Review
Pharmacology & Pharmacy
Mengyuan Kan, Blanca E. Himes
Summary: Glucocorticoid drugs are widely used in the treatment of diseases, but there is still much to learn about their cell type-specific mechanisms and why patients respond differently. Recent studies have used genomics, transcriptomics, and other omics approaches to address these questions, but there are still knowledge gaps to be filled related to glucocorticoid action mechanisms.
PHARMACOLOGY & THERAPEUTICS
(2021)
Review
Biochemistry & Molecular Biology
Qiaolifan Aerqin, Zuo-Teng Wang, Kai-Min Wu, Xiao-Yu He, Qiang Dong, Jin-Tai Yu
Summary: This review summarizes the progress made in the discovery of reliable Alzheimer's disease (AD) biomarkers using genomics, transcriptomics, proteomics, and metabolomics. The importance of these biomarkers in the diagnosis and treatment of AD is discussed.
CELLULAR AND MOLECULAR LIFE SCIENCES
(2022)
Review
Plant Sciences
Milan Jockovic, Sinisa Jocic, Sandra Cvejic, Ana Marjanovic-Jeromela, Jelena Jockovic, Aleksandra Radanovic, Dragana Miladinovic
Summary: The review emphasizes the importance of systematic approaches to sunflower breeding, highlighting the lack of desirable genetic variation in the field. By integrating information from various omics technologies, a comprehensive understanding of the molecular mechanisms in sunflower can be achieved, leading to more efficient breeding strategies.
Review
Nutrition & Dietetics
Omar Ramos-Lopez, J. Alfredo Martinez, Fermin Milagro
Summary: The combination of multiple omics approaches provides a comprehensive view of human diseases and their underlying molecular and physiological events, aiding in the understanding of metabolic phenotypes and disease associations, guiding dietary treatments and prognosis. However, challenges include ethical and regulatory issues, lack of reliable and reproducible results, high cost and high-dimensional data analysis.
Article
Health Care Sciences & Services
Yadu Gautam, Elisabet Johansson, Tesfaye B. Mersha
Summary: This article provides an overview of the current status and development of omics studies in asthma, including genomics, transcriptomics, epigenomics, proteomics, exposomics, and metabolomics. Biomarker discovery through multi-omics profiling can be useful for better phenotyping and subtyping of asthma, ultimately leading to advances in precision medicine.
JOURNAL OF PERSONALIZED MEDICINE
(2022)
Article
Obstetrics & Gynecology
Lina Youssef, Lea Testa, Francesca Crovetto, Fatima Crispi
Summary: Preeclampsia is a pregnancy-specific disease with an unknown precise cause. Multi-omics approaches have been used to study the molecular mechanisms of preeclampsia, and various genetic variants, altered gene expressions, potential biomarkers, and metabolic changes have been identified. Microbiomics studies have also found dysbiosis in the microbiota of pregnant women with preeclampsia. Further research is needed to integrate and translate these findings into clinical practice.
BEST PRACTICE & RESEARCH CLINICAL OBSTETRICS & GYNAECOLOGY
(2024)
Article
Biochemistry & Molecular Biology
Catarina M. Stein, Ralf Weiskirchen, Frederik Damm, Paulina M. Strzelecka
Summary: Single-cell sequencing methods provide high-resolution insight into cellular heterogeneity, serving as powerful tools for scientists. Application of these methods in the biomedical field can help unravel disease pathogenesis.
