Department of Molecular Biology and Genetics

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  • ItemOpen Access
    Microfluidics-integrated microwave sensors for single cells size discrimination
    (Institute of Electrical and Electronics Engineers, 2021-04-01) Seçme, Arda; Pisheh, Hadi Sedaghat; Uslu, H. Dilara; Akbulut, Özge; Erdoğan, R. Tufan; Hanay, M. Selim; Akbulut, Özge; Erdoğan, R. Tufan; Seçme, Arda; Pisheh, Hadi Sedaghat; Uslu, H. Dilara; Hanay, M. Selim
    The size of a cell is one of the most fundamental biophysical parameters it possesses. Traditionally size measurements are done by using optical microscopy and quantitative phase imaging. However, a sensor with higher resolution, high throughput and lower cost is still needed. Here, a novel microfluidics-integrated microwave sensor is demonstrated to characterize single cells in real-time without labelling. Coplanar waveguide resonator is designed with a bowtie-shaped sensing electrodes separated by 50 μm. Cells are transported to sensing region by microfluidic channels and their sizes are measured simultaneously by the microwave sensors and optical microscopy. To enhance the microwave resolution, the microwave resonator is equipped with external heterodyne measurement circuitry detecting each and every cell passing through the sensing region. By comparing quantitative microscopic image analysis with frequency shifts, we show that microwave sensors can effectively measure cellular size. Our results indicate that microfluidics-integrated microwave sensors (MIMS) can be used for detecting.
  • ItemOpen Access
    Author Correction: A global effort to dissect the human genetic basis of resistance to SARS-CoV-2 infection (Nature Immunology, (2022), 23, 2, (159-164), 10.1038/s41590-021-01030-z)
    (Springer Nature, 2022-02) Andreakos, Evangelos; Abel, Laurent; Vinh, Donald C.; Kaja, Elżbieta; Drolet, Beth A.; Zhang, Qian; O’Farrelly, Cliona; Novelli, Giuseppe; Rodríguez-Gallego, Carlos; Haerynck, Filomeen; Prando, Carolina; Pujol, Aurora; Bastard, Paul; Biggs, Catherine M.; Bigio, Benedetta; Boisson, Bertrand; Bolze, Alexandre; Bondarenko, Anastasiia; Brodin, Petter; Chakravorty, Samya; Christodoulou, John; Cobat, Aurelié; Condino-Neto, Antonio; Constantinescu, Stefan N.; Feldman, Hagit Baris; Fellay, Jacques; Halwani, Rabih; Jouanguy, Emmanuelle; Lau, Yu-Lung; Meyts, Isabelle; Mogensen, Trine H.; Okada, Satoshi; Okamoto, Keisuke; Özçelik, Tayfun; Pan-Hammarström, Qiang; Planas, Anna M.; Puel, Anne; Quintana-Murci, Lluis; Renia, Laurent; Resnick, Igor; Sediva, Anna; Shcherbina, Anna; Slaby, Ondrej; Tancevski, Ivan; Turvey, Stuart E.; Uddin, K. M. Furkan; van de Beek, Diederik; Zatz, Mayana; Zawadzki, Pawel; Zhang, Shen-Ying; Su, Helen C.; Casanova, Jean-Laurent; Spaan, András N.; Özçelik, Tayfun
  • ItemOpen Access
    Fulminant viral hepatitis in two siblings with inherited IL-10RB deficiency
    (Springer, 2022-10-29) Korol, Cecilia B.; Belkaya, Serkan; Alsohime, Fahad; Lorenzo, Lazaro; Boisson-Dupuis, Stéphanie; Brancale, Joseph; Neehus, Anna-Lena; Vilarinho, Silvia; Zobaida, Alsum; Halwani, Rabih; Al-Muhsen, Saleh; Casanova, Jean-Laurent; Jouanguy, Emmanuelle; Belkaya, Serkan
    Fulminant viral hepatitis (FVH) caused by hepatitis A virus (HAV) is a life-threatening disease that typically strikes otherwise healthy individuals. The only known genetic etiology of FVH is inherited IL-18BP deficiency, which unleashes IL-18-dependent lymphocyte cytotoxicity and IFN-γ production. We studied two siblings who died from a combination of early-onset inflammatory bowel disease (EOIBD) and FVH due to HAV. The sibling tested was homozygous for the W100G variant of IL10RB previously described in an unrelated patient with EOIBD. We show here that the out-of-frame IL10RB variants seen in other EOIBD patients disrupt cellular responses to IL-10, IL-22, IL-26, and IFN-λs in overexpression conditions and in homozygous cells. By contrast, the impact of in-frame disease-causing variants varies between cases. When overexpressed, the W100G variant impairs cellular responses to IL-10, but not to IL-22, IL-26, or IFN-λ1, whereas cells homozygous for W100G do not respond to IL-10, IL-22, IL-26, or IFN-λ1. As IL-10 is a potent antagonist of IFN-γ in phagocytes, these findings suggest that the molecular basis of FVH in patients with IL-18BP or IL-10RB deficiency may involve excessive IFN-γ activity during HAV infections of the liver. Inherited IL-10RB deficiency, and possibly inherited IL-10 and IL-10RA deficiencies, confer a predisposition to FVH, and patients with these deficiencies should be vaccinated against HAV and other liver-tropic viruses. © 2022, The Author(s).
