Article
Computer Science, Interdisciplinary Applications
Koyel Mandal, Rosy Sarnnah, Dhruba Kumar Bhattacharyya, Jugal Kumar Kalita, Bhogeswar Borah
Summary: Effective biomarkers are crucial for early diagnosis and monitoring of breast cancer. Analyzing breast cancer miRNA data helps identify biomarkers that contribute to better understanding of the disease and making important clinical decisions. Our proposed rank-preserving biclustering algorithm outperforms other algorithms in relevance and recovery, showcasing its effectiveness in identifying biclusters for breast cancer data.
MEDICAL & BIOLOGICAL ENGINEERING & COMPUTING
(2021)
Review
Biochemistry & Molecular Biology
Matthew G. Davey, Aoife J. Lowery, Nicola Miller, Michael J. Kerin
Summary: Breast cancer treatment has evolved from solely relying on radical surgical resection to incorporating chemotherapy, radiotherapy, targeted therapy, and refined surgical approaches. MiRNAs serve as important biomarkers in predicting treatment response, improving therapeutic strategies, and enhancing prognosis for breast cancer patients.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Genetics & Heredity
Mengying Zhou, Menglu Dong, Xue Yang, Jun Gong, Xinghua Liao, Qi Zhang, Zeming Liu
Summary: Breast cancer, with its high molecular heterogeneity, is the leading cause of cancer deaths in women. N6-methyladenosine (m6A), the most common mRNA internal modification in eukaryotic cells, has reversible modification process regulated by writer, reader, and eraser enzymes. Abnormal m6A modifications in breast cancer can impact key signaling pathways and serve as markers, targets, or regulators for diagnosis, prognosis prediction, and treatment.
FRONTIERS IN GENETICS
(2022)
Article
Biochemistry & Molecular Biology
Anamika Thalor, Hemant Kumar Joon, Gagandeep Singh, Shikha Roy, Dinesh Gupta
Summary: Tumor heterogeneity and unclear metastasis mechanisms are the main challenges in treating Triple-negative breast cancer (TNBC). In this study, gene expression datasets were analyzed to identify gene signatures that can differentiate TNBC from other breast cancer subtypes. Machine learning algorithms were used to evaluate the performance of these signatures, and potential prognostic genes were discovered. Pathway enrichment analyses revealed the functional role of these genes in the metastasis cascade.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Article
Agriculture, Dairy & Animal Science
Jingting Shu, Yifan Liu, Yanju Shan, Gaige Ji, Xiaojun Ju, Yunjie Tu, Shiying Shi, Zhongwei Sheng, Ming Zhang, Jianmin Zou
Summary: This study investigated the miRNAs and related pathways involved in the development of Wooden Breast (WB) in modern commercial broiler chickens. Through small RNA sequencing, 23 significantly differentially expressed miRNAs were identified, indicating their involvement in biological processes and pathways related to energy metabolism, apoptosis, focal adhesion, and development of blood vessels. Four differentially expressed miRNAs were validated by quantitative real-time polymerase chain reaction (qRT-PCR), including gga-miR155, gga-miR-29c, and gga-miR-133.
Article
Oncology
Phatchariya Phannasil, Chareeporn Akekawatchai, Sarawut Jitrapakdee
Summary: Breast cancer is a global public health concern with increasing incidence rate. Metastasis is the primary cause of death in breast cancer. Dysregulation of miRNAs is involved in carcinogenesis, cancer cell proliferation, and metastasis. This study assessed miRNAs associated with breast cancer metastasis and found 46 differentially expressed miRNAs between low-metastatic MCF-7 and highly metastatic MDA-MB-231 cell lines. Among them, miR-222-3p was upregulated in MDA-MB-231 cells and its suppression resulted in reduced proliferation and migration. Bioinformatic analysis identified potential mRNA targets for miR-222-3p. Overall, miR-222-3p may play a role in the aggressive phenotype of MDA-MB-231 cells.
