Article
Biochemistry & Molecular Biology
Eichi Watabe, Marina Togo-Ohno, Yuma Ishigami, Shotaro Wani, Keiko Hirota, Mariko Kimura-Asami, Sharmin Hasan, Satomi Takei, Akiyoshi Fukamizu, Yutaka Suzuki, Tsutomu Suzuki, Hidehito Kuroyanagi
Summary: The homeostasis of SAM synthetase in C. elegans is maintained through alternative splicing regulation and m(6)A modification, with splicing regulation achieved through NMD and regulated by U6 snRNA methyltransferase.
Review
Virology
Md Robel Ahmed, Zhiyou Du
Summary: The interaction between viruses and hosts is dynamic and evolutionary. Eukaryotic hosts have multiple defense mechanisms against viral infection, including the nonsense-mediated mRNA decay (NMD) system. NMD ensures the accuracy of mRNA translation by degrading abnormal mRNAs. Many RNA viruses have internal stop codons (iTC), which activate NMD and lead to degradation of viral genomes. Some viruses are sensitive to NMD-mediated antiviral defense, while others have evolved mechanisms to overcome or escape NMD. This review summarizes the current understanding of NMD-mediated viral RNA degradation and the ways in which viruses compromise NMD for better infection.
Article
Cell Biology
Andrew C. Cicchetto, Elsie C. Jacobson, Hannah Sunshine, Blake R. Wilde, Abigail S. Krall, Kelsey E. Jarrett, Leslie Sedgeman, Martin Turner, Kathrin Plath, M. Luisa Iruela-Arispe, Thomas Q. de Aguiar Vallim, Heather R. Christofk
Summary: Cellular metabolism is regulated by growth factor signaling, and this study identifies the ZFP36/L1/L2 family of RNA-binding proteins and mRNA decay factors as key regulators of metabolic rewiring downstream of acute growth factor signaling. The researchers found that ZFP36 directly promotes the degradation of multiple metabolic enzyme and nutrient transporter mRNAs, including those encoding rate-limiting steps in metabolic pathways. They also demonstrated that ZFP36-mediated mRNA decay affects the expression and activity of Enolase 2 (Eno2), and plays a role in VEGF-stimulated developmental retinal angiogenesis.
Article
Microbiology
Alicia Vachon, Grace E. Seo, Nishi H. Patel, Carla S. Coffin, Eric Marinier, Eduardo Eyras, Carla Osiowy
Summary: This study evaluated the composition and proportionality of serum hepatitis B virus (HBV) RNA transcripts in chronic hepatitis B (CHB) infection patients using PCR-cDNA nanopore sequencing. The results showed that HBV pregenomic RNA (pgRNA) was the most frequently observed transcript isoform, followed by other pgRNA spliced variants, 3' truncated variants and HBx mRNA. The type and proportion of transcripts were influenced by HBV genotype and HBeAg status. The study demonstrated the utility of long-read sequencing for studying the serum HBV transcriptome.
FRONTIERS IN MICROBIOLOGY
(2023)
Letter
Biochemistry & Molecular Biology
Jin Ji, Rui Chen, Lin Zhao, Yalong Xu, Zhi Cao, Huan Xu, Xi Chen, Xiaolei Shi, Yasheng Zhu, Ji Lyu, Junfeng Jiang, Yue Wang, Tie Zhou, Jingyi He, Xuedong Wei, Jason Boyang Wu, Bo Yang, Fubo Wang
Summary: The study developed an optimized detection strategy for emRNAs and identified novel emRNA signatures for the detection of prostate cancer.
Review
Virology
Liying Zhang, Yichen Ju, Si Chen, Linzhu Ren
Summary: Recent research has shown that exosomes, small vesicles released by most tissue and cell types, play a crucial role in cell-to-cell communication and the transfer of biologically active molecules. Studies on RNA viruses have highlighted the significance of exosomes in delivering regulatory factors and genetic elements during infection processes. Further research is needed to clarify the mechanisms involved in exosome pathways and their effects in physiological/pathological contexts.
