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Article: Investigating G-quadruplex structures in

Donato, Luigi / Scimone, Concetta / Alibrandi, Simona / Mordà, Domenico / Anchesi, Ivan / Scalinci, Sergio Zaccaria / Rinaldi, Carmela / D'Angelo, Rosalia / Sidoti, Antonina

Heliyon

2024 Volume 10, Issue 8, Page(s) e29828

Abstract: Aims: This pilot study investigates the potential pathogenic role of G-quadruplex (G4) structures ...

Abstract	Aims: This pilot study investigates the potential pathogenic role of G-quadruplex (G4) structures in Main methods: We conducted whole genome amplification experiments and next-generation sequencing to detect the blockade of polymerase activity by G4 structures. Our specific focus was the Key findings: Our data confirmed the obstruction of DNA polymerase enzymes by G4 structures, particularly when stabilized by the compound pyridostatin. This obstruction was evident in the reduced amplification of Significance: Our findings suggest that G4 formation in the
Language	English
Publishing date	2024-04-18
Publishing country	England
Document type	Journal Article
ZDB-ID	2835763-2
ISSN	2405-8440
ISSN	2405-8440
DOI	10.1016/j.heliyon.2024.e29828
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Article ; Online: Scaling up Functional Analyses of the G Protein-Coupled Receptor Rhodopsin.

Scott, Benjamin M / Chen, Steven K / Van Nynatten, Alexander / Liu, Jing / Schott, Ryan K / Heon, Elise / Peisajovich, Sergio G / Chang, Belinda S W

Journal of molecular evolution

2024 Volume 92, Issue 1, Page(s) 61–71

Abstract: Eukaryotic cells use G protein-coupled receptors (GPCRs) to convert external stimuli into internal ...

Abstract	Eukaryotic cells use G protein-coupled receptors (GPCRs) to convert external stimuli into internal signals to elicit cellular responses. However, how mutations in GPCR-coding genes affect GPCR activation and downstream signaling pathways remain poorly understood. Approaches such as deep mutational scanning show promise in investigations of GPCRs, but a high-throughput method to measure rhodopsin activation has yet to be achieved. Here, we scale up a fluorescent reporter assay in budding yeast that we engineered to study rhodopsin's light-activated signal transduction. Using this approach, we measured the mutational effects of over 1200 individual human rhodopsin mutants, generated by low-frequency random mutagenesis of the GPCR rhodopsin (RHO) gene. Analysis of the data in the context of rhodopsin's three-dimensional structure reveals that transmembrane helices are generally less tolerant to mutations compared to flanking helices that face the lipid bilayer, which suggest that mutational tolerance is contingent on both the local environment surrounding specific residues and the specific position of these residues in the protein structure. Comparison of functional scores from our screen to clinically identified rhodopsin disease variants found many pathogenic mutants to be loss of function. Lastly, functional scores from our assay were consistent with a complex counterion mechanism involved in ligand-binding and rhodopsin activation. Our results demonstrate that deep mutational scanning is possible for rhodopsin activation and can be an effective method for revealing properties of mutational tolerance that may be generalizable to other transmembrane proteins.
MeSH term(s)	Humans ; Rhodopsin/genetics ; Rhodopsin/chemistry ; Rhodopsin/metabolism ; Receptors, G-Protein-Coupled/genetics ; Receptors, G-Protein-Coupled/chemistry ; Signal Transduction ; Protein Structure, Secondary ; Mutation
Chemical Substances	Rhodopsin (9009-81-8) ; Receptors, G-Protein-Coupled
Language	English
Publishing date	2024-02-07
Publishing country	Germany
Document type	Journal Article
ZDB-ID	120148-7
ISSN	1432-1432 ; 0022-2844
ISSN (online)	1432-1432
ISSN	0022-2844
DOI	10.1007/s00239-024-10154-3
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Article: Bayesian network models identify co-operative GPCR:G protein interactions that contribute to G protein coupling.

