Article
Medicine, Research & Experimental
Anna Maria Rachiglio, Luca De Sabato, Cristin Roma, Michele Cennamo, Mariano Fiorenza, Daniela Terracciano, Raffaella Pasquale, Francesca Bergantino, Ernesta Cavalcanti, Gerardo Botti, Gabriele Vaccari, Giuseppe Portella, Nicola Normanno
Summary: This study successfully obtained the complete genomes of 27 nasopharyngeal swabs from citizens of the Italian Campania region who tested positive for SARS-CoV-2 in March-April 2020 using a highly automated sequencing method, revealing various mutations, with 10 non-synonymous variants found in ORF1ab. The Genexus system was effective in sequencing the complete genomes of SARS-CoV-2, even in cases with low viral copies, and may help standardize sequencing protocols and identify novel variants faster during the pandemic.
JOURNAL OF TRANSLATIONAL MEDICINE
(2021)
Article
Multidisciplinary Sciences
Valentina Curini, Massimo Ancora, Lucija Jurisic, Valeria Di Lollo, Barbara Secondini, Luana Fiorella Mincarelli, Marialuigia Caporale, Ilaria Puglia, Luigina Di Gialleonardo, Iolanda Mangone, Marco Di Domenico, Adriano Di Pasquale, Alessio Lorusso, Maurilia Marcacci, Cesare Camma
Summary: Whole genome sequencing (WGS) of SARS-CoV-2 is essential for public health control strategies, allowing for tracking viral spread and monitoring the emergence of variants. The study found that Illumina COVIDSeq Test is the most cost-effective and time-efficient approach for producing consensus sequences.
Article
Virology
Nathalie Mugnier, Aurelien Griffon, Bruno Simon, Maxence Rambaud, Hadrien Regue, Antonin Bal, Gregory Destras, Maud Tournoud, Magali Jaillard, Abel Betraoui, Emmanuelle Santiago, Valerie Cheynet, Alexandre Vignola, Veronique Ligeon, Laurence Josset, Karen Brengel-Pesce
Summary: In this study, researchers developed a web-based application called EPISEQ SARS-CoV-2 for the analysis of SARS-CoV-2 NGS data. The application showed a strong agreement with a reference pipeline in strain and mutation identification, and revealed reagent-related sequencing issues.
Review
Biochemical Research Methods
Matteo Chiara, Anna Maria D'Erchia, Carmela Gissi, Caterina Manzari, Antonio Parisi, Nicoletta Resta, Federico Zambelli, Ernesto Picardi, Giulio Pavesi, David S. Horner, Graziano Pesole
Summary: Various NGS-based strategies have been used to trace infectious agent origins and develop molecular diagnostic tests. The ongoing COVID-19 pandemic has caused severe societal and economic costs, emphasizing the importance of efficient sequencing methods. However, different technologies and approaches have their own advantages and limitations, highlighting the need for better integration and sharing of data.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Biology
Scott Burkholz, Michael Rubsamen, Luke Blankenberg, Richard T. Carback III, Daria Mochly-Rosen, Paul E. Harris
Summary: Analysis of next-generation sequencing data linked with clinical metadata reveals that Omicron reinfections occur at a higher frequency and within a shorter time interval compared to pre-Omicron variants. This suggests that a single infection may not generate the protective immunity required to defend against Omicron reinfections. Continued next-generation sequencing and inclusion of clinical metadata is necessary for effective surveillance, treatment, vaccine development, and public health recommendations.
COMMUNICATIONS BIOLOGY
(2023)
Article
Multidisciplinary Sciences
Lyora A. Cohen-Aharonov, Annie Rebibo-Sabbah, Adar Yaacov, Roy Z. Granit, Merav Strauss, Raul Colodner, Ori Cheshin, Shai Rosenberg, Ronen Eavri
Summary: In this study, the researchers proposed a solution for large-scale viral screening and specific variant analysis by integrating DNA barcoding technology, sample pooling, and Next Generation Sequencing (NGS) methods. The solution allows high throughput testing with high sensitivity and specificity, and enables variant analysis at a single nucleotide resolution.
