Article
Oncology
Amrit L. Pappula, Shayaan Rasheed, Golrokh Mirzaei, Ruben C. Petreaca, Renee A. Bouley
Summary: Glioma patients with IDH1 mutation show significant genetic differences compared to patients with wild-type IDH1, including co-mutations and gene expression levels, which may contribute to a better prognosis.
Article
Multidisciplinary Sciences
Mingyi Yang, Omer Ali, Magnar Bjoras, Junbai Wang
Summary: In this article, a non-coding SNVs analysis tool called bpb3 is proposed to identify functional mutation blocks (FMBs) by integrating genome sequencing and transcriptome data. A two-level Bayesian approach with a biophysical model is implemented to compute TF-DNA binding affinity changes based on clustered position weight matrices (PWMs) from over 1700 TF-motifs. By testing datasets from follicular lymphoma and melanoma, bpb3 automatically and robustly identifies FMBs, providing insights into patho-mechanisms and therapeutic targets.
Article
Multidisciplinary Sciences
Shizhe Yu, Haoren Wang, Lingpeng Yang, Yingxue Yan, Qiang Cai, Duo Ma, Long Jiang, Zehai Gao, Zhiyong Yu, Zongping Xia
Summary: The comprehensive study of the spatial-cellular anatomy of the human liver is crucial for understanding the cellular origins of liver disease. In this study, spatial transcriptomics were conducted on normal human liver tissue sections, providing detailed transcriptional information on liver zonation. A total of 6581 high-quality spots from normal livers were analyzed, mainly consisting of hepatocytes, which were classified into four sub-groups. These data serve as a reliable reference for studying the spatial heterogeneity of liver lobules.
Article
Cell Biology
Ying Jiang, Baotong Zheng, Yang Yang, Xiangmei Li, Junwei Han
Summary: This study developed a software package SMDIC for the automated identification of immune cells driven by specific somatic mutations, providing a novel pipeline to discover mutation-specific immune cells and contribute to understanding the mechanisms underlying anticancer immune response.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Review
Hematology
Johann-Christoph Jann, Zuzana Tothova
Summary: The cohesin complex plays an essential role in healthy and malignant hematopoiesis, with its mutations recurrently found in various hematologic and solid malignancies. However, the mechanisms by which these mutations drive clonal expansion and disease progression are still poorly understood.
Article
Genetics & Heredity
Shadi Darvish Shafighi, Szymon M. Kielbasa, Julieta Sepulveda-Yanez, Ramin Monajemi, Davy Cats, Hailiang Mei, Roberta Menafra, Susan Kloet, Hendrik Veelken, Cornelis A. M. van Bergen, Ewa Szczurek
Summary: CACTUS is a probabilistic model that integrates whole exome, single-cell RNA, and B cell receptor sequencing data to map single cells to imperfect genotypes of tumor clones. The integration of independent measurements increases model certainty and improves performance in drawing genotype-to-phenotype maps in tumors.
Review
Oncology
Kartika Venugopal, Yang Feng, Daniil Shabashvili, Olga A. Guryanova
Summary: DNMT3A is one of the most frequently mutated genes in hematologic malignancies and plays a crucial role in epigenetic regulation. Mutations in DNMT3A have significant effects on DNA methylation and gene expression, contributing to the pathogenesis of hematologic malignancies.
Article
Biochemistry & Molecular Biology
Ivan Kiselev, Maxim Kozin, Natalia Baulina, Maria Pisklova, Ludmila Danilova, Alexandr Zotov, Olga Chumakova, Dmitry Zateyshchikov, Olga Favorova
Summary: Hypertrophic cardiomyopathy (HCM) is the most common inherited heart disease, and its pathogenesis is characterized by significant genetic and phenotypic heterogeneity. This study analyzed gene expression profiles and DNA methylation profiles in hypertrophied myocardia of HCM patients to identify new genes involved in HCM development. The results showed that innervation-associated genes are implicated in HCM, providing new insights into disease pathogenesis.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Multidisciplinary Sciences
Margot Jarrige, Helene Polveche, Alexandre Carteron, Stephane Janczarski, Marc Peschanski, Didier Auboeuf, Cecile Martinat
Summary: Human pluripotent stem cells have brought forth a new era in disease modeling, drug discovery, and cell therapy development. SISTEMA, a curated gene expression database, serves as a one-stop resource for the stem cell community to easily evaluate gene expression levels and compare them across different conditions.
