Review
Genetics & Heredity
Dharmendra Kumar Soni, Roopa Biswas
Summary: ncRNAs, especially miRNAs and lncRNAs, play crucial regulatory roles in lung diseases, and their dysregulation is associated with various pulmonary disorders. Research suggests that exploring the interactions between miRNAs and lncRNAs, as well as their functions in regulating mRNA expression, may help in early diagnosis and the development of novel therapeutic approaches for lung diseases.
FRONTIERS IN GENETICS
(2021)
Review
Cell Biology
Monika Vilimova, Sebastien Pfeffer
Summary: A significant portion of miRNA genes in animal genomes tend to cluster together. These miRNA clusters are transcribed as polycistronic transcripts, benefiting from common transcriptional regulation. However, there are discrepancies in the accumulation of mature miRNAs produced from the same cluster, suggesting unforeseen post-transcriptional regulatory mechanisms.
WILEY INTERDISCIPLINARY REVIEWS-RNA
(2023)
Article
Biochemistry & Molecular Biology
Wing-Keung Chu, Li-Man Hung, Chun-Wei Hou, Jan-Kan Chen
Summary: This study found that MIR630 represses the expression of NANOG through transcriptional and post-transcriptional regulation, leading to the differentiation of NT2/D1 cells. MIR630 may have multiple binding sites in the 3'UTR of NANOG and may act together with other miRNAs to maximally suppress NANOG expression.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Biochemical Research Methods
Mattia Furlan, Stefano de Pretis, Mattia Pelizzola
Summary: Despite RNA abundance being commonly assumed as a proxy for transcriptional activity, it is now possible to calculate how synthesis, processing, and degradation rates collectively determine the abundance of each gene's RNA. Different transcriptional outputs can correspond to different combinations of kinetic rates, indicating the existence of markedly different modes of gene expression regulation and their profound effects on gene self-expression regulation.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Biochemistry & Molecular Biology
Ullas Valiya Chembazhi, Wesley S. Tung, Hyojeong Hwang, Yuexi Wang, Aryan Lalwani, Ka Lam Nguyen, Sushant Bangru, Danielle Yee, Kristy Chin, Jing Yang, Auinash Kalsotra, Wenyan Mei
Summary: Intestinal epithelial regeneration is driven by intestinal stem cells. Upon the loss of intestinal stem cells, differentiated intestinal epithelial cells, such as Paneth cells, are capable of acquiring multipotency and contributing to regeneration. Depletion of an RNA-binding protein named PTBP1 in mouse intestinal epithelial cells leads to intestinal stem cell death and epithelial regeneration failure.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Valeria Canu, Sara Donzelli, Andrea Sacconi, Federica Lo Sardo, Claudio Pulito, Noa Bossel, Anna Di Benedetto, Paola Muti, Claudio Botti, Eytan Domany, Silvio Bicciato, Sabrina Strano, Yosef Yarden, Giovanni Blandino
Summary: SPAG5 is a crucial driver of cell mitotic spindle, and its overexpression in breast cancer is associated with poor prognosis. It is a direct target of miR-10b-3p and is involved in an oncogenic feedback loop with YAP and TAZ.
CELL DEATH AND DIFFERENTIATION
(2021)
Review
Toxicology
Tomas Smutny, Lucie Hyrsova, Albert Braeuning, Magnus Ingelman-Sundberg, Petr Pavek
Summary: The pregnane X receptor (PXR) is a key transcription factor known for regulating xenobiotic detoxification, but it is also involved in endogenous metabolism and various pathological states. Non-coding RNAs, especially microRNAs, have been shown to post-transcriptionally regulate PXR expression. In addition, PXR is controlled by multiple transcription factors and genetic polymorphisms, with long non-coding RNAs also playing a role in PXR expression regulation.
ARCHIVES OF TOXICOLOGY
(2021)
Review
Cell Biology
Qiuqin Ma, Shihui Long, Zhending Gan, Gianluca Tettamanti, Kang Li, Ling Tian
Summary: Autophagy, a widely conserved process in eukaryotes, is regulated by nutrient deprivation, energy stress, and other unfavorable conditions through multiple pathways. It is primarily governed at the RNA and protein levels in a synergistic manner.
Article
Biochemistry & Molecular Biology
Emily J. Collins, Mariana P. Cervantes-Silva, George A. Timmons, James R. O'Siorain, Annie M. Curtis, Jennifer M. Hurley
Summary: The circadian clock plays a crucial role in immunity, with post-transcriptional regulation influencing macrophage clock regulatory output significantly, particularly in metabolic pathways. Daily variations in metabolic pathways, ATP production, mitochondrial morphology, and phagocytosis correspond to post-transcriptional temporal-gating and are essential for determining the response of macrophages to immune stimuli.
