Article
Medicine, Research & Experimental
Yutong Zhang, Lijuan Zhao, Yaping Bi, Jinyuan Zhao, Chao Gao, Xiaojie Si, Honglin Dai, Moges Dessale Asmamaw, Qiurong Zhang, Wenchao Chen, Hongmin Liu
Summary: Tumor metastasis is a major cause of cancer-related death, and new tumor metastasis regulators are needed for diagnosis and treatment. Long non-coding RNA (lncRNA) plays a role in promoting tumor metastasis through various mechanisms. Additionally, lncRNA can be found in exosomes and may serve as potential biomarkers and therapeutic targets for cancer metastasis.
BIOMEDICINE & PHARMACOTHERAPY
(2023)
Article
Medical Laboratory Technology
Parisa Vosough, Seyyed Hossein Khatami, Ali Hashemloo, Amir Tajbakhsh, Farzaneh Karimi-Fard, Sina Taghvimi, Mortaza Taheri-Anganeh, Elahe Soltani Fard, Amir Savardashtaki, Ahmad Movahedpour
Summary: Gastrointestinal cancer is a major global health issue and early diagnosis is difficult due to the lack of reliable biomarkers. However, circulating exosomes are showing promise as non-invasive diagnostic tools with limited risks. In particular, exosomal long non-coding RNAs are emerging as potential biomarkers in gastrointestinal cancer. This review provides an overview of the extraction and detection of exosomal lncRNAs, focusing on their role in gastrointestinal cancer.
CLINICA CHIMICA ACTA
(2023)
Review
Biochemistry & Molecular Biology
Wuwen Zhang, Qinshi Wang, Yi Yang, Siyuan Zhou, Ping Zhang, Tongbao Feng
Summary: Exosomes play a crucial role in cell-cell communication within the cancer microenvironment. Exosomal long noncoding RNAs (lncRNAs) are key regulators in cancer development, involved in processes such as cancer cell proliferation, metastasis, drug resistance, and immunomodulation. Changes in exosomal lncRNAs levels often correlate with cancer occurrence and progression, making them valuable biomarkers for cancer diagnosis and prognosis.
EXPERIMENTAL AND MOLECULAR MEDICINE
(2021)
Editorial Material
Genetics & Heredity
Claire Wilson, Aditi Kanhere
Summary: This study speculates on the potential role of variants of lncRNAs in cancer development by drawing upon emerging research findings.
TRENDS IN GENETICS
(2021)
Review
Oncology
Yuntong Sun, Fengtian Sun, Jianhua Jin, Wenrong Xu, Hui Qian
Summary: Exosomes are nanosized vesicles secreted by cells and contain various bioactive molecules, such as proteins and nucleic acids, that reflect the pathophysiological state of donor cells. Recent research has focused on the long non-coding RNAs (lncRNAs) present in exosomes, which play important roles in gastrointestinal cancer progression. Exosomal lncRNAs derived from blood samples show potential as important indicators for liquid biopsy and offer a new diagnosis strategy for gastrointestinal cancer. Furthermore, exosomes can deliver certain lncRNAs with anti-tumor effects. This review article summarizes recent work in this field and evaluates the opportunities and challenges of using exosomal lncRNAs for the diagnosis and treatment of gastrointestinal cancer.
Review
Oncology
Ya-Ting Chuang, Jun-Ping Shiau, Jen-Yang Tang, Ammad Ahmad Farooqi, Fang-Rong Chang, Yi-Hong Tsai, Ching-Yu Yen, Hsueh-Wei Chang
Summary: Cancer cells release exosomes containing tumor-promoting effects, and natural products can block exosome processing and inhibit cancer progression. However, the correlation between exosomal lncRNAs and natural product treatments is not well understood. By using bioinformatics, this study fills the gap by exploring the interaction between exosomal lncRNAs, miRNAs, and exosomal processing genes, and summarizes their roles in cancer progression and the anticancer effects of natural products.
Article
Oncology
Haiming Huang, Jialin Du, Bo Jin, Lu Pang, Nan Duan, Chenwei Huang, Jiayin Hou, Wei Yu, Han Hao, Haixia Li
Summary: The study identified tumor progression-related mRNAs and lncRNAs in urine exosomes for the detection of bladder cancer. After RNA sequencing and validation in TCGA database, five dysregulated RNAs were found to have the highest diagnostic potential to distinguish BCa or early stage BCa patients from healthy controls.