  • ItemOpen Access
    Leishmania kinetoplast DNA contributes to parasite burden in infected macrophages: Critical role of the cGAS-STING-TBK1 signaling pathway in macrophage parasitemia
    (Frontiers Media S.A., 2022-11-02) Yilmaz, Ismail Cem; Dunuroglu, Emre; Ayanoglu, Ihsan Cihan; Ipekoglu, Emre Mert; Yıldırım, Muzaffer; Girginkardesler, Nogay; Ozbel, Yusuf; Toz, Seray; Ozbilgin, Ahmet; Aykut, Gamze; Gursel, Ihsan; Yıldırım, Muzaffer; Aykut, Gamze; Gursel, Ihsan
    Leishmania parasites harbor a unique network of circular DNA known as kinetoplast DNA (kDNA). The role of kDNA in leishmania infections is poorly understood. Herein, we show that kDNA delivery to the cytosol of Leishmania major infected THP-1 macrophages provoked increased parasite loads when compared to untreated cells, hinting at the involvement of cytosolic DNA sensors in facilitating parasite evasion from the immune system. Parasite proliferation was significantly hindered in cGAS- STING- and TBK-1 knockout THP-1 macrophages when compared to wild type cells. Nanostring nCounter gene expression analysis on L. major infected wild type versus knockout cells revealed that some of the most upregulated genes including, Granulysin (GNLY), Chitotriosidase-1 (CHIT1), Sialomucin core protein 24 (CD164), SLAM Family Member 7 (SLAMF7), insulin-like growth factor receptor 2 (IGF2R) and apolipoprotein E (APOE) were identical in infected cGAS and TBK1 knockout cells, implying their involvement in parasite control. Amlexanox treatment (a TBK1 inhibitor) of L. major infected wild type cells inhibited both the percentage and the parasite load of infected THP-1 cells and delayed footpad swelling in parasite infected mice. Collectively, these results suggest that leishmania parasites might hijack the cGAS-STING-TBK1 signaling pathway to their own advantage and the TBK1 inhibitor amlexanox could be of interest as a candidate drug in treatment of cutaneous leishmaniasis. Copyright © 2022 Yilmaz, Dunuroglu, Ayanoglu, Ipekoglu, Yildirim, Girginkardesler, Ozbel, Toz, Ozbilgin, Aykut, Gursel and Gursel.
  • ItemOpen Access
    Doxorubicin induces prolonged DNA damage signal in cells overexpressing DEK isoform-2
    (Public Library of Science, 2022-10-03) Özçelik, Emrah; Kalaycı, Ahmet; Çelik, Büşra; Avcı, Açelya; Akyol, Hasan; Kılıç, İrfan Baki; Güzel, Türkan; Çetin, Metin; Öztürk, Merve Tuzlakoğlu; Çalışkaner, Zihni Onur; Tombaz, Melike; Yoleri, Dilan; Konu, Özlen; Kandilci, Ayten; Tombaz, Melike; Konu, Özlen
    DEK has a short isoform (DEK isoform-2; DEK2) that lacks amino acid residues between 49–82. The full-length DEK (DEK isoform-1; DEK1) is ubiquitously expressed and plays a role in different cellular processes but whether DEK2 is involved in these processes remains elusive. We stably overexpressed DEK2 in human bone marrow stromal cell line HS-27A, in which endogenous DEKs were intact or suppressed via short hairpin RNA (sh-RNA). We have found that contrary to ectopic DEK1, DEK2 locates in the nucleus and nucleolus, causes persistent үH2AX signal upon doxorubicin treatment, and couldn’t functionally compensate for the loss of DEK1. In addition, DEK2 overexpressing cells were more sensitive to doxorubicin than DEK1-cells. Expressions of DEK1 and DEK2 in cell lines and primary tumors exhibit tissue specificity. DEK1 is upregulated in cancers of the colon, liver, and lung compared to normal tissues while both DEK1 and DEK2 are downregulated in subsets of kidney, prostate, and thyroid carcinomas. Interestingly, only DEK2 was downregulated in a subset of breast tumors suggesting that DEK2 can be modulated differently than DEK1 in specific cancers. In summary, our findings show distinct expression patterns and subcellular location and suggest non-overlapping functions between the two DEK isoforms. © 2022 Ozçelik et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
  • ItemOpen Access
    A new triazolothiadiazine derivative inhibits stemness and induces cell death in HCC by oxidative stress dependent JNK pathway activation
    (Nature Research, 2022-09-07) Kahraman, Deniz Cansen; Bilget Guven, Ebru; Aytac, Peri S.; Aykut, Gamze; Tozkoparan, Birsen; Cetin Atalay, Rengul; Bilget Guven, Ebru; Aykut, Gamze
    Hepatocellular carcinoma (HCC) is a highly heterogeneous cancer, and resistant to both conventional and targeted chemotherapy. Recently, nonsteroidal anti-inflammatory drugs (NSAIDs) have been shown to decrease the incidence and mortality of different types of cancers. Here, we investigated the cellular bioactivities of a series of triazolothiadiazine derivatives on HCC, which have been previously reported as potent analgesic/anti-inflammatory compounds. From the initially tested 32 triazolothiadiazine NSAID derivatives, 3 compounds were selected based on their IC50 values for further molecular assays on 9 different HCC cell lines. 7b, which was the most potent compound, induced G2/M phase cell cycle arrest and apoptosis in HCC cells. Cell death was due to oxidative stress-induced JNK protein activation, which involved the dynamic involvement of ASK1, MKK7, and c-Jun proteins. Moreover, 7b treated nude mice had a significantly decreased tumor volume and prolonged disease-free survival. 7b also inhibited the migration of HCC cells and enrichment of liver cancer stem cells (LCSCs) alone or in combination with sorafenib. With its ability to act on proliferation, stemness and the migration of HCC cells, 7b can be considered for the therapeutics of HCC, which has an increased incidence rate of ~ 3% annually. © 2022, The Author(s).
