Article
Medicine, Research & Experimental
Bo-Yi Sung, Yi-Hsin Lin, Qiongman Kong, Pali D. Shah, Joan Glick Bieler, Scott Palmer, Kent J. Weinhold, Hong-Ru Chang, Hailiang Huang, Robin K. Avery, Jonathan Schneck, Yen-Ling Chiu
Summary: This study reveals a molecular mechanism governing T cell polyfunctionality, involving the activation of Wnt signaling and the role of PRMT1. Wnt activation inhibits T cell differentiation and promotes the generation of highly polyfunctional cells, with persistent effects even after the removal of the drug. PRMT1 is involved in regulating T cell polyfunctionality, particularly the production of IL-2. These findings highlight PRMT1 as a potential target for T cell immunotherapy.
JOURNAL OF CLINICAL INVESTIGATION
(2022)
Review
Biochemistry & Molecular Biology
Olga Sergeeva, Timofei Zatsepin
Summary: RNA helicases play a crucial role in regulating the activity of key cell cycle regulators at the transcription and translation levels. Some RNA helicases, such as eIF4A, DDX3, and DDX5, have been identified as promising therapeutic targets. However, targeting RNA helicases may lead to side effects, underscoring the importance of caution in their use.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Biochemistry & Molecular Biology
Valeria Pietropaolo, Carla Prezioso, Ugo Moens
Summary: Tumor viruses such as HTLV-1, HCV, MCPyV, HR-HPVs, EBV, KSHV, and HBV play a role in approximately 15% of all human cancers, using similar mechanisms to convey cancer hallmarks to infected cells. Perturbed gene expression and epigenetic processes, including DNA methylation and histone modification, are key mechanisms in virus-induced carcinogenesis. Increasing evidence shows that oncoviruses cause epigenetic modifications which are crucial in cancer development.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Multidisciplinary Sciences
Johanna Diener, Arianna Baggiolini, Mattias Pernebrink, Damian Dalcher, Luigi Lerra, Phil F. Cheng, Sandra Varum, Jessica Hausel, Salome Stierli, Mathias Treier, Lorenz Studer, Konrad Basler, Mitchell P. Levesque, Reinhard Dummer, Raffaella Santoro, Claudio Cantu, Lukas Sommer
Summary: Melanoma cells rely on developmental programs during tumor initiation and progression. SALL4 is a negative regulator of melanoma phenotype switching where its loss leads to the acquisition of an invasive phenotype. This is mediated through interaction with HDAC2 and co-binding to a set of invasiveness genes.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Jin-Yu Lee, Nai-Lin Chou, Ya-Ru Yu, Hsin-An Shih, Hung-Wei Lin, Chine-Kuo Lee, Mau-Sun Chang
Summary: In this study, the importance of PHRF1 in IgA switching was investigated in CH12F3-2A cells and CD19-Cre mice. The results showed that the loss of PHRF1 decreased IgA production and the levels of PARP1, NELF-A, and NELF-D. Interestingly, IgA switching was not significantly reduced in PHRF1 deficient splenic B lymphocytes.
Article
Oncology
Laurynas Vilys, Inga Peciuliene, Egle Jakubauskiene, Ruta Zinkeviciute, Yuichi Makino, Arvydas Kanopka
Summary: The splicing machinery is crucial for cellular adaptability and hypoxia can alter RNA splicing, leading to the formation of different Fas mRNA isoforms.
EXPERIMENTAL CELL RESEARCH
(2021)
Article
Microbiology
Isabelle Gennart, Astrid Petit, Laetitia Wiggers, Srdan Pejakovic, Nicolas Dauchot, Sylvie Laurent, Damien Coupeau, Benoit Muylkens
Summary: GaHV-2 infection suppresses the expression of gga-miR-126, which is considered a tumor suppressor. The reduced expression of miR-126 may be related to hypermethylation at a CpG island in the miR-126 host gene EGFL-7. Restoration of miR-126 inhibits cell proliferation and reduces CRK protein levels.