Article
Virology
Jiratchaya Puenpa, Vorthon Sawaswong, Pattaraporn Nimsamer, Sunchai Payungporn, Patthaya Rattanakomol, Nutsada Saengdao, Jira Chansaenroj, Ritthideach Yorsaeng, Kamol Suwannakarn, Yong Poovorawan
Summary: This study conducted complete genome sequencing of 210 samples to investigate the SARS-CoV-2 lineages circulating in Thailand and their evolutionary history, revealing multiple lineage introductions before the emergence of the omicron variant. The evolutionary rate for the spike gene of SARS-CoV-2 was estimated, and certain predominant mutations in the ORF3a gene were identified during the Thailand outbreaks. Complete genome sequencing can enhance the prediction of future variant changes and is crucial for vaccine strain development.
Article
Biochemistry & Molecular Biology
Marius Ilie, Jonathan Benzaquen, Veronique Hofman, Elodie Long-Mira, Sandra Lassalle, Jacques Boutros, Christophe Bontoux, Virginie Lespinet-Fabre, Olivier Bordone, Virginie Tanga, Maryline Allegra, Myriam Salah, Julien Fayada, Sylvie Leroy, Matteo Vassallo, Irit Touitou, Johan Courjon, Julie Contenti, Michel Carles, Charles-Hugo Marquette, Paul Hofman
Summary: As new SARS-CoV-2 variants emerge, it is important to improve the efficiency and availability of viral genome sequencing, especially in samples with low viral load. In this study, retrospective SARS-CoV-2 genome sequencing was performed on 175 positive samples, and the analysis successfully detected Delta and Omicron variants in low viral load samples. The results showed that there was no significant difference in viral load between patients infected with the Omicron variant and those infected with the Delta variant.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Editorial Material
Multidisciplinary Sciences
Ewen Callaway
Summary: New technologies may offer stronger or wider immunity, but they will face competition for market share.
Article
Engineering, Chemical
Antoine Dara, Bourema Kouriba, Amadou Daou, Abdoul Karim Sangare, Djibril Kassogue, Charles Dara, Abdoulaye A. Djimde
Summary: NGS has become essential in genomic epidemiology, especially during the COVID-19 pandemic. By adapting a lab setup for malaria research, we successfully generated the first complete SARS-CoV-2 genome locally, demonstrating the capacity to produce high-quality genomes with limited resources and emphasizing the importance of developing genomics capacity locally.
Article
Microbiology
Annika Brinkmann, Sophie-Luisa Ulm, Steven Uddin, Sophie Foerster, Dominique Seifert, Rainer Oehme, Merle Corty, Lars Schaade, Janine Michel, Andreas Nitsche
Summary: Since December 2019, the scientific community has been sharing real-time data on the SARS-CoV-2 virus, facilitating analyses like virus evolution, transmission chain tracking, protein modeling, and therapeutic target identification. They have developed and evaluated an amplification-based approach for whole-genome sequencing of SARS-CoV-2, which can prepare sequencing libraries in 10 minutes.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Immunology
Orna Mor, Michal Mandelboim, Shay Fleishon, Efrat Bucris, Dana Bar-Ilan, Michal Linial, Ital Nemet, Limor Kliker, Yaniv Lustig, Ella S. Mendelson, Neta S. Zuckerman
Summary: The study identified a new variant B.1.362+L452R of SARS-CoV-2, carrying the L452R mutation associated with increased infection and reduced neutralization. This variant infected hundreds of individuals in Israel but declined due to the dominance of the Alpha variant, highlighting the importance of routine surveillance and detection of novel variants in preventing disease spread.
Article
Biology
David P. Maison, Lauren L. Ching, Sean B. Cleveland, Alanna C. Tseng, Eileen Nakano, Cecilia M. Shikuma, Vivek R. Nerurkar
Summary: This study evaluated sequencing data on two Hawai'i isolates and other SARS-CoV-2 variants using a rule-based algorithm to monitor virus evolution and emergence for vaccine design. The results showed that the worldwide spread and evolution of SARS-CoV-2 have led to variants containing mutations that decrease vaccine efficacy. The researchers developed an algorithm to monitor the evolution of SARS-CoV-2 in the context of vaccines and monoclonal antibodies, based on spike protein changes. The algorithm showed a strong positive correlation between spike protein changes and predictive value, which can be utilized in designing vaccines with relevant immunogenic epitopes.