Article
Forestry
Qiao-Lu Zang, Yao Zhang, Su-Ying Han, Wan-Feng Li, Li-Wang Qi
Summary: The study investigated the expression and regulatory mechanisms of miR171 and its target gene LaSCL6 during somatic embryogenesis in Larix kaempferi. It identified five members of the miR171 family that cleave LaSCL6 mRNA at different sites and improved a method for measuring miRNA activity. The expression patterns of mature miR171s and their primary transcripts differed during somatic embryogenesis, indicating regulation of MIR171 gene transcription and cleavage of intermediate products.
TREES-STRUCTURE AND FUNCTION
(2021)
Review
Biochemistry & Molecular Biology
Rocio Soledad Tognacca, Javier Francisco Botto
Summary: Seed dormancy is a crucial developmental stage regulated by temperature and light, with a delicate balance of hormone signaling. Chromatin remodeling and alternative splicing play important roles in seed germination. Understanding post-transcriptional processes in crop seeds may lead to genotypes with improved performance and productivity.
PLANT COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Jeong-Ryul Hwang, Donghwan Kim, Jung-Ah Kang, Sang-Heon Park, Sung-Gyoo Park
Summary: Notch1 plays important roles in T cell development and is highly expressed in activated CD4(+) T cells. The transcription of Notch1 in activated CD4(+) T cells is upregulated via the PI3K-PDK1-NF-kappa B signaling pathway. The -300 to -270 region of the Notch1 promoter is crucial for its transcription in activated T cells.
SCIENTIFIC REPORTS
(2023)
Article
Multidisciplinary Sciences
Ana Rodriguez-Galan, Sara G. Dosil, Manuel Jose Gomez, Irene Fernandez-Delgado, Lola Fernandez-Messina, Fatima Sanchez-Cabo, Francisco Sanchez-Madrid
Summary: T cell activation results in changes in the miRNA repertoire, with some individual miRNAs being specifically upregulated. Using next-generation sequencing, differential expression of multiple miRNAs not previously linked to T cell activation was identified. Upregulated miRNAs showed a higher frequency of 3' adenylation, which may serve a protective function in the adverse environment and could be utilized to improve miRNA stability for T cell-targeted therapy.
Article
Immunology
Ruth P. Duecker, Ines De Mir Messa, Silvija-Pera Jerkic, Annalena Kochems, Gabriele Gottwald, Antonio Moreno-Galdo, Martin Rosewich, Lucia Gronau, Stefan Zielen, Andreas Geburtig-Chiocchetti, Hermann Kreyenberg, Ralf Schubert
Summary: This study aimed to define biomarkers for post-infectious bronchiolitis obliterans (PiBO) by analyzing the miRNA expression profile using next-generation sequencing (NGS). The results showed that patients with PiBO had decreased lung function values and increased airway inflammation compared to controls. NGS analysis revealed dysregulated miRNAs, which are involved in cytokine-cytokine receptor interaction, TGF-beta signaling, and FoxO signaling pathway. These dysregulated miRNAs may serve as potential biomarkers and therapeutic targets for PiBO.
CLINICAL & TRANSLATIONAL IMMUNOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Pasi K. Korhonen, Tao Wang, Neil D. Young, Gangi R. Samarawickrama, Deepani D. Fernando, Guangxu Ma, Robin B. Gasser, Katja Fischer
Summary: This study revealed significant negative and positive correlations between miRNAs and gene transcription levels between different developmental stages of Sarcoptes scabiei, which may be associated with processes such as metabolism and genetic information processing.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Oncology
Shoko Yamashita, Yuji Morine, Satoru Imura, Tetsuya Ikemoto, Yu Saito, Chie Takasu, Shinichiro Yamada, Kazunori Tokuda, Shohei Okikawa, Katsuki Miyazaki, Takeshi Oya, Koichi Tsuneyama, Mitsuo Shimada
Summary: IHCC can be classified into different groups based on the protein expression levels of SSTR2 and Bcl2, with distinct clinicopathological features and prognoses. Patients with SSTR2 negative and Bcl2 positive expression showed better 5-year survival rates, while those with SSTR2 positive and Bcl2 negative expression had more severe clinical and pathological characteristics.
