Review
Hematology
Marta Kulis, Jose Ignacio Martin-Subero
Summary: Chronic lymphocytic leukaemia (CLL) is characterized by both driver genetic alterations and extensive epigenetic changes. Epigenomic studies have revealed the DNA methylome, chromatin accessibility, histone modifications, and 3D genome architecture of CLL. The DNA methylome contains information about the cellular origin and proliferative history of CLL cells, which are independent prognostic factors. Integrative analyses of chromatin marks have identified novel regulatory elements and altered transcription factor networks in CLL. Additionally, CLL cells display disease-specific patterns of 3D genome interactions. Single-cell analyses are becoming increasingly important in CLL research.
BRITISH JOURNAL OF HAEMATOLOGY
(2023)
Review
Pharmacology & Pharmacy
Yu Li, Yuanyuan Zhao, Xiaona Li, Liuqun Zhai, Hua Zheng, Ying Yan, Qiang Fu, Jinlian Ma, Haier Fu, Zhenqiang Zhang, Zhonghua Li
Summary: Alzheimer's disease is a common neurodegenerative disease with no cure. Lysine-specific demethylase 1 (LSD1) plays an important role in the pathogenesis of AD and has potential therapeutic benefits for treatment.
FRONTIERS IN PHARMACOLOGY
(2022)
Review
Genetics & Heredity
Jie Zhang, Shixiao Wang, Baohua Liu
Summary: Biological aging is characterized by various factors such as cell cycle blockade, decreased tissue regeneration capacity, and increased risk of age-related diseases and mortality. Genes and epigenetic factors play important roles in regulating aging, including abnormal gene expression, DNA methylation, histone modifications, and protein translation homeostasis. Understanding the genetic and epigenetic mechanisms of aging can help identify aging-related markers and develop interventions to reverse the aging process.
Review
Biochemistry & Molecular Biology
Carlos Wilson, Alfredo Caceres
Summary: This article reviews the role of epigenetic mechanisms in regulating axonal specificity, growth, and guidance, as well as the importance of splicing in axonal growth. Exploring the connection between epigenetics and axonal growth raises new questions and perspectives for understanding the development of axons in physiological and pathological contexts.
Review
Biochemistry & Molecular Biology
Alexandra Wagner, Helena Kosnacova, Miroslav Chovanec, Dana Jurkovicova
Summary: Mitochondria play a crucial role in cellular metabolism and bioenergetics, and are involved in cancer development and treatment response. Studying the genetic and epigenetic control of mitochondria can provide insights into cancer therapy response and aid in the development of new therapeutic strategies.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Oncology
Sumera I. Ilyas, Silvia Affo, Lipika Goyal, Angela Lamarca, Gonzalo Sapisochin, Ju Dong Yang, Gregory J. Gores
Summary: Cholangiocarcinoma still has a poor prognosis and better understanding of the disease biology is needed for early detection and treatment. In the past 5 years, significant advances have been made in the scientific understanding and clinical management of cholangiocarcinoma, including insights into the tumor microenvironment, progress in liquid biopsy approaches, targeted therapies, immunotherapies, and reassessment of liver transplantation.
NATURE REVIEWS CLINICAL ONCOLOGY
(2023)
Review
Immunology
Hanli Xu, Shuye Lin, Ziyun Zhou, Duoduo Li, Xiting Zhang, Muhan Yu, Ruoyi Zhao, Yiheng Wang, Junru Qian, Xinyi Li, Bohan Li, Chuhan Wei, Keqiang Chen, Teizo Yoshimura, Ji Ming Wang, Jiaqiang Huang
Summary: Over the past thirty years, the importance of chemokines and their receptors has been recognized in various immune processes and disease pathogenesis. The genetic and nongenetic regulation of chemokines and receptors leads to functional heterogeneity and their imbalances contribute to various diseases. Understanding the molecular basis and interactions of chemokines and receptors will advance the application of precision medicine.