  • ItemOpen Access
    Functional analysis of co-expression networks of zebrafish ace2 reveals enrichment of pathways associated with development and disease
    (Canadian Science Publishing, 2022-02-02) Keşkuş, Ayşe Gökçe; Tombaz, Melike; Arıcı, Burçin İrem; Dinçaslan, Fatma Betül; Nabi, Afshan; Shehwana, Huma; Konu, Özlen; Keşkuş, Ayşe Gökçe; Tombaz, Melike; Arıcı, Burçin İrem; Dinçaslan, Fatma Betül; Nabi, Afshan; Shehwana, Huma; Konu, Özlen
    Human Angiotensin I Converting Enzyme 2 (ACE2) plays an essential role in blood pressure regulation and SARS-CoV-2 entry. ACE2 has a highly conserved, one-to-one ortholog (ace2) in zebrafish, which is an important model for human diseases. However, the zebrafish ace2 expression profile has not yet been studied during early development, between genders, across different genotypes, or in disease. Moreover, a network-based meta-analysis for the extraction of functionally enriched pathways associated with differential ace2 expression is lacking in the literature. Herein, we first identified significant development-, tissue-, genotype-, and gender-specific modulations in ace2 expression via meta-analysis of zebrafish Affymetrix transcriptomics datasets (ndatasets = 107); and the correlation analysis of ace2 meta-differential expression profile revealed distinct positively and negatively correlated local functionally enriched gene networks. Moreover, we demonstrated that ace2 expression was significantly modulated under different physiological and pathological conditions related to development, tissue, gender, diet, infection, and inflammation using additional RNA-seq datasets. Our findings implicate a novel translational role for zebrafish ace2 in organ differentiation and pathologies observed in the intestines and liver.
  • ItemOpen Access
    ER Stress-induced sphingosine-1-phosphate lyase phosphorylation potentiates the mitochondrial unfolded protein response
    (American Society for Biochemistry and Molecular Biology Inc., 2022-10) Yıldırım, Aslı Dilber; Citir, Mevlut; Doğan, Aslı Ekin; Veli, Zehra; Yıldırım, Zehra; Tufanli, Ozlem; Traynor-Kaplan, Alexis; Schultz, Carsten; Erbay, Ebru; Yıldırım, Aslı Dilber; Doğan, Aslı Ekin; Veli, Zehra; Yıldırım, Zehra
    The unfolded protein response (UPR) is an elaborate signaling network that evolved to maintain proteostasis in the endoplasmic reticulum (ER) and mitochondria (mt). These organelles are functionally and physically associated, and consequently, their stress responses are often intertwined. It is unclear how these two adaptive stress responses are coordinated during ER stress. The inositol-requiring enzyme-1 (IRE1), a central ER stress sensor and proximal regulator of the UPRER, harbors dual kinase and endoribonuclease (RNase) activities. IRE1 RNase activity initiates the transcriptional layer of the UPRER, but IRE1’s kinase substrate(s) and their functions are largely unknown. Here, we discovered that sphingosine 1-phosphate (S1P) lyase (SPL), the enzyme that degrades S1P, is a substrate for the mammalian IRE1 kinase. Our data show that IRE1-dependent SPL phosphorylation inhibits SPL’s enzymatic activity, resulting in increased intracellular S1P levels. S1P has previously been shown to induce the activation of mitochondrial UPR (UPRmt) in nematodes. We determined that IRE1 kinase-dependent S1P induction during ER stress potentiates UPRmt signaling in mammalian cells. Phosphorylation of eukaryotic translation initiation factor 2α (eif2α) is recognized as a critical molecular event for UPRmt activation in mammalian cells. Our data further demonstrate that inhibition of the IRE1-SPL axis abrogates the activation of two eif2α kinases, namely double-stranded RNA-activated protein kinase (PKR) and PKR–like ER kinase upon ER stress. These findings show that the IRE1-SPL axis plays a central role in coordinating the adaptive responses of ER and mitochondria to ER stress in mammalian cells. © 2022 THE AUTHORS.
  • ItemOpen Access
    PACT establishes a posttranscriptional brake on mitochondrial biogenesis by promoting the maturation of miR-181c
    (American Society for Biochemistry and Molecular Biology Inc., 2022-07) Doğan, Aslı Ekin; Hamid, Syed M.; Yıldırım, Aslı Dilber; Yıldırım, Zehra; Sen, Ganes; Riera, Celine E.; Gottlieb, Roberta A.; Erbay, Ebru; Doğan, Aslı Ekin; Yıldırım, Aslı Dilber; Yıldırım, Zehra
    The double-stranded RNA-dependent protein kinase activating protein (PACT), an RNA-binding protein that is part of the RNA-induced silencing complex, plays a key role in miR-mediated translational repression. Previous studies showed that PACT regulates the expression of various miRs, selects the miR strand to be loaded onto RNA-induced silencing complex, and determines proper miR length. Apart from PACT's role in mediating the antiviral response in immune cells, what PACT does in other cell types is unknown. Strikingly, it has also been shown that cold exposure leads to marked downregulation of PACT protein in mouse brown adipose tissue (BAT), where mitochondrial biogenesis and metabolism play a central role. Here, we show that PACT establishes a posttranscriptional brake on mitochondrial biogenesis (mitobiogenesis) by promoting the maturation of miR-181c, a key suppressor of mitobiogenesis that has been shown to target mitochondrial complex IV subunit I (Mtco1) and sirtuin 1 (Sirt1). Consistently, we found that a partial reduction in PACT expression is sufficient to enhance mitobiogenesis in brown adipocytes in culture as well as during BAT activation in mice. In conclusion, we demonstrate an unexpected role for PACT in the regulation of mitochondrial biogenesis and energetics in cells and BAT. © 2022 The Authors
  • ItemOpen Access
    3D-MSCs A151 ODN-loaded exosomes are immunomodulatory and reveal a proteomic cargo that sustains wound resolution
