Scholarly Publications - Molecular Biology and Genetics

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

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Open Access
Microfluidics-integrated microwave sensors for single cells size discrimination
(Institute of Electrical and Electronics Engineers, 2021-04) Seçme, Arda; Pisheh, Hadi Sedaghat; Uslu, H. Dilara; Akbulut, Özge; Erdoğan, R. Tufan; Hanay, Mehmet 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.
Open Access
Rafting on the plasma membrane: Lipid rafts in signaling and disease
(Springer Singapore, 2023-01-18) Işık, Özlem Aybüke; Çizmecioğlu, Onur
The plasma membrane is not a uniform phospholipid bilayer; it has specialized membrane nano- or microdomains called lipid rafts. Lipid rafts are small cholesterol and sphingolipid-rich plasma membrane islands. Although their existence was long debated, their presence in the plasma membrane of living cells is now well accepted with the advent of super-resolution imaging techniques. It is interesting to note that lipid rafts function to compartmentalize receptors and their regulators and substantially modulate cellular signaling. In this review, we will examine the role of lipid rafts and caveolae-lipid raft-like microdomains with a distinct 3D morphology—in cellular signaling. Moreover, we will investigate how raft compartmentalized signaling regulates diverse physiological processes such as proliferation, apoptosis, immune signaling, and development. Also, the deregulation of lipid raft-mediated signaling during tumorigenesis and metastasis will be explored.
Open Access
Genetic investigation of severe viral diseases in children
(Wiley-Blackwell Publishing, 2023-01) Belkaya, Serkan
Open Access
Toxic PARP trapping upon cAMP-induced DNA damage reinstates the efficacy of endocrine therapy and CDK4/6 inhibitors in treatment-refractory ER+ breast cancer
(Nature Research, 2023-11-02) Saatci, O.; Cetin, M; Uner, M.; Tokat, Ünal Metin; Chatzistamou, I.; Ersan, P. G.; Montaudon, E.; Akyol, A.; Aksoy, S.; Uner, A.; Marangoni, E.; Sajish, M.
Resistance to endocrine therapy and CDK4/6 inhibitors, the standard of care (SOC) in estrogen receptor-positive (ER+) breast cancer, greatly reduces patient survival. Therefore, elucidating the mechanisms of sensitivity and resistance to SOC therapy and identifying actionable targets are urgently needed. Here, we show that SOC therapy causes DNA damage and toxic PARP1 trapping upon generation of a functional BRCAness (i.e., BRCA1/2 deficiency) phenotype, leading to increased histone parylation and reduced H3K9 acetylation, resulting in transcriptional blockage and cell death. Mechanistically, SOC therapy downregulates phosphodiesterase 4D (PDE4D), a novel ER target gene in a feedforward loop with ER, resulting in increased cAMP, PKA-dependent phosphorylation of mitochondrial COXIV-I, ROS generation and DNA damage. However, during SOC resistance, an ER-to-EGFR switch induces PDE4D overexpression via c-Jun. Notably, combining SOC with inhibitors of PDE4D, EGFR or PARP1 overcomes SOC resistance irrespective of the BRCA1/2 status, providing actionable targets for restoring SOC efficacy. © 2023, The Author(s).
Open Access
Retraction Note: TRIB2 confers resistance to anti-cancer therapy by activating the serine/threonine protein kinase AKT
(Nature Research, 2023-07-19) Hill, R.; Madureira, P. A.; Ferreira, B.; Baptista, I.; Machado, S.; Colaҫo, L.; dos Santos, M.; Liu, N.; Dopazo, A.; Ugurel, S.; Adrienn, A.; Kiss-Toth, E.; İşbilen, Murat; Gure, A. O.; Link, W.
Retraction to: Nature Communications, published online 09 March 2017 The authors have retracted this article as it has come to their attention that several images were inappropriately processed and duplicated in multiple figures. In particular, the data were duplicated, and in some cases inverted, across several panels in Figures 2c, 2b, 3d and Supplementary Figure 5. Erroneous data were also included in Figure 2e, Supplementary Figure 1 and Supplementary Figure 8. We apologize to the scientific community for any confusion this article may have caused. Richard Hill, Patricia Madureira, Bibiana I. Ferreira, Susana Machado, Ana Dopazo, Selma Ugurel, Endre Kiss-Toth, Murat isbilen and Wolfgang Link agree with this retraction. Inês Baptista, Laura Colaço, Marta dos Santos, Ningshu Liu, Angyal Adrienn and Ali O. Gure have not responded to correspondence from the Publisher about this retraction. © 2023, The Author(s).