Mukhaleva, Elizaveta / Ma, Ning / van der Velden, Wijnand J C / Gogoshin, Grigoriy / Branciamore, Sergio / Bhattacharya, Supriyo / Rodin, Andrei S / Vaidehi, Nagarajan

bioRxiv : the preprint server for biology

2023

Abstract: ... to identify the residue pairs that show high cooperativity and their allosteric effect in the interface of G ... protein-coupled receptor (GPCR) complexes with G proteins. Our results reveal a strong co-dependency ... in the formation of interface GPCR:G protein contacts. This observation indicates that cooperativity of GPCR:G ...

Abstract	Cooperative interactions in protein-protein interfaces demonstrate the interdependency or the linked network-like behavior of interface interactions and their effect on the coupling of proteins. Cooperative interactions also could cause ripple or allosteric effects at a distance in protein-protein interfaces. Although they are critically important in protein-protein interfaces it is challenging to determine which amino acid pair interactions are cooperative. In this work we have used Bayesian network modeling, an interpretable machine learning method, combined with molecular dynamics trajectories to identify the residue pairs that show high cooperativity and their allosteric effect in the interface of G protein-coupled receptor (GPCR) complexes with G proteins. Our results reveal a strong co-dependency in the formation of interface GPCR:G protein contacts. This observation indicates that cooperativity of GPCR:G protein interactions is necessary for the coupling and selectivity of G proteins and is thus critical for receptor function. We have identified subnetworks containing polar and hydrophobic interactions that are common among multiple GPCRs coupling to different G protein subtypes (Gs, Gi and Gq). These common subnetworks along with G protein-specific subnetworks together confer selectivity to the G protein coupling. This work underscores the potential of data-driven Bayesian network modeling in elucidating the intricate dependencies and selectivity determinants in GPCR:G protein complexes, offering valuable insights into the dynamic nature of these essential cellular signaling components.
Language	English
Publishing date	2023-10-12
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.10.09.561618
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Article ; Online: An Upstream G-Quadruplex DNA Structure Can Stimulate Gene Transcription.

Chen, Yuqi / Simeone, Angela / Melidis, Larry / Cuesta, Sergio Martinez / Tannahill, David / Balasubramanian, Shankar

ACS chemical biology

2024 Volume 19, Issue 3, Page(s) 736–742

Abstract: Four-stranded G-quadruplexes (G4s) are DNA secondary structures that can form in the human genome ... to the corresponding G4-negative control promoter in a way that is not dependent on primary sequence or inherent G ...

Abstract	Four-stranded G-quadruplexes (G4s) are DNA secondary structures that can form in the human genome. G4 structures have been detected in gene promoters and are associated with transcriptionally active chromatin and the recruitment of transcription factors and chromatin remodelers. We adopted a controlled, synthetic biology approach to understand how G4s can influence transcription. We stably integrated G4-forming sequences into the promoter of a synthetic reporter gene and inserted these into the genome of human cells. The integrated G4 sequences were shown to fold into a G4 structure within a cellular genomic context. We demonstrate that G4 structure formation within a gene promoter stimulates transcription compared to the corresponding G4-negative control promoter in a way that is not dependent on primary sequence or inherent G-richness. Systematic variation in the stability of folded G4s showed that in this system, transcriptional levels increased with higher stability of the G4 structure. By creating and manipulating a chromosomally integrated synthetic promoter, we have shown that G4 structure formation in a defined gene promoter can cause gene transcription to increase, which aligns with earlier observational correlations reported in the literature linking G4s to active transcription.
MeSH term(s)	Humans ; G-Quadruplexes ; DNA/genetics ; DNA/chemistry ; Promoter Regions, Genetic ; Transcription, Genetic ; Chromatin
Chemical Substances	DNA (9007-49-2) ; Chromatin
Language	English
Publishing date	2024-02-28
Publishing country	United States
Document type	Journal Article
ISSN	1554-8937
ISSN (online)	1554-8937
DOI	10.1021/acschembio.3c00775
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Article: Photocatalytic Activity of Ag Nanoparticles Deposited on Thermoexfoliated g-C

Portillo-Cortez, Karina / Caudillo-Flores, Uriel / Sánchez-López, Perla / Smolentseva, Elena / Dominguez, David / Fuentes-Moyado, Sergio

Nanomaterials (Basel, Switzerland)

2024 Volume 14, Issue 7

Abstract: ... photocatalysis. Graphitic carbon nitride (g-C ...