    (Elsevier B.V., 2022-11) Camões, Sérgio P.; Bulut, Özlem; Yazar, Volkan; Gaspar, Maria M.; Simões, Sandra; Ferreira, Rita; Vitorino, Rui; Santos, Jorge M.; Gürsel, İhsan; Miranda, Joana P.; Bulut, Özlem; Gürsel, İhsan
    Introduction: Non-healing wounds remain a major burden due to the lack of effective treatments. Mesenchymal stem cell-derived exosomes (MSC-Exo) have emerged as therapeutic options given their pro-regenerative and immunomodulatory features. Still, little is known on the exact mechanisms mediated by MSC-Exo. Importantly, modulation of their efficacy through 3D-physiologic cultures together with loading strategies continues underexplored. Objectives: To uncover the MSC-Exo-mediated mechanism via proteomic analyses, and to use 3D-culture and loading technologies to expand MSC-Exo efficacy for cutaneous wound healing. Methods: MSC-Exo were produced in either 3D or 2D cultures (Exo3D/Exo2D) and loaded with an exogenous immunosuppressive oligodeoxynucleotide (A151 ODN). Both, loaded and naïve exosomes were characterised regarding size, morphology and the presence of specific protein markers; while IPA analyses enabled to correlate their protein content with the effects observed in vitro and in vivo. The Exo3D/Exo2D regenerative potential was evaluated in vitro by assessing keratinocyte and fibroblast mitogenicity, motogenicity, and cytokine secretion as well as using an in vivo wound splinting model. Accordingly, the modulation of inflammatory and immune responses by A151-loaded Exo3D/Exo2D was also assessed. Results: Exo3D stimulated mitogenically and motogenically keratinocytes and fibroblasts in vitro, with upregulation of IL-1α and VEGF-α or increased secretion of TGF-β, TNF-α and IL-10. In vivo, Exo3D reduced the granulation tissue area and promoted complete re-epithelization of the wound. These observations were sustained by the proteomic profiling of the Exo3D cargo that identified wound healing-related proteins, such as TGF-β, ITGA1-3/5, IL-6, CDC151, S100A10 and Wnt5α. Moreover, when loaded with A151 ODN, Exo3D differentially mediated wound healing-related trophic factors reducing the systemic levels of IL-6 and TNF-α at the late stage of wound healing in vivo. Conclusion: Our results support the potential of A151-loaded Exo3D for the treatment of chronic wounds by promoting skin regeneration, while modulating the systemic levels of the pro-inflammatory cytokines. © 2022
  • ItemOpen Access
    Small RNA-seq dataset of wild type and 16C Nicotiana benthamiana leaves sprayed with naked dsRNA using the high-pressure spraying technique
    (Elsevier Inc., 2022-12) Çalışır, Kübra; Krczal, Gabi; Uslu, Veli Vural; Çalışır, Kübra
    Double-stranded RNA (dsRNA) applications have emerged as promising alternatives to chemical plant pesticides. It has been proposed that the protective effect of dsRNA is mediated by the RNA interference (RNAi) mechanism. Small RNAs (sRNAs) are one of the landmarks of RNAi mechanisms. Two classes of sRNAs appear upon RNAi, triggered by dsRNA: The cleavage products of the dsRNA mapping directly to the dsRNA sequence and the transitive sRNAs mapping to the target transcript outside of the dsRNA sequence. Therefore, the sRNA-seq data obtained from dsRNA-treated plants have been exclusively analysed in the context of the target genes and the outcome has been considered essential to evaluate the underlying mechanism of dsRNA mediated plant protection. Using high-pressure spraying technology (HPST), we have applied a GFP targeting 139bp-long dsRNA on wild type (WT) and GFP expressing (16C) Nicotiana benthamiana plants in biological triplicates. As a control, we applied water with HPST on 16C N. benthamiana. We have acquired sRNA-seq data on the treated and control leaves 5 days post spraying. In this dataset, we have expanded our sRNA-seq analysis from the target GFP transgene sequence to the whole transcriptome of N. benthamiana to provide the community with a resource for the small RNA landscape after high-pressure spraying in 16C and WT samples. Furthermore, we have provided a comparison of sRNA landscape between WT and 16C lines. © 2022 The Author(s)
  • ItemOpen Access
    Characterization of differential expression patterns of the extracellular purinergic enzymes in colorectal cancer
    (Trakya University, 2022-10-15) Göktuna, Serkan; Göktuna, Serkan
    The aim of this study is to characterize tumor cell specific expression of purinergic ecto-enzymes CD39 and CD73, and to associate prognostic significance of these expression patterns in colorectal cancer (CRC) patients. Protein and gene expression of the target genes in various CRC cell lines were assessed via Western Blot (WB) analysis and Real Time PCR (RT-PCR). Additionally, tumor vs stromal cell expression of the target genes was analyzed from publicly available patient expression datasets. Finally, the correlation between CD39 and CD73 expression with patient prognosis was analyzed via The Cancer Genome Atlas (TCGA) datasets. In CRC cell lines, CD39 was found to be not expressed at all while CD73 was expressed extensively in most cell lines via WB and RT-PCR analyses. Patient microarray expression data confirmed the results from CRC cell lines that CD39 expression was very low in epithelial/tumor cells relative to other stromal cell types yet CD73 was expressed abundantly in every cell type within patient tumor samples. Interestingly, CD39 expression in patient tumors was correlated with favorable prognosis while CD73 expression was associated with worse prognosis. Although CD39 and CD73 are related enzymes involved in extracellular purinergic signaling, their expression patterns in tumor cells and prognostic effects in patients show opposing outcomes. Therefore, better insights in understanding the functional involvement of purinergic ecto-enzymes in colorectal tumor development is needed via further mechanistic studies.