Open Access
Oncogenic CALR mutant C-terminus mediates dual binding to the thrombopoietin receptor triggering complex dimerization and activation
(Nature Research, 2023-04-05) Papadopoulos, N.; Nédélec, A.; Derenne, A.; Şulea, T. A.; Pecquet, C.; Chachoua, Ilyas; Vertenoeil, G.; Tilmant, T.; Petrescu, A.; Mazzucchelli, G.; Iorga, B. I.; Vertommen, D.; Constantinescu, S. N.
Calreticulin (CALR) frameshift mutations represent the second cause of myeloproliferative neoplasms (MPN). In healthy cells, CALR transiently and non-specifically interacts with immature N-glycosylated proteins through its N-terminal domain. Conversely, CALR frameshift mutants turn into rogue cytokines by stably and specifically interacting with the Thrombopoietin Receptor (TpoR), inducing its constitutive activation. Here, we identify the basis of the acquired specificity of CALR mutants for TpoR and define the mechanisms by which complex formation triggers TpoR dimerization and activation. Our work reveals that CALR mutant C-terminus unmasks CALR N-terminal domain, rendering it more accessible to bind immature N-glycans on TpoR. We further find that the basic mutant C-terminus is partially α-helical and define how its α-helical segment concomitantly binds acidic patches of TpoR extracellular domain and induces dimerization of both CALR mutant and TpoR. Finally, we propose a model of the tetrameric TpoR-CALR mutant complex and identify potentially targetable sites. © 2023, The Author(s).
Open Access
Newly synthesized 6-substituted piperazine/phenyl-9-cyclopentyl containing purine nucleobase analogs act as potent anticancer agents and induce apoptosis via inhibiting Src in hepatocellular carcinoma cells
(Royal Society of Chemistry, 2023-11-10) Guven, Ebru Bilget; Durmaz Şahin, İrem; Altiparmak, Duygu; Servili, Burak; Essiz, Sebnem; Cetin-Atalay, Rengul; Tuncbilek, Meral
Newly synthesized 6-substituted piperazine/phenyl-9-cyclopentyl-containing purine nucleobase analogs were tested for their in vitro anticancer activity against human cancer cells. Compounds 15, 17–24, 49, and 56 with IC50 values less than 10 μM were selected for further examination on an enlarged panel of liver cancer cell lines. Experiments revealed that compound 19 utilizes its high cytotoxic potential (IC50 < 5 μM) to induce apoptosis in vitro. Compound 19 displayed a KINOMEscan selectivity score S35 of 0.02 and S10 of 0.01 and demonstrated a significant selectivity against anaplastic lymphoma kinase (ALK) and Bruton's tyrosine kinase (BTK) over other kinases. Compounds 19, 21, 22, 23, and 56 complexed with ALK, BTK, and (discoidin domain-containing receptor 2) DDR2 were analyzed structurally for binding site interactions and binding affinities via molecular docking and molecular dynamics simulations. Compounds 19 and 56 displayed similar interactions with the activation loop of the kinases, while only compound 19 reached toward the multiple subsites of the active site. Cell cycle and signaling pathway analyses exhibited that compound 19 decreases phosho-Src, phospho-Rb, cyclin E, and cdk2 levels in liver cancer cells, eventually inducing apoptosis.
Embargo
The potential of gene editing for Huntington’s disease
(Elsevier, 2023-05) Wenzhen, D.; Urani, Ece; Mattson, M. P.
Huntington’s disease (HD) is a dominantly inherited neurodegenerative disorder caused by a trinucleotide repeat expansion in the huntingtin gene resulting in long stretches of polyglutamine repeats in the huntingtin protein. The disease involves progressive degeneration of neurons in the striatum and cerebral cortex resulting in loss of control of motor function, psychiatric problems, and cognitive deficits. There are as yet no treatments that can slow disease progression in HD. Recent advances in gene editing using clustered regularly interspaced short palindromic repeats (CRISPR)–CRISPR-associated protein 9 (Cas9) systems and demonstrations of their ability to correct gene mutations in animal models of a range of diseases suggest that gene editing may prove effective in preventing or ameliorating HD. Here we describe (i) potential CRISPR-Cas designs and cellular delivery methods for the correction of mutant genes that cause inherited diseases, and (ii) recent preclinical findings demonstrating the efficacy of such gene-editing approaches in animal models, with a focus on HD.
