Article
Geriatrics & Gerontology
Devin Wahl, Alyssa N. Cavalier, Meghan Smith, Douglas R. Seals, Thomas J. LaRocca
Summary: The study shows that healthy aging interventions globally reduce transcripts of noncoding repetitive elements, while aging and high-fat diet increase their expression. The reduction of RE transcripts with healthy aging interventions is associated with biological/physiological processes linked to aging.
JOURNALS OF GERONTOLOGY SERIES A-BIOLOGICAL SCIENCES AND MEDICAL SCIENCES
(2021)
Article
Multidisciplinary Sciences
Tatsuya Ohhata, Maya Suzuki, Satoshi Sakai, Kosuke Ota, Hazuki Yokota, Chiharu Uchida, Hiroyuki Niida, Masatoshi Kitagawa
Summary: This study developed a program called CCIVR that comprehensively identifies cis-natural antisense transcripts (cis-NATs) using RNA-seq data. CCIVR was demonstrated to be effective in identifying cis-NAT pairs in various organisms. Furthermore, CCIVR identified cis-NAT pairs that exhibit inversely correlated expression upon TGF beta stimulation, with some cis-NATs functioning to repress their partner genes through epigenetic alterations in the promoters.
SCIENTIFIC REPORTS
(2022)
Article
Cell Biology
Dongming Wu, Shihua Deng, Li Li, Teng Liu, Ting Zhang, Jing Li, Ye Yu, Ying Xu
Summary: The study revealed that TGF-beta 1-mediated exosomal lnc-MMP2-2 increases BBB permeability to promote NSCLC brain metastasis by modulating miR-1207-5p and EPB41L5. Thus, exosomal lnc-MMP2-2 may serve as a potential therapeutic target for lung cancer brain metastasis.
CELL DEATH & DISEASE
(2021)
Article
Biochemistry & Molecular Biology
Fan Gao, Fang Wang, Huifen Cao, Yue Chen, Yong Diao, Philipp Kapranov
Summary: The human genome contains various noncoding transcripts that have been traditionally categorized into long or small based on their lengths. However, the functions and biological significance of most of these transcripts are still unknown. In this study, a high-throughput assay was developed to test the functionality of small noncoding RNAs (sncRNAs) by overexpressing them in human cells. Surprisingly, a significant fraction of unannotated sncRNAs were found to have biological relevance, challenging the assumption that they are merely degradation products. These findings suggest the potential existence of multiple functional sncRNAs in the small noncoding transcriptome.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Multidisciplinary Sciences
Parisa Sooshtari, Biao Feng, Saumik Biswas, Michael Levy, Hanxin Lin, Zhaoliang Su, Subrata Chakrabarti
Summary: This study found that ANRIL gene alteration may play an important role in diabetic nephropathy by regulating the expression of multiple pathogenetic molecules, affecting various metabolic pathways, apoptosis, and synthesis and degradation of extracellular matrix proteins. ANRIL may be a potential drug target for DN and other chronic diabetic complications.
Article
Medicine, Research & Experimental
Xiang He, Xinzhong Li, Yuan Han, Guojun Chen, Tong Xu, Donghua Cai, Yili Sun, Shifei Wang, Yanxian Lai, Zhonghua Teng, Senlin Huang, Wangjun Liao, Yulin Liao, Jianping Bin, Jiancheng Xiu
Summary: This study demonstrates that circChordc1 plays a role in modulating VSMC phenotype and growth, suppressing abdominal aortic aneurysm formation and reducing rupture risk. By inducing vimentin degradation and increasing the activity of the GSK3 beta/beta-catenin pathway, circChordc1 optimizes VSMC phenotype and reverses pathological aneurysm progression.
MOLECULAR THERAPY-NUCLEIC ACIDS
(2022)
Article
Biology
Tao Shen, Wangxiao Xia, Sainan Min, Zixuan Yang, Lehua Cheng, Wei Wang, Qianxi Zhan, Fanghong Shao, Xuehan Zhang, Zhiyu Wang, Yan Zhang, Guodong Shen, Huafeng Zhang, Li-Ling Wu, Guang-Yan Yu, Qing-Peng Kong, Xiangting Wang
Summary: This study identified a lncRNA gene related to Chr3q29 in tongue squamous carcinoma and demonstrated how its two variants, 887S and 887L, play opposing roles in tumor progression through the common target CA9. The mechanisms involve the activation of CA9 transcription by 887L through recruiting HIF1 alpha, while 887S suppresses CA9 through DNMT1-mediated DNA methylation. The findings highlight the fine control of hypoxia adaptation through CA9 by these two antagonistic lncRNA variants.