  • ItemOpen Access
    Inherited Irak-4 deficiency in acute human Herpesvirus-6 encephalitis
    (Springer, 2022-10-07) Tepe, Zeynep Güneş; Yazıcı, Yılmaz Yücehan; Tank, Umut; Köse, Ladin Işık; Özer, Murat; Aytekin, Caner; Belkaya, Serkan; Tepe, Zeynep Güneş; Yazıcı, Yılmaz Yücehan; Tank, Umut; Köse, Ladin Işık; Belkaya, Serkan
    Human herpesvirus-6 (HHV-6) infection can rarely cause life-threatening conditions, such as encephalitis, in otherwise healthy children, with unclear pathogenesis. We studied a child who presented with acute HHV-6 encephalitis at the age of 10 months and who was homozygous for a novel missense mutation in IRAK4, encoding interleukin-1 receptor-associated kinase 4, identified by whole-exome sequencing. We tested the damaging impact of this mutation in silico by molecular dynamics simulations and in vitro by biochemical and functional experiments utilizing cell lines and patient’s cells. We found that the mutation is severely hypomorphic, impairing both the expression and function of IRAK-4. Patient’s leukocytes had barely detectable levels of IRAK-4 and diminished anti-viral immune responses to various stimuli inducing different Toll-like receptors and cytosolic nucleic acid sensors. Overall, these findings suggest that acute HHV-6 encephalitis can result from inborn errors of immunity to virus. This study represents the first report of isolated acute HHV-6 infection causing encephalitis in an inherited primary immunodeficiency, notably autosomal recessive (AR) partial IRAK-4 deficiency, and the first report of AR IRAK-4 deficiency presenting with a severe viral disease, notably HHV-6 encephalitis upon an acute infection, thereby expanding the clinical spectrum of IRAK-4 deficiency.
  • ItemOpen Access
    Respiratory viral infections in otherwise healthy humans with inherited IRF7 deficiency
    (Rockefeller University Press, 2022) Özçelik, Tayfun; Campbell, Tessa Mollie; Liu, Zhiyong; Zhang, Qian; Moncada-Velez, Marcela; Covill, Laura E.; Zhang, Peng; Darazam, Ilad Alavi; Bastard, Paul; Bizien, Lucy; Bucciol, Giorgia; Enoksson, Sara Lind; Jouanguy, Emmanuelle; Karabela, Şemsi Nur; Khan, Taushif; Kendir-Demirkol, Yasemin; Arias, Andres Augusto; Mansouri, Davood; Marits, Per; Marr, Nico; Migeotte, Isabelle; Moens, Leen; Pellier, Isabelle; Sendel, Anton; Shahrooei, Mohammad; Edvard Smith C.I.; Vandernoot, Isabelle; Willekens, Karen; Bergman, Peter; Abel, Laurent; Cobat, Aurélie; Casanova, Jean-Laurent; Meyts, Isabelle; Bryceson, Yenan T.; Özçelik, Tayfun
    Autosomal recessive IRF7 deficiency was previously reported in three patients with single critical influenza or COVID-19 pneumonia episodes. The patients’ fibroblasts and plasmacytoid dendritic cells produced no detectable type I and III IFNs, except IFN-β. Having discovered four new patients, we describe the genetic, immunological, and clinical features of seven IRF7-deficient patients from six families and five ancestries. Five were homozygous and two were compound heterozygous for IRF7 variants. Patients typically had one episode of pulmonary viral disease. Age at onset was surprisingly broad, from 6 mo to 50 yr (mean age 29 yr). The respiratory viruses implicated included SARS-CoV-2, influenza virus, respiratory syncytial virus, and adenovirus. Serological analyses indicated previous infections with many common viruses. Cellular analyses revealed strong antiviral immunity and expanded populations of influenza-and SARS-CoV-2–specific memory CD4+ and CD8+ Tcells. IRF7-deficient individuals are prone to viral infections of the respiratory tract but are otherwise healthy, potentially due to residual IFN-β and compensatory adaptive immunity. © 2022 Campbell et al.
  • ItemOpen Access
    Recessive inborn errors of type I IFN immunity in children with COVID-19 pneumonia
    (Rockefeller University Press, 2022-08-01) Özçelik, Tayfun; Zhang, Qian; Matuozzo, Daniela; Le Pen, Jérémie; Moens, Leen; Asano, Takaki; Bohlen, Jonathan; Liu, Zhiyong; Moncada-Velez, Marcela; Kendir-Demirkol, Yasemin; Jing, Huie; Bizien, Lucy; Marchal, Astrid; Abolhassani, Hassan; Delafontaine, Selket; Bucciol, Giorgia; Bayhan, Gulsum Ical; Keles, Sevgi; Kiykim, Ayca; Hancerli, Selda; Haerynck, Filomeen; Florkin, Benoit; Hatipoğlu, Nevin; Morelle, Guillaume; Zatz, Mayana; Ng, Lisa F. P.; Lye, David Chien; Young, Barnaby Edward; Leo, Yee-Sin; Dalgard, Clifton L.; Lifton, Richard P.; Renia, Laurent; Meyts, Isabelle; Jouanguy, Emmanuelle; Hammarström, Lennart; Pan-Hammarström, Qiang; Boisson, Bertrand; Bastard, Paul; Su, Helen C.; Boisson-Dupuis, Stéphanie; Abel, Laurenta; Rice, Charles M.; Zhang, Shen-Ying; Cobat, Aurélie; Casanova, Jean-Laurent; Özçelik, Tayfun
    Recessive or dominant inborn errors of type I interferon (IFN) immunity can underlie critical COVID-19 pneumonia in unvaccinated adults. The risk of COVID-19 pneumonia in unvaccinated children, which is much lower than in unvaccinated adults, remains unexplained. In an international cohort of 112 children (<16 yr old) hospitalized for COVID-19 pneumonia, we report 12 children (10.7%) aged 1.5–13 yr with critical (7 children), severe (3), and moderate (2) pneumonia and 4 of the 15 known clinically recessive and biochemically complete inborn errors of type I IFN immunity: X-linked recessive TLR7 deficiency (7 children) and autosomal recessive IFNAR1 (1), STAT2 (1), or TYK2 (3) deficiencies. Fibroblasts deficient for IFNAR1, STAT2, or TYK2 are highly vulnerable to SARS-CoV-2. These 15 deficiencies were not found in 1,224 children and adults with benign SARS-CoV-2 infection without pneumonia (P = 1.2 × 10−11) and with overlapping age, sex, consanguinity, and ethnicity characteristics. Recessive complete deficiencies of type I IFN immunity may underlie ∼10% of hospitalizations for COVID-19 pneumonia in children. © 2022 Zhang et al.