JOURNAL OF CELLULAR BIOCHEMISTRY
(2021)
Article
Cell Biology
Fei Yuan, Xiaoyu Cao, Yu-Hang Zhang, Lei Chen, Tao Huang, ZhanDong Li, Yu-Dong Cai
Summary: This study conducted a computational investigation on lung cancer driver genes, involving four omics levels. Through a screening process and intersection operation, novel driver genes involving two omics levels were identified, which were found to be associated with the fundamental pathological mechanisms of lung cancer.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Ranjan K. Shaw, Yusen Shen, Huifang Yu, Xiaoguang Sheng, Jiansheng Wang, Honghui Gu
Summary: Clubroot disease caused by Plasmodiophora brassicae poses a significant threat to Brassica crops. The application of omics technologies has provided valuable insights into the resistance mechanisms of Brassica crops against clubroot. This review summarizes the recent advances in utilizing various omics approaches to breed clubroot-resistant Brassica crops and discusses the challenges and future directions in this area.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Biochemistry & Molecular Biology
Annamaria Tisi, Sakthimala Palaniappan, Mauro Maccarrone
Summary: This article presents the application of advanced omics techniques, such as genomics, transcriptomics, and epigenomics, in cochlear research. The article also introduces the latest technologies, including single-cell omics and spatial omics, for investigating molecular events at a single-cell resolution with spatial information.
Article
Biochemistry & Molecular Biology
Otilia Menyhart, Balazs Gyorffy
Summary: Multi-omics data integration offers unparalleled opportunities for understanding complex diseases like cancer, but faces challenges such as uneven maturity of different omics approaches and limited data processing capacity. Efforts to standardize sample processing, train experts for data analysis, and close the gap between data generation and processing are crucial for the translatability of theoretical findings.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)
Review
Plant Sciences
Manish Tiwari, Baljinder Singh, Doohong Min, S. V. Krishna Jagadish
Summary: Conventional breeding techniques for lentils have limitations, leading to exploration of alternative routes like genomics and transcriptomics for identifying genes related to stress tolerance. New technologies such as NGS and HTP improve breeding efficiency, while proteomics and metabolomics studies aid in understanding gene regulation mechanisms under different stresses.
FRONTIERS IN PLANT SCIENCE
(2022)
Review
Cell Biology
Mafalda Rizzuti, Luca Sali, Valentina Melzi, Simone Scarcella, Gianluca Costamagna, Linda Ottoboni, Lorenzo Quetti, Lorenzo Brambilla, Dimitra Papadimitriou, Federico Verde, Antonia Ratti, Nicola Ticozzi, Giacomo Pietro Comi, Stefania Corti, Delia Gagliardi
Summary: This article provides an overview of the research progress in investigating the molecular mechanisms of ALS using genomics, epigenomics, transcriptomics, and microRNAs. It reports the most relevant genes implicated in ALS pathogenesis and discusses the use of different high-throughput sequencing techniques and the role of epigenomic modifications. Furthermore, it presents the latest advances in transcriptomic studies and discusses the potential of microRNAs as biomarkers and molecular intervention tools.
AGEING RESEARCH REVIEWS
(2023)
Review
Food Science & Technology
Karolinny Cristiny de Oliveira Vieira, Hevelin Regiane Augusto da Silva, Isabela Poletto Masselli Rocha, Emmanuel Barboza, Lizziane Kretli Winkelstroter Eller
Summary: Outbreaks and deaths related to Foodborne Diseases (FBD) are constantly occurring worldwide, largely due to consumption of contaminated foodstuffs with pathogens. This review discusses the main omic techniques applied in foodborne pathogens and their potential in ensuring food safety. Omics have been shown to integrate variables that contribute to food safety and improve consumer health, costs, and product quality.
CRITICAL REVIEWS IN FOOD SCIENCE AND NUTRITION
(2022)
Review
Biochemistry & Molecular Biology
Sara Rega, Floriana Farina, Silvia Bouhuis, Silvia de Donato, Mattia Chiesa, Paolo Poggio, Laura Cavallotti, Giorgia Bonalumi, Ilaria Giambuzzi, Giulio Pompilio, Gianluca L. Perrucci
Summary: Thoracic aortic aneurysm (TAA) is a serious condition without etiological therapy. Recent studies have shown that integrating biological targets and etiological mechanisms through -omics approaches, especially metabolomics, can provide valuable insights for TAA diagnosis and therapy.