COMMUNICATIONS BIOLOGY
(2022)
Review
Immunology
Xiaomin Chen, Yutong Kang, Jing Luo, Kun Pang, Xin Xu, Jinyu Wu, Xiaokun Li, Shengwei Jin
Summary: The ongoing COVID-19 pandemic caused by the novel coronavirus SARS-CoV-2 has highlighted the importance of next-generation sequencing in understanding the virus. NGS analysis has provided insights into the origin and transmission of SARS-CoV-2, as well as related factors like ACE2 expression levels, gut microbiota dysbiosis, and immunogenetics of patients. These sequencing techniques have the potential to identify new hosts, aid in diagnostic development, and discover therapeutic targets, offering crucial support in the fight against future public health emergencies.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2021)
Article
Infectious Diseases
Tom Loney, Hamda Khansaheb, Sathishkumar Ramaswamy, Divinlal Harilal, Zulfa Omar Deesi, Rupa Murthy Varghese, Aydah Belal Al Ali, Anees Khadeeja, Hanan Al Suwaidi, Abdulmajeed Alkhajeh, Laila Mohamed AlDabal, Mohammed Uddin, Mubarak Al Faresi, Madhvi Joshi, Abiola Senok, Norbert Nowotny, Alawi Alsheikh-Ali, Ahmad Abou Tayoun
Summary: The study conducted in Dubai, UAE, explored the global molecular epidemiology of SARS-CoV-2 and the relationship between different viral strains and disease severity. Findings demonstrated that older age, being overweight/obese, or having diabetes were associated with increased likelihood of hospitalization and ICU admission for COVID-19. The research also highlighted the continued community-based transmission of European strains in the Dubai population.
TRANSBOUNDARY AND EMERGING DISEASES
(2022)
Article
Oncology
Csilla Olah, Henning Reis, Michele J. Hoffmann, Fabian Mairinger, Saskia Ting, Boris Hadaschik, Ulrich Krafft, Viktor Gruenwald, Peter Nyirady, Melinda Varadi, Balazs Gyorffy, Andras Kiss, Eszter Szekely, Gottfrid Sjodahl, Tibor Szarvas
Summary: The study proposed a method for molecular classification of bladder cancer samples, and evaluated the impact of subtypes on survival after adjuvant chemotherapy. The results showed that luminal subtypes had better survival with chemotherapy, while basal subtypes did not show significant differences. High APOBEC3G expression was associated with better survival in platinum-treated patients. The proposed method is reliable for classifying tissue samples and subtypes have a significant impact on adjuvant chemotherapy.
Review
Multidisciplinary Sciences
Balazs Gyorffy, Boglarka Weltz, Istvan Szabo
Summary: A grant decision support tool was established in Hungary to rank the scientific productivity of researchers. The introduction of this tool increased the correlation between grant selection and scientometric parameters, leading to enhanced transparency in the review process.
Article
Oncology
Melinda Varadi, Nikolett Nagy, Henning Reis, Boris Hadaschik, Christian Niedworok, Orsolya Modos, Attila Szendroi, Jason Ablat, Peter C. Black, David Keresztes, Anita Csizmarik, Csilla Olah, Nadine T. Gaisa, Andras Kiss, Jozsef Timar, Erika Toth, Erzsebet Csernak, Arpad Gerstner, Vinay Mittal, Sofia Karkampouna, Marianna Kruithof de Julio, Balazs Gyorffy, Gabor Bedics, Michael Rink, Margit Fisch, Peter Nyirady, Tibor Szarvas
Summary: In this study, a data-processing pipeline was developed for the detection and interpretation of genetic alterations in two rare cancers. The analysis revealed a high rate of actionable mutations, suggesting potential feasibility for the treatment of urachal adenocarcinoma and primary bladder adenocarcinoma.
Article
Oncology
N. Woldmar, A. Schwendenwein, M. Kuras, B. Szeitz, K. Boettiger, A. Tisza, V Laszlo, L. Reiniger, A. G. Bago, Z. Szallasi, J. Moldvay, A. M. Szasz, J. Malm, P. Horvatovich, L. Pizzatti, G. B. Domont, F. Renyi-Vamos, K. Hoetzenecker, M. A. Hoda, G. Marko-Varga, K. Schelch, Z. Megyesfalvi, M. Rezeli, B. Dome
Summary: This study investigated the proteomic differences between primary lung adenocarcinoma (LADC) and corresponding brain metastases. The results revealed differential expression of proteins related to the immune system, cell-cell interactions, migration, metabolism, translation, and vesicle formation. Additionally, differences were observed in the proteomic profiles of fast-progressing patients compared to slow-progressing individuals. The findings provide insights into the biology of LADC brain metastases and may contribute to the development of personalized follow-up strategies.