CELLULAR & MOLECULAR IMMUNOLOGY
(2023)
Article
Biochemical Research Methods
Yuanyuan Li
Summary: Epigenetics refers to molecular modifications on DNA that regulate gene activity independent of DNA sequence, with DNA methylation, histone modifications, and non-coding RNAs being the most recognized regulations. Recent advances in the field require thorough methodologies and advanced technologies to push epigenetics to the forefront of molecular biology.
Review
Oncology
Garrett W. Cooper, Andrew L. Hong
Summary: Loss of SMARCB1 is associated with the occurrence of rare pediatric and adult cancers. This review highlights the recent advances in our understanding of the function of SMARCB1 and the importance of discovering potential therapeutic vulnerabilities to improve patient outcomes.
Review
Oncology
Benluvankar Varghese, Nunzio Del Gaudio, Gilda Cobellis, Lucia Altucci, Angela Nebbioso
Summary: Breast cancer is the second leading cause of cancer death in women, with genetic mutations and epigenetic modifications playing a critical role in its progression. The KDM4 enzymes are considered potential therapeutic targets for breast cancer, but the lack of selective inhibitors has hindered their entry into clinical trials.
FRONTIERS IN ONCOLOGY
(2021)
Article
Medicine, General & Internal
Yanghui Chen, Xin Xu, Linlin Wang, Ke Li, Yang Sun, Lei Xiao, Jiaqi Dai, Man Huang, Yan Wang, Dao Wen Wang
Summary: This study identified therapeutic targets associated with aortic aneurysms and found that inhibiting PLAU and PSMA(4) could reduce the risk of aortic aneurysms.
Review
Genetics & Heredity
Waleed Iqbal, Wanding Zhou
Summary: Understanding tissue heterogeneity requires analyzing intercellular epigenetic differences at the single-cell level. Recent advances in single-cell DNA methylome profiling have provided the tools to study this heterogeneity in detail. However, these advances also bring challenges in data analysis and interpretation.
GENOMICS PROTEOMICS & BIOINFORMATICS
(2023)
Article
Biochemical Research Methods
Itika Arora, Trygve O. Tollefsbol
Summary: The field of epigenetics plays a crucial role in regulating genomic interactions and has significant implications for diseases such as cancer. Researchers analyze epigenetics data through genome-wide studies and high-throughput methods, utilizing bioinformatics tools to identify key modifications. Next-generation sequencing technology is used for high-throughput genomic profiling, allowing researchers to understand various epigenetic modifications accurately and in parallel.
Review
Endocrinology & Metabolism
Matthew Dapas, Andrea Dunaif
Summary: Polycystic ovary syndrome (PCOS) is a common disorder in women of reproductive age, characterized by reproductive abnormalities, insulin resistance, and obesity. Genetic and environmental factors contribute to the development of PCOS. Genomic studies have provided insights into disease pathways and highlighted the limitations of current diagnostic criteria. Future research will focus on understanding the genetic mechanisms of PCOS.
Review
Urology & Nephrology
Katherine R. Tuttle, Rajiv Agarwal, Charles E. Alpers, George L. Bakris, Frank C. Brosius, Peter Kolkhof, Jaime Uribarri
Summary: Diabetic kidney disease is a global burden that increases the risk of kidney failure and cardiovascular events. There is a need to understand the molecular mechanisms of the disease and find new therapies. Inflammatory and fibrotic mediators play important roles in the pathophysiology of the disease. Recent clinical trials have shown promising drug therapies and dietary strategies for treating diabetic kidney disease.
KIDNEY INTERNATIONAL
(2022)
Article
Biochemistry & Molecular Biology
Soudabeh Sabetian, Mahboubeh Zarei, Bahia Namavar Jahromi, Mohammad Hossein Morowvat, Seyed Mohammad Bagher Tabei, Claudia Cava
Summary: Non-obstructive azoospermia (NOA) is a common clinical problem in infertility, with most patients having unknown molecular mechanisms. This study identified differentially expressed mRNAs, miRNAs, and lncRNAs in testicular tissue of NOA patients. The study provides new insights into the regulatory roles of miRNAs and lncRNAs in idiopathic azoospermia pathogenesis.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Multidisciplinary Sciences
Claudia Cava, Alexandros Armaos, Benjamin Lang, Gian G. Tartaglia, Isabella Castiglioni
Summary: Using bioinformatics algorithms, we identified differentially expressed genes, long non-coding RNAs, and RNA binding proteins for different subtypes of breast cancer, and proposed potential signature biomarkers specific to each subtype. We validated these biomarkers using a machine learning approach and found some novel prognostic biomarkers and therapeutic targets.