WORLD JOURNAL OF SURGICAL ONCOLOGY
(2021)
Article
Oncology
Shunichi Toki, Tetsuro Yoshimaru, Yosuke Matsushita, Hitoshi Aihara, Masaya Ono, Koichi Tsuneyama, Koichi Sairyo, Toyomasa Katagiri
Summary: The study reveals a novel function of the BIG3-PHB2 complex in regulating apoptosis pathway activation in osteosarcoma cells. Disruption of the mitochondrial BIG3-PHB2 complex leads to inhibition of cell growth and activation of apoptotic pathways, suggesting it as a potential therapeutic strategy for osteosarcoma.
Article
Medicine, General & Internal
Hironori Tanaka, Yoshihito Saijo, Tetsu Tomonari, Takahiro Tanaka, Tatsuya Taniguchi, Shusuke Yagi, Koichi Okamoto, Hiroshi Miyamoto, Masahiro Sogabe, Yasushi Sato, Naoki Muguruma, Koichi Tsuneyama, Masataka Sata, Tetsuji Takayama
Summary: A 42-year-old woman presented with syncope and was diagnosed with congenital extrahepatic portosystemic shunt type II and FNH-like nodules. After undergoing B-RTO, her intrahepatic portal vein developed normally, multiple liver nodules completely regressed, and her pulmonary hypertension also improved.
Article
Pathology
Tomoko Kobayashi, Mayuko Ichimura-Shimizu, Takeshi Oya, Hirohisa Ogawa, Minoru Matsumoto, Yuki Morimoto, Satoshi Sumida, Takumi Kakimoto, Michiko Yamashita, Mitsuko Sutoh, Shunji Toyohara, Ryoji Hokao, Chunmei Cheng, Koichi Tsuneyama
Summary: This study compared the role of hyperglycemia in hepatocellular carcinoma development using 4CS mice and DIAR mice with different treatments. The results suggest that hyperglycemia may play a role in the onset and progression of hepatocellular carcinoma, while streptozotocin treatment could be a key factor in carcinogenesis.
PATHOLOGY RESEARCH AND PRACTICE
(2021)
Article
Pathology
Mayuko Ichimura-Shimizu, Yosuke Tsuchiyama, Yuki Morimoto, Minoru Matsumoto, Tomoko Kobayashi, Satoshi Sumida, Takumi Kakimoto, Takeshi Oya, Hirohisa Ogawa, Michiko Yamashita, Satoru Matsuda, Katsuhisa Omagari, Shu Taira, Koichi Tsuneyama
Summary: This study utilized a HFCC diet to induce a NASH-related fibrosis model in A/J mice, showing aggravated inflammation and fibrosis in the liver tissue compared to C57BL/6J mice. The presence of lipid-laden macrophage aggregation and cholesterol crystals adjacent to fibrotic lesions provided histological evidence of fibrosis initiation. Mass spectrometry analysis identified specific molecules in the aggregated macrophages, shedding light on the pathophysiology of NASH-related fibrosis.
AMERICAN JOURNAL OF PATHOLOGY
(2022)
Article
Pharmacology & Pharmacy
Mai Nagaoka, Tatsuki Fukami, Fumiya Kisui, Takuya Yamada, Yoshiyuki Sakai, Kiyomichi Tashiro, Takuo Ogiso, Keigo Konishi, Shiori Honda, Keiya Hirosawa, Masataka Nakano, Miki Nakajima
Summary: This study demonstrated the significance of AADAC in ketoconazole-induced toxicity through experiments on Aadac knockout mice, showing that AADAC deficiency exacerbates liver injury and steroidogenesis inhibition caused by ketoconazole. The findings suggest that the hydrolysis of ketoconazole by AADAC can mitigate ketoconazole-induced toxicities.
BIOCHEMICAL PHARMACOLOGY
(2022)
Article
Immunology
Hitoshi Nishijima, Minoru Matsumoto, Junko Morimoto, Kazuyoshi Hosomichi, Nobuko Akiyama, Taishin Akiyama, Takeshi Oya, Koichi Tsuneyama, Hideyuki Yoshida, Mitsuru Matsumoto
Summary: The deficiency of Aire leads to autoimmunity, and Aire indirectly induces the expression of TRAs by controlling the heterogeneity of mTECs. Analysis of transcriptomic data from Aire-augmented and Aire-deficient mTECs reveals that many Aire-dependent genes may not be direct transcriptional targets of Aire, while Ccl25 is identified as a canonical target of Aire.