Abstract	The limited access to fresh water and the increased presence of emergent pollutants (EPs) in wastewater has increased the interest in developing strategies for wastewater remediation, including photocatalysis. Graphitic carbon nitride (g-C
Language	English
Publishing date	2024-04-02
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2662255-5
ISSN	2079-4991
ISSN	2079-4991
DOI	10.3390/nano14070623
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Article ; Online: Genetic interactions of G-quadruplexes in humans.

Zyner, Katherine G / Mulhearn, Darcie S / Adhikari, Santosh / Martínez Cuesta, Sergio / Di Antonio, Marco / Erard, Nicolas / Hannon, Gregory J / Tannahill, David / Balasubramanian, Shankar

eLife

2019 Volume 8

Abstract: G-quadruplexes (G4) are alternative nucleic acid structures involved in transcription, translation ...

Abstract	G-quadruplexes (G4) are alternative nucleic acid structures involved in transcription, translation and replication. Aberrant G4 formation and stabilisation is linked to genome instability and cancer. G4 ligand treatment disrupts key biological processes leading to cell death. To discover genes and pathways involved with G4s and gain mechanistic insights into G4 biology, we present the first unbiased genome-wide study to systematically identify human genes that promote cell death when silenced by shRNA in the presence of G4-stabilising small molecules. Many novel genetic vulnerabilities were revealed opening up new therapeutic possibilities in cancer, which we exemplified by an orthogonal pharmacological inhibition approach that phenocopies gene silencing. We find that targeting the WEE1 cell cycle kinase or USP1 deubiquitinase in combination with G4 ligand treatment enhances cell killing. We also identify new genes and pathways regulating or interacting with G4s and demonstrate that the DDX42 DEAD-box helicase is a newly discovered G4-binding protein.
MeSH term(s)	Apoptosis ; Cell Line, Tumor ; Cell Nucleus/metabolism ; G-Quadruplexes ; Genes, Neoplasm ; Genetic Testing ; Genome, Human ; Humans ; Ligands ; Neoplasm Proteins/genetics ; Neoplasm Proteins/metabolism ; Neoplasms/genetics ; RNA, Small Interfering/metabolism ; Signal Transduction/genetics
Chemical Substances	Ligands ; Neoplasm Proteins ; RNA, Small Interfering
Language	English
Publishing date	2019-07-09
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2687154-3
ISSN	2050-084X ; 2050-084X
ISSN (online)	2050-084X
ISSN	2050-084X
DOI	10.7554/eLife.46793
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Article: One-Pot Thermal Synthesis of g-C

Pérez-Molina, Álvaro / Pastrana-Martínez, Luisa M / Pérez-Poyatos, Lorena T / Morales-Torres, Sergio / Maldonado-Hódar, Francisco J

Nanomaterials (Basel, Switzerland)

2022 Volume 12, Issue 3

Abstract: Graphitic carbon nitride (g-C ...

Abstract	Graphitic carbon nitride (g-C
Language	English
Publishing date	2022-01-21
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2662255-5
ISSN	2079-4991
ISSN	2079-4991
DOI	10.3390/nano12030340
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Article ; Online: Differential mRNA expression in the induction of DNA damage, G

Rondina, Débora Berbel Lirio / de Lima, Luan Vitor Alves / da Silva, Matheus Felipe / Zanetti, Thalita Alves / Felicidade, Ingrid / Marques, Lilian Areal / Coatti, Giuliana Castello / Mantovani, Mario Sergio

Toxicology in vitro : an international journal published in association with BIBRA

2022 Volume 85, Page(s) 105474

Abstract: Zerumbone (ZER) is a phytochemical with antioxidant and antiproliferative properties. This study evaluated the cytoxicity of ZER combined with chemotherapeutic agents and the expression of mRNA genes related to cell cycle, cell death, xenobiotic ... ...