  • ItemOpen Access
    Extraction and prioritization of a gene-cancer-by-survival network involved in homeostasis of intracellular calcium concentrations using TCGA PANCAN data
    (Mary Ann Liebert, Inc. Publishers, 2022-05-26) Tombaz, Melike; Yanyatan, Çağdaş; Keşküş, Ayşe Gökçe; Konu, Özlen; Tombaz, Melike; Yanyatan, Çağdaş; Keşküş, Ayşe Gökçe; Konu, Özlen
    Regulation of intracellular calcium concentrations, [Ca++]i is important in maintaining the viability of normal as well as cancer cells and can be mediated by tumor microenvironment. Calcium release-activated calcium channel protein (ORAI) calcium channels on the plasma membrane (PM) become physically connected by stromal interaction molecules (STIMs) to the endoplasmic reticulum (ER), on which paralogous receptors of inositol phosphate and of ryanodine are also present along with ATP2A/SERCA (sarco/endoplasmic reticulum calcium ATPases) subunits (also known as PM-ER geneset). Proper expression of this functionally and physically interconnected geneset is essential for the maintenance of [Ca++]i, yet has not been interrogated as a whole for its role in cancer prognosis using multivariable Cox regression. In the present study, we examined whether the expression profile of the PM-ER geneset exhibited prognostic significance across different cancers found in The Cancer Genome Atlas (TCGA) by generating gene-cancer-by-survival networks, in which the nodes represented either genes or cancers and the edges, the logarithmically transformed hazard ratios for overall survival (OS). We then applied network clustering to identify the gene-cancer subnetworks with high connectivity, among which uveal melanoma (UVM) emerged exhibiting the highest degree of genes (k = 10). BAP1, a well-known [Ca++]i regulator and a tumor suppressor, was not found to be significant in predicting OS by PM-ER geneset for UVM, yet it was for several others, including mesothelioma (MESO). Moreover, the best subset of the PM-ER geneset obtained by lasso predicted OS in the TCGA UVM cohort with an area under the receiver operating characteristics (AUC) of 91.4%, comparable to or better than previous prognostic signatures in the literature. Our findings indicate that homeostasis of [Ca++]i is an essential determinant of prognosis in multiple cancers and particularly in UVM. The proposed gene-cancer-by-survival network approach can be extended with other gene sets as well as different survival types.
  • ItemOpen Access
    Intercepting IRE1 kinase-FMRP signaling prevents atherosclerosis progression
    (EMBO Press, 2022-02-22) Yıldırım, Zehra; Baboo, S.; Hamid, S.M.; Doğan, Asli E.; Tufanlı, Ö.; Robichaud, S.; Emerton, C.; Diedrich, J.K.; Vatandaşlar, H.; Nikolos, F.; Gu, Y.; Iwawaki, T.; Tarling, E.; Ouimet, M.; Nelson, D.L.; Yates, J.R.; Walter, P.; Erbay, E.; Yıldırım, Zehra; Doğan, Asli E.
    Fragile X Mental Retardation protein (FMRP), widely known for its role in hereditary intellectual disability, is an RNA-binding protein (RBP) that controls translation of select mRNAs. We discovered that endoplasmic reticulum (ER) stress induces phosphorylation of FMRP on a site that is known to enhance translation inhibition of FMRP-bound mRNAs. We show ER stress-induced activation of Inositol requiring enzyme-1 (IRE1), an ER-resident stress-sensing kinase/endoribonuclease, leads to FMRP phosphorylation and to suppression of macrophage cholesterol efflux and apoptotic cell clearance (efferocytosis). Conversely, FMRP deficiency and pharmacological inhibition of IRE1 kinase activity enhances cholesterol efflux and efferocytosis, reducing atherosclerosis in mice. Our results provide mechanistic insights into how ER stress-induced IRE1 kinase activity contributes to macrophage cholesterol homeostasis and suggests IRE1 inhibition as a promising new way to counteract atherosclerosis.