Article
Chemistry, Multidisciplinary
Szonja Anna Kovacs, Janos Tibor Fekete, Balazs Gyorffy
Summary: Immune-checkpoint inhibitors have shown promising effects in the treatment of various tumor types. This study established a database and web platform to identify biomarkers of response to immunotherapy and facilitate further analysis and validation of new biomarker candidates.
ACTA PHARMACOLOGICA SINICA
(2023)
Article
Oncology
Zsuzsanna Valko, Zsolt Megyesfalvi, Anna Schwendenwein, Christian Lang, Sandor Paku, Nandor Barany, Bence Ferencz, Anita Horvath-Rozsas, Ildiko Kovacs, Erzsebet Schlegl, Veronika Pozonec, Kristiina Boettiger, Melinda Rezeli, Gyorgy Marko-Varga, Ferenc Renyi-Vamos, Mir Alireza Hoda, Thomas Klikovits, Konrad Hoetzenecker, Michael Grusch, Viktoria Laszlo, Balazs Dome, Karin Schelch
Summary: This study demonstrates the subtype specificity of BCL-2 expression and reveals the mechanism of venetoclax resistance in SCLC. Moreover, it provides preclinical evidence that combined BCL-2 and MCL-1 targeting is an effective approach to overcome venetoclax resistance in high BCL-2-expressing SCLCs with intact BAX.
BRITISH JOURNAL OF CANCER
(2023)
Review
Oncology
Jozsef Timar, Kenneth V. Honn, Mary J. C. Hendrix, Gyorgy Marko-Varga, Sirpa Jalkanen
Summary: Cancer plasticity, characterized by disturbances of cell differentiation programs, is a recognized hallmark of cancer. It includes various forms such as epithelial-mesenchymal transition (EMT), vasculogenic mimicry, and megakaryocytic mimicry. Immunogenic mimicry (IGM), a type of cancer plasticity, involves the expression of immune cell genes regulated by interferons (IFNs), often due to gene amplifications. These IGM genes play a role in immune escape of cancers and offer potential targets for immunotherapeutics.
CANCER AND METASTASIS REVIEWS
(2023)
Article
Obstetrics & Gynecology
J. Cadenas, L. C. Poulsen, D. Nikiforov, M. L. Grondahl, A. Kumar, K. Bahnu, A. L. M. Englund, J. Malm, G. Marko-Varga, I Pla, A. Sanchez, S. E. Pors, C. Yding Andersen
Summary: This study investigates the substances and signal transduction pathways involved in the regulation of human oocyte maturation downstream to the effects of FSH and LH. The results reveal that human oocyte maturation is a multifactorial process involving several different signal transduction pathways. Various pathways, including those involving CNP, EGF-related peptides, TGF-beta family members, activins/inhibins, FF-MAS, and MDK, are potentially active, while the GDF9 and BMP15 pathways show less pronounced influence.
HUMAN REPRODUCTION
(2023)
Article
Biochemistry & Molecular Biology
Aron Bartha, Zsuzsanna Darula, Gyoengyi Munkacsy, Eva Klement, Peter Nyirady, Balazs Gyorffy
Summary: This research used a proteotranscriptomic approach to differentiate normal and tumor tissues in clear cell renal cell carcinoma (ccRCC). Top genes over-expressed in ccRCC were identified using transcriptomic data of patients with malignant and normal tissue samples. Protein level analysis and mass spectrometry further validated the differential protein abundance of these genes. A minimal panel of proteins highly specific for ccRCC tissues was identified using transcriptomic and proteomic data.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Biochemistry & Molecular Biology
Gyongyi Munkacsy, Libero Santarpia, Balazs Gyorffy
Summary: Triple-negative breast cancer is the most aggressive subtype of breast cancer, characterized by the absence of estrogen receptor, progesterone receptor, and human epidermal growth receptor 2 expression. It has genomic and transcriptional heterogeneity and an immunosuppressive tumor microenvironment with high levels of tumor-infiltrating lymphocytes.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Medicine, Research & Experimental
Ines Barone, Luca Gelsomino, Felice Maria Accattatis, Francesca Giordano, Balazs Gyorffy, Salvatore Panza, Mario Giuliano, Bianca Maria Veneziani, Grazia Arpino, Carmine De Angelis, Pietro De Placido, Daniela Bonofiglio, Sebastiano Ando, Cinzia Giordano, Stefania Catalano
Summary: Obesity is a known risk factor for various chronic diseases, including breast cancer. This study found that the expression levels of miR-126-3p, miR-4772-3p, and miR-10a-5p in circulating extracellular vesicles were negatively correlated with survival in obese breast cancer patients.
