Article
Chemistry, Multidisciplinary
Yuchong Yang, Tanya K. Ronson, Jieyu Zheng, Nozomi Mihara, Jonathan R. Nitschke
Summary: The binding of fluoride to boron centers within metal-organic cages can regulate cage conformations and modulate host-guest binding. Tetrahedral and octahedral cages respond differently to fluoride binding, inhibiting or enhancing the binding of a second guest, respectively. Allosteric regulation between the tetrahedral and octahedral cages is also possible, with guests transferring between the two cages upon binding of fluoride to both.
Article
Biochemistry & Molecular Biology
Pan Li, Yuwei Chen, Xiumei Ke, Ruoyu Zhang, Ling Zuo, Meng Wang, Zhiwei Chen, Xianqin Luo, Jianwei Wang
Summary: This study provides evidence that baicalin alleviates alcohol-induced hepatic steatosis by regulating SREBP1c-mediated competitive binding of PNPLA3 to ATGL. Baicalin significantly attenuated metabolic disorders and hepatic steatosis in alcohol-induced rats, normalized the levels of hepatic triglyceride, alanine aminotransferase, and aspartate aminotransferase, and reduced hepatic vacuolization and Oil Red O staining area caused by alcohol. Baicalin also relieved alcohol-induced hepatic fibrosis. Mechanistically, baicalin activated hepatic lipolysis by suppressing the binding of PNPLA3 to ABHD5, leading to a decline in the hydrolysis capacity in liver lipid droplets. Overall, baicalin is a promising natural product for preventing alcohol-induced hepatic steatosis.
ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS
(2022)
Article
Oncology
Charlotte Zoe Angel, Mei Yu Cynthia Stafford, Christopher J. J. McNally, Heather Nesbitt, Declan J. J. McKenna
Summary: This study investigates the link between hypoxia and microRNA-21 (miR-21) in prostate cancer cells. It is found that hypoxia can induce the up-regulation of miR-21 expression in prostate cells, which promotes the progression of prostate cancer by suppressing the expression of the tumor suppressor gene RHOB. Additionally, miR-21 shows potential as a biomarker of hypoxia that can aid in the diagnosis and prognosis of prostate cancer.
Article
Immunology
Mengyuan Zhu, Han Han, Lei Hu, Yu Cao, Zhipeng Fan
Summary: IGFBP5 regulates the balance between Th17 and Treg cells by inhibiting Th17 differentiation and promoting Treg differentiation, alleviating colitis severity in mice models. In addition, IGFBP5 can suppress pro-inflammatory cytokines and its function can be inhibited by ERK or JNK pathway inhibitors.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Genetics & Heredity
Junyu Yan, Yalan Yang, Xinhao Fan, Yijie Tang, Zhonglin Tang
Summary: This study revealed the expression and function of circHipk2 in skeletal myogenesis, showing that circHipk2 can inhibit ribosome translation, and is regulated by the transcription factor Sp1, playing an important role in ribosome biogenesis and muscle cell proliferation and differentiation.
Article
Cell Biology
Laura Hakanpaa, Amr Abouelezz, An-Sofie Lenaerts, Seyda Culfa, Michael Algie, Jenny Barlund, Pekka Katajisto, Harvey McMahon, Leonardo Almeida-Souza
Summary: Hakanpaa et al. discovered that reticular adhesions are formed at flat clathrin lattices, a process inhibited by fibronectin and its receptor integrin alpha 5 beta 1. This novel adhesion assembly mechanism is involved in cell migration and reveals a unique crosstalk between cell-matrix adhesions.