JOURNAL OF IMMUNOLOGY
(2022)
Article
Cell Biology
Junko Morimoto, Minoru Matsumoto, Ryuichiro Miyazawa, Hideyuki Yoshida, Koichi Tsuneyama, Mitsuru Matsumoto
Summary: This study reveals the significance of the interaction between mTECs and DCs coordinated by Aire in establishing thymic tolerance. Aire deficiency leads to abnormal expression of CTLA-4 in mTECs, which removes CD80/CD86 ligands from DCs, attenuating their ability to provide co-stimulatory signals and present self-antigens transferred from mTECs, resulting in impaired Treg production and organ-specific autoimmunity.
Article
Biochemistry & Molecular Biology
Takeo Minamikawa, Eiji Hase, Mayuko Ichimura-Shimizu, Yuki Morimoto, Akihiro Suzuki, Takeshi Yasui, Satoko Nakamura, Akemi Tsutsui, Koichi Takaguchi, Koichi Tsuneyama
Summary: In this study, second-harmonic generation microscopy was used to quantitatively assess the ultra-early stage of fibrosis in NAFLD patients. The results showed that SHG microscopy can effectively visualize fibrotic structures and early fibrosis in liver tissues, which is challenging to identify with conventional histopathological methods. Additionally, SHG emission directionality analysis can assess the maturation of collagen fibers in each patient.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Chemistry, Multidisciplinary
Mayuko Ichimura-Shimizu, Soichiro Ishimaru, Christine (Yee-Yan) Wai, Takeo Minamikawa, Takaaki Tsunematsu, Aiko Endo, Takumi Kojima, Minoru Matsumoto, Tomoko Kobayashi, Satoshi Sumida, Takumi Kakimoto, Yuko Miyakami, Hirohisa Ogawa, Takeshi Oya, Koichi Tsuneyama
Summary: This study generated a mouse model of shellfish allergy through epicutaneous sensitization, which can be used to explore the pathogenesis of skin sensitization. Raman microscopy may also provide valuable insights into subtle skin changes leading to sensitization.
APPLIED SCIENCES-BASEL
(2022)
Article
Biochemistry & Molecular Biology
Wenhua Shao, Orgil Jargalsaikhan, Mayuko Ichimura-Shimizu, Qinyi Cai, Hirohisa Ogawa, Yuko Miyakami, Kengo Atsumi, Mitsuru Tomita, Mitsuko Sutoh, Shunji Toyohara, Ryoji Hokao, Yasusei Kudo, Takeshi Oya, Koichi Tsuneyama
Summary: The GS-negative tumors of TSOD mice exhibit characteristics similar to various subtypes of human hepatocellular adenoma (HCA), suggesting that TSOD mice may share similar mechanisms of HCA development as in humans.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Yuki Tada, Kaichi Kasai, Nana Makiuchi, Naoya Igarashi, Koudai Kani, Shun Takano, Hiroe Honda, Tsutomu Yanagibashi, Yasuharu Watanabe, Fumitake Usui-Kawanishi, Yukihiro Furusawa, Mayuko Ichimura-Shimizu, Yoshiaki Tabuchi, Kiyoshi Takatsu, Koichi Tsuneyama, Yoshinori Nagai
Summary: Macrophages play a critical role in the development of non-alcoholic steatohepatitis (NASH), but it is unclear which macrophage subset is specifically involved in inflammation and fibrosis. In this study, we found that in TSNO mice with advanced liver fibrosis resembling human NASH, recruited macrophages were more abundant than Kupffer cells (KCs) and formed hepatic crown-like structures (hCLS). The recruited macrophages consisted of CD11c(+)/Ly6C(-) and CD11c(-)/Ly6C(+) subsets, with CD11c(+)/Ly6C(-) cells promoting liver fibrosis and hepatic stellate cell (HSC) activation, while CD11c(-)/Ly6C(+) cells exhibited an anti-inflammatory role and promoted tissue repair.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Kaichi Kasai, Naoya Igarashi, Yuki Tada, Koudai Kani, Shun Takano, Tsutomu Yanagibashi, Fumitake Usui-Kawanishi, Shiho Fujisaka, Shiro Watanabe, Mayuko Ichimura-Shimizu, Kiyoshi Takatsu, Kazuyuki Tobe, Koichi Tsuneyama, Yukihiro Furusawa, Yoshinori Nagai
Summary: The gut microbiota plays a potential role in the development of non-alcoholic fatty liver disease. Antibiotic treatments in non-obese mice fed a high-fat/cholesterol/cholate-based diet exacerbated liver damage, steatohepatitis, and fibrosis. This effect was attributed to changes in gut microbiota, particularly an increase in Gram-positive organisms, and the modulation of bile acid levels and composition.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Mayuko Ichimura-Shimizu, Shiro Watanabe, Yuka Kashirajima, Ami Nagatomo, Hitomi Wada, Koichi Tsuneyama, Katsuhisa Omagari
Summary: This study demonstrates the direct impact of dietary cholic acid (CA) on the progression of nonalcoholic steatohepatitis (NASH) induced by a high-fat and high-cholesterol diet. Adding CA to the diet exacerbates hepatic steatosis, inflammation, and fibrosis, leading to cirrhosis. These findings provide further evidence of the hepatotoxicity of CA.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Pathology
Yuki Morimoto, Takeshi Oya, Mayuko Ichimura-Shimizu, Minoru Matsumoto, Hirohisa Ogawa, Tomoko Kobayashi, Satoshi Sumida, Takumi Kakimoto, Michiko Yamashita, Chunmei Cheng, Koichi Tsuneyama
Summary: Probe electrospray ionization-MS (PESI-MS) shows promising potential as a novel diagnostic modality for swiftly acquiring specific cytological information. The study results demonstrate the ability of PESI-MS to distinguish different cancer cell types and accurately identify normal cells.