JOURNAL OF TRANSLATIONAL MEDICINE
(2023)
Article
Pharmacology & Pharmacy
Balazs Gyorffy
Summary: This study established a comprehensive database of transcriptome-level data for lung cancer, which can be used to identify and rank the most promising biomarkers and therapeutic targets for different subtypes of lung cancer.
BRITISH JOURNAL OF PHARMACOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Cinzia Giordano, Felice Maria Accattatis, Luca Gelsomino, Piercarlo Del Console, Balazs Gyorffy, Mario Giuliano, Bianca Maria Veneziani, Grazia Arpino, Carmine De Angelis, Pietro De Placido, Erica Pietroluongo, Francesco Zinno, Daniela Bonofiglio, Sebastiano Ando, Ines Barone, Stefania Catalano
Summary: This study identified novel miRNA signatures, miRNA-27a and miRNA-128, in breast cancer by analyzing the expression profiles of EV-derived miRNAs in the blood circulation. These miRNAs showed diagnostic accuracy in distinguishing breast cancer patients from non-cancer controls.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Multidisciplinary Sciences
Peter Szluka, Edit Csajbok, Balazs Gyorffy
Summary: An increasing interest in demonstrating the prestige and status of higher education institutions has led to the establishment of several international ranking systems. These rankings often include parameters related to scientific productivity. In this study, we examined the differences between different rankings and their correlation with bibliometric parameters and disciplines for the top universities. The results showed that the most important parameters defining ranking positions include citations, international reputation, and the number of researchers. However, the strength of correlation varied among ranking systems. The absolute number of publications and citations were particularly important in certain rankings, while scientific category normalized citation impact played a central role in others. Additionally, there were variations in performance across different disciplines, with some ranking systems favoring universities with more publications in social sciences and others favoring universities with more publications in science, technology, and medicine fields.
SCIENTIFIC REPORTS
(2023)
Article
Oncology
Esther Cabanas Morafraile, Cristina Saiz-Ladera, Cristina Nieto-Jimenez, Balazs Gyorffy, Adam Nagy, Guillermo Velasco, Pedro Perez-Segura, Alberto Ocana
Summary: This study describes a novel therapeutic strategy for treating colorectal cancer (CRC) patients with BRAF mutations. By identifying upregulated proteins on the surface of tumor cells as treatment targets and observing the transcriptional profile associated with antigen presenting cells, it is suggested that a combination of anti PD(L)1 with other co-inhibitor receptors can be explored for treating BRAF-mutated CRC patients.
Review
Infectious Diseases
Allison M. Hitchcock, Wesley D. Kufel, Keri A. Mastro Dwyer, Eric F. Sidman
Summary: Lenacapavir is a novel HIV-1 treatment option for patients with multidrug-resistant (MDR) HIV-1 infection. It has a favorable pharmacokinetic profile and has shown good tolerability and efficacy in clinical trials.
INTERNATIONAL JOURNAL OF ANTIMICROBIAL AGENTS
(2024)
Article
Infectious Diseases
Roberta Gagliardini, Alessandro Tavelli, Stefano Rusconi, Sergio Lo Caputo, Vincenzo Spagnuolo, Maria Mercedes Santoro, Andrea Costantini, Alessandra Vergori, Franco Maggiolo, Andrea Giacomelli, Giulia Burastero, Giordano Madeddu, Eugenia Quiros Roldan, Antonella d'Arminio Monforte, Andrea Antinori, Alessandro Cozzi-Lepri
Summary: This study evaluated multiple treatment failures to modern antiretroviral therapy in HIV-infected individuals and found that approximately 4% of them were difficult to treat. The difficult to treat group, compared to the non-difficult to treat group, was characterized by older age, higher prevalence of AIDS, lower CD4+ cell count, and higher risk of treatment failure.
INTERNATIONAL JOURNAL OF ANTIMICROBIAL AGENTS
(2024)