Article
Microbiology
Han Xiao, Emanuel Wyler, Miha Milek, Bastian Grewe, Philipp Kirchner, Arif Ekici, Ana Beatriz Oliveira Villela Silva, Doris Jungnickl, Florian Full, Marco Thomas, Markus Landthaler, Armin Ensser, Klaus Ueberla
Summary: The HIV-1 Rev protein is crucial for nuclear export of unspliced and incompletely spliced HIV-1 RNAs. Depletion of proteins like CRNKL1 can significantly enhance levels of unspliced HIV-1 RNA in the cytoplasm, potentially revealing a cellular mechanism exploited by HIV-1 to regulate its complex splicing pattern.
Review
Biochemistry & Molecular Biology
Yumin Wang, Yan Wang, Harsh Patel, Jichao Chen, Jinhua Wang, Zhe-Sheng Chen, Hongquan Wang
Summary: Divergent N-6-methyladenosine (m(6)A) modifications, mediated by m(6)A regulators, play a dynamic and reversible role in posttranscriptional RNA modifications. Aberrant m(6)A modifications are associated with cancer occurrence, development, progression, and prognosis. This review summarizes the current roles of m(6)A regulators in cancer and explores the epigenetic regulatory mechanisms of m(6)A regulators in cancer genesis.
Article
Cell Biology
Yumeng Zhu, Xiaojun Liu, Yang Wang, Yongbo Pan, Xiaoqi Han, Bo Peng, Xu Zhang, Shaoxi Niu, He Wang, Qinong Ye, Yinmin Gu, Shan Gao
Summary: This study identified a lncRNA DMDRMR/miR-378a-5p/DAB2IP axis that activates the VEGFA/VEGFR2 signaling pathway, leading to angiogenesis and drug resistance in clear cell renal cell carcinoma (ccRCC). This axis is clinically relevant to ccRCC pathogenesis and prognosis, and may serve as a novel target for diagnosis and therapy of ccRCC patients.
CELL DEATH & DISEASE
(2022)
Article
Oncology
Hua You, Zijun Y. Xu-Monette, Li Wei, Harry Nunns, Mate L. Nagy, Govind Bhagat, Xiaosheng Fang, Feng Zhu, Carlo Visco, Alexandar Tzankov, Karen Dybkaer, April Chiu, Wayne Tam, Youli Zu, Eric D. Hsi, Fredrick B. Hagemeister, Jooryung Huh, Maurilio Ponzoni, Andres J. M. Ferreri, Michael B. Moller, Benjamin M. Parsons, J. Han Van Krieken, Miguel A. Piris, Jane N. Winter, Yong Li, Qingyan Au, Bing Xu, Maher Albitar, Ken H. Young
Summary: The study identified the associations of KMT2D and TP53 mutations with increased mutation numbers in DLBCL, and the poor clinical outcomes associated with high mutation numbers. The underlying mechanisms were revealed through gene-expression profiling and the correlation of MUThigh with decreased T cells in patients with DLBCL. Furthermore, MUThigh was linked to lower PD-1 and PD-L1 expression, suggesting a potential positive impact on immune responses in DLBCL patients.
Article
Biotechnology & Applied Microbiology
Chen Yang, Siqi Wu, Zezhong Mou, Quan Zhou, Xiyu Dai, Yuxi Ou, Xinan Chen, Yiling Chen, Chenyang Xu, Yun Hu, Limin Zhang, Lujia Zou, Shengming Jin, Jimeng Hu, Shanhua Mao, Haowen Jiang
Summary: This study identified differentially expressed circRNAs in bladder cancer tissue and exosomes, and investigated their roles in cancer cell behavior and immune function. The findings revealed the regulatory function of exosome-derived circTRPS1 in BCa cells and provided potential therapeutic targets for BCa.
Article
Oncology
Yifan Li, Qiaozhen Zhu, Shuchang Zhou, Jiangtao Chen, Aoyu Du, Changjiang Qin
Summary: In this study, we identified a prognostic and immune-related marker for hepatocellular carcinoma (HCC) from the RNA splicing pathway. This marker, thioredoxin like 4A (TXNL4A), was found to be highly expressed in HCC tumors and correlated with HCC survival. Additionally, TXNL4A was found to be associated with CD8 T cell infiltration in HCC.