Abstract	Zerumbone (ZER) is a phytochemical with antioxidant and antiproliferative properties. This study evaluated the cytoxicity of ZER combined with chemotherapeutic agents and the expression of mRNA genes related to cell cycle, cell death, xenobiotic metabolism, DNA damage, and endoplasmic reticulum (ER) stress in HepG2/C3A cells. ZER was cytotoxic (IC
MeSH term(s)	Cytochrome P-450 CYP1A2 ; Cytochrome P-450 CYP2C19 ; Cisplatin/pharmacology ; Antioxidants/pharmacology ; NF-kappa B ; Cytochrome P-450 CYP2D6/pharmacology ; Cytochrome P-450 CYP1A1 ; Xenobiotics/pharmacology ; Sesquiterpenes/pharmacology ; Apoptosis ; DNA Damage ; Antineoplastic Agents/pharmacology ; Phytochemicals/pharmacology ; RNA, Messenger ; Doxorubicin/pharmacology ; Fluorouracil/pharmacology ; Cell Line, Tumor
Chemical Substances	zerumbone (471-05-6) ; Cytochrome P-450 CYP1A2 (EC 1.14.14.1) ; Cytochrome P-450 CYP2C19 (EC 1.14.14.1) ; Cisplatin (Q20Q21Q62J) ; Antioxidants ; NF-kappa B ; Cytochrome P-450 CYP2D6 (EC 1.14.14.1) ; Cytochrome P-450 CYP1A1 (EC 1.14.14.1) ; Xenobiotics ; Sesquiterpenes ; Antineoplastic Agents ; Phytochemicals ; RNA, Messenger ; Doxorubicin (80168379AG) ; Fluorouracil (U3P01618RT)
Language	English
Publishing date	2022-09-16
Publishing country	England
Document type	Journal Article
ZDB-ID	639064-x
ISSN	1879-3177 ; 0887-2333
ISSN (online)	1879-3177
ISSN	0887-2333
DOI	10.1016/j.tiv.2022.105474
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Zs.A 2223: Show issues

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Article ; Online: Association of TAP1 1177A>G and 2090A>G gene polymorphisms with latent tuberculosis infections in sheltered populations, in the metropolitan area of Guadalajara, Mexico: a pilot study.

Cazarez-Navarro, Gerardo / Palomares-Marín, Jaime / Rodríguez-Preciado, Sergio Yair / Pereira-Suárez, Ana Laura / Martínez-López, Erika / Bacilio-Medrano, Eva Adriana / Huerta-Olvera, Selene / Hernández-Cañaveral, Iván Isidro

Revista do Instituto de Medicina Tropical de Sao Paulo

2021 Volume 63, Page(s) e55

Abstract: ... aimed to determine the association between TAP1 gene 1177A>G (rs1057141) and 2090A>G (rs1135216 ... analyzed (46 were LTBI-positive and 92 were controls). Genotyping of the rs11352216 (2090A>G) and rs1057141 ... 1177A>G) gene IDs was performed using the Applied Biosystems Step One Thermal Cycler Real-Time PCR ...

Abstract	Latent tuberculosis infection (LTBI) is a condition that has no clinical signs and symptoms. LTBI patients are characterized by persistent immune responses to Mycobacterium tuberculosis, and approximately 5-10% of these infected individuals will develop active TB at some point in their lives. The antigen transporter associated with antigen processing (TAP1) is a protein involved in the transport of the antigen from the cytoplasm to the endoplasmic reticulum by means of the association with MHC class I molecules. It plays a fundamental role in the immune response, promoting the clearance of intracellular pathogens. Our pilot study aimed to determine the association between TAP1 gene 1177A>G (rs1057141) and 2090A>G (rs1135216) genetic polymorphisms with susceptibility to LTBI. In this case-control study, 153 individuals from shelters were analyzed (46 were LTBI-positive and 92 were controls). Genotyping of the rs11352216 (2090A>G) and rs1057141 (1177A>G) gene IDs was performed using the Applied Biosystems Step One Thermal Cycler Real-Time PCR allelic discrimination technology. The haplotypic analyses were performed with the Arlequin 3.5 program. Social assistance centers and shelters that serve vulnerable populations represent high-risk sites due to overcrowding and the impaired nutritional status of their residents. The G allele (OR=1.99, CI=1.109-3.587, p=0.021) and the GG genotype of rs11352216 (A>G) were associated with susceptibility to LTBI, according to the codominant genetic model (OR=8.32, CI=1.722-61.98, p=0.007). The rs1057141 (A>G) polymorphism was not associated with LTBI risk. The results suggest that carriers of the G allele of rs1135216 (A>G) are susceptible to LTBI.
MeSH term(s)	ATP Binding Cassette Transporter, Subfamily B, Member 2/genetics ; Case-Control Studies ; Genetic Predisposition to Disease ; Humans ; Latent Tuberculosis/genetics ; Mexico ; Mycobacterium tuberculosis ; Pilot Projects ; Polymorphism, Single Nucleotide
Chemical Substances	ATP Binding Cassette Transporter, Subfamily B, Member 2 ; TAP1 protein, human
Language	English
Publishing date	2021-07-05
Publishing country	Brazil
Document type	Journal Article
ZDB-ID	128928-7
ISSN	1678-9946 ; 0036-4665
ISSN (online)	1678-9946
ISSN	0036-4665
DOI	10.1590/S1678-9946202163055
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Article: Somatic multicomorbidity and disability in patients with psychiatric disorders in comparison to the general population: a quasi-epidemiological investigation in 54,826 subjects from 40 countries (COMET-G study).