Review
Biochemistry & Molecular Biology
Lisa Padroni, Laura De Marco, Valentina Fiano, Lorenzo Milani, Giorgia Marmiroli, Maria Teresa Giraudo, Alessandra Macciotta, Fulvio Ricceri, Carlotta Sacerdote
Summary: The analysis of circulating tumor cells and tumor-derived materials, such as circulating tumor DNA, circulating miRNAs (cfmiRNAs), and extracellular vehicles, provides crucial information in cancer research, especially in breast cancer cases. However, the current studies on cfmiRNA levels exhibit high risk of bias and lack standardized protocols, highlighting the need for more robust study designs, standardized procedures, and larger sample sizes for accurate and reliable results. The identified cfmiRNAs show potential as diagnostic and prognostic biomarkers, but further validation studies in different populations are required for clinical application.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Medical Laboratory Technology
Meilan Zhang, Xue Bai, Xuemei Zeng, Jiangrong Liu, Feng Liu, Zhiwei Zhang
Summary: Breast cancer has the highest incidence rate among women and the circRNA-miRNA-mRNA axis plays a crucial role in its progression, serving as a potential marker for early diagnosis and treatment.
CLINICA CHIMICA ACTA
(2021)
Review
Medicine, Research & Experimental
Bashdar Mahmud Hussen, Hazha Jamal Hidayat, Abbas Salihi, Dana K. Sabir, Mohammad Taheri, Soudeh Ghafouri-Fard
Summary: MicroRNAs (miRNAs) are small non-coding RNAs that play a critical role in cancer by post-transcriptionally controlling gene expression. They are involved in the initiation, progression, and metastasis of cancer, and can be used to classify genes affecting cancer pathways.
BIOMEDICINE & PHARMACOTHERAPY
(2021)
Article
Medical Laboratory Technology
David De Gonzalo-Calvo, Ivan D. Benitez, Lucia Pinilla, Amara Carratala, Anna Moncusi-Moix, Clara Gort-Paniello, Marta Molinero, Jessica Gonzalez, Gerard Torres, Maria Bernal, Silvia Pico, Raquel Almansa, Noelia Jorge, Alicia Ortega, Elena Bustamante-Munguira, Jose Manuel Gomez, Milagros Gonzalez-Rivera, Dariela Micheloud, Pablo Ryan, Amalia Martinez, Luis Tamayo, Cesar Aldecoa, Ricard Ferrer, Adrian Ceccato, Laia Fernandez-Barat, Ana Motos, Jordi Riera, Rosario Menendez, Dario Garcia-Gasulla, Oscar Penuelas, Antoni Torres, Jesus F. Bermejo-Martin, Ferran Barbe
Summary: This study demonstrated a close association between the circulating miRNA profile of COVID-19 patients and disease severity. Analysis of miRNA levels proved useful in distinguishing between ICU patients and ward patients, as well as between ICU nonsurvivors and survivors. The potential of miRNA signatures in predicting disease progression in critical COVID-19 patients was found to be superior to traditional laboratory parameters such as leukocyte counts, CRP, and D-dimer levels.
TRANSLATIONAL RESEARCH
(2021)
Article
Oncology
Ming Wu, Yujie Zhao, Nanxi Peng, Zuo Tao, Bo Chen
Summary: This study explored the mechanism of chemotherapy resistance in breast cancer through miRNA analysis, identifying differentially expressed miRNAs and genes, and highlighting the importance of cell signaling pathways like the ErbB and PI3K/AKT/mTOR pathways in cancer proliferation and drug resistance. The findings may provide new insights for enhancing chemotherapy effectiveness in breast cancer patients.
INVESTIGATIONAL NEW DRUGS
(2021)
Article
Oncology
Filippo Valle, Matteo Osella, Michele Caselle
Summary: This paper presents an application of topic modeling techniques for the identification of breast cancer subtypes. By integrating different layers of gene expression data, the authors were able to accurately distinguish healthy from tumor samples and classify different breast cancer subtypes. The inclusion of microRNA data significantly improved the accuracy of subtype classification and revealed genes and microRNAs associated with breast cancer development and survival probability.