Open Access
The effect of exosomes released from apheresis platelet concentrates under the impact of gamma irradiation and storage time upon platelet aggregation and hemostasis
(Edizioni SIMTI, 2023) Bal, Salih H.; Sağdilek, E.; Karaçay, M.; Kızmaz, Muhammed A.; Kumaş, Levent T.; Can, Fatma E.; Yıldırım, M.; Canavar-Yıldırım, Tuğçe; Koşay-Gülkaya, D.; Yöyen-Ermiş, D.; Budak, F.; Heper, Y.
Open Access
Zebrafish optomotor response to second-order motion illustrates that age-related changes in motion detection depend on the activated motion system
(Elsevier Inc., 2023-06-10) Karaduman, Ayşenur; Karoğlu-Eravşar, Elif Tuğçe; Kaya, Utku; Aydın, Alaz; Adams, Michelle Marie; Kafalıgönül, Hulusi
Various aspects of visual functioning, including motion perception, change with age. Yet, there is a lack of comprehensive understanding of age-related alterations at different stages of motion processing and in each motion system. To understand the effects of aging on second-order motion processing, we investigated optomotor responses (OMR) in younger and older wild-type (AB-strain) and acetylcholinesterase (achesb55/+) mutant zebrafish. The mutant fish with decreased levels of acetylcholinesterase have been shown to have delayed age-related cognitive decline. Compared to previous results on first-order motion, we found distinct changes in OMR to second-order motion. The polarity of OMR was dependent on age, such that second-order stimulation led to mainly negative OMR in the younger group while older zebrafish had positive responses. Hence, these findings revealed an overall aging effect on the detection of second-order motion. Moreover, neither the genotype of zebrafish nor the spatial frequency of motion significantly changed the response magnitude. Our findings support the view that age-related changes in motion detection depend on the activated motion system. © 2023 Elsevier Inc.
Open Access
Caloric restriction reinforces the stem cell pool in the aged brain without affecting overall proliferation status
(Elsevier BV, 2022-11-01) Erbaba, Begün; Macaroğlu, Duygu; Avcı, N. İlgim Ardıç; Ergül , Ayça Arslan; Adams, Michelle M.
Overfeeding (OF) and obesity increase the risk for brain aging and neurodegenerative diseases due to increased oxidative stress and neuroinflammation, which likely contribute to cellular dysfunction. In contrast, caloric restriction (CR) is an intervention known for its effects on extending both life- and health-span. In the current study, the effects on the aging brain of two short-term feeding regimens, OF and CR, were investigated. We applied these diets for 12 weeks to both young and aged zebrafish. We performed protein and mRNA level analysis to examine diet-mediated effects on any potential age-related alterations in the brain. Markers implicated in the regulation of brain aging, cell cycle, proliferation, inflammation, and cytoskeleton were analyzed. The most prominent result observed was a downregulation in the expression levels of the stem cell marker, Sox2, in CR-fed animals as compared to OF-fed fish. Furthermore, our data highlighted significant age-related downregulations in Tp53, Myca, and L-plastin levels. The multivariate analyses of all datasets suggested that as opposed to OF, the adaptive mechanisms increasing lifespan via CR are likely exerting their effects by reinforcing the stem cell pool and downregulating inflammation. The data reveal important therapeutic targets with respect to the state of nutrient uptake for the slowing down of the detrimental effects of aging, resulting in a healthy and extended lifespan, as well as lowering the risk for neurodegenerative disease.