FRONTIERS IN ONCOLOGY
(2021)
Review
Oncology
Hangsheng Zhou, Hongyuan Wan, Yanyan Feng, Lijie Zhu, Yuanyuan Mi
Summary: This article summarizes the research on the diagnostic roles and mechanistic functions of exosomal lncRNAs in prostate cancer.
CLINICAL & TRANSLATIONAL ONCOLOGY
(2023)
Review
Cell Biology
Julio Cesar Villegas-Pineda, Melida del Rosario Lizarazo-Taborda, Adrian Ramirez-de-Arellano, Ana Laura Pereira-Suarez
Summary: The tumor microenvironment consists of molecular and cellular components, with ncRNAs playing a key role in modulating the development of cancer. Communication between different cell types within the tumor microenvironment through exosomal vesicles influences the behavior of tumor cells.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Review
Cardiac & Cardiovascular Systems
Zhu Yuan, Weiqiang Huang
Summary: Long non-coding RNAs (lncRNAs) in exosomes play important roles in cardiovascular diseases, with potential diagnostic and therapeutic effects. Research focuses on atherosclerosis, myocardial infarction, myocardial ischemia-reperfusion injury, and other cardiovascular diseases, highlighting the challenges and prospects in clinical applications.
FRONTIERS IN CARDIOVASCULAR MEDICINE
(2021)
Review
Pharmacology & Pharmacy
Liangyun Li, Yihui Bi, Shaoxi Diao, Xiaofeng Li, Tong Yuan, Tao Xu, Cheng Huang, Jun Li
Summary: This review article highlights the role of exosomal lncRNAs in the development of HCC, showing their crucial involvement in the growth and progression of HCC and their potential as therapeutic targets.
BIOCHEMICAL PHARMACOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Jing-Dong J. Han
Summary: During cellular senescence and organismal aging, cells undergo molecular and morphological changes. This review focuses on the roles of long noncoding RNAs (lncRNAs) in senescence-associated nuclear architecture and morphological changes, particularly RNA double-strand DNA triplexes as a nexus between lncRNAs, DNA, and proteins. The future of deciphering direct links between lncRNA changes and nuclear morphology changes with the help of artificial intelligence and genetic perturbations is also discussed.
TRENDS IN BIOCHEMICAL SCIENCES
(2023)
Article
Medicine, Research & Experimental
Maliheh Entezari, Maryam Ghanbarirad, Afshin Taheriazam, Mehrdokht Sadrkhanloo, Amirhossein Zabolian, Mohammad Ali Shekhi Beig Goharrizi, Kiavash Hushmandi, Amir Reza Aref, Milad Ashrafizadeh, Ali Zarrabi, Noushin Nabavi, Navid Rabiee, Mehrdad Hashemi, Saeed Samarghandian
Summary: This review focuses on lncRNAs and exosomal lncRNAs in lung cancer, highlighting their roles in regulating proliferation and metastasis. LncRNAs play a significant role in the development of lung cancer through various molecular mechanisms, and have the potential to serve as biomarkers and diagnostic tools.
BIOMEDICINE & PHARMACOTHERAPY
(2022)
Review
Oncology
Wenqin Zhang, Yuanliang Yan, Jinwu Peng, Abhimanyu Thakur, Ning Bai, Keda Yang, Zhijie Xu
Summary: The tumor microenvironment plays a crucial role in cancer progression through the communication between cellular and noncellular components. Exosomal lncRNAs in the tumor microenvironment are important factors that can interfere with immune responses and affect therapeutic efficiency. This review summarizes the roles of exosomal lncRNAs in tumor-immune regulation and proposes potential treatment strategies.
Review
Plant Sciences
Juncheng Lin, Qingshun Quinn Li
Summary: Precise regulation of gene expression is essential for plant survival. Pre-mRNA polyadenylation, as a cotranscriptional regulatory mechanism, plays a crucial role in fine-tuning gene expression. Epigenetic modification, including DNA methylation, histone modifications, and epitranscriptomic modification, has been found to be involved in regulating polyadenylation in plants. This article summarizes the links between epigenetics and polyadenylation and discusses their novel biological efficacy for plant development and environmental responses.