Article
Multidisciplinary Sciences
Phaedra R. Theodoridis, Michael Bokros, Dane Marijan, Nathan C. Balukoff, Dazhi Wang, Chloe C. Kirk, Taylor D. Budine, Harris D. Goldsmith, Miling Wang, Timothy E. Audas, Stephen Lee
Summary: This study investigates how solid-like amyloid bodies coordinate local nuclear protein synthesis during stress. It was found that these solid-like condensates facilitate translation by accumulating translationally active ribosomes. Additionally, regulatory ribosomal proteins and translation factors relocate to amyloid bodies to sustain nuclear protein synthesis.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biochemistry & Molecular Biology
Adriano Biasini, Baroj Abdulkarim, Stefano de Pretis, Jennifer Y. Tan, Rajika Arora, Harry Wischnewski, Rene Dreos, Mattia Pelizzola, Constance Ciaudo, Ana Claudia Marques
Summary: Translation is necessary for miRNA-dependent transcript destabilization, and coding and noncoding transcripts are differently affected by miRNAs.
Review
Biochemistry & Molecular Biology
Seung Wan Son, Ba Da Yun, Mun Gyu Song, Jin Kyeong Lee, Soo Young Choi, Hyo Jeong Kuh, Jong Kook Park
Summary: Hypoxia, regulated by HIFs, influences cancer hallmarks and therapeutic resistance, with dysregulated lncRNAs being considered as potential candidates for cancer control.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Oncology
Mina Zamani, Ali-Mohammad Foroughmand, Mohammad-Reza Hajjari, Babak Bakhshinejad, Rory Johnson, Hamid Galehdari
Summary: Cancer is a genetic disorder that alters cellular information flow, and noncoding variations in the genome have been found to drive important cancer phenotypes. In this study, increased expression of certain genes was observed in colorectal cancer, and these genes were associated with clinicopathological characteristics of the disease. The noncoding transcripts were found to significantly participate in the regulation network of the MYC gene and in the carcinogenesis of colorectal cells.
FRONTIERS IN ONCOLOGY
(2022)
Article
Agronomy
Jianghua Liao, Haoling Rong, Lili You, Kai Xia, Minghui Wang, Peng Han, Chao Li, Jiang Zhang
Summary: By targeting the beta-Actin gene of the Colorado potato beetle, transplastomic plants can trigger a strong resistance to CPB. However, there is still dsRNA accumulation in the tubers, which is unnecessary and may pose a potential food exposure issue. In this study, we compared the activities of two promoters (PrbcL and PpsbD) with the Prrn promoter and found that PpsbD is an effective promoter to reduce dsRNA accumulation in potato tubers while maintaining resistance to CPB in the leaves.
PEST MANAGEMENT SCIENCE
(2023)
Article
Engineering, Environmental
Ke Zhang, Joseph Hodge, Anamika Chatterjee, Tae Seok Moon, Kimberly M. Parker
Summary: Double-stranded RNA undergoes alkaline hydrolysis at orders-of-magnitude slower rates compared to single-stranded RNA, and can remain intact for months at neutral pH. Increasing pH effectively attenuates enzymatic degradation of dsRNA without inducing alkaline hydrolysis, which differs significantly from ssRNA. Understanding these unique properties of dsRNA allows for greater control of stability in RNAi technology and provides insights into various applications, including isolation, detection, and inactivation of dsRNA viruses.
ENVIRONMENTAL SCIENCE & TECHNOLOGY
(2021)
Article
Oncology
Sen Liu, Xu Chen, Tianxin Lin
Summary: The article summarizes the molecular mechanisms of lymphatic metastasis in bladder cancer, including lymphangiogenesis, noncoding RNAs, and microenvironment-associated molecules. Newly discovered radiomics and genomics approaches have improved the preoperative diagnostic accuracy of lymph node metastasis, potentially leading to promising therapeutic strategies.