Article
Oncology
Lu Huang, Huimin Zhu, Zhenhua Luo, Chukun Luo, Linjiang Luo, Baoting Nong, Shiyu Zhang, Chengcheng Wan, Yanzhi Wang, Zhou Songyang, Yuanyan Xiong
Summary: Gene fusions play a crucial role in tumorigenesis and have become important biomarkers and therapeutic targets. However, there is a lack of interactive analysis tools. Fusion Profiling Interactive Analysis (FPIA) is a web server that allows researchers to perform customizable and interactive analysis on fusion genes, enabling exploration of fusion-associated biological and molecular differences.
INTERNATIONAL JOURNAL OF CANCER
(2022)
Article
Agriculture, Dairy & Animal Science
Yingjie Wu, Lihua Zhao, Yinghe Qin
Summary: This study aimed to investigate the relationship between the severity of clinical signs and pathological observations in rabbit mastitis and analyze the differentially expressed genes (DEGs). The results showed that rabbits with mild and severe mastitis had higher rectal temperatures compared to the control group. The somatic cell count in milk was significantly higher in severe mastitis, while the number of heterophils in histological sections was significantly higher in mild mastitis. RNA-sequencing identified 1,096 DEGs between the control and mastitis mammary glands, with up-regulated genes enriched in response to stimulus, signal transduction, and cell communication, and downregulated genes mainly enriched in metabolic processes and pathways.
JOURNAL OF ANIMAL SCIENCE
(2023)
Article
Biochemical Research Methods
Benedek Danko, Peter Szikora, Tamas Por, Alexa Szeifert, Endre Sebestyen
Summary: Current tools investigating patterns of alternative splicing check for coordinated changes in the expression or relative ratio of RNA isoforms, but the stochastic nature of the splicing process can lead to changes in RNA isoform diversity for a gene between different conditions.
Review
Oncology
Irene Pastor-Galan, Ivan Martin, Blanca Ferrer, Juan-Carlos Hernandez-Boluda
Summary: Myelofibrosis is a chronic neoplasm characterized by diverse clinical manifestations, driven by mutations in the JAK-STAT pathway. Molecular profiling plays a crucial role in predicting the prognosis of MF patients and guiding transplantation for high-risk individuals.
CANCER TREATMENT REVIEWS
(2022)
Article
Biochemistry & Molecular Biology
Stephanie M. Zimmerman, Robin Fropf, Bridget R. Kulasekara, Maddy Griswold, Oliver Appelbe, Arya Bahrami, Rich Boykin, Derek L. Buhr, Kit Fuhrman, Margaret L. Hoang, Quoc Huynh, Lesley Isgur, Andrew Klock, Alecksandr Kutchma, Alexa E. Lasley, Yan Liang, Jill McKay-Fleisch, Jeffrey S. Nelson, Karen Nguyen, Erin Piazza, Aric Rininger, Daniel R. Zollinger, Michael Rhodes, Joseph M. Beechem
Summary: Emerging spatial profiling technology allows high-plex molecular profiling in biological tissues while preserving the spatial and morphological context of gene expression. By expanding the chemistry for the Digital Spatial Profiling platform, researchers have successfully quantified whole transcriptomes in human and mouse tissues, enabling applications in cancer research, molecular pathology, and developmental biology.