Open Access
Evaluation of the relationship between aromatase/sirtuin1 interaction and miRNA expression in human neuroblastoma cells
(Bentham Science Publishers, 2022-10-21) Kartal, Yasemin; Tokat, Ünal Metin; Uğur, Pelin Kelicen; Yılmaz, Serkan; Karahan, Sevilay; Budak, Murat Timur
Background: Changes in activation/inhibition of Sirtuin-1 (SIRT1) and aromatase play an important role in a plethora of diseases. MicroRNAs (miRNAs) modulate multiple molecular pathways and affect a substantial number of physiological and pathological processes. Objective: The aim of this study was to investigate any possible interaction between aromatase and SIRT1 in SH-SY5Y cells and to see how there is a connection between this interaction and miRNA expression, if there is an interaction. Methods: In this study, cells were incubated in serum-deprived media for 6, 12, and 24 h. Aromatase and SIRT1 expressions were evaluated by Western blot. The IC50 concentration of SIRT1 activator (SRT1720), SIRT1 inhibitor (EX527), and aromatase inhibitors (letrozole and fadrozole) was determined by the XTT method. Then, CYP19A1 and SIRT1 levels were evaluated in the presence of SIRT1 siRNA or IC50 values for each activator/inhibitor. Finally, CYP19A1, SIRT1 expression and miRNA target gene were assessed with bioinformatic approaches. Results: Aromatase and SIRT1 protein levels were significantly elevated in the cells incubated at 24 h in serum-deprived media (p ≤ 0.05). SIRT1 also positively regulated CYP19A1 in SH-SY5Y cells in media with/without FBS. Serum deprivation depending on time course caused changes in the oxidant/ antioxidant system. While oxidative stress index tended to decrease in the absence of FBS at 24 h compared to the control, it showed a significant decrease at 48 h in a serum-deprived manner (p ≤ 0.001). As a result of bioinformatics analysis, we determined 3 miRNAs that could potentially regulate SIRT1 and CYP19A1. hsa-miR-27a-3p and hsa-miR-181a-5p correlated in terms of their expressions at 24 h compared to 12 h, and there was a significant decrease in the expression of these miRNAs. On the contrary, the expression of hsa-miR-30c-5p significantly increased at 24 h compared to 12 h. Conclusion: Considering the results, a direct link between aromatase and SIRT1 was observed in human neuroblastoma cells. The identification of key miRNAs, hsa-miR-27a-3p, hsa-miR-30c-5p, and hsa-miR-181a-5p targeting both aromatase and SIRT1, provides an approach with novel insights on neurology-associated diseases.
Open Access
Cholesterol biogenesis is a PTEN-dependent actionable node for the treatment of endocrine therapy-refractory cancers
(Wiley, 2023-09-14) Kaysudu, Irmak; Güngül, T. B.; Atıcı, S.; Yılmaz, S.; Bayram, E.; Güven, G.; Çizmecioğlu, N. T.; Şahin, Ö.; Yeşilöz, Gürkan; Haznedaroğlu, B. Z.; Çizmecioğlu, Onur
PTEN and PIK3CA mutations are the most prevalent PI3K pathway alterations in prostate, breast, colorectal, and endometrial cancers. p110β becomes the prominent PI3K isoform upon PTEN loss. In this study, we aimed to understand the molecular mechanisms of PI3K dependence in the absence of PTEN. Using online bioinformatical tools, we examined two publicly available microarray datasets with aberrant PI3K activation. We found that the rate-limiting enzyme of cholesterol biogenesis, SQLE, was significantly upregulated in p110β-hyperactivated or PTEN-deficient mouse prostate tumors. Concomitantly, the expression of cholesterol biosynthesis pathway enzymes was directly correlated with PI3K activation status in microarray datasets and diminished upon PTEN re-expression in PTEN-null prostate cancer cells. Particularly, PTEN re-expression decreased SQLE protein levels in PTEN-deficient prostate cancer cells. We performed targeted metabolomics and detected reduced levels of cholesteryl esters as well as free cholesterol upon PTEN re-expression. Notably, PTEN-null prostate and breast cancer cell lines were more sensitive to pharmacological intervention with the cholesterol pathway than PTEN-replete cancer cells. Since steroid hormones use sterols as structural precursors, we studied whether cholesterol biosynthesis may be a metabolic vulnerability that enhances antihormone therapy in PTEN-null castration-resistant prostate cancer cells. Coinhibition of cholesterol biosynthesis and the androgen receptor enhanced their sensitivity. Moreover, PTEN suppression in endocrine therapy-resistant luminal-A breast cancer cells leads to an increase in SQLE expression and a corresponding sensitization to the inhibition of cholesterol synthesis. According to our data, targeting cholesterol biosynthesis in combination with the hormone receptor signaling axis can potentially treat hormone-resistant prostate and breast cancers.