Article
Biochemistry & Molecular Biology
Chairmandurai Aravindraja, Syam Jeepipalli, William Duncan, Krishna Mukesh Vekariya, Sakshee Bahadekar, Edward K. L. Chan, Lakshmyya Kesavalu
Summary: T. forsythia infection results in significant downregulation of miRNA expression in mouse mandibles, which is associated with periodontitis. Some of these downregulated miRNAs have also been detected in gingival tissue and saliva of periodontitis patients.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Biochemistry & Molecular Biology
Alejandro Garrido-Palacios, Ana Maria Rojas Carvajal, Ana Maria Nunez-Negrillo, Jonathan Cortes-Martin, Juan Carlos Sanchez-Garcia, Maria Jose Aguilar-Cordero
Summary: This systematic review and meta-analysis investigated dysregulated miRNA biomarkers and their diagnostic accuracy in breast cancer. The study found that 34 microRNAs were significantly dysregulated and could be considered as biomarkers for breast cancer. Individually, miR-155 showed better diagnostic results compared to mammography. However, using a panel of multiple miRNAs improved sensitivity and specificity rates, and they can be associated with classic biomarkers such as CA-125 or CEA. Based on the results, miR-155 holds promise as a diagnostic biomarker for breast cancer.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Genetics & Heredity
Meng An, Xiaowen Zang, Jimin Wang, Jie Kang, Xiaoyu Tan, Bo Fu
Summary: This study identified 739 differentially expressed lncRNAs, 115 differentially expressed miRNAs, and 5749 differentially expressed mRNAs associated with breast cancer brain metastasis. Hub genes such as PTBP1, NUP98, and HYOU1 were found to be associated with BCBM. The lncRNA-miRNA-mRNA network revealed a potential mechanism of BCBM involving lncRNAs FIRRE and RP11-169F17.1 interacting with miR-501-5p to regulate gene expression.
Article
Biochemical Research Methods
Valeria Boscaino, Antonino Fiannaca, Laura La Paglia, Massimo La Rosa, Riccardo Rizzo, Alfonso Urso
BMC BIOINFORMATICS
(2019)
Article
Biochemical Research Methods
Antonino Fiannaca, Laura La Paglia, Massimo La Rosa, Riccardo Rizzo, Alfonso Urso
BMC BIOINFORMATICS
(2020)
Article
Biochemistry & Molecular Biology
Aiti Vizzini, Angela Bonura, Laura La Paglia, Antonino Fiannaca, Massimo La Rosa, Alfonso Urso, Vincenzo Arizza
Summary: The TGF-beta family of cytokines play a crucial role in regulating cell fate through multiple signaling pathways, such as Wintless, FOXO, and Hedgehog, to maintain tissue homeostasis. Research indicates that in Ciona robusta, interactions between miRNA, pseudogenes, and mRNA 3'UTR elements are integral in post-transcriptional regulation.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Oncology
Gaia Morello, Valeria Cancila, Massimo La Rosa, Giovanni Germano, Daniele Lecis, Vito Amodio, Federica Zanardi, Fabio Iannelli, Daniele Greco, Laura La Paglia, Antonino Fiannaca, Alfonso M. Urso, Giulia Graziano, Francesco Ferrari, Serenella M. Pupa, Sabina Sangaletti, Claudia Chiodoni, Giancarlo Pruneri, Alberto Bardelli, Mario P. Colombo, Claudio Tripodo
Summary: Rare subsets of tumor-infiltrating T cells were found to express transcripts associated with TCR specificity revision in the tumor microenvironment, providing evidence of a microniche within TIL involved in TCR shaping.
