Article
Evolutionary Biology
Zoe Vance, Lukasz Niezabitowski, Laurence D. Hurst, Aoife McLysaght
Summary: Research has shown that duplicated genes evolve at a faster rate compared to singleton genes in multiple lineages. This phenomenon is not restricted to a single lineage and has implications for the interpretation of gene duplication. Additionally, some singleton genes appear to evolve faster due to homology detection failure and unidentified paralogs.
GENOME BIOLOGY AND EVOLUTION
(2022)
Article
Engineering, Civil
Mengdie Chen, Sujith Mangalathu, Jong-Su Jeon
Summary: This study proposes a novel framework for computing transportation network fragilities following earthquakes to assess the likelihood of functionality of bridge routes, assisting emergency responders and bridge owners in evaluating availability post-seismic events.
ENGINEERING STRUCTURES
(2021)
Article
Biology
Wei-luo Cai, Mo Cheng, Yi Wang, Pei-hang Xu, Xi Yang, Zheng-wang Sun, Wang-jun Yan
Summary: Cancer metastasis is a major cause of cancer progression and treatment difficulty. This study identified genes associated with different tissue metastases and proposed a CNN-based model, MDCNN, for predicting metastasis occurrence. The model achieved satisfactory prediction accuracy and outperformed other methods. Further analysis revealed pathways and immune infiltration associated with bone metastasis.
COMPUTERS IN BIOLOGY AND MEDICINE
(2024)
Article
Oncology
Meng-jie Shan, Ling-bing Meng, Peng Guo, Yuan-meng Zhang, Dexian Kong, Ya-bin Liu
Summary: This study identified CDH3, LEF1, and MMP7 as potential biomarkers for gastric cancer through gene expression analysis, and established a neural network model for early diagnosis.
FRONTIERS IN ONCOLOGY
(2021)
Article
Oncology
Yan Chen, Xuan Sun, Jiaxing Yang
Summary: This paper introduces a method for identifying gastric cancer related genes. By constructing a heterogeneous network and using graph transformer network and deep belief network to process and reduce the dimension of features, the accuracy is improved and it performed the best.
FRONTIERS IN ONCOLOGY
(2022)
Article
Cell Biology
Tingna Chen, Qiuming He, Zhenxian Xiang, Rongzhang Dou, Bin Xiong
Summary: The study utilized WGCNA to identify three gene modules significantly correlated with gastric cancer and analyzed differentially correlated gene pairs within these modules using DiffCorr. GEMIN5 and PFDN2 were identified as key genes in the regulatory network, with their differential expression validated in cell lines and patient tissues.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Rhys Gillman, Matt A. Field, Ulf Schmitz, Rozemary Karamatic, Lionel Hebbard
Summary: Cancer, a heterogeneous disease with a strong genetic component, can benefit from precision medicine approaches to identify molecular drivers. Single-tumour methods based on gene interaction networks have limitations and require further research for evaluation.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Article
Plant Sciences
Bingqian Tang, Lingling Xie, Huiping Yang, Xiumin Li, Ying Chen, Xuexiao Zou, Feng Liu, Xiongze Dai
Summary: The mechanism of resistance to cold temperatures in plants, specifically in pepper, is not well understood. This study utilized cluster analysis to classify expressed genes during cold treatment and identified differentially expressed genes associated with metabolic processes and membrane compositions. By comparing the expression levels of ICE-CBF-COR module genes, the study also identified positive and negative regulators in pepper. The findings shed light on the relationship between these genes and their role in cold stress adaptation. This study provides valuable resources for cold tolerance research and genetic modification of cold stress regulators.
FRONTIERS IN PLANT SCIENCE
(2022)
Review
Cell Biology
Rocio I. R. Macias, Maria J. Monte, Maria A. Serrano, Jesus M. Gonzalez-Santiago, Isabel Martin-Arribas, Andre L. Simao, Rui E. Castro, Javier Gonzalez-Gallego, Jose L. Mauriz, Jose J. G. Marin
Summary: Aging leads to gradual deterioration of organs and functions, making elderly patients more susceptible to liver cancer. Certain age-related characteristics may play a role in liver carcinogenesis in the elderly, but there is still controversy over the treatment of liver tumors in elderly patients.