SCIENTIFIC REPORTS
(2022)
Article
Medicine, General & Internal
Matteo Interlenghi, Christian Salvatore, Veronica Magni, Gabriele Caldara, Elia Schiavon, Andrea Cozzi, Simone Schiaffino, Luca Alessandro Carbonaro, Isabella Castiglioni, Francesco Sardanelli
Summary: A machine learning model based on radiomics was developed to predict the BI-RADS category of ultrasound-detected suspicious breast lesions, supporting medical decision-making regarding follow-up intervals or tissue sampling. The ensemble of support vector machines showed the ability to decrease the biopsy rate of benign lesions by 15% to 18% while maintaining sensitivity above 94%.
Article
Biochemistry & Molecular Biology
Ida Manna, Francesco Fortunato, Selene De Benedittis, Ilaria Sammarra, Gloria Bertoli, Angelo Labate, Antonio Gambardella
Summary: Temporal lobe epilepsy is the most common form of focal epilepsy, considered a network disorder associated with structural changes. Non-coding RNAs, acting as epigenetic factors, participate in the regulation of the pathophysiological processes of epilepsy and can be used as biomarkers for diagnosis and treatment response.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Chemistry, Multidisciplinary
Veronica Quarato, Salvatore D'Antona, Petronilla Battista, Roberta Zupo, Rodolfo Sardone, Isabella Castiglioni, Danilo Porro, Marco Frasca, Claudia Cava
Summary: This study explored differentially expressed genes in the hippocampus of Alzheimer's disease patients, identifying potential drug targets and gene networks involved in various biological processes. The findings shed light on the genetic mechanisms of the disease and provide insights for further research.
APPLIED SCIENCES-BASEL
(2022)
Article
Biochemistry & Molecular Biology
Gloria Bertoli, Antonella Panio, Claudia Cava, Francesca Gallivanone, Martina Alini, Giulia Strano, Federico Molfino, Loredana Brioschi, Paola Viani, Danilo Porro
Summary: Prostate cancer is a common male neoplasm and is the second leading cause of cancer death in American men. Traditional diagnosis of prostate cancer relies on prostate secreted antigen (PSA) evaluation, but false positives are common, making additional tests necessary. This study explores the role of miR-153 in controlling cell growth and invasion in high Gleason Score prostate cancer, and suggests that miR-153 could serve as a circulating biomarker for diagnosis.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Chiara Foglieni, Maria Lombardi, Davide Lazzeroni, Riccardo Zerboni, Edoardo Lazzarini, Gloria Bertoli, Annalinda Pisano, Francesca Girolami, Annapaola Andolfo, Cinzia Magagnotti, Giovanni Peretto, Carmem L. Sartorio, Iacopo Olivotto, Giovanni La Canna, Ottavio Alfieri, Ornella E. Rimoldi, Lucio Barile, Giulia D'Amati, Paolo G. Camici
Summary: Hypertrophic cardiomyopathy (HCM) is a common genetic cardiac disorder. This study investigated the molecular mechanisms underlying HCM phenotypes and found that certain genes and proteins, as well as a network of myosin-encoded microRNA and long-noncoding RNAs, play a modulatory role in HCM myocardium, potentially contributing to phenotypic diversity and providing therapeutic targets.
Review
Cell Biology
Daniel Ruben Akiola Sanya, Claudia Cava, Djamila Onesime
Summary: RNA-binding proteins (RBPs) play important roles in various biological processes, including transcription regulation, splicing, R-loop homeostasis, DNA rearrangement, miRNA function, and ribosome biogenesis. They directly or indirectly interact with their target RNAs or mRNAs to perform crucial biological functions, which can lead to disease or normal biological events. This review summarizes the current understanding of RBPs' functions, highlighting their emerging roles in regulating diverse pathways, physiological processes, and their molecular links to diseases.