Article
Multidisciplinary Sciences
Zhenyu Zhang, Kyle Hernandez, Jeremiah Savage, Shenglai Li, Dan Miller, Stuti Agrawal, Francisco Ortuno, Louis M. Staudt, Allison Heath, Robert L. Grossman
Summary: The goal of National Cancer Institute's Genomic Data Commons (GDC) is to provide the cancer research community with a data repository of uniformly processed genomic and clinical data to support precision medicine through data sharing and collaborative analysis. The initial dataset includes various data types from NCI TCGA and TARGET projects, and data production started in June 2015 using an OpenStack-based private cloud. The GDC has analyzed more than 50,000 raw sequencing data inputs and generated different data types using the latest human genome reference build GRCh38, which are available for download and exploratory analysis at GDC Data Portal and Legacy Archive.
NATURE COMMUNICATIONS
(2021)
Article
Dermatology
Simona Pisanti, Teresa Mencherini, Tiziana Esposito, Valeria D'Amato, Tania Re, Maurizio Bifulco, Rita P. Aquino
Summary: This study critically compares medieval and modern dermocosmetics through the analysis of Trotula de Ruggiero's works. The results highlight Trotula's focus on female care, beauty and well-being, as well as the extraordinary combination of tradition and modernity in her work.
JOURNAL OF COSMETIC DERMATOLOGY
(2023)
Review
Biochemistry & Molecular Biology
Maurizio Bifulco, Erika Di Zazzo, Fabiana Napolitano, Anna Maria Malfitano, Giuseppe Portella
Summary: Since the nineteenth century, reports have shown that cancer patients occasionally experience clinical remission called Saint Peregrine tumor as a result of natural infections. The oncolytic activity of viruses, known as oncolytic viruses (OVs), which selectively infect and kill cancer cells, has been discovered. However, early attempts to increase OVs specificity, efficacy, and safety were inconclusive/negative, leading to a decline in research in this field. The renewal of interest in virotherapy occurred in the late 1990s with the development of genetic engineering techniques and a better understanding of cancer cells, resulting in the generation of potent and safe OVs.
Review
Oncology
Cristina Pagano, Erika di Zazzo, Giorgio Avilia, Beatrice Savarese, Giovanna Navarra, Maria Chiara Proto, Donatella Fiore, Monica Rienzo, Patrizia Gazzerro, Chiara Laezza, Maurizio Bifulco
Summary: The epidemic spread of obesity is recognized as a global burden, and its link with cancer, known as adiponcosis, is of great interest in the scientific community. The mechanisms underlying adiponcosis, which may vary depending on cancer type, involve insulin resistance, chronic inflammation, and adipose tissue-derived hormones and cytokines. This review summarizes the current evidence on pathways, hormones, and interventions for obesity-related breast and colorectal cancers. It also discusses current targets and drugs for cancer treatment and potential therapeutic mechanisms.
INTERNATIONAL JOURNAL OF CANCER
(2023)
Review
Biochemistry & Molecular Biology
Cristina Pagano, Beatrice Savarese, Laura Coppola, Giovanna Navarra, Giorgio Avilia, Chiara Laezza, Maurizio Bifulco
Summary: Cannabis sativa-derived compounds, such as THC and CBD, and components of the endocannabinoid system, such as AEA and 2-AG, have been extensively studied for their antioxidant effects. Many diseases are characterized by imbalanced ROS production, and these compounds have shown potential in reducing ROS levels in various pathological conditions. Further research on the antioxidant properties of cannabis sativa-derived compounds could have future clinical applications.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Chemistry, Multidisciplinary
Laura Aliisa Saarimaki, Jack Morikka, Alisa Pavel, Seela Korpilahde, Giusy del Giudice, Antonio Federico, Michele Fratello, Angela Serra, Dario Greco
Summary: Mechanistic toxicology serves as a powerful tool for assessing chemical safety and developing safe-by-design compounds. However, the implementation of toxicogenomics into the regulatory framework is hindered by uncertainties in data analysis and interpretation. To overcome these challenges and fully leverage the potential of AOPs, robust associations between AOPs and molecular alterations need to be established.