Article
Physics, Multidisciplinary
Liwen Zhang, Linying Xiang, Jiawei Zhu
Summary: This paper explains from a mathematical perspective the relationship between fragility and resilience in networked systems. Analytical and numerical evidence is provided to support the finding that fragility increases and resilience decreases when the network is attacked.
PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS
(2022)
Article
Biotechnology & Applied Microbiology
Yuan Zhu, Houwang Zhang, Yuanhang Yang, Chaoyang Zhang, Le Ou-Yang, Litai Bai, Minghua Deng, Ming Yi, Song Liu, Chao Wang
Summary: This study successfully identified potential pan-cancer-related genes by establishing a pan-cancer network and using integrative network analysis, demonstrating the potential of the method for further biological experimental verification.
BRIEFINGS IN FUNCTIONAL GENOMICS
(2022)
Article
Oncology
Rui Wu, Hao Zhuang, Yu-Kun Mei, Jin-Yu Sun, Tao Dong, Li-Li Zhao, Zhi-Ning Fan, Li Liu
Summary: By combining DEGs and WGCNA, CCNB1 was identified as the hub gene in esophageal cancer, upregulated in tumor tissues, and associated with poor prognosis in esophageal cancer patients with higher expression.
CANCER CELL INTERNATIONAL
(2021)
Article
Genetics & Heredity
Shao-Wu Zhang, Jing-Yu Xu, Tong Zhang
Summary: DGMP is a novel method that uses multi-omics pan-cancer data to identify cancer driver genes. It combines directed graph convolutional network (DGCN) and multilayer perceptron (MLP) to learn gene features and topological structure features in gene regulatory networks (GRNs). The experimental results show that DGMP outperforms other existing methods in identifying cancer driver genes.
GENOMICS PROTEOMICS & BIOINFORMATICS
(2022)
Article
Multidisciplinary Sciences
Sharaf J. Malebary, Yaser Daanial Khan
Summary: Cancer is primarily driven by various types of genetic changes and variations. Identifying cancer driver genes is crucial for precise oncological analysis. A proposed model, PCDG-Pred, utilizes sequencing data to distinguish cancer driver genes from passenger genes effectively, showing promising results in identifying and prioritizing cancer driver genes.
SCIENTIFIC REPORTS
(2021)
Article
Engineering, Civil
Mohammadreza Parvizi, Kiarash Nasserasadi, Ehsan Tafakori
Summary: This study employs a soft computing approach and trains artificial neural networks to estimate the parameters of fragility functions, reducing computational costs and increasing estimation accuracy. The results show the reliability and accuracy of this method for predicting fragility functions.
Article
Biochemistry & Molecular Biology
Maria Vittoria Cavicchioli, Mariangela Santorsola, Nicola Balboni, Daniele Mercatelli, Federico Manuel Giorgi
Summary: The correlation between the metabolome and transcriptome can provide insights into cancer, biomarker discovery, and prediction of metabolite quantities based on transcriptomics data.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Stephanie A. Carmack, Janaina C. M. Vendruscolo, M. Adrienne McGinn, Jorge Miranda-Barrientos, Vez Repunte-Canonigo, Gabriel D. Bosse, Daniele Mercatelli, Federico M. Giorgi, Yu Fu, Anthony J. Hinrich, Francine M. Jodelka, Karen Ling, Robert O. Messing, Randall T. Peterson, Frank Rigo, Scott Edwards, Pietro P. Sanna, Marisela Morales, Michelle L. Hastings, George F. Koob, Leandro F. Vendruscolo
Summary: This study explores the mechanistic role of extrahypothalamic stress systems in driving opioid addiction and finds that glucocorticoid receptor antagonism with mifepristone reduces opioid addiction-like behaviors and decreases the firing of corticotropin-releasing factor neurons in the rat amygdala.
MOLECULAR PSYCHIATRY
(2022)
Article
Virology
Yu Fu, Irene Lorrai, Barry Zorman, Daniele Mercatelli, Chase Shankula, Jorge Marquez Gaytan, Celine Lefebvre, Giordano de Guglielmo, Hyunjae Ryan Kim, Pavel Sumazin, Federico M. Giorgi, Vez Repunte-Canonigo, Pietro Paolo Sanna
Summary: Substance use disorders are common in people with HIV, and excessive opioid intake can lead to neurotoxicity and cognitive impairment.
Review
Biology
Federico M. Giorgi, Carmine Ceraolo, Daniele Mercatelli
Summary: This article reviews the development of the R programming language from its inception to the present day, describing its current features and capabilities, as well as its relationship with other programming languages. It also provides a detailed introduction to the major tools and applications of R, and discusses its role in science.
