altogether, this study accesses to the structure and dynamics of IL37 complexes, revealing the structural underpinnings of the IL37’s modulatory effect on the IL18 signaling pathway.