Open Access
Two target gene activation pathways for orphan ERR nuclear receptors
(Nature Publishing Group, 2023-01-16) Nakadai, T.; Shimada, M.; Ito, K.; Cevher, Murat Alper; Chu, C.-S.; Kumegawa, K.; Maruyama, R.; Malik, S.; Roeder, R. G.
Estrogen-related receptors (ERRα/β/γ) are orphan nuclear receptors that function in energy-demanding physiological processes, as well as in development and stem cell maintenance, but mechanisms underlying target gene activation by ERRs are largely unknown. Here, reconstituted biochemical assays that manifest ERR-dependent transcription have revealed two complementary mechanisms. On DNA templates, ERRs activate transcription with just the normal complement of general initiation factors through an interaction of the ERR DNA-binding domain with the p52 subunit of initiation factor TFIIH. On chromatin templates, activation by ERRs is dependent on AF2 domain interactions with the cell-specific coactivator PGC-1α, which in turn recruits the ubiquitous p300 and MED1/Mediator coactivators. This role of PGC-1α may also be fulfilled by other AF2-interacting coactivators like NCOA3, which is shown to recruit Mediator selectively to ERRβ and ERRγ. Importantly, combined genetic and RNA-seq analyses establish that both the TFIIH and the AF2 interaction-dependent pathways are essential for ERRβ/γ-selective gene expression and pluripotency maintenance in embryonic stem cells in which NCOA3 is a critical coactivator.
Open Access
Gene network landscape of mouse splenocytes reveals integrin complex as the A151 ODN-responsive hub molecule in the immune transcriptome
(Cell Press, 2023-02-01) Yazar, Volkan; Yılmaz, İsmail Cem; Bülbül, Artun; Klinman, D. M.; Gürsel, İhsan
Homeostatic restoration of an inflammatory response requires quenching of the immune system after pathogen threats vanish. A continued assault orchestrated by host defense results in tissue destruction or autoimmunity. A151 is the epitome of synthetic oligodeoxynucleotides (ODNs) that curb the immune response by a subset of white corpuscles through repetitive telomere-derived TTAGGG sequences. Currently, the genuine effect of A151 on the immune cell transcriptome remains unknown. Here, we leveraged an integrative approach where weighted gene co-expression network analysis (WGCNA), differential gene expression analysis, and gene set enrichment analysis (GSEA) of our in-house microarray datasets aided our understanding of how A151 ODN suppresses the immune response in mouse splenocytes. Our bioinformatics results, together with experimental validations, indicated that A151 ODN acts on components of integrin complexes, Itgam and Itga6, to interfere with immune cell adhesion and thereby suppresses the immune response in mice. Moreover, independent lines of evidence in this work converged on the observation that cell adhesion by integrin complexes serves as a focal point for cellular response to A151 ODN treatment in immune cells. Taken together, the outcome of this study sheds light on the molecular basis of immune suppression by a clinically useful DNA-based therapeutic agent.
Open Access
An infant with zoonotic pulmonary tuberculosis due to mycobacterium bovis
(2023-04-12) Üstündaǧ, G.; Şahin, A.; Yazıcı, Yücehan Yılmaz; Aksay, A.; Biçmen, C.; Belkaya, Serkan; Yilmaz, D.