Review
Oncology
A. Acha-Sagredo, P. Ganguli, F. D. Ciccarelli
Summary: Somatic variation is an important factor in cancer initiation and early detection. The extent of somatic variation varies across tissues depending on their intrinsic features and exposure to endogenous and exogenous insults. Mutations in tumor suppressor genes involved in chromatin modification and cell growth signaling are tissue-specific drivers of clonal expansion. Understanding the factors triggering the transformation of somatic variation into malignant clones is crucial for cancer prevention and early detection.
ANNALS OF ONCOLOGY
(2022)
Article
Biochemical Research Methods
Daniele Mercatelli, Chiara Cabrelle, Pierangelo Veltri, Federico M. Giorgi, Pietro H. Guzzi
Summary: Cell surface proteins play important roles in cancer research as diagnostic and prognostic markers, as well as targets for anticancer agents. The integrated network analysis on transcriptomic data can infer the activity of these proteins and identify surface signaling hubs. This study demonstrates the application of the SURFACER method in cancer datasets, discovering relevant knowledge and stratifying different cancers based on surface activity.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Genetics & Heredity
Giorgio Milazzo, Giovanni Perini, Federico M. Giorgi
Summary: This study identified a global senescence signature and reduced proliferation in NBL cells treated with panobinostat, as well as transcriptional responses compatible with early neuronal differentiation. Through master regulator analysis, BAZ1A, HCFC1, MAZ, and ZNF146 were identified as the transcriptional regulators most significantly repressed by panobinostat, and experimental silencing confirmed their role in sustaining NBL cell proliferation in vitro.
Article
Genetics & Heredity
Hrvoje Misetic, Mohamed Reda Keddar, Jean-Pierre Jeannon, Francesca D. D. Ciccarelli
Summary: In this study, the significant interactions between cancer-specific genetic drivers and anti- and pro-tumour features of the tumour immune microenvironment (TIME) were computed using Lasso regularised ordinal regression in 32 cancer types. The functional networks linking specific TIME driver alterations to the associated TIME state were reconstructed for head and neck squamous cancer (HNSC). The study identified 477 TIME drivers that are multifunctional genes, predicted the immune profiles of HNSC molecular subtypes, and provided insights into the immune-regulatory role of TIME drivers.
Article
Biology
Daria Messelodi, Silvia Strocchi, Salvatore Nicola Bertuccio, Pascale Baden, Valentina Indio, Federico M. Giorgi, Alberto Taddia, Salvatore Serravalle, Sabrina Valente, Alessio di Fonzo, Emanuele Frattini, Roberto Bernardoni, Annalisa Pession, Daniela Grifoni, Michela Deleidi, Annalisa Astolfi, Andrea Pession
Summary: Gaucher Disease (GD), caused by mutations in the GBA1 gene, has a wide range of phenotypes, from mild to severe neurological involvement. Our study using Drosophila dGBA1b loss-of-function models and GD patient-derived iPSCs reveals that GD neuronal cells have impaired growth mechanisms, with increased cell death and reduced proliferation. This impairment is associated with downregulation of several Hippo transcriptional targets and exclusion of YAP from nuclei. Targeting the Hippo pathway may be a promising therapeutic approach for neuronopathic GD.
COMMUNICATIONS BIOLOGY
(2023)
Article
Neurosciences
Pietro Paolo Sanna, Chiara Cabrelle, Tomoya Kawamura, Daniele Mercatelli, Nathan O'Connor, Amanda J. Roberts, Vez Repunte-Canonigo, Federico M. Giorgi
Summary: Repeated alcohol intoxication can hasten neurocognitive impairment in a mouse model of Alzheimer's disease (AD). Through single nucleus RNA sequencing of 113,242 cells in the prefrontal cortex, we identified a broad dysregulation of gene expression related to neuronal excitability, neurodegeneration, and inflammation. Our findings suggest that alcohol promotes transcriptional changes consistent with AD progression, and our gene expression dataset provides a unique resource for investigating the detrimental role of excessive alcohol intake in AD.