Editorial Material
Endocrinology & Metabolism
Monica Rienzo, Cristina Pagano, Felice Crocetto, Erika Di Zazzo
FRONTIERS IN ENDOCRINOLOGY
(2023)
Article
Biochemical Research Methods
Emanuele Di Lieto, Angela Serra, Simo Iisakki Inkala, Laura Aliisa Saarimaki, Giusy del Giudice, Michele Fratello, Veera Hautanen, Maria Annala, Antonio Federico, Dario Greco
Summary: Biological data repositories provide valuable research evidence, but the lack of a common metadata annotation strategy results in low FAIRness of the data. ESPERANTO is an innovative framework that enables the standardized harmonization and integration of toxicogenomics metadata, increasing their FAIRness in a Good Laboratory Practice-compliant fashion. The tool facilitates user-friendly metadata harmonization, regardless of the user's background and expertise. ESPERANTO and its user manual are freely available for academic use.
Article
Oncology
Marianna Aprile, Simona Cataldi, Caterina Perfetto, Antonio Federico, Alfredo Ciccodicola, Valerio Costa
Summary: This study identified a specific metabolic gene signature in BRAF-mutated tumors, characterized by enhanced glycolysis and increased expression of Hif-1 alpha-modulated glycolytic genes. Inhibitory effects of BRAFi on these genes and on cell viability were counteracted by Hif-1 alpha stabilization. Treatment with BRAFi and diclofenac combination could restrain the glycolytic phenotype and synergistically reduce tumor cells' viability.
BRITISH JOURNAL OF CANCER
(2023)
Article
Cell Biology
Katariina Maaninka, Maarit Neuvonen, Erja Kerkela, Kati Hyvarinen, Mari Palviainen, Masood Kamali-Moghaddam, Antonio Federico, Dario Greco, Saara Laitinen, Katariina Oorni, Pia R. M. Siljander
Summary: Platelet extracellular vesicles (PEVs) generated upon platelet activation, particularly in the presence of oxLDL, contribute to the pathogenesis of atherosclerosis by promoting inflammation and macrophage dysfunction. The combination of thrombin, collagen, and oxLDL induces the formation of PEVs that contain inflammatory proteins and alter macrophage gene expression. Scavenger receptor CD36 plays a significant role in oxLDL-induced PEV formation, while HDL has a slight suppressive effect. Pathways related to cell cycle, gene expression regulation, and immune system signaling are affected in macrophages treated with oxLDL-induced PEVs.
EUROPEAN JOURNAL OF CELL BIOLOGY
(2023)
Editorial Material
Biochemistry & Molecular Biology
Amelia Casamassimi, Alfredo Ciccodicola, Monica Rienzo
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Medicine, General & Internal
Felice Crocetto, Biagio Barone, Giulio D'Aguanno, Alfonso Falcone, Rosamaria de Vivo, Monica Rienzo, Laura Recchia, Erika Di Zazzo
Summary: Prostate cancer is a common cancer in men and a leading cause of death. Recent studies suggest that vitamin D supplementation does not have an impact on prostate health. Further research is needed to confirm this finding.
JOURNAL OF CLINICAL MEDICINE
(2023)
Article
Biochemical Research Methods
Antonio Federico, Michele Fratello, Alisa Pavel, Lena Mobus, Giusy del Giudice, Angela Serra, Dario Greco
Summary: Drug repurposing, which involves the re-usage of approved drugs for different therapeutic indications, has limited translatability into clinical practice. The lack of integration between mechanistic and chemocentric approaches is one of the major obstacles. This study introduces DREAM, an R package that integrates these two approaches and provides druggability evaluation and optimized combination therapy predictions.
Article
Biochemical Research Methods
Alisa Pavel, Giusy del Giudice, Michele Fratello, Leo Ghemtio, Antonio Di Lieto, Jari Yli-Kauhaluoma, Henri Xhaard, Antonio Federico, Angela Serra, Dario Greco
Summary: In this study, a network mapping approach (KNeMAP) was proposed for comparing transcriptomic profiles. By grouping genes into similarity groups based on multiple levels of prior information, KNeMAP provided a higher-level view and showed higher accuracy in identifying compounds with similar molecular responses compared to traditional methods.