JOURNAL OF CELL BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Jingwen Song, Syed Nabeel-Shah, Shuye Pu, Hyunmin Lee, Ulrich Braunschweig, Zuyao Ni, Nujhat Ahmed, Edyta Marcon, Guoqing Zhong, Debashish Ray, Kevin C. H. Ha, Xinghua Guo, Zhaolei Zhang, Timothy R. Hughes, Benjamin J. Blencowe, Jack F. Greenblatt
Summary: Alternative polyadenylation (APA) enhances gene regulatory potential by increasing the diversity of mRNA transcripts. A study found that the transcription factor Sp1 binds RNA and is a common repressor of distal poly(A) site usage. Sp1 inhibits cleavage at distal sites by interacting with the subunits of the core cleavage and polyadenylation (CPA) machinery.
Article
Biochemistry & Molecular Biology
Xiyi Lu, Jing Wang, Wei Wang, Chenfei Lu, Tianyu Qu, Xuezhi He, Xinyin Liu, Renhua Guo, Erbao Zhang
Summary: This study identified an oncogenic long non-coding RNA (lncRNA) called MELTF-AS1 that is significantly upregulated in non-small cell lung cancer (NSCLC). MELTF-AS1 was found to regulate cell proliferation and metastasis, and its knockdown specifically modulated genes associated with cell proliferation, apoptosis, and migration. Furthermore, MELTF-AS1 was shown to directly bind and drive the phase separation of YBX1, an RNA-binding protein involved in tumorigenesis, leading to the activation of ANXA8 transcription and promotion of NSCLC tumorigenesis.
Article
Biochemistry & Molecular Biology
Ferbian Milas Siswanto, Ami Oguro, Susumu Imaoka
Summary: Nrf2, a critical transcription factor regulating cellular responses to oxidative stress, is controlled by Keap1 and WDR23 through distinct pathways. Interaction mechanisms between Keap1 and WDR23 for Nrf2 regulation remain unclear.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2021)
Article
Endocrinology & Metabolism
Huaiyun Tang, Linqing Pan, Yun Xiong, Leilei Wang, Yugui Cui, Jiayin Liu, Lisha Tang
Summary: The study revealed that increased levels of microRNA-4497 in placental villus tissues of recurrent miscarriage patients may down-regulate SP1 protein expression, leading to trophoblast apoptosis and potentially contributing to the pathogenesis of recurrent miscarriage.
REPRODUCTIVE BIOLOGY AND ENDOCRINOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Yongliang Fan, Abdelaziz Adam Idriss Arbab, Huimin Zhang, Yi Yang, Xubin Lu, Ziyin Han, Zhangping Yang
Summary: The study confirms that miRNA193a-5p regulates PUFAs metabolism in BMECs by targeting FADS1, indicating that miRNA-193a-5p and FADS1 are underlying factors that improve PUFAs content in bovine milk.
Article
Immunology
Renjie Chang, Qing Chu, Weiwei Zheng, Lei Zhang, Tianjun Xu
Summary: The study reveals that miR-15b negatively regulates the antiviral response triggered by SCRV by targeting TBK1, leading to enhanced viral replication. Additionally, miR-15b feedback regulates the antiviral innate immune response through NF-kappa B and IRF3 signaling pathways. These findings suggest that miR-15b plays a crucial role in regulating virus-host interactions and outlines a new mechanism of fish's innate immune responses.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Multidisciplinary Sciences
Shenqi Wang, Zimin Zhou, Rini Rahiman, Grace Sheen Yee Lee, Yuan Kai Yeo, Xin Yang, On Sun Lau
Summary: Developmental outcomes in plants are shaped by the interplay between intrinsic and external factors, with light playing a key role in promoting stomatal development. The study by Wang et al. reveals that the light-regulated transcription factor HY5 activates the expression of STOMAGEN, a mesophyll-derived secreted peptide that stabilizes the master regulator of stomatal development in the epidermis, leading to enhanced stomatal production. This work highlights a molecular link between light signaling and stomatal development across different tissue layers.