FRONTIERS IN ONCOLOGY
(2023)
Article
Biology
Davia Blake, Caleb M. Radens, Max B. Ferretti, Matthew R. Gazzara, Kristen W. Lynch
Summary: The study investigates the impact of CD28 costimulation on alternative splicing in T cells activated through the T cell receptor (TCR). It is found that CD28 signaling has minimal impact on splicing alone but enhances the extent of change in TCR-induced alternative splicing events. Interestingly, enhanced splicing events occur within genes encoding key components of the apoptotic signaling pathway. Experimental evidence shows that isoforms induced by CD3/CD28 costimulation promote resistance to apoptosis and changes in these genes function combinatorially to further promote cell viability. The JNK signaling pathway is also found to be required for these splicing events, highlighting their co-regulation.
Review
Cell Biology
Yuanjie Ding, Yuanchun Yao, Xingmu Gong, Qi Zhuo, Jinhua Chen, Miao Tian, Maryam Farzaneh
Summary: JMJD3 is a key histone demethylase that regulates H3K27me3 and plays a crucial role in stem cell fate determination during the process of cell reprogramming.
CELL COMMUNICATION AND SIGNALING
(2021)
Article
Ecology
Priscila Silva Matos, Cristiane Figueira da Silva, Marcos Gervasio Pereira, Eliane Maria Ribeiro da Silva, Ricardo Martinez Tarre, Andre Luiz Custodio Franco, Everaldo Zonta
Summary: This research assessed the effects of different land uses on the arbuscular mycorrhizal fungi (AMF) community and glomalin-related soil protein (GRSP) production. The study found that land use type significantly influenced the AMF community and GRSP, while seasonality had a minimal impact. The management practices in agroforestry systems affected AMF sporulation and species diversity. Additionally, there were correlations between the AMF community and key soil parameters, such as soil aggregate stability and soil organic carbon (SOC).
ACTA OECOLOGICA-INTERNATIONAL JOURNAL OF ECOLOGY
(2022)
Article
Oncology
Biswendu Biswas, Rady Chaaban, Shrena Chakraborty, Alexandre Devaux, Ana Luisa Dian, Anna Minello, Jenny Kaur Singh, Stephan Vagner, Patricia Uguen, Sarah Lambert, Martin Dutertre, Aura Carreira
Summary: This article synthesizes scientific presentations from two international courses held at Institute Curie in 2021, focusing on post-transcriptional gene regulation and genome instability and human disease, bringing together knowledge on RNA metabolism and genome stability maintenance.
BULLETIN DU CANCER
(2022)
Article
Environmental Sciences
Julio Cesar Ribeiro, Adriano Portz, Fabiana Soares Dos Santos, Marcos Gervasio Pereira, Everaldo Zonta
Summary: This study evaluated the potential use of different doses of onshore oil well drill cuttings and sunflower cake on the growth of sunflower plants and soil chemical attributes. The results provide recommendations for safe application doses and show that a mixture of sunflower cake and drill cuttings can promote plant growth and soil fertility without causing significant increases in sodium content.
ENVIRONMENTAL TECHNOLOGY
(2023)
Article
Oncology
Anne-Sophie Hatat, Clara Benoit-Pilven, Amelie Pucciarelli, Florence de Fraipont, Lucie Lamothe, Pascal Perron, Amandine Rey, Matteo Giaj Levra, Anne-Claire Toffart, Didier Auboeuf, Beatrice Eymin, Sylvie Gazzeri
Summary: This study identifies an alternative splicing event involving the autophagic gene ATG16-L1 as a potential mechanism for acquired resistance to EGFR-TKIs in NSCLC. Overexpression of the splice variant ATG16-L1 beta was found to be associated with resistance to EGFR-TKI treatment. Mechanistically, ATG16-L1 beta impairs gefitinib-induced autophagy, leading to cell survival and resistance. Neutralization of ATG16-L1 beta restores autophagy and sensitizes cells to gefitinib-induced apoptosis. These findings highlight the importance of splicing regulation in EGFR-targeted cancer therapy.