Fountoulakis, Konstantinos N / Karakatsoulis, Grigorios N / Abraham, Seri / Adorjan, Kristina / Ahmed, Helal Uddin / Alarcón, Renato D / Arai, Kiyomi / Auwal, Sani Salihu / Berk, Michael / Bjedov, Sarah / Bobes, Julio / Bobes-Bascaran, Teresa / Bourgin-Duchesnay, Julie / Bredicean, Cristina Ana / Bukelskis, Laurynas / Burkadze, Akaki / Cabrera Abud, Indira Indiana / Castilla-Puentes, Ruby / Cetkovich, Marcelo /

Colon-Rivera, Hector / Corral, Ricardo / Cortez-Vergara, Carla / Crepin, Piirika / De Berardis, Domenico / Zamora Delgado, Sergio / Lucena, David De / Sousa, Avinash De / Stefano, Ramona Di / Dodd, Seetal / Priyanka Elek, Livia / Elissa, Anna / Erdelyi-Hamza, Berta / Erzin, Gamze / Etchevers, Martin J / Falkai, Peter / Farcas, Adriana / Fedotov, Ilya / Filatova, Viktoriia / Fountoulakis, Nikolaos K / Frankova, Iryna / Franza, Francesco / Frias, Pedro / Galako, Tatiana / Garay, Cristian J / Garcia-Álvarez, Leticia / García-Portilla, Maria Paz / Gonda, Xenia / Gondek, Tomasz M / Morera González, Daniela / Gould, Hilary / Grandinetti, Paolo / Grau, Arturo / Groudeva, Violeta / Hagin, Michal / Harada, Takayuki / Hasan, Tasdik M / Azreen Hashim, Nurul / Hilbig, Jan / Hossain, Sahadat / Iakimova, Rossitza / Ibrahim, Mona / Iftene, Felicia / Ignatenko, Yulia / Irarrazaval, Matias / Ismail, Zaliha / Ismayilova, Jamila / Jakobs, Asaf / Jakovljević, Miro / Jakšić, Nenad / Javed, Afzal / Kafali, Helin Yilmaz / Karia, Sagar / Kazakova, Olga / Khalifa, Doaa / Khaustova, Olena / Koh, Steve / Kopishinskaia, Svetlana / Kosenko, Korneliia / Koupidis, Sotirios A / Kovacs, Illes / Kulig, Barbara / Lalljee, Alisha / Liewig, Justine / Majid, Abdul / Malashonkova, Evgeniia / Malik, Khamelia / Malik, Najma Iqbal / Mammadzada, Gulay / Mandalia, Bilvesh / Marazziti, Donatella / Marčinko, Darko / Martinez, Stephanie / Matiekus, Eimantas / Mejia, Gabriela / Memon, Roha Saeed / Meza Martínez, Xarah Elenne / Mickevičiūtė, Dalia / Milev, Roumen / Mohammed, Muftau / Molina-López, Alejandro / Morozov, Petr / Muhammad, Nuru Suleiman / Mustač, Filip / Naor, Mika S / Nassieb, Amira / Navickas, Alvydas / Okasha, Tarek / Pandova, Milena / Panfil, Anca-Livia / Panteleeva, Liliya / Papava, Ion / Patsali, Mikaella E / Pavlichenko, Alexey / Pejuskovic, Bojana / Pinto Da Costa, Mariana / Popkov, Mikhail / Popovic, Dina / Raduan, Nor Jannah Nasution / Vargas Ramírez, Francisca / Rancans, Elmars / Razali, Salmi / Rebok, Federico / Rewekant, Anna / Ninoska Reyes Flores, Elena / Rivera-Encinas, María Teresa / Saiz, Pilar / Sánchez de Carmona, Manuel / Saucedo Martínez, David / Saw, Jo Anne / Saygili, Görkem / Schneidereit, Patricia / Shah, Bhumika / Shirasaka, Tomohiro / Silagadze, Ketevan / Sitanggang, Satti / Skugarevsky, Oleg / Spikina, Anna / Mahalingappa, Sridevi Sira / Stoyanova, Maria / Szczegielniak, Anna / Tamasan, Simona Claudia / Tavormina, Giuseppe / Tavormina, Maurilio Giuseppe Maria / Theodorakis, Pavlos N / Tohen, Mauricio / Tsapakis, Eva Maria / Tukhvatullina, Dina / Ullah, Irfan / Vaidya, Ratnaraj / Vega-Dienstmaier, Johann M / Vrublevska, Jelena / Vukovic, Olivera / Vysotska, Olga / Widiasih, Natalia / Yashikhina, Anna / Prezerakos, Panagiotis E / Smirnova, Daria