TRENDS IN PLANT SCIENCE
(2023)
Article
Oncology
Elias A. T. Koch, Anne Petzold, Anja Wessely, Edgar Dippel, Michael Erdmann, Lucie Heinzerling, Bettina Hohberger, Harald Knorr, Ulrike Leiter, Friedegund Meier, Peter Mohr, Farnaz Rahimi, Beatrice Schell, Max Schlaak, Patrick Terheyden, Beatrice Schuler-Thurner, Selma Ugurel, Jochen Utikal, Julio Vera, Michael Weichenthal, Fabian Ziller, Carola Berking, Markus Heppt
Summary: The study identified that a good response to immune checkpoint blockade, radiation therapy, or liver-directed treatments were associated with prolonged overall survival. Conversely, a poor ECOG performance status and elevated serum LDH were linked to a poorer overall survival. Long-term survivors often had more organs affected by metastasis, while patients with liver metastases only were more common among short-term survivors.
CANCER IMMUNOLOGY IMMUNOTHERAPY
(2022)
Article
Oncology
Xin Lai, Jinfei Zhou, Anja Wessely, Markus Heppt, Andreas Maier, Carola Berking, Julio Vera, Le Zhang
Summary: This study demonstrates the utilization of a deep learning model to integrate genomics data, a disease network, and machine learning techniques to classify melanoma patients for prognosis, assess the impact of genomic features on classification, and provide interpretation to the impactful features at molecular levels. The approach successfully identifies disease subgroups and quantifies the impact of genomic features on patient classification, leading to a better understanding of melanoma heterogeneity and potential pathways associated with the disease.
INTERNATIONAL JOURNAL OF CANCER
(2022)
Letter
Hematology
Hannah Reimann, Anita N. Kremer, Viktoria Blumenberg, Katja Schmidt, Michael Aigner, Benedikt Jacobs, Nina Eisenhauer, Alina Kaempf, Wolf Roesler, Soraya Kharboutli, Dimitrios Mougiakakos, Vanessa Lang, Christopher Lischer, Pascal Irrgang, Moritz Leppkes, Julio Vera Gonzalez, Gerhard Kroenke, Andreas E. Kremer, Matthias Tenbusch, Heiko Bruns, Thomas Harrer, Fabian Mueller, Georg Schett, Andreas Mackensen, Marion Subklewe, Simon Voelkl
Review
Biochemical Research Methods
Ryley Dorney, Bijay P. Dhungel, John E. J. Rasko, Lionel Hebbard, Ulf Schmitz
Summary: This review highlights the importance of gene fusions in cancer, including chromosomal rearrangement-independent fusion transcripts and complex fusion structures. It proposes a classification system for gene and transcript fusions and discusses the use of long-read sequencing and bioinformatic tools to detect and characterize fusions.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Oncology
Raheleh Amirkhah, Kathryn Gilroy, Sudhir B. B. Malla, Tamsin R. M. Lannagan, Ryan M. M. Byrne, Natalie C. C. Fisher, Shania M. M. Corry, Noha-Ehssan Mohamed, Hojjat Naderi-Meshkin, Megan L. L. Mills, Andrew D. D. Campbell, Rachel A. A. Ridgway, Baharak Ahmaderaghi, Richard Murray, Antoni Berenguer Llergo, Rebeca Sanz-Pamplona, Alberto Villanueva, Eduard Batlle, Ramon Salazar, Mark Lawler, Owen J. J. Sansom, Philip D. D. Dunne
Summary: In this study, three approaches for classifying human-to-mouse CRC tissue were developed, with MmCMS-C, a combined pathway system, showing the best accuracy in classifying epithelial-like subtypes (CMS2/3) of tumors. The results provide guidance for researchers to select suitable mouse models for studying human CRC subtypes.
BRITISH JOURNAL OF CANCER
(2023)
Article
Cell Biology
Tamara Treleaven, Matthew Zada, Rajini Nagarajah, Charles G. Bailey, John E. J. Rasko, Michael B. Morris, Margot L. Day
Summary: L-proline has been found to improve the development of mouse embryos and enhance embryo development during in vitro fertilization. The presence of neutral amino acid transporter B(0)AT1 and its accessory protein ACE2 in mouse preimplantation embryos has been identified. The uptake of Pro in embryos is regulated by B(0)AT1, and addition of Pro to the culture medium improves embryo development.