Article
Multidisciplinary Sciences
Yongsuk Ku, Joo-Hwan Park, Ryeongeun Cho, Yongki Lee, Hyoung-Min Park, MinA Kim, Kyunghoon Hur, Soo Young Byun, Jun Liu, Young-Suk Lee, David Shum, Dong-Yeop Shin, Youngil Koh, Je-Yoel Cho, Sung-Soo Yoon, Junshik Hong, Yoosik Kim
Summary: This study uncovers the mechanism of viral mimicry and cell death triggered by decitabine through the activation of endogenous retroviruses (ERVs), highlighting the essential role of the double-stranded RNA-binding protein Staufen1 (Stau1) and providing a novel target for predicting the efficacy of DNMTis.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Review
Biochemistry & Molecular Biology
Nicole Wagner, Kay-Dietrich Wagner
Summary: Peroxisome proliferator activated receptors (PPARs) are ligand-activated transcription factors that play important roles in glucose and lipid metabolism. They are also involved in reducing inflammation and atherosclerosis. Different types of PPARs have specific synthetic agonists, which are used to treat dyslipidemia and Type 2 diabetes mellitus. The safety of PPAR activators in cardiovascular diseases is still controversial.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Oncology
Alexandra Mousset, Enora Lecorgne, Isabelle Bourget, Pascal Lopez, Kitti Jenovai, Julien Cherfils-Vicini, Chloe Dominici, Geraldine Rios, Cedric Girard-Riboulleau, Bodu Liu, David L. Spector, Sidse Ehmsen, Shufang Renault, Caroline Hego, Fatima Mechta-Grigoriou, Francois-Clement Bidard, Mikkel Green Terp, Mikala Egeblad, Cedric Gaggioli, Jean Albrengues
Summary: Metastasis is a major cause of cancer death, often accompanied by therapy resistance. In this study, we discovered that chemotherapy induces neutrophil recruitment and NET formation, leading to reduced therapy response in breast cancer lung metastasis mouse models. We further elucidate that chemotherapy-treated cancer cells secrete IL-1(3, which triggers NET formation. NET-associated proteins, integrin-αv(β3 and matrix metalloproteinase 9, play crucial roles in activating latent TGF-β3 and promoting chemoresistance. Our findings suggest that targeting the IL-1(3-NET-TGF-β3 axis could potentially reduce or prevent chemoresistance in the metastatic setting.
Review
Cell Biology
Paul Hofman, Marc G. Denis
Summary: The assessment of minimal residual disease (MRD) from blood samples has potential in optimizing patient care for resected non-small cell lung carcinoma (NSCLC). Evaluating MRD status can improve overall survival for early stage NSCLC patients and reduce the toxic effects and financial burden of treatment. Clinical trials have examined MRD in early stage NSCLC, highlighting the need to bridge the gap between research and routine practice. Further action is necessary to assess the relevance of MRD detection in interventional clinical studies, comparing different techniques, time points, and cutoffs. This article investigates and provides recommendations for optimizing MRD evaluation in NSCLC.
Review
Biochemistry & Molecular Biology
Serena Janho Dit Hreich, Paul Hofman, Valerie Vouret-Craviari
Summary: This article focuses on the role of the purinergic receptor P2RX7 in controlling tumor growth by releasing IL-18 and modulating anti-tumor immunity. It summarizes the receptor activities of P2RX7 and how IL-18 controls tumor growth. Furthermore, the potential of targeting the P2RX7/IL-18 pathway in combination with classical immunotherapies to fight cancer is discussed.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Marius Ilie, Jonathan Benzaquen, Veronique Hofman, Elodie Long-Mira, Sandra Lassalle, Jacques Boutros, Christophe Bontoux, Virginie Lespinet-Fabre, Olivier Bordone, Virginie Tanga, Maryline Allegra, Myriam Salah, Julien Fayada, Sylvie Leroy, Matteo Vassallo, Irit Touitou, Johan Courjon, Julie Contenti, Michel Carles, Charles-Hugo Marquette, Paul Hofman
Summary: As new SARS-CoV-2 variants emerge, it is important to improve the efficiency and availability of viral genome sequencing, especially in samples with low viral load. In this study, retrospective SARS-CoV-2 genome sequencing was performed on 175 positive samples, and the analysis successfully detected Delta and Omicron variants in low viral load samples. The results showed that there was no significant difference in viral load between patients infected with the Omicron variant and those infected with the Delta variant.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Editorial Material
Biochemistry & Molecular Biology
Nicole Wagner, Kay-Dietrich Wagner
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Oncology
Olivia Vidal-Cruchez, Victoria J. Nicolini, Tifenn Rete, Karine Jacquet, Roger Rezzonico, Caroline Lacoux, Marie-Angela Domdom, Barnabe Romeo, Jeremie Roux, Arnaud Hubstenberger, Bernard Mari, Baharia Mograbi, Paul Hofman, Patrick Brest
Summary: Cancer therapies targeting the MAPK pathway lead to drug resistance. Overexpression of RAS has been linked to this resistance, but the underlying mechanisms are unclear. This study shows that MEK inhibitors increase translation of KRAS and NRAS oncogenes through liquid-liquid phase separation, specifically P-body dissolution. This feedback loop involving P-bodies and phase separation could be important for future targeted therapies.