Article
Chemistry, Analytical
Michele Protti, Marco Cirrincione, Sarah Palano, Eleonora Poeta, Giorgia Babini, Maria Chiara Magnifico, Simona Nicole Barile, Nicola Balboni, Francesca Massenzio, Mohammadreza Mahdavijalal, Federico M. Giorgi, Roberto Mandrioli, Francesco M. Lasorsa, Barbara Monti, Laura Mercolini
Summary: Accurate characterization of metabolic profiles is essential for studying cellular metabolic pathways and understanding human diseases. A liquid chromatography-tandem mass spectrometry (LC-MS/MS) approach was developed for the qualitative and quantitative analysis of compounds in cell cultures. The method showed good sensitivity, selectivity, linearity, and precision, making it suitable for studying biochemical pathways in central nervous system diseases.
JOURNAL OF PHARMACEUTICAL AND BIOMEDICAL ANALYSIS
(2023)
Article
Biochemistry & Molecular Biology
Ensieh M. Poursani, Daniele Mercatelli, Prahlad Raninga, Jessica L. Bell, Federica Saletta, Felix V. Kohane, Daniel P. Neumann, Ye Zheng, Jourdin R. C. Rouaen, Toni Rose Jue, Filip T. Michniewicz, Piper Schadel, Erin Kasiou, Maria Tsoli, Giuseppe Cirillo, Shafagh Waters, Tyler Shai-Hee, Riccardo Cazzoli, Merryn Brettle, Iveta Slapetova, Maria Kasherman, Renee Whan, Fernando Souza-Fonseca-Guimaraes, Linda Vahdat, David Ziegler, John G. Lock, Federico M. Giorgi, KumKum Khanna, Orazio Vittorio
Summary: Metastatic cancer cells use Epithelial-mesenchymal-transition (EMT) to enhance migration, invasion, and treatment resistance, and elevated levels of copper are implicated in cancer progression and metastasis. Copper chelation therapy can inhibit metastasis by reducing TGF-beta levels and EMT signaling, making it a potentially effective therapeutic approach for targeting TGF-beta and inhibiting EMT in various cancers.
CELL AND BIOSCIENCE
(2023)
Article
Environmental Sciences
Livia Beccacece, Filippo Costa, Jennifer Paola Pascali, Federico Manuel Giorgi
Summary: In recent decades, the persistence of per- and polyfluoroalkyl substances (PFASs) in the environment and their detrimental effects on living organisms have drawn widespread attention. This study collected 2144 publicly available samples from seven different animal species to investigate molecular responses to PFAS exposure and determine any conserved responses. Comparative transcriptional analysis revealed that PFAS exposure induces conserved molecular responses across different tissues, molecules, and species. The study identified several genes and pathways that exhibit consistent and evolutionarily conserved transcriptional responses to PFASs, providing evidence for the impact of PFAS exposure on living organisms and the environment.
Article
Evolutionary Biology
Ella F. Gunady, Kathryn E. Ware, Sarah Hoskinson Plumlee, Nicolas Devos, David Corcoran, Joseph Prinz, Hrvoje Misetic, Francesca D. Ciccarelli, Tara M. Harrison, Jeffrey L. Thorne, Robert Schopler, Jeffrey Everitt, William C. Eward, Jason A. Somarelli
Summary: The mutational landscape of hepatocellular carcinoma in lemurs shows similarities and unique features compared to human hepatocellular carcinomas, suggesting potential differences in the etiology and progression of this cancer in lemurs and humans.
EVOLUTION MEDICINE AND PUBLIC HEALTH
(2022)
Article
Biotechnology & Applied Microbiology
Lisa Dressler, Michele Bortolomeazzi, Mohamed Reda Keddar, Hrvoje Misetic, Giulia Sartini, Amelia Acha-Sagredo, Lucia Montorsi, Neshika Wijewardhane, Dimitra Repana, Joel Nulsen, Jacki Goldman, Marc Pollitt, Patrick Davis, Amy Strange, Karen Ambrose, Francesca D. Ciccarelli
Summary: This study compiled a literature-based repertoire of 3355 well-known or predicted drivers of cancer and non-cancer somatic evolution in 122 cancer types and 12 non-cancer tissues. The analysis of these genes revealed that the known compendium of drivers is still incomplete and biased towards frequently occurring coding mutations. There is a high overlap between drivers of cancer and non-cancer somatic evolution, although significant differences exist in their recurrence. Additionally, a set of evolutionarily conserved and essential genes were identified, and alteration in even one of these genes is sufficient to drive clonal expansion but not malignant transformation.