MOLECULAR ONCOLOGY
(2022)
Article
Oncology
Biswendu Biswas, Ramdane Guemiri, Mandy Cadix, Celine M. Labbe, Alina Chakraborty, Martin Dutertre, Caroline Robert, Stephan Vagner
Summary: The eIF4A inhibitor silvestrol selectively inhibits the translation of alternatively polyadenylated mRNAs encoding key immune-related proteins, providing a promising approach for anti-cancer therapy targeting the translation initiation complex eIF4F. Through high-throughput analysis, it has been shown that silvestrol differentially inhibits the translation of APA isoforms of various genes in T cells, highlighting the importance of considering mRNA heterogeneity in the understanding of the anti-tumor activities of eIF4A inhibitors.
Article
Biochemistry & Molecular Biology
Alina Chakraborty, Mandy Cadix, Sebastien Relier, Nicolo Taricco, Tina Alaeitabar, Alexandre Devaux, Celine M. Labbe, Sylvain Martineau, Amelie Heneman-Masurel, Pierre Gestraud, Alberto Inga, Nicolas Servant, Stephan Vagner, Martin Dutertre
Summary: This study reveals differential regulation of intronic polyadenylation (IPA) isoform ratio across subcellular compartments during drug response, suggesting distinct patterns of IPA isoform regulation in the transcriptome and translatome, as well as between the nucleus and cytosol.
Article
Biochemistry & Molecular Biology
Rym Sfaxi, Biswendu Biswas, Galina Boldina, Mandy Cadix, Nicolas Servant, Huimin Chen, Daniel R. Larson, Martin Dutertre, Caroline Robert, Stephan Vagner
Summary: The recognition of polyadenylation signals (PAS) in eukaryotic pre-mRNAs is usually coupled to transcription termination, occurring while pre-mRNA is chromatin-bound. However, for some pre-mRNAs, this 3'-end processing occurs post-transcriptionally, i.e., through a co-transcriptional cleavage (CoTC) event downstream of the PAS, leading to chromatin release and subsequent PAS cleavage in the nucleoplasm. These findings indicate that CoTC-type cleavage of pre-mRNAs, followed by PAS cleavage in the nucleoplasm, allows certain pre-mRNAs to escape 3'-end processing inhibition in response to UV-induced DNA damage.
Article
Engineering, Environmental
Julia Barra Netto-Ferreira, Fernanda Palmeira Gabetto, Ana Carolina Muniz de Araujo, Ricardo de Castro Dias, Nelson Moura Brasil do Amaral Sobrinho, Everaldo Zonta
Summary: Using urban residues to produce organomineral fertilizers (OMF) is an environmentally friendly strategy that can enhance soil fertility. The study investigated the availability of N, P, and K under organomineral fertilization in sandy soils. The results showed that OMFs have the potential to alter nutrient availability dynamics, serving as a strategy for nutrient management in agriculture.
ENVIRONMENTAL GEOCHEMISTRY AND HEALTH
(2023)
Article
Engineering, Civil
Amanda Sales Alves, Nivaldo Schultz, Bruno Antonio Augusto Faria Conforto, Everaldo Zonta, Daniel Fonseca de Carvalho
Summary: The aim of this study was to evaluate the loss of soil, water and nutrients, as well as the financial impact resulting from the loss of nutrients, in an area with and without fertilisation with chicken litter under simulated rainfall in different rainfall patterns. The results showed that the rainfall pattern affected the loss of N, P, and K, and the financial losses from the loss of nutrients caused by water erosion can be even more marked in areas with greater slope.