Article
Biochemistry & Molecular Biology
Le Zhang, Shiwei Fan, Julio Vera, Xin Lai
Summary: Cancer is a heterogeneous disease driven by abnormal gene perturbations in regulatory networks. A network medicine approach was developed to identify common and specific perturbed genes and investigate drug repurposing across cancer types. Prioritized genes in cancer-specific networks were identified using a network-based method. These cancer genes showed extensive perturbation and strong regulatory interaction, and demonstrated remarkable performances in discriminating tumors and predicting survival times of cancer patients. A network proximity approach was used to systematically screen drugs, resulting in the identification of potential repurposable candidates in several cancer types.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Article
Cell Biology
Vahid Moghimi, Jeiran Rahvarian, Zohreh Esmaeilzadeh, Najmeh Mohammad-Pour, Danial Babaki, Fatemeh Sadeghifar, Reza Jafarzadeh Esfehani, Hamid Reza Bidkhori, Nema Mohamadian Roshan, Madjid Momeni-Moghaddam, Hojjat Naderi-Meshkin
Summary: This study investigates the feasibility and effectiveness of using decellularized HAM (dAM) and stromal HAM (sAM) in combination with adipose-derived human mesenchymal stem cells (AdMSCs) to promote wound healing. The results showed that the expression level of VEGF was significantly higher in the sAM/AdMSCs group compared to the dAM/AdMSCs group. In vivo experiments demonstrated that wounds treated with sAM/AdMSCs had more vascularization and thicker collagen deposition compared to untreated wounds and wounds treated with dAM/AdMSCs.
Article
Genetics & Heredity
Mehdi Sadeghi, Mohammad Reza Karimi, Amir Hossein Karimi, Nafiseh Ghorbanpour Farshbaf, Abolfazl Barzegar, Ulf Schmitz
Summary: In this study, a differentially expressed co-expression module of mRNAs in EMT-type gastric tumors was identified using Weighted Gene Co-expression Network Analysis (WGCNA). Through network analysis and linear discriminant analysis, mRNA motifs and microRNA-based models with strong prognostic and diagnostic relevance were determined. Additionally, the DMD/ITGA1/CAV1 motif was identified as the top motif with consistent relevance to prognosis. The molecular functions of the identified models indicate the central roles of MAPK, Hh, and cGMP/cAMP signaling in the pathology of the EMT subtype of gastric cancer and highlight their potential utility in precision therapeutic approaches.
Article
Cell & Tissue Engineering
Laertis Ikonomou, Natividad Cuende, Miguel Forte, Bambi J. Grilley, Aaron D. Levine, Megan Munsie, John E. J. Rasko, Leigh Turner, Hamid R. Bidkhori, Rachele Ciccocioppo, Felix Grignon, Alok Srivastava, Daniel J. Weiss, Patricia Zettler, Bruce L. Levine
Summary: The field of regenerative medicine is growing rapidly, but it also faces challenges with the commercialization of unproven cell and gene-based products. The International Society for Cell & Gene Therapy opposes premature commercialization and advocates for evidence-based advanced therapy products.
Article
Cell Biology
Shun Hay Pun, Karla M. O'Neill, Kevin S. Edgar, Eleanor K. Gill, Arya Moez, Hojjat Naderi-Meshkin, Sudhir B. Malla, Michelle B. Hookham, Mohammed Alsaggaf, Vinuthna Vani Madishetti, Bianca Botezatu, William King, Coy Brunssen, Henning Morawietz, Philip D. Dunne, Derek P. Brazil, Reinhold J. Medina, Chris J. Watson, David J. Grieve
Summary: This study aimed to investigate and define the contribution of NOX4 NADPH oxidase to hypoxia-induced dysfunction and explore its potential as a therapeutic target. The results showed that activation of the PLAC8-NOX4 signaling axis improved the angiogenic functions of CB-ECFCs under hypoxic conditions.
Review
Biochemistry & Molecular Biology
Siyuan Wu, Ulf Schmitz
Summary: Single-cell sequencing technologies have revolutionized life sciences and biomedical research by providing high-resolution data on cell heterogeneity. Computational algorithms and mathematical models have been developed to make sense of the data and simulate biological processes, leading to breakthroughs in understanding cell differentiation and tissue composition. Long-read sequencing technologies have further enhanced the investigation of alternative splicing, isoform expression, genome assembly, and the detection of complex structural variants.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Article
Biochemistry & Molecular Biology
Jimmy Retzlaff, Xin Lai, Carola Berking, Julio Vera
Summary: Recent progress in understanding cancer relies on systematic profiling of patient samples using high-throughput techniques like transcriptomics. Omics data alone cannot provide insights into the spatiotemporal aspects of tumor progression. A computational workflow to integrate transcriptomics data into hybrid, multi-scale cancer models is presented, identifying scenarios of therapy resistance.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
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)