NATURE COMMUNICATIONS
(2021)
Article
Cell Biology
Ashrafur Rahman, Peter Lorincz, Raksha Gohel, Aniko Nagy, Gabor Csordas, Yan Zhang, Gabor Juhasz, Ioannis P. Nezis
Summary: Selective autophagy receptors and adapters contain LIR motifs that interact with Atg8-family proteins. Mutation in the LDS of Atg8a leads to accumulation of autophagy substrates and reduced lifespan in Drosophila. The study identifies GMAP as a LIR motif-containing protein that modulates Golgi morphology and size through its interaction with Atg8a.
Article
Immunology
Lesly Calderon, Karina Schindler, Stephen G. Malin, Alexandra Schebesta, Qiong Sun, Tanja Schwickert, Chiara Alberti, Maria Fischer, Markus Jaritz, Hiromi Tagoh, Anja Ebert, Martina Minnich, Adrian Liston, Luisa Cochella, Meinrad Busslinger
Summary: Pax5 plays a crucial role in mature B cells by inhibiting PTEN protein expression, which promotes differentiation and survival of B cells, thereby enhancing humoral immunity.
SCIENCE IMMUNOLOGY
(2021)
Article
Cardiac & Cardiovascular Systems
Zhijian Yang, Erin Macdonald-Dunlop, Jiantao Chen, Ranran Zhai, Ting Li, Anne Richmond, Lucija Klaric, Nicola Pirastu, Zheng Ning, Chenqing Zheng, Yipeng Wang, Tingting Huang, Yazhou He, Huiming Guo, Kejun Ying, Stefan Gustafsson, Bram Prins, Anna Ramisch, Emmanouil T. Dermitzakis, Grace Png, Niclas Eriksson, Jeffrey Haessler, Xiaowei Hu, Daniela Zanetti, Thibaud Boutin, Shih-Jen Hwang, Eleanor Wheeler, Maik Pietzner, Laura M. Raffield, Anette Kalnapenkis, James E. Peters, Ana Vinuela, Arthur Gilly, Solve Elmstahl, George Dedoussis, John R. Petrie, Ozren Polasek, Lasse Folkersen, Yan Chen, Chen Yao, Urmo Vosa, Erola Pairo-Castineira, Sara Clohisey, Andrew D. Bretherick, Konrad Rawlik, Tonu Esko, Stefan Enroth, Asa Johansson, Ulf Gyllensten, Claudia Langenberg, Daniel Levy, Caroline Hayward, Themistocles L. Assimes, Charles Kooperberg, Ani W. Manichaikul, Agneta Siegbahn, Lars Wallentin, Lars Lind, Eleftheria Zeggini, Jochen M. Schwenk, Adam S. Butterworth, Karl Michaelsson, Yudi Pawitan, Peter K. Joshi, J. Kenneth Baillie, Anders Malarstig, Alexander P. Reiner, James F. Wilson, Xia Shen
Summary: In this study, genetic correlations between plasma ACE2 levels and cardiovascular disease, COVID-19, and other related diseases were identified. Mendelian randomization analysis showed a causal effect of elevated ACE2 levels on COVID-19 severity, hospitalization, and infection. The study also revealed that ACE2 regulatory variants were enriched for DNA methylation sites in blood immune cells.
Article
Multidisciplinary Sciences
Marcin Kierczak, Nima Rafati, Julia Hoglund, Hadrien Gourle, Valeria Lo Faro, Daniel Schmitz, Weronica E. Ek, Ulf Gyllensten, Stefan Enroth, Diana Ekman, Bjorn Nystedt, Torgny Karlsson, Asa Johansson
Summary: Despite the success of genome-wide association studies, the genetic contribution to complex traits remains unexplained. This study analyzed whole-genome sequencing data to evaluate the impact of rare genetic variants on plasma proteins. The findings suggest that rare variants have a limited contribution to heritability but may play a role in precision medicine applications.