Editorial Material
Cell Biology
Nicole Wagner, Kay-Dietrich Wagner
Editorial Material
Cell Biology
Nicole Wagner, Kay-Dietrich Wagner
Article
Cardiac & Cardiovascular Systems
Sandra Diaz del Moral, Maha Benaouicha, Cristina Villa del Campo, Miguel Torres, Nicole Wagner, Kay-Dietrich Wagner, Ramon Munoz-Chapuli, Rita Carmona
Summary: The Wilms tumor suppressor gene (Wt1) encodes a C2H2-type zinc-finger transcription factor involved in various cellular processes. It has a crucial role in the development of multiple organs. Silencing or deletion of Wt1 in cardiomyocytes leads to abnormal cardiac development and increased susceptibility to damage. These findings suggest that WT1 plays a novel role in cardiac physiology and protection against damage.
JOURNAL OF CARDIOVASCULAR DEVELOPMENT AND DISEASE
(2023)
Review
Oncology
Edwin Roger Parra, Marius Ilie, Ignacio I. Wistuba, Paul Hofman
Summary: Over the past decade, there has been a revolution in cancer treatment with the shift towards targeted molecular therapies and immune-based therapies, particularly immune-checkpoint inhibitors (ICIs). However, not all patients with advanced non-small cell lung cancer (aNSCLC) benefit equally from immunotherapy, and there is a need for additional predictive markers for ICIs efficacy. Multiplex immunostaining, which evaluates multiple molecules in the tumor at the same time, shows promise in optimizing patient selection for ICIs. This review aims to explore the role of multiplex immunostaining in immuno-thoracic oncology and its current advantages and limitations in clinical practice.
BRITISH JOURNAL OF CANCER
(2023)
Review
Oncology
Patrick Brest, Baharia Mograbi, Gilles Pages, Paul Hofman, Gerard Milano
Summary: The combination of immune checkpoint inhibitors and anti-angiogenic agents shows promise in cancer treatment by enhancing response rates and prolonging progression-free survival. However, it also comes with increased side effects and requires careful monitoring.
BRITISH JOURNAL OF CANCER
(2023)
Article
Biochemistry & Molecular Biology
Nicola Normanno, Jose Carlos Machado, Edoardo Pescarmona, Simonetta Buglioni, Lara Navarro, Riziero Esposito Abate, Anabela Ferro, Rob Mensink, Matilde Lambiase, Virginie Lespinet-Fabre, Byron Calgua, Philip M. Jermann, Marius Ilie, Paul Hofman
Summary: This multicenter study evaluated the performance of the Oncomine Dx Express Test on the Ion Torrent Genexus System for detecting DNA and RNA variants in solid tumors. The test showed high accuracy and sensitivity, providing results in a short turnaround time, which can support timely decision-making for targeted therapeutic interventions.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Oncology
Paul Hofman
Summary: The introduction of liquid biopsies has provided new therapeutic opportunities in thoracic oncology, especially for advanced nonsquamous non-small cell lung cancer patients. In Europe, liquid biopsies are frequently used for patients receiving tyrosine kinase inhibitors (TKIs) when tumor progression occurs. Tissue biopsies are necessary if the liquid biopsy fails to detect TKI resistance mechanisms. Liquid biopsy is recommended before first-line therapy if tissue or cytological material is inaccessible or insufficient in quantity or quality. Simultaneous performance of liquid biopsy and tissue biopsy before treatment or tumor progression is rare and its benefits to patient care need further evaluation. This review updates the complementarity of liquid biopsy and tissue biopsy for care of aNS-NSCLC patients.
TRANSLATIONAL ONCOLOGY
(2023)
Review
Pathology
Paul Hofman, Sabina Berezowska, Daniel Kazdal, Baharia Mograbi, Marius Ilie, Albrecht Stenzinger, Veronique Hofman
Summary: The evolving treatment options in thoracic oncology require regular updates in diagnostic algorithms by pathologists. The pathologist plays a crucial role in deciding whether to send specimens for further analysis and can quickly obtain more material if needed. Inadequate algorithms and sampling workflow can lead to inaccurate results, impacting treatment choices and patient outcomes.