Bovine tuberculosis might be seen in low-income countries, especially in children fed with raw milk. The most common transmission route is fecal-oral way, and it is most likely through unpasteurized dairy products. Although clinical and radiological findings are like non-zoonotic tuberculosis, treatment approaches may differ in individuals with zoonotic tuberculosis. Prevention of zoonotic diseases requires multidisciplinary approaches. These approaches include the development of veterinary and surveillance studies for the detection of communicable diseases in farm animals, as well as informing the public about raw milk consumption. In this case report, a patient with zoonotic pulmonary tuberculosis related to Mycobacterium bovis because of consumption of raw milk was presented. A five-month-old male was admitted to the hospital due to a persistent, feverless, non-productive cough since birth. Empirical antibiotic treatment was started with a preliminary diagnosis of pneumonia because of left upper lobe and right pericardial infiltration on chest X-ray. However, after two weeks of antimicrobial therapy, the patient's clinical and laboratory findings did not improve. This led to the referral for a computed tomography imaging, which revealed tracheomalacia, consolidation on the right upper lobe, an indistinguishable mass or consolidation on the left middle lobe of the lung, peribronchial thickening on the basal segment of the lower lobe, and mediastinal lymphadenopathy. Three consecutive days of fasting gastric lavage fluid was sent to the reference laboratory for acid-resistant bacillus examination, polymerase chain reaction (PCR) and culture studies. As the clinical findings were compatible and PCR was positive, the patient was started on quadruple antituberculous therapy. After initiation of anti-tuberculosis drugs, the patient's findings radiologically and clinically were improved. Mycobacterium bovis was grown in the culture. In the meantime, it was discovered that the patient was fed with raw milk. Due to the patient's clinical symptoms and the growth of Mycobacterium bovis in the gastric lavage fluid culture, the diagnosis of bovine tuberculosis was made. The culprit was that the milk of the cow belonging to the patient's family, which was later found to be infected with M.bovis, was milked and given to the patient without boiling. Today, unpasteurized dairy products continue to be consumed, especially in rural areas. One of the most important steps to prevent zoonotic diseases is to raise awareness about not consuming raw milk and undercooked meat. To elucidate the epidemiological link in childhood, taking a good anamnesis, including questioning raw milk consumption, is essential in the diagnosis of tuberculosis. © 2023 Ankara Microbiology Society. All rights reserved.
Open Access
A small non-interface surface epitope in human IL18 mediates the dynamics and self-assembly of IL18-IL18BP heterodimers
(Elsevier, 2023-07-01) Yazıcı, Yılmaz Yücehan; Belkaya, Serkan; Timuçin, E.
Interleukin 18 (IL18) is a pro-inflammatory cytokine that modulates innate and adaptive immune responses. IL18 activity is tightly controlled by the constitutively secreted IL18 binding protein (IL18BP). PDB structures of human IL18 showed that a short stretch of amino acids between 68 and 81 adopted a disordered conformation in all IL18-IL18BP complexes while adopting a 310 helical structure in other IL18 structures, including the receptor complexes. The C74 of human IL18, which was reported to form a novel intermolecular disulfide bond in the human tetrameric assembly, is also located in this short epitope. These observations reflected the importance of this short surface epitope for the structure and dynamics of the IL18-IL18BP heterodimers. We have analyzed all known IL18-IL18BP complexes in the PDB by all-atom MD simulations. The analysis also included two computed complex models adopting a helical structure for the surface epitope. Heterodimer simulations showed a stabilizing impact of the small surface region at the helical form by reducing flexibility of the complex backbone. Analysis of the symmetry-related human IL18-IL18BP tetramer showed that the unfolding of this small surface region also contributed to the IL18-IL18BP stability through a completely exposed C74 sidechain to form an intermolecular disulfide bond in the self-assembled human IL18-IL18BP dimer. Our findings showed how the conformation of the short IL18 epitope between amino acids 68 and 81 would affect IL18 activity by mediating the intermolecular interactions of IL18.
Open Access
A novel gene list identifies tumors with a stromal-mesenchymal phenotype and worse prognosis in gastric cancer
(MDPI, 2023-06-02) Demirkol Canlı, Seçil; Üner, M.; Küçükkaraduman, Barış; Karaoğlu, D. A.; Işık, A.; Turhan, N.; Akyol, A.; Gömceli, I.; Güre, A. O. A
Background: Molecular biomarkers that predict disease progression can help identify tumor subtypes and shape treatment plans. In this study, we aimed to identify robust biomarkers of prognosis in gastric cancer based on transcriptomic data obtained from primary gastric tumors. Methods: Microarray, RNA sequencing, and single-cell RNA sequencing-based gene expression data from gastric tumors were obtained from public databases. Freshly frozen gastric tumors (n = 42) and matched FFPE (formalin-fixed, paraffin-embedded) (n = 40) tissues from a Turkish gastric cancer cohort were used for quantitative real-time PCR and immunohistochemistry-based assessments of gene expression, respectively. Results: A novel list of 20 prognostic genes was identified and used for the classification of gastric tumors into two major tumor subgroups with differential stromal gene expression (“Stromal-UP” (SU) and “Stromal-DOWN” (SD)). The SU group had a more mesenchymal profile with an enrichment of extracellular matrix-related gene sets and a poor prognosis compared to the SD group. Expression of the genes within the signature correlated with the expression of mesenchymal markers ex vivo. A higher stromal content in FFPE tissues was associated with shorter overall survival. Conclusions: A stroma-rich, mesenchymal subgroup among gastric tumors identifies an unfavorable clinical outcome in all cohorts tested.