Article
Psychology, Multidisciplinary
Martina Caramenti, Isabella Castiglioni
Summary: This study found a strong association between self-perceived health rating and not only physical health aspects but also mental health and cognitive functioning. Factors such as BMI, chronic diseases, muscle strength, and mobility issues had a strong effect on self-perceived health, while quality of life, depression, and verbal fluency had smaller effects. Therefore, public health and prevention interventions should target all aspects of well-being, not just physical health.
BEHAVIORAL SCIENCES
(2022)
Article
Genetics & Heredity
Salvatore D'Antona, Gita A. Pathak, Dora Koller, Danilo Porro, Claudia Cava, Renato Polimanti
Summary: In this study, we conducted a phenome-wide analysis of ALS genetic liability using genome-wide association statistics from a large study and identified 46 genetically correlated traits. We also conducted a latent causal variable analysis to assess the directionality of these genetic correlations. The study highlights the widespread pleiotropy linking ALS with several health domains.
Article
Genetics & Heredity
Claudia Cava, Salvatore D'Antona, Francesca Maselli, Isabella Castiglioni, Danilo Porro
Summary: Sporadic Alzheimer's disease (AD) is a complex neurological disorder with multiple risk loci and various symptoms. Early diagnosis is crucial for early treatment, but current methods are not always accurate and can be time-consuming and invasive. This study analyzed the association of AD with other traits and disorders, and found 65 correlated traits grouped into 9 clusters. Additionally, the study compared different neural network models for gene expression analysis and found that a simple basic model performed better than more complex methods.
FUNCTIONAL & INTEGRATIVE GENOMICS
(2023)
Article
Biochemistry & Molecular Biology
Paolo Rainone, Silvia Valtorta, Chiara Villa, Sergio Todde, Massimiliano Cadamuro, Gloria Bertoli, Donatella Conconi, Marialuisa Lavitrano, Rosa Maria Moresco
Summary: Breast cancer is the most common cancer in women and the second leading cause of death. Breast cancer cells show a metabolic shift towards increased glycolysis, making it an interesting target for metabolic drugs such as metformin. Recent studies have found that the antihypertensive drug syrosingopine, when combined with metformin, has a synergistic effect on various cancers. However, there is a need to develop in vivo biomarkers that can detect early clinical response.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Medicine, General & Internal
Matteo Interlenghi, Giancarlo Sborgia, Alessandro Venturi, Rodolfo Sardone, Valentina Pastore, Giacomo Boscia, Luca Landini, Giacomo Scotti, Alfredo Niro, Federico Moscara, Luca Bandi, Christian Salvatore, Isabella Castiglioni
Summary: This study developed an explainable AI-based system using radiomics and deep learning to predict the presence of early signs of AMD and stratify patients. The system achieved high sensitivity and specificity in detecting explainable features associated with AMD using ultra-widefield fundus retinographies.
Article
Oncology
Nicola Lambri, Simone Leopoldo Antonetti, Damiano Dei, Luisa Bellu, Stefania Bramanti, Ricardo Coimbra Brioso, Carmelo Carlo-Stella, Isabella Castiglioni, Elena Clerici, Leonardo Crespi, Chiara De Philippis, Carmela Galdieri, Daniele Loiacono, Pierina Navarria, Giacomo Reggiori, Roberto Rusconi, Stefano Tomatis, Marta Scorsetti, Pietro Mancosu
Summary: Delivery of total marrow (lymph node) irradiation (TMI/TMLI) takes longer than standard radiotherapy treatments due to patient's extremity movements. The study evaluated the reproducibility of TMI/TMLI patient's extremities in order to find the best positioning and minimize unwanted movements.
Review
Biochemical Research Methods
Francesca Gallivanone, Gloria Bertoli, Danilo Porro
Summary: Breast cancer is a heterogeneous disease, and early detection is crucial for survival. Recent advances in image processing and -omics technologies have been applied to breast cancer diagnosis, allowing for personalized diagnostic and therapeutic approaches.
METHODS AND PROTOCOLS
(2022)