CELL AND BIOSCIENCE
(2023)
Article
Biology
Diane Duroux, Hector Climente-Gonzalez, Chloe-Agathe Azencott, Kristel Van Steen
Summary: The study proposes a multi-step protocol for detecting epistasis at the gene level, which reduces the number of tests performed and provides interpretable interactions while controlling for errors. Applying this protocol to a genome-wide association study dataset on inflammatory bowel disease yields different results, overlapping with known disease characteristics. The proposed pipeline also demonstrates the potential for additional discoveries when incorporating prior biological knowledge into epistasis detection.
Article
Gastroenterology & Hepatology
Monica P. de Andres, Richard J. Jackson, Irene Felipe, Sladjana Zagorac, Christian Pilarsky, Anna Melissa Schlitter, Jaime Martinez de Villareal, Gun Ho Jang, Eithne Costello, Steve Gallinger, Paula Ghaneh, William Greenhalf, Thomas Knoesel, Daniel H. Palmer, Petra Ruemmele, Wilko Weichert, Markus Buechler, Thilo Hackert, John P. Neoptolemos, Faiyaz Notta, Nuria Malats, Paola Martinelli, Francisco X. Real
Summary: GATA4 and GATA6 cooperate to maintain the classical phenotype in pancreatic ductal adenocarcinoma (PDAC), and their expression is associated with patient prognosis and therapeutic response, providing a theoretical basis for using them as biomarkers of prognosis and therapeutic response.
Article
Cell & Tissue Engineering
Dafni Chondronasiou, Jaime Martinez de Villarreal, Elena Melendez, Cian J. Lynch, Natalia del Pozo, Marta Kovatcheva, Monica Aguilera, Neus Prats, Francisco X. Real, Manuel Serrano
Summary: This study revealed the cellular reprogramming process in the pancreas using single-cell RNA sequencing and identified markers associated with cell dedifferentiation and reprogramming. Some cells do not dedifferentiate during the reprogramming process and exhibit stress markers. Additionally, markers of intermediate reprogramming were also observed in the stomach, colon, and cultured fibroblasts expressing OSKM, suggesting their potential role in tissue regeneration and rejuvenation.
Article
Environmental Sciences
Alice Hinchliffe, Juan Alguacil, Wendy Bijoux, Manolis Kogevinas, Florence Menegaux, Marie-Elise Parent, Beatriz Perez Gomez, Sanni Uuksulainen, Michelle C. Turner
Summary: This study found no clear evidence for an association between occupational heat exposure and prostate cancer risk.
ENVIRONMENTAL RESEARCH
(2023)
Article
Genetics & Heredity
Emilie Abby, Stefan C. C. Dentro, Michael W. J. Hall, Joanna C. C. Fowler, Swee Hoe Ong, Roshan Sood, Albert Herms, Gabriel Piedrafita, Irina Abnizova, Christian W. W. Siebel, Moritz Gerstung, Benjamin A. A. Hall, Philip H. H. Jones
Summary: Notch1 mutations have opposite effects in normal and tumor cells of the mouse esophagus. Notch1 blockade reduces premalignant tumor growth and may be used as a prevention strategy for squamous esophageal cancer. NOTCH1 mutant clones are more common in normal human esophagus but less prevalent in esophageal cancers, suggesting that these mutations promote clonal expansion but hinder carcinogenesis. Further experiments confirmed the competitive advantage conferred by Notch1 mutations in mouse esophagus and the potential therapeutic effect of Notch1 blockade in preventing esophageal cancer.
Article
Environmental Sciences
Manolis Kogevinas, Marianna Karachaliou, Ana Espinosa, Ruth Aguilar, Gemma Castano-Vinyals, Judith Garcia-Aymerich, Anna Carreras, Beatriz Cortes, Vanessa Pleguezuelos, Kyriaki Papantoniou, Rocio Rubio, Alfons Jimenez, Marta Vidal, Pau Serra, Daniel Parras, Pere Santamaria, Luis Izquierdo, Marta Cirach, Mark Nieuwenhuijsen, Payam Dadvand, Kurt Straif, Gemma Moncunill, Rafael de Cid, Carlota Dobano, Cathryn Tonne
Summary: This study found an association between long-term exposure to air pollution and a lower antibody response to COVID-19 vaccines. Among vaccinated individuals without prior infection, higher levels of exposure to PM2.5, NO2, BC, and O3 were associated with lower vaccine antibody responses. This association persisted over time since vaccination.