Article
Biochemistry & Molecular Biology
Rucong Liu, Zibaguli Wubulikasimu, Runze Cai, Fanyi Meng, Qinghua Cui, Yuan Zhou, Yang Li
Summary: NAT10-catalyzed N-4-acetylcytidine (ac(4)C) plays an important role in post-transcriptional regulation of mRNA stability. This study shows that NAT10 expression is correlated with pluripotency and that ac(4)C modification preferentially targets core pluripotency transcription factors in hESCs. Inactivation of NAT10 leads to decreased ac(4)C levels, decay of core pluripotency regulator OCT4 transcript, and impairment of self-renewal and early differentiation in hESCs.
NUCLEIC ACIDS RESEARCH
(2023)
Review
Cell Biology
Scott Berry, Lucas Pelkmans
Summary: The relationship between mRNA transcript abundance and cell size, as well as the regulation of RNA polymerase II activity and abundance, are discussed in this article. Feedback mechanisms that adjust mRNA synthesis rates, nuclear export, and degradation are also identified, allowing cells to compensate for changes in one aspect by adjusting others. Researchers are integrating findings from different fields to understand the mechanisms underlying transcript homeostasis and its connection to other aspects of the cellular phenotype.
TRENDS IN CELL BIOLOGY
(2022)
Article
Gastroenterology & Hepatology
Xiaopei Zhao, Hongxia Fan, Xi Chen, Xiaoqing Zhao, Xu Wang, Yujie Feng, Min Liu, Shengping Li, Hua Tang
Summary: Long noncoding RNAs (lncRNAs) have been associated with infection and hepatitis B virus (HBV)-related diseases, though the underlying mechanisms remain unclear. Our study found that HOTTIP is significantly upregulated in HBV-HCC, leading to suppression of HBV replication. Additionally, HBV DNA polymerase attenuates HBV replication through activation of the CREB1-HOTTIP-HOXA13 axis.
Article
Biochemistry & Molecular Biology
Shaoying Chen, Yanchun Zhou, Pei Peng, Liqun Xu, Quandong Tang, Weibin Chen, Wei Gu
Summary: This study reveals a novel function of lncRNA SNHG15 in mediating breast cancer cell invasion through regulating the local translation of CDH2 mRNA. SNHG15 forms a complex with nucleolin and transports it to the cell protrusions, stabilizing local CDH2 mRNA and promoting cell invasive potential.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Immunology
Hongyun Wang, Jiangpeng Feng, Cong Zeng, Jiejie Liu, Zhiying Fu, Dehe Wang, Yafen Wang, Lu Zhang, Jiali Li, Ao Jiang, Miao He, Yuanyuan Cao, Kun Yan, Hao Tang, Deyin Guo, Ke Xu, Xiang Zhou, Li Zhou, Ke Lan, Yu Zhou, Yu Chen
Summary: NSUN2, a typical m(5)C methyltransferase, negatively regulates type I interferon responses during various viral infections by mediating m(5)C methylation of IRF3 mRNA and accelerating its degradation. Knockout or knockdown of NSUN2 enhances type I interferon and downstream ISGs during viral infection in vitro. Moreover, various viral infections decrease endogenous levels of NSUN2, further increasing type I interferon and downstream ISGs.
EMERGING MICROBES & INFECTIONS
(2023)
Article
Biochemistry & Molecular Biology
Hiromichi Dansako, Masanori Ikeda, Yasuo Ariumi, Yosuke Togashi, Nobuyuki Kato
Summary: RNA viruses produce dsRNA during viral genome replication, which triggers the production of interferon-beta and activates the immune response. The NS5B protein derived from hepatitis C virus (HCV) induces the dimerization of MDA5 and the production of dsRNA, leading to an innate immune response in human hepatocytes.
Article
Chemistry, Multidisciplinary
Shenshen Wu, Jun Yun, Weiyan Tang, Giuseppe Familiari, Michela Relucenti, Jiong Wu, Xiaobo Li, Hanqing Chen, Rui Chen
Summary: Although therapeutic targets have been developed for colorectal cancer (CRC) therapy, the therapeutic effects are not ideal and the survival rate for CRC patients remains poor. Reduced ALKBH5 mediates aberrant m(6)A modification and tumor progression in CRC. ALKBH5 mRNA-loaded folic acid-modified exosome-liposome hybrid nanoparticles significantly inhibit the progression of CRC in preclinical tumor models by modulating the ALKBH5/JMJD8/PKM2 axis and inhibiting glycolysis.