CANCER IMMUNOLOGY RESEARCH
(2021)
Article
Immunology
Valeria Longo, Alessandra Longo, Giorgia Adamo, Antonino Fiannaca, Sabrina Picciotto, Laura La Paglia, Daniele Romancino, Massimo La Rosa, Alfonso Urso, Fabio Cibella, Antonella Bongiovanni, Paolo Colombo
Summary: PBDE-47 can affect the expression of intracellular miRNAs and interfere with the biogenesis of sEVs, leading to an overload of specific immune-related miRNAs. Studies have shown that sEVs derived from PBDE-47 can modulate macrophage immune responses.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Aiti Vizzini, Angela Bonura, Laura La Paglia, Antonino Fiannaca, Massimo La Rosa, Alfonso Urso, Manuela Mauro, Mirella Vazzana, Vincenzo Arizza
Summary: Research shows that cytochrome gene expression and miRNA regulation play important roles in the inflammatory response induced by LPS in Ciona robusta, with different cytochrome subfamilies being deregulated. The interactions of miRNA networks and regulation are key areas of focus in studying the inflammatory response.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biology
Davide Vacca, Antonino Fiannaca, Fabio Tramuto, Valeria Cancila, Laura La Paglia, Walter Mazzucco, Alessandro Gulino, Massimo La Rosa, Carmelo Massimo Maida, Gaia Morello, Beatrice Belmonte, Alessandra Casuccio, Rosario Maugeri, Gerardo Iacopino, Carmela Rita Balistreri, Francesco Vitale, Claudio Tripodo, Alfonso Urso
Summary: In this study, direct RNA sequencing technology was used to directly identify SARS-CoV-2 sequences from samples of patients infected with the virus in Sicily, Italy. Mutations were found in the nucleocapsid gene, and the technique used offers the advantages of true native RNA sequencing without amplification steps that could introduce errors. This study provides novel information relevant to next-generation sequencing strategies for SARS-CoV-2.
Article
Biochemistry & Molecular Biology
Laura La Paglia, Mirella Vazzana, Manuela Mauro, Francesca Dumas, Antonino Fiannaca, Alfonso Urso, Vincenzo Arizza, Aiti Vizzini
Summary: Through bioinformatics and in vivo experiments, it was found that LPS induction activates the expression of multiple immune genes in granulocyte hemocytes, leading to the activation of the Nf-kB signaling pathway and downstream pro-inflammatory gene expression. The study reveals the evolutionarily conserved functional link between the Mif-Csn-Nf-kB axis in the ascidian C. robusta during LPS-mediated inflammation response, which is finely regulated by non-coding molecules such as microRNAs.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemical Research Methods
Antonino Fiannaca, Massimo La Rosa, Laura La Paglia, Salvatore Gaglio, Alfonso Urso
Summary: Single-cell RNA-sequencing enables the characterization of cell types and estimation of cell population composition. This study presents a GOWDL model, which combines gene ontology and marker genes, for cell type classification and demonstrates its effectiveness in multiple tissues.
BRIEFINGS IN BIOINFORMATICS
(2023)
Proceedings Paper
Computer Science, Artificial Intelligence
Gianmarco Coppola, Antonino Fiannaca, Massimo La Rosa, Laura La Paglia, Alfonso Urso, Salvatore Gaglio
Summary: Recent advances in single-cell RNA-sequencing and the availability of more data have led to the development of algorithms for analyzing single cells in gene expression data. This study proposes an artificial intelligence architecture that classifies cell types in human tissue. Combining a deep learning model based on convolutional neural network (CNN) with a wide model, the architecture integrates the concept of functional genes neighborhood from Gene Ontology into the CNN model and incorporates information on biologically relevant marker genes for each cell type in the underlying human tissue. The proposed architecture was tested on seven human tissue datasets and compared with three reference literature algorithms, showing equal or better performance than the other models within each tissue.
ENGINEERING APPLICATIONS OF NEURAL NETWORKS, EAAAI/EANN 2022
(2022)
Article
Biochemistry & Molecular Biology
Massimo La Rosa, Antonino Fiannaca, Laura La Paglia, Alfonso Urso
Summary: This study presents a graph neural network (GNN) approach for analyzing RNA interference-messenger RNA interaction networks. The GNN method has the ability to predict the efficacy of siRNA and achieves high accuracy on benchmark datasets.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Proceedings Paper
Biochemical Research Methods
Antonino Fiannaca, Laura La Paglia, Massimo La Rosa, Giosue Lo Bosco, Riccardo Rizzo, Alfonso Urso
COMPUTATIONAL INTELLIGENCE METHODS FOR BIOINFORMATICS AND BIOSTATISTICS, CIBB 2018
(2020)