ENVIRONMENTAL HEALTH PERSPECTIVES
(2023)
Article
Public, Environmental & Occupational Health
Anna Palomar-Cros, Bernard Srour, Valentina A. Andreeva, Leopold K. Fezeu, Alice Bellicha, Emmanuelle Kesse-Guyot, Serge Hercberg, Dora Romaguera, Manolis Kogevinas, Mathilde Touvier
Summary: This study investigated the longitudinal associations of meal timing, number of eating occasions, and night-time fasting duration with the incidence of type 2 diabetes (T2D). The findings showed that individuals who habitually ate breakfast after 9 AM had a higher risk of developing T2D, while the timing of the last meal was not associated with T2D incidence. Each additional eating occasion was associated with a lower risk of T2D. The duration of night-time fasting was not associated with T2D incidence, except for those who had breakfast before 8 AM and fasted for more than 13 hours overnight. This study suggests that breakfast timing affects the incidence of T2D, and an early breakfast should be considered for T2D prevention.
INTERNATIONAL JOURNAL OF EPIDEMIOLOGY
(2023)
Article
Oncology
Miriam Marques, Sonia Corral, Maria Sanchez-Diaz, Natalia del Pozo, Jaime Martinez de Villarreal, Norbert Schweifer, Ivana Zagorac, Frank Hilberg, Francisco X. Real
Summary: Bladder cancer is a prevalent tumor that requires the development of novel therapies. Nintedanib, an angio-kinase inhibitor, has shown efficacy in combination with chemotherapy for locally advanced muscle-invasive bladder cancer. Our study investigated the mechanisms of action of nintedanib and identified potential markers and treatment strategies to overcome resistance.
MOLECULAR CANCER THERAPEUTICS
(2023)
Review
Oncology
Lisa M. C. van Hoogstraten, Alina Vrieling, Antoine G. van der Heijden, Manolis Kogevinas, Anke Richters, Lambertus A. Kiemeney
Summary: Bladder cancer is a significant burden for healthcare systems worldwide due to its high incidence and mortality. The occurrence of bladder cancer is influenced by factors such as population growth, aging, and exposure to risk factors like tobacco smoking. Primary prevention efforts are crucial in reducing the burden of bladder cancer, and less-invasive diagnostic approaches using urinary biomarkers show promise. Increasing awareness of risk factors and symptoms among healthcare professionals and high-risk groups is also important. Further research on the relationship between lifestyle factors and bladder cancer outcomes should be prioritized.
NATURE REVIEWS CLINICAL ONCOLOGY
(2023)
Review
Oncology
Belen Caramelo, Sladjana Zagorac, Sonia Corral, Miriam Marques, Francisco X. Real
Summary: Bladder cancer is a highly prevalent tumor, especially among men. The tumor microenvironment, specifically the cancer-associated fibroblasts, play an important role in tumor development and progression. However, the role of cancer-associated fibroblasts in bladder cancer is not well understood.