Article
Cell Biology
Rebecca A. Mosig, Allison N. Castaneda, Jacob C. Deslauriers, Landon P. Frazier, Kevin L. He, Naseem Maghzian, Aarati Pokharel, Camille T. Schrier, Lily Zhu, Nobuya Koike, John J. Tyson, Carla B. Green, Joseph S. Takahashi, Shihoko Kojima
Summary: In mammals, the Per2AS transcript inhibits Per2 expression in a double negative feedback loop, maintaining Per2 levels within the oscillatory range. This regulation is important for the circadian clock machinery and cannot be solely explained by Per2 interaction.
GENES & DEVELOPMENT
(2021)
Article
Biochemistry & Molecular Biology
John H. Kim, Matthew S. Modena, Enisha Sehgal, Annie Courney, Celine W. Neudorf, Joshua A. Arribere
Summary: NMD is a mechanism that protects cells from the effects of truncated proteins, and previous studies have identified a novel NMD intermediate where ribosomes stall on cleaved stop codons. Our research shows that this intermediate is the result of mRNA cleavage by the endonuclease SMG-6.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Surgery
Naruhiko Honmyo, Tsuyoshi Kobayashi, Shintaro Kuroda, Kentaro Ide, Masahiro Ohira, Hiroyuki Tahara, Hiroshi Morimoto, Naoki Tanimine, Michinori Hamaoka, Megumi Yamaguchi, Masateru Yamamoto, Daisuke Takei, Hiroshi Aikata, Kazuaki Chayama, Hideki Ohdan
Summary: This study identified risk factors for hepatocellular carcinoma (HCC) development after splenectomy for portal hypertension. The etiology of cirrhosis, presence of HCC history, and preoperative hemoglobin level were found to be associated with HCC development. The predictive model constructed in this study may assist in surveillance for HCC after splenectomy in patients with portal hypertension.
Article
Gastroenterology & Hepatology
Yutaro Ogawa, Takashi Nakahara, Masafumi Ono, Takumi Kawaguchi, Hiroshi Isoda, Akira Hiramatsu, Shinsuke Uchikawa, Hatsue Fujino, Eisuke Murakami, Tomokazu Kawaoka, Masami Yamauchi, Masataka Tsuge, Kensuke Munekage, Tsunehiro Ochi, C. Nelson Hayes, Michio Imamura, Hiroshi Aikata, Hirokazu Takahashi, Takuji Torimura, Kazuaki Chayama
Summary: This study evaluated blood glucose variability in patients with chronic liver disease using a continuous glucose monitoring system (CGMS) and examined the discrepancy between hemoglobin A1c (HbA1c) levels estimated from average blood glucose levels and HbA1c. The results showed that as hepatic functional reserve decreased, average blood glucose and insulin resistance increased while HbA1c decreased. A formula was created to calculate HbA1c without using CGMS. CGMS was useful in assessing accurate glycemic control and detecting hyperglycemia and hypoglycemia. Correction of hepatic functional reserve is necessary for glycemic control in patients with chronic liver disease.
JOURNAL OF GASTROENTEROLOGY AND HEPATOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Naohiro Kamiya, Takahiko Sugimoto, Hiromi Abe-Chayama, Rie Akiyama, Yasunori Tsuboi, Akira Mogami, Michio Imamura, C. Nelson Hayes, Kazuaki Chayama
Summary: In this study, a robust method was established to untie mature rcDNA into linear DNA, which can be used for quantification and visualization of cccDNA. Precise quantification was achieved by combining the method with plasmid-safe DNase and T5 exonuclease preprocessing and digesting cccDNA with a restriction enzyme. The method was successfully applied to an infection model and demonstrated the possibility of evaluating cccDNA levels accurately.