  • ItemOpen Access
    The risk of COVID-19 death is much greater and age dependent with type I IFN autoantibodies
    (National Academy of Sciences, 2022-05-16) Manry, J.; Bastard, P.; Gervais, A.; Le Voyer, T.; Rosain, J.; Philippot, Q.; Michailidis, E.; Hoffmann, H.; Eto, S.; Garcia-Prat, M.; Bizien, L.; Parra-Martínez, A.; Yang, R.; Haljasmägi, L.; Migaud, M.; Särekannu, K.; Maslovskaja, J.; de Prost, N.; Tandjaoui-Lambiotte, Y.; Luyt, C.; Amador-Borrero, B.; Gaudet, A.; Poissy, J.; Morel, P.; Richard, P.; Cognasse, F.; Troya, J.; Trouillet-Assant, S.; Belot, A.; Saker, K.; Garçpn, P.; Rivière, J. G.; Lagier, J.; Gentile, S.; Rosen, L. B.; Shaw, E.; Morio, T.; Tanaka, J.; Dalmau, D.; Tharaux, P.; Sene, D.; Stepanian, A.; Mégarbane, B.; Triantafyllia, V.; Fekkar, A.; Heath, J. R.; Franco, J. L.; Anaya, J.; Solé-Violán, J.; Imberti, L.; Biondi, A.; Bonfanti, P.; Castagnoli, R.; Delmonte, O. M.; Zhang, Y.; Snow, A. L.; Holland, S. M.; Biggs, C. M.; Moncada-Vélez, M.; Arias, A. A.; Lorenzo, L.; Boucherit, S.; Anglicheau, D.; Planas, A. M.; Haerynck, F.; Duvlis, S.; Ozcelik, Tayfun; Keles, S.; Bousfiha, A. A.; El Bakkouri, J.; Ramirez-Santana, C.; Paul, S.; Pan-Hammarström, Q.; Hammarström, L.; Dupont, A.; Kurolap, A.; Metz, C. N.; Aiuti, A.; Casari, G.; Lampasona, V.; Ciceri, F.; Barreiros, L. A.; Dominguez-Garrido, E.; Vidigal, M.; Zatz, M.; van de Beek, D.; Sahanic, S.; Tancevski, I.; Stepanovskyy, Y.; Boyarchuk, O.; Nukui, Y.; Tsumura, M.; Vidaur, L.; Tangye, S. G.; Burrel, S.; Duffy, D.; Quintana-Murci, L.; Klocperk, A.; Kann, N. Y.; Shcherbina, A.; Lau, Y.; Leung, D.; Coulongeat, M.; Marlet, J.; Koning, R.; Reyes, L. F.; Chauvineau-Grenier, A.; Venet, F.; Monneret, G.; Nussenzweig, M. C.; Arrestier, R.; Boudhabhay, I.; Baris-Feldman, H.; Hagin, D.; Wauters, J.; Meyts, I.; Dyer, A. H.; Kennelly, S. P.; Bourke, N. M.; Halwani, R.; Sharif-Askari, F. S.; Dorgham, K.; Sallette, J.; Sedkaoui, S. M.; AlKhater, S.; Rigo-Bonnin, R.; Morandeira, F.; Roussel, L.; Vinh, D. C.; Erikstrup, C.; Condino-Neto, A.; Prando, C.; Bondarenko, A.; Spaan, A. N.; Gilardin, L.; Fellay, J.; Lyonnet, S.; Bilguvar, K.; Lifton, R. P.; Mane, S.; Anderson, M. S.; Boisson, B.; Béziat, V.; Zhang, S.; Andreakos, E.; Hermine, O.; Pujol, A.; Peterson, P.; Mogensen, T. H.; Rowen, L.; Mond, J.; Debette, S.; de Lamballerie, X.; Burdet, C.; Bouadma, L.; Zins, M.; Soler-Palacin, P.; Colobran, R.; Gorochov, G.; Solanich, X.; Susen, S.; Martinez-Picado, J.; Raoult, D.; Vasse, M.; Gregersen, P. K.; Piemonti, L.; Rodríguez-Gallego, C.; Notarangelo, L. D.; Su, H. C.; Kisand, K.; Okada, S.; Puel, A.; Jouanguy, E.; Rice, C. M.; Tiberghien, P.; Zhang, Q.; Casanova, J.; Abel, L.; Cobat, A.; Ozcelik, Tayfun
    Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection fatality rate (IFR) doubles with every 5 y of age from childhood onward. Circulating autoantibodies neutralizing IFN-α, IFN-ω, and/or IFN-β are found in ∼20% of deceased patients across age groups, and in ∼1% of individuals aged [removed]4% of those >70 y old in the general population. With a sample of 1,261 unvaccinated deceased patients and 34,159 individuals of the general population sampled before the pandemic, we estimated both IFR and relative risk of death (RRD) across age groups for individuals carrying autoantibodies neutralizing type I IFNs, relative to noncarriers. The RRD associated with any combination of autoantibodies was higher in subjects under 70 y old. For autoantibodies neutralizing IFN-α2 or IFN-ω, the RRDs were 17.0 (95% CI: 11.7 to 24.7) and 5.8 (4.5 to 7.4) for individuals <70 y and ≥70 y old, respectively, whereas, for autoantibodies neutralizing both molecules, the RRDs were 188.3 (44.8 to 774.4) and 7.2 (5.0 to 10.3), respectively. In contrast, IFRs increased with age, ranging from 0.17% (0.12 to 0.31) for individuals <40 y old to 26.7% (20.3 to 35.2) for those ≥80 y old for autoantibodies neutralizing IFN-α2 or IFN-ω, and from 0.84% (0.31 to 8.28) to 40.5% (27.82 to 61.20) for autoantibodies neutralizing both. Autoantibodies against type I IFNs increase IFRs, and are associated with high RRDs, especially when neutralizing both IFN-α2 and IFN-ω. Remarkably, IFRs increase with age, whereas RRDs decrease with age. Autoimmunity to type I IFNs is a strong and common predictor of COVID-19 death.