EUROPEAN UROLOGY ONCOLOGY
(2023)
Article
Urology & Nephrology
Stella Koutros, Lambertus A. Kiemeney, Parichoy Pal Choudhury, Roger L. Milne, Evangelina Lopez de Maturana, Yuanqing Ye, Vijai Joseph, Oscar Florez-Vargas, Lars Dyrskjot, Jonine Figueroa, Diptavo Dutta, Graham G. Giles, Michelle A. T. Hildebrandt, Kenneth Offit, Manolis Kogevinas, Elisabete Weiderpass, Marjorie L. McCullough, Neal D. Freedman, Demetrius Albanes, Charles Kooperberg, Victoria K. Cortessis, Margaret R. Karagas, Alison Johnson, Molly R. Schwenn, Dalsu Baris, Helena Furberg, Dean F. Bajorin, Olivier Cussenot, Geraldine Cancel-Tassin, Simone Benhamou, Peter Kraft, Stefano Porru, Angela Carta, Timothy Bishop, Melissa C. Southey, Giuseppe Matullo, Tony Fletcher, Rajiv Kumar, Jack A. Taylor, Philippe Lamy, Frederik Prip, Mark Kalisz, Stephanie J. Weinstein, Jan G. Hengstler, Silvia Selinski, Mark Harland, Mark Teo, Anne E. Kiltie, Adonina Tardon, Consol Serra, Alfredo Carrato, Reina Garcia-Closas, Josep Lloreta, Alan Schned, Petra Lenz, Elio Riboli, Paul Brennan, Anne Tjonneland, Thomas Otto, Daniel Ovsiannikov, Frank Volkert, Sita H. Vermeulen, K. K. Aben, Tessel E. Galesloot, Constance Turman, Immaculata De Vivo, Edward Giovannucci, David J. Hunter, Chancellor Hohensee, Rebecca Hunt, Alpa V. Patel, Wen-Yi Huang, Gudmar Thorleifsson, Manuela Gago-Dominguez, Pilar Amiano, Klaus Golka, Mariana C. Stern, Wusheng Yan, Jia Liu, Shengchao Alfred, Shilpa Katta, Amy Hutchinson, Belynda Hicks, William A. Wheeler, Mark P. Purdue, Katherine A. McGlynn, Cari M. Kitahara, Christopher A. Haiman, Mark H. Greene, Thorunn Rafnar, Nilanjan Chatterjee, Stephen J. Chanock, Xifeng Wu, Francisco X. Real, Debra T. Silverman, Montserrat Garcia-Closas, Kari Stefansson, Ludmila Prokunina-Olsson, Nuria Malats, Nathaniel Rothman
Summary: A meta-analysis of 32 studies identified novel genetic variants associated with bladder cancer risk and constructed a polygenic risk score (PRS) to stratify lifetime risk. These findings provide insights into the biological underpinnings of bladder cancer and have the potential to inform future preventive strategies.
Article
Immunology
Ahmed Tawfik, Takahisa Kawaguchi, Meiko Takahashi, Kazuya Setoh, Izumi Yamaguchi, Yasuharu Tabara, Kristel Van Steen, Anavaj Sakuntabhai, Fumihiko Matsuda
Summary: This study investigated the immunogenicity of influenza vaccine in two independent groups. The results showed that a single dose of the vaccine provided equal protection after three months for both annually vaccinated adults and first-time vaccine receivers.
EXPERT REVIEW OF VACCINES
(2023)
Article
Biochemical Research Methods
Jaime Martinez de Villarreal, Mark Kalisz, Gabriel Piedrafita, Osvaldo Grana-Castro, Dafni Chondronasiou, Manuel Serrano, Francisco X. Real
Summary: Transposable elements have played a major role in shaping mammalian genomes, but little is known about their cell-type-specific expression. A cost-efficient single-cell-resolution TE expression analytical approach is needed.
Review
Biochemistry & Molecular Biology
Maria Ramal, Sonia Corral, Mark Kalisz, Eleonora Lapi, Francisco X. Real
Summary: This study systematically analyzed the transcription factors (TFs) in urothelium and bladder cancer using RNA-Seq and ATAC-Seq data. The results identified known TFs associated with luminal and basal phenotypes, as well as novel candidate TFs involved in bladder cancer and differentiation. Additionally, several TF families were suggested to be involved in urothelial cell differentiation and bladder cancer.
Article
Health Care Sciences & Services
Denis Horgan, Jasmina Koeva-Balabanova, Ettore Capoluongo, Beata Jagielska, Ivana Cattaneo, Marta Kozaric, Birute Tumiene, Jean-Paul El Ahl, Jonathan A. Lal, Dipak Kalra, Nuria Malats
Summary: The current delicate balance of funding rare disease research and development in Europe is facing new threats from forthcoming policy changes, which may reduce incentives and disrupt the flow of innovative treatments.