JOURNAL OF HYDROLOGY
(2023)
Article
Biochemistry & Molecular Biology
Jean-Philippe Villemin, Laia Bassaganyas, Didier Pourquier, Florence Boissiere, Simon Cabello-Aguilar, Evelyne Crapez, Rita Tanos, Emmanuel Cornillot, Andrei Turtoi, Jacques Colinge
Summary: The study of cellular networks mediated by ligand-receptor interactions has been a hot topic recently due to single-cell omics. However, there is a lack of comparable bulk data and clinical information in single-cell studies. Spatial transcriptomic analyses offer a revolutionary tool in biology, particularly those relying on multicellular resolution. In this study, we introduce BulkSignalR, an R package that infers ligand-receptor networks from bulk data, integrates downstream pathways, and provides statistical significance estimation and visualization methods, including those specific to spatial data. Our results demonstrate the relevance and superior quality of BulkSignalR inferences compared to other spatial transcriptomic packages.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Soil Science
Tiago Paula da Silva, Igor de Sousa Morais, Gilsonley Lopes dos Santos, Everaldo Zonta, Luiz Alberto da Silva Rodrigues Pinto, Hugo de Souza Fagundes, Marcos Gervasio Pereira
Summary: Sandy texture soils are a challenge for agriculture due to their low water retention capacity, rapid organic matter decomposition, and nutrient loss. This study evaluated different soil management systems and vegetation covers to assess their impact on aggregate formation pathways, nutrient contents, and organic matter fractions. Results showed that the percentage of biogenic aggregates was higher than physicogenic ones, and there were no significant influences of vegetation coverage or management system. The conventional system generally exhibited higher chemical properties, while C2 and S.P covers provided the greatest improvements for chemical properties and carbon content.
REVISTA BRASILEIRA DE CIENCIA DO SOLO
(2023)
Article
Agronomy
Altina Lacerda Nascimento, Maria Clara Oliveira Duraes, Regynaldo Arruda Sampaio, Geraldo Ribeiro Zuba Junior, Fabiano Barbosa De Souza Prates, Luiz Arnaldo Fernandes, Everaldo Zonta, Nelson Moura Brasil Do Amaral Sobrinho
Summary: This study investigated the impact of different stabilization processes of sewage sludge (SS) on the levels of heavy metals in the soil and castor bean plant. Fertilization with solarized sewage sludge (SSS), composted sewage sludge (CSS), and vermi composted sewage sludge (VSS) resulted in the highest increase in soil zinc (Zn) levels, mainly in the surface layer. In the leaf tissues, higher levels of Zn and copper (Cu) were observed with the control (CO) and SSS treatments, while nickel (Ni) levels were higher with SSS, CSS, VSS, and mineral fertilizer (MF) treatments. Overall, Zn and Cu levels were higher in the leaf limb than in the petiole, whereas Ni, lead (Pb), and chromium (Cr) levels were higher in the petiole. However, no toxicity symptoms in the plants and no risk of soil contamination were observed with any of the fertilization treatments.
Article
Soil Science
Priscila Silva Matos, Luiz Alberto da Silva Rodrigues Pinto, Sandra Santana de Lima, Thassiany de Castro Alves, Eduardo Pellegrino Cerri, Marcos Gervasio Pereira, Everaldo Zonta
Summary: Adopting land-uses that contribute with a considerable litter input affects soil organic carbon accumulation and the physical fractions of soil organic matter. This study aimed to determine the impact of agroforestry systems on soil organic carbon content and physical fractions, as well as the influence of seasonality on the compartmentalization of soil organic matter. The results showed significant changes in soil organic carbon contents and physical fractions after a short period of implementing agroforestry systems, with the particulate fraction being particularly affected. The Carbon Management Index was found to be sensitive in detecting changes and revealed that the agroforestry system with the highest species density had the highest carbon accumulation in the soil.
REVISTA BRASILEIRA DE CIENCIA DO SOLO
(2023)
Article
Agriculture, Multidisciplinary
Priscila Silva Matos, Cristiane Figueira da Silva, Junior Melo Damian, Carlos Eduardo Pellegrino Cerri, Marcos Gervasio Pereira, Everaldo Zonta
Summary: Reducing soil degradation and its impacts on the environment is a major challenge in the 21st century, especially due to the link between population growth and soil degradation. Beneficial microorganisms, particularly arbuscular mycorrhizal fungi (AMF), play a crucial role in soil amelioration. Glomalin produced by AMF contributes to mitigating soil degradation. Understanding the role of glomalin and AMF in the restoration of degraded soils can improve sustainable restoration efforts.