NATURE COMMUNICATIONS
(2022)
Article
Oncology
Ulf Gyllensten, Julia Hedlund-Lindberg, Johanna Svensson, Johanna Manninen, Torbjorn Ost, Jon Ramsell, Matilda Aslin, Emma Ivansson, Marta Lomnytska, Maria Lycke, Tomas Axelsson, Ulrika Liljedahl, Jessica Nordlund, Per-Henrik Edqvist, Tobias Sjoblom, Mathias Uhlen, Karin Stalberg, Karin Sundfeldt, Mikael Aberg, Stefan Enroth
Summary: Ovarian cancer is the eighth most common cancer in women, but its survival rate is low. Current biomarkers for early detection of cancer lack sensitivity and specificity, and new biomarkers are needed. This study measured protein biomarkers and found that combinations of 4-7 proteins can accurately detect early- and late-stage ovarian cancer.
Article
Oncology
Holger Weishaupt, Matko Cancer, Gabriela Rosen, Karl O. Holmberg, Susana Haggqvist, Ignas Bunikis, Yiwen Jiang, Smitha Sreedharan, Ulf Gyllensten, Oren J. Becher, Lene Uhrbom, Adam Ameur, Fredrik J. Swartling
Summary: This study demonstrates a novel approach to tagging glioma genes using retroviral integration sites. By using a high-throughput pipeline coupled to a tumor model system, the researchers were able to detect retroviral integration sites in malignant stem cell lines from glioma biopsies. The results identified genes that have been dysregulated in glioma and also discovered novel potential cancer-causing genes.
Article
Biochemistry & Molecular Biology
Josefin Johansson, Sarah Lideus, Carina Frykholm, Cecilia Gunnarsson, Filip Mihalic, Sanna Gudmundsson, Sara Ekvall, Anna-Maja Molin, Mai Pham, Mauno Vihinen, Kristina Lagerstedt-Robinson, Ann Nordgren, Per Jemth, Adam Ameur, Goeran Anneren, Maria Wilbe, Marie-Louise Bondeson
Summary: This study reveals the genetic and molecular factors underlying Gustavson syndrome, and identifies a novel in-frame deletion in the RBMX gene associated with this syndrome, leading to disrupted RNA polymerase II transcription and potentially reduced SH3 binding. These findings provide new insights into the pathogenesis of RBMX-related intellectual disabilities.
EUROPEAN JOURNAL OF HUMAN GENETICS
(2023)
Article
Cell Biology
Caroline Gelabert, Panagiotis Papoutsoglou, Irene Golan, Eric Ahlstrom, Adam Ameur, Carl-Henrik Heldin, Laia Caja, Aristidis Moustakas
Summary: This study demonstrates that LINC00707 interacts with Smad proteins, limiting the output of TGF beta signaling and suppressing cancer cell invasion.
CELL COMMUNICATION AND SIGNALING
(2023)
Article
Multidisciplinary Sciences
Kristine Bilgrav Saether, Daniel Nilsson, Hakan Thonberg, Emma Tham, Adam Ameur, Jesper Eisfeldt, Anna Lindstrand
Summary: The majority of rare diseases are genetic, and despite advances in genomics-based investigations, a large percentage of patients remain undiagnosed. A significant contributing factor to this is the limited understanding of transposable elements (TE), which make up a substantial portion of the human genome. This study aims to bridge this knowledge gap by characterizing TE insertions in different populations and highlights the potential clinical implications in rare disease diagnostics.
Article
Multidisciplinary Sciences
Josefin Johansson, Sarah Lideus, Ida Hoijer, Adam Ameur, Sanna Gudmundsson, Goeran Anneren, Marie-Louise Bondeson, Maria Wilbe
Summary: Researchers developed a novel strategy called XCI-ONT, which combines amplification-free Cas9 enrichment and Oxford nanopore technologies sequencing, to investigate and accurately quantify X-chromosome inactivation (XCI). The XCI-ONT strategy was shown to be more useful and reliable than the PCR-based golden standard technique, and it provides a valuable tool for studying X-linked traits in clinical and research settings.