Article
Pharmacology & Pharmacy
Paola Orlandi, Marta Banchi, Francesca Vaglini, Marco Carli, Stefano Aringhieri, Arianna Bandini, Carla Pardini, Cristina Viaggi, Michele Lai, Greta Ali, Alessandra Ottani, Eleonora Vandini, Patrizia Guidi, Margherita Bernardeschi, Veronica La Rocca, Giulio Francia, Gabriella Fontanini, Mauro Pistello, Giada Frenzilli, Daniela Giuliani, Marco Scarselli, Guido Bocci
Summary: This study investigates the role of MC4R in melanoma and the use of the selective antagonist ML in combination with vemurafenib. The results show that ML can inhibit melanoma cell proliferation and induce apoptosis through the inhibition of ERK1/2 phosphorylation and reduction of BCL-XL expression. The combination of vemurafenib and ML exhibits a synergistic effect in vitro and inhibits tumor growth in vivo without causing adverse effects.
BIOCHEMICAL PHARMACOLOGY
(2024)
Article
Pharmacology & Pharmacy
Conor J. Bloxham, Katina D. Hulme, Fabrizio Fierro, Christian Fercher, Cassandra L. Pegg, Shannon L. O'Brien, Simon R. Foster, Kirsty R. Short, Sebastian G. B. Furness, Melissa E. Reichelt, Masha Y. Niv, Walter G. Thomas
Summary: Bitter taste receptors (T2Rs) are a type of G protein-coupled receptors that allow humans to detect aversive and toxic substances. This study characterized the functional properties of previously identified T2Rs in human cardiac tissues and their naturally occurring polymorphisms. The results showed differences in signaling among different T2R variants, and revealed a potential association between the T2R50 Tyr203 variant and cardiovascular disease.
BIOCHEMICAL PHARMACOLOGY
(2024)
Article
Pharmacology & Pharmacy
Lu Chen, Huanying Shi, Wenxin Zhang, Yongjun Zhu, Haifei Chen, Zimei Wu, Huijie Qi, Jiafeng Liu, Mingkang Zhong, Xiaojin Shi, Tianxiao Wang, Qunyi Li
Summary: This study demonstrates that Carfilzomib exhibits potent anti-tumor activity against esophageal squamous cell carcinoma (ESCC) by triggering mitochondrial apoptosis and reprogramming cellular metabolism. It has been identified that activating transcription factor 3 (ATF3) plays a crucial role as a cellular target in ESCC cells treated with Carfilzomib. Overexpression of ATF3 effectively counteracts the effects of Carfilzomib on ESCC cell proliferation, apoptosis, and metabolic reprogramming. Furthermore, ATF3 mediates the anti-tumor activity of Carfilzomib, suggesting its potential as a therapeutic agent for ESCC.
BIOCHEMICAL PHARMACOLOGY
(2024)
Review
Pharmacology & Pharmacy
Xing Zhang, Xiang Li, Ran Xia, Hong-Sheng Zhang
Summary: This review summarizes recent progress on the mechanisms of ferroptosis resistance in cancer and highlights the role of redox status and metabolism. Combination therapy for ferroptosis has great potential in treating resistant malignant tumors.
BIOCHEMICAL PHARMACOLOGY
(2024)