JOURNAL OF GENERAL VIROLOGY
(2022)
Correction
Gastroenterology & Hepatology
Heather J. Cordell, James J. Fryett, Kazuko Ueno, Rebecca Darlay, Yoshihiro Aiba, Yuki Hitomi, Minae Kawashima, Nao Nishida, Seik-Soon Khor, Olivier Gervais, Yosuke Kawai, Masao Nagasaki, Katsushi Tokunaga, Ruqi Tang, Yongyong Shi, Zhiqiang Li, Brian D. Juran, Elizabeth J. Atkinson, Alessio Gerussi, Marco Carbone, Rosanna Asselta, Angela Cheung, Mariza de Andrade, Aris Baras, Julie Horowitz, Manuel A. R. Ferreira, Dylan Sun, David E. Jones, Steven Flack, Ann Spicer, Victoria L. Mulcahy, Jinyoung Byun, Younghun Han, Richard N. Sandford, Konstantinos N. Lazaridis, Christopher I. Amos, Gideon M. Hirsch, Michael F. Seldin, Pietro Invernizzi, Katherine A. Siminovitch, Xiong Ma, Minoru Nakamura, George F. Mells
JOURNAL OF HEPATOLOGY
(2022)
Article
Infectious Diseases
Haruna Hatooka, Yumi Shimomura, Michio Imamura, Yuji Teraoka, Kei Morio, Hatsue Fujino, Atsushi Ono, Takashi Nakahara, Eisuke Murakami, Masami Yamauchi, Tomokazu Kawaoka, Grace Naswa Makokha, Daiki Miki, Masataka Tsuge, Akira Hiramatsu, Hiromi Abe-Chayama, C. Nelson Hayes, Hiroshi Aikata, Shinji Tanaka, Kazuaki Chayama
Summary: The study developed an antibody against preS1 and an ELISA system for measuring serum preS1 levels. PreS1 may serve as a novel tool to predict the need for antiviral therapy in HBeAg-negative HBV-infected patients.
JOURNAL OF INFECTION
(2022)
Article
Virology
Toshitada Takemori, Akiko Sugimoto-Ishige, Hironori Nishitsuji, Yushi Futamura, Michishige Harada, Tomomi Kimura-Someya, Takehisa Matsumoto, Teruki Honma, Miho Tanaka, Masami Yaguchi, Kyoichi Isono, Haruhiko Koseki, Hiroyuki Osada, Daiki Miki, Takashi Saito, Takashi Tanaka, Takehiro Fukami, Toshio Goto, Mikako Shirouzu, Kunitada Shimotohno, Kazuaki Chayama
Summary: Entry inhibitors are being developed to enhance the treatment of HBV patients with oral nucleoside/nucleotide analogues (NA). Therapeutic MAbs with neutralizing activity against HBs antigens have been developed to amplify the effectiveness of NA therapy. Targeting NTCP can provide an effective treatment option for patients with chronic hepatitis B, regardless of viral genotype, mutations, and the presence of subviral particles.
JOURNAL OF VIROLOGY
(2022)
Review
Gastroenterology & Hepatology
C. Nelson Hayes, Michio Imamura, Junko Tanaka, Kazuaki Chayama
Summary: Since its discovery in 1989, the road to a cure for hepatitis C virus (HCV) has been slow, but most patients can now expect to achieve a sustained virological response (SVR). Adverse events are rare or mild, and patients with compensated cirrhosis and other co-morbidities are often eligible for treatment. However, a small number of patients fail to eradicate the virus even after retreatment.
LIVER INTERNATIONAL
(2022)
Article
Chemistry, Multidisciplinary
Ryotaro Ota, Daichi Karasawa, Mizuki Oshima, Koichi Watashi, Noriko Shimasaki, Yoshinori Nishii
Summary: The asymmetric total synthesis of four lignans and the relationship between enantiomeric structure and anti-viral activity were investigated in this study.
Article
Biochemistry & Molecular Biology
Atsushi Hijikata, Clara Shionyu-Mitsuyama, Setsu Nakae, Masafumi Shionyu, Motonori Ota, Shigehiko Kanaya, Takatsugu Hirokawa, Shogo Nakajima, Koichi Watashi, Tsuyoshi Shirai
Summary: This study evaluated the potential of natural analogues of Cepharanthine as anti-coronavirus disease 2019 drugs through molecular docking simulations and cell-based SARS-CoV-2 infection assays. The diphenyl ester moiety of the molecules was suggested as a putative pharmacophore for the CEP analogues according to the docking conformations.