Open Access
Inborn errors of OAS–RNase L in SARS-CoV-2–related multisystem inflammatory syndrome in children
(American Association for the Advancement of Science (AAAS), 2022-12-20) Lee, D.; Pen, J. L.; Yatim, A.; Dong, B.; Aquino, Y.; Ogishi, M.; Pescarmona, R.; Talouarn, E.; Rinchai, D.; Zhang, P.; Perret, M.; Liu, Z.; Jordan, L.; Bozdemir, S. E.; Bayhan, G. I.; Beaufils, C.; Bizien, L.; Bisiaux, A.; Lei, W.; Hasan, M.; Chen, J.; Gaughan, C.; Asthana, A.; Libri, V.; Luna, Joseph M.; Jaffré, Fabrice; Hoffmann, H.; Michailidis, E.; Moreews, M.; Seeleuthner, Y.; Bilguvar, K.; Mane, S.; Flores, C.; Zhang, Y.; Arias, A. A.; Bailey, R.; Schlüter, A.; Milisavljevic, B.; Bigio, B.; Voyer, T. L.; Materna, M.; Gervais, A.; Moncada-Velez, M.; Pala, F.; Lazarov, T.; Levy, R.; Neehus, A.; Rosain, J.; Peel, J.; Chan, Y.; Morin, M.; Pino-Ramirez, R. M.; Belkaya, Serkan; Lorenzo, L.; Anton, J.; Delafontaine, S.; Toubiana, J.; Bajolle, F.; Fumadó, V.; DeDiego, M. L.; Fidouh, N.; Rozenberg, F.; Pérez-Tur, J.; Chen, S.; Evans, T.; Geissmann, F.; Lebon, P.; Weiss, S. R.; Bonnet, D.; Duval, X.; Cohort§, C.; Effort, C.; Pan-Hammarström, Q.; Planas, A. M.; Meyts, I.; Haerynck, F.; Pujol, A.; Sancho-Shimizu, V.; Dalgard, C.; Bustamante, J.; Puel, A.; Boisson-Dupuis, S.; Boisson, B.; Maniatis, T.; Zhang, Q.; Bastard, P.; Notarangelo, L.; Béziat, V.; Diego, R.; Rodriguez-Gallego, C.; Su, H. C.; Lifton, R. P.; Jouanguy, E.; Cobat, A.; Alsina, L.; Keles, S.; Haddad, E.; Abel, L.; Belot, A.; Quintana-Murci, L.; Rice, C. M.; Silverman, R. H.; Zhang, S.; Casanova, J.
Multisystem inflammatory syndrome in children (MIS-C) is a rare and severe condition that follows benign COVID-19. We report autosomal recessive deficiencies of OAS1, OAS2, or RNASEL in five unrelated children with MIS-C. The cytosolic double-stranded RNA (dsRNA)-sensing OAS1 and OAS2 generate 2'-5'-linked oligoadenylates (2-5A) that activate the single-stranded RNA-degrading ribonuclease L (RNase L). Monocytic cell lines and primary myeloid cells with OAS1, OAS2, or RNase L deficiencies produce excessive amounts of inflammatory cytokines upon dsRNA or severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) stimulation. Exogenous 2-5A suppresses cytokine production in OAS1-deficient but not RNase L-deficient cells. Cytokine production in RNase L-deficient cells is impaired by MDA5 or RIG-I deficiency and abolished by mitochondrial antiviral-signaling protein (MAVS) deficiency. Recessive OAS-RNase L deficiencies in these patients unleash the production of SARS-CoV-2-triggered, MAVS-mediated inflammatory cytokines by mononuclear phagocytes, thereby underlying MIS-C.
Open Access
Isolated subcutaneous abscess: A rare presentation of extrapulmonary tuberculosis
(Lippincott Williams & Wilkins, 2023-08-01) Sahin, A.; Kara-Aksay, A.; Bicmen, C.; Belkaya, Serkan; Kaya, A.; Yilmaz, D.