  • ItemOpen Access
    Human genetic and immunological determinants of critical COVID-19 pneumonia
    (Springer Nature, 2022-03-24) Zhang, Qian; Bastard, Paul; Karbuz, Adem; Gervais, Adrian; Tayoun, Ahmad Abou; Aiuti, Alessandro; Belot, Alexandre; Bolze, Alexandre; Gaudet, Alexandre; Bondarenko, Anastasiia; Liu, Zhiyong; Spaan, András N.; Guennoun, Andrea; Arias, Andres Augusto; Planas, Anna M.; Sediva, Anna; Shcherbina, Anna; Neehus, Anna-Lena; Puel, Anne; Froidure, Antoine; Novelli, Antonio; Parlakay, Aslınur Özkaya; Pujol, Aurora; Yahşi, Aysun; Gülhan, Belgin; Bigio, Benedetta; Boisson, Bertrand; Drolet, Beth A.; Franco, Carlos Andres Arango; Flores, Carlos; Rodríguez-Gallego, Carlos; Prando, Carolina; Biggs, Catherine M.; Luyt, Charles-Edouard; Dalgard, Clifton L.; O’Farrelly, Cliona; Matuozzo, Daniela; Dalmau, David; Perlin, David S.; Mansouri, Davood; van de Beek, Diederik; Vinh, Donald C.; Dominguez-Garrido, Elena; Hsieh, Elena W. Y.; Erdeniz, Emine Hafize; Jouanguy, Emmanuelle; Şevketoglu, Esra; Talouarn, Estelle; Quiros-Roldan, Eugenia; Andreakos, Evangelos; Husebye, Eystein; Alsohime, Fahad; Haerynck, Filomeen; Casari, Giorgio; Novelli, Giuseppe; Aytekin, Gökhan; Morelle, Guillaume; Alkan, Gulsum; Bayhan, Gulsum Iclal; Feldman, Hagit Baris; Su, Helen C.; von Bernuth, Horst; Resnick, Igor; Bustos, Ingrid; Meyts, Isabelle; Migeotte, Isabelle; Tancevski, Ivan; Bustamante, Jacinta; Fellay, Jacques; El Baghdadi, Jamila; Martinez-Picado, Javier; Casanova, Jean-Laurent; Rosain, Jeremie; Manry, Jeremy; Chen, Jie; Christodoulou, John; Bohlen, Jonathan; Franco, José Luis; Li, Juan; Anaya, Juan Manuel; Rojas, Julian; Ye, Junqiang; Uddin, K. M. Furkan; Yasar, Kadriye Kart; Kisand, Kai; Okamoto, Keisuke; Chaïbi, Khalil; Mironska, Kristina; Maródi, László; Abel, Laurent; Renia, Laurent; Lorenzo, Lazaro; Hammarström, Lennart; Ng, Lisa F. P.; Quintana-Murci, Lluis; Erazo, Lucia Victoria; Notarangelo, Luigi D.; Reyes, Luis Felipe; Allende, Luis M.; Imberti, Luisa; Renkilaraj, Majistor Raj Luxman Maglorius; Moncada-Velez, Marcela; Materna, Marie; Anderson, Mark S.; Gut, Marta; Chbihi, Marwa; Ogishi, Masato; Emiroglu, Melike; Seppänen, Mikko R. J.; Uddin, Mohammed J.; Shahrooei, Mohammed; Alexander, Natalie; Hatipoglu, Nevin; Marr, Nico; Akçay, Nihal; Boyarchuk, Oksana; Slaby, Ondrej; Akcan, Ozge Metin; Zhang, Peng; Soler-Palacín, Pere; Gregersen, Peter K.; Brodin, Petter; Garçon, Pierre; Morange, Pierre-Emmanuel; Pan-Hammarström, Qiang; Zhou, Qinhua; Philippot, Quentin; Halwani, Rabih; de Diego, Rebeca Perez; Levy, Romain; Yang, Rui; Öz, Şadiye Kübra Tüter; Muhsen, Saleh Al; Kanık-Yüksek, Saliha; Espinosa-Padilla, Sara; Ramaswamy, Sathishkumar; Okada, Satoshi; Bozdemir, Sefika Elmas; Aytekin, Selma Erol; Karabela, Şemsi Nur; Keles, Sevgi; Senoglu, Sevtap; Zhang, Shen-Ying; Duvlis, Sotirija; Constantinescu, Stefan N.; Boisson-Dupuis, Stephanie; Turvey, Stuart E.; Tangye, Stuart G.; Asano, Takaki; Özcelik, Tayfun; Le Voyer, Tom; Maniatis, Tom; Morio, Tomohiro; Mogensen, Trine H.; Sancho-Shimizu, Vanessa; Beziat, Vivien; Solanich, Xavier; Bryceson, Yenan; Lau, Yu-Lung; Itan, Yuval; Cobat, Aurélie; Casanova, Jean-Laurent; Özçelik, Tayfun
    SARS-CoV-2 infection is benign in most individuals but, in around 10% of cases, it triggers hypoxaemic COVID-19 pneumonia, which leads to critical illness in around 3% of cases. The ensuing risk of death (approximately 1% across age and gender) doubles every five years from childhood onwards and is around 1.5 times greater in men than in women. Here we review the molecular and cellular determinants of critical COVID-19 pneumonia. Inborn errors of type I interferons (IFNs), including autosomal TLR3 and X-chromosome-linked TLR7 deficiencies, are found in around 1–5% of patients with critical pneumonia under 60 years old, and a lower proportion in older patients. Pre-existing auto-antibodies neutralizing IFNα, IFNβ and/or IFNω, which are more common in men than in women, are found in approximately 15–20% of patients with critical pneumonia over 70 years old, and a lower proportion in younger patients. Thus, at least 15% of cases of critical COVID-19 pneumonia can be explained. The TLR3- and TLR7-dependent production of type I IFNs by respiratory epithelial cells and plasmacytoid dendritic cells, respectively, is essential for host defence against SARS-CoV-2. In ways that can depend on age and sex, insufficient type I IFN immunity in the respiratory tract during the first few days of infection may account for the spread of the virus, leading to pulmonary and systemic inflammation. © 2022, Springer Nature Limited.
  • ItemOpen Access
    IKBKE-driven_TPL2_and_MEK1_phosphorylations_sustain_constitutive_ERK1_2_activation_in_tumor_cells
    (EXCLI Journal, 2022-02-17) Göktuna, Serkan İsmail; Göktuna, Serkan İsmail
    IKBKE have been associated with numerous cancers. As a result, IKBKE have emerged as potential target for cancer therapy. Accumulating evidence support that IKBKE orchestrate tumor cell survival in cancers. Here we evaluated the possible link between IKBKE and ERK phosphorylation. The effects of IKBKE silencing on MAPK activation in tumor vs. normal cells were evaluated via WB and RT-PCR. Ectopically expressed IKBKE, TPL2 or MEK1 constructs were used to examine the possible interactions among them via co-IP. In vitro kinase assays were performed to understand nature of the observed interactions. In tumors, IKBKE regulates MEK/ERK constitutive activations in vitro and in vivo. IKBKE and TPL2 physically interact and this interaction leads to TPL2 phosphorylation. We describe here a novel regulatory link between IKBKE and constitutive ERK1/2 activation in tumor cells. This new circuitry may be relevant for tumor cell survival in various malignancies.