Article
Microbiology
Masaaki Toyama, Koichi Watashi, Masanori Ikeda, Atsuya Yamashita, Mika Okamoto, Kohji Moriishi, Masamichi Muramatsu, Takaji Wakita, Ashoke Sharon, Masanori Baba
Summary: Novel neplanocin A derivatives have shown potency in inhibiting HBV replication in vitro, reducing HBV RNA levels and antigen production, with a mechanism of action different from clinically approved anti-HBV agents.
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY
(2022)
Article
Infectious Diseases
Diane Delobel, Yutaka Furutani, Sumiko Nagoshi, Akihito Tsubota, Akio Miyasaka, Koichi Watashi, Takaji Wakita, Tomokazu Matsuura, Kengo Usui
Summary: SmartAmp-Eprimer binary code (SEB) genotyping is a novel isothermal amplification method that can be used for rapid genotyping of any variable target of interest. By producing specific binary codes, SEB genotyping can accurately identify the 8 main genotypes of HBV.
BMC INFECTIOUS DISEASES
(2022)
Article
Multidisciplinary Sciences
Jae-Hyun Park, Masashi Iwamoto, Ji-Hye Yun, Tomomi Uchikubo-Kamo, Donghwan Son, Zeyu Jin, Hisashi Yoshida, Mio Ohki, Naito Ishimoto, Kenji Mizutani, Mizuki Oshima, Masamichi Muramatsu, Takaji Wakita, Mikako Shirouzu, Kehong Liu, Tomoko Uemura, Norimichi Nomura, So Iwata, Koichi Watashi, Jeremy R. H. Tame, Tomohiro Nishizawa, Weontae Lee, Sam-Yong Park
Summary: Around 250 million people worldwide are infected with hepatitis B virus (HBV), and 15 million of them may also carry hepatitis D virus (HDV), which increases the risk of severe liver disease. The structure of the HBV receptor NTCP has not been solved, but using cryo-electron microscopy, the structure of NTCP bound to an antibody has been determined. Comparison with other related proteins reveals a common mechanism of bile acid transport, and the NTCP structure presents a new pocket for potential drug design.
Article
Biotechnology & Applied Microbiology
Shinji Kamisuki, Hisanobu Shibasaki, Hironobu Murakami, Kan Fujino, Senko Tsukuda, Ikumi Kojima, Koudai Ashikawa, Kazuki Kanno, Tomohiro Ishikawa, Tatsuo Saito, Fumio Sugawara, Koichi Watashi, Kouji Kuramochi
Summary: Three novel compounds were isolated from the culture broth of a vanitaracin A-producing fungus, and their structures were determined. The antiviral activity of these compounds against bovine leukemia virus was evaluated, and vanitaracin B, vanitaraphilone A, and 2-hydroxy-4-(hydroxymethyl)-6-methylbenzaldehyde were found to exhibit activity against the virus. These findings suggest potential candidates for the development of anti-bovine leukemia virus drugs.
JOURNAL OF ANTIBIOTICS
(2023)
Review
Virology
Ashraf Elbahrawy, Hassan Atalla, Mohamed Alboraie, Ahmed Alwassief, Ali Madian, Mohammed El Fayoumie, Ashraf A. Tabll, Hussein H. Aly
Summary: Vaccination is the safest and often the only method to protect against infectious diseases. Vaccines have successfully controlled diseases such as smallpox and polio. Hepatitis viruses, including HAV, HBV, HCV, HDV, and HEV, can cause severe liver infections and result in many deaths worldwide. However, effective vaccines are available to prevent hepatitis A and B, and ongoing research is focused on developing vaccines against the other major hepatitis viruses.
Article
Cell Biology
Koichi Ogami, Keima Ogawa, Shoko Sanpei, Fumito Ichikawa, Tsuyoshi Udagawa, Shin-ichi Hoshino
Summary: During early embryonic development, the RNA-binding protein CPEB mediates cytoplasmic polyadenylation and translational activation through a combinatorial code defined by the cytoplasmic polyadenylation element (CPE). In non-neuronal somatic cells, CPEB accelerates deadenylation to repress c-myc mRNA translation through a combination of tandemly arranged consensus (cCPE) and non-consensus (ncCPE) cytoplasmic polyadenylation elements (CPEs). CPEB binds to cCPEs with high affinity and ncCPEs with low affinity, enhancing the recruitment of deadenylases and repression of c-myc mRNAs.