CNS spectrums

2024 Volume 29, Issue 2, Page(s) 126–149

Abstract: ... males; 1.11% nonbinary gender) from 40 countries (COMET-G study). The analysis was based ...

Abstract	Background: The prevalence of medical illnesses is high among patients with psychiatric disorders. The current study aimed to investigate multi-comorbidity in patients with psychiatric disorders in comparison to the general population. Secondary aims were to investigate factors associated with metabolic syndrome and treatment appropriateness of mental disorders. Methods: The sample included 54,826 subjects (64.73% females; 34.15% males; 1.11% nonbinary gender) from 40 countries (COMET-G study). The analysis was based on the registration of previous history that could serve as a fair approximation for the lifetime prevalence of various medical conditions. Results: About 24.5% reported a history of somatic and 26.14% of mental disorders. Mental disorders were by far the most prevalent group of medical conditions. Comorbidity of any somatic with any mental disorder was reported by 8.21%. One-third to almost two-thirds of somatic patients were also suffering from a mental disorder depending on the severity and multicomorbidity. Bipolar and psychotic patients and to a lesser extent depressives, manifested an earlier (15-20 years) manifestation of somatic multicomorbidity, severe disability, and probably earlier death. The overwhelming majority of patients with mental disorders were not receiving treatment or were being treated in a way that was not recommended. Antipsychotics and antidepressants were not related to the development of metabolic syndrome. Conclusions: The finding that one-third to almost two-thirds of somatic patients also suffered from a mental disorder strongly suggests that psychiatry is the field with the most trans-specialty and interdisciplinary value and application points to the importance of teaching psychiatry and mental health in medical schools and also to the need for more technocratically oriented training of psychiatric residents.
MeSH term(s)	Male ; Female ; Humans ; Metabolic Syndrome/epidemiology ; Metabolic Syndrome/drug therapy ; Mental Disorders/epidemiology ; Mental Disorders/drug therapy ; Antipsychotic Agents/therapeutic use ; Mental Health ; Comorbidity
Chemical Substances	Antipsychotic Agents
Language	English
Publishing date	2024-01-25
Publishing country	United States
Document type	Journal Article
ZDB-ID	2008418-3
ISSN	2165-6509 ; 1092-8529
ISSN (online)	2165-6509
ISSN	1092-8529
DOI	10.1017/S1092852924000026
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