SCIENTIFIC REPORTS
(2023)
Article
Genetics & Heredity
Daniel Schmitz, Zhiwei Li, Valeria Lo Faro, Mathias Rask-Andersen, Adam Ameur, Nima Rafati, Asa Johansson
Summary: This study characterized CNVs in a Swedish cohort using whole-genome sequencing and identified CNVs associated with plasma proteins. Validations were done using long-read sequencing. The findings provide insights into the structure and effects of common CNVs on the plasma proteome.
Article
Genetics & Heredity
Kimberly Sturk-Andreaggi, Martin Bodner, Joseph D. Ring, Adam Ameur, Ulf Gyllensten, Walther Parson, Charla Marshall, Marie Allen
Summary: The study analyzed the mitochondrial DNA (mtDNA) reads from the SweGen whole genome sequencing dataset to characterize mitogenome variation in Sweden. A total of 934 forensic-quality mitogenome haplotypes were identified, with almost 45% belonging to haplogroup H. The majority (99.1%) of the mitogenome haplotypes were assigned to European haplogroups, as expected. The study also observed signature haplogroups from northern Sweden and Finland, consistent with previous nuclear DNA analyses. The complete mitogenome analysis showed high haplotype diversity and a low random match probability.
Article
Genetics & Heredity
Gregory Lazarian, Bernard Leroy, Floriane Theves, Myriam Hormi, Remi Letestu, Virginie Eclache, Giulia Tueur, Adam Ameur, Audrey Bidet, Pascale Cornillet-Lefebvre, Frederic Davi, Eric Delabesse, Marie-Helene Estienne, Pascaline Etancelin, Olivier Kosmider, Sophy Laibe, Marc Muller, Nathalie Nadal, Dina Naguib, Cedric Pastoret, Stephanie Poulain, Pierre Sujobert, Lauren Veronese, Samia Imache, Valerie Lefebvre, Florence Cymbalista, Fanny Baran-Marszak, Thierry Soussi
Summary: TP53 aberrations are a major predictive factor for resistance to chemoimmunotherapy in CLL. This study analyzed 1,056 TP53 variants from 683 patients in France and compared them to a dataset of 5,173 TP53 variants from published articles. The analysis identified CLL-specific hotspot mutations and a novel splice variant. The study also found frequent copy-neutral loss of heterozygosity in CLL and the presence of multiple TP53 variants in a high proportion of patients.
Meeting Abstract
Biochemistry & Molecular Biology
Josefin Johansson, Sarah Lideus, Filip Mihalic, Mauno Vihinen, Carina Frykholm, Sanna Gudmundsson, Adam Ameur, Per Jemth, Marie-Louise Bondeson, Maria Wilbe
EUROPEAN JOURNAL OF HUMAN GENETICS
(2023)
Meeting Abstract
Biochemistry & Molecular Biology
Jonas Mattisson, Moeen Riaz, Galina Polekhina, Andrew Bakshi, Jonatan Halvardson, Marcus Danielsson, Adam Ameur, John McNeil, Lars Forsberg, Paul Lacaze
EUROPEAN JOURNAL OF HUMAN GENETICS
(2023)
Article
Oncology
Wesley Schaal, Adam Ameur, Ulla Olsson-Stromberg, Monica Hermanson, Lucia Cavelier, Ola Spjuth
Summary: This project aimed to implement long-read sequencing for screening TKI resistance mutations in patients with chronic myeloid leukemia, successfully establishing automated analysis processes and an information system for better sensitivity and early detection of emerging mutations.
CANCER INFORMATICS
(2022)
Article
Medicine, Research & Experimental
Stefan Enroth, Emma Ivansson, Julia Hedlund Lindberg, Maria Lycke, Jessica Bergman, Anna Reneland, Karin Stalberg, Karin Sundfeldt, Ulf Gyllensten
Summary: This study developed a risk score based on an 11-protein plasma assay to distinguish between benign and malignant ovarian tumors. The assay showed robust performance in diagnostic work-up and predicting clinical course.
COMMUNICATIONS MEDICINE
(2022)