Review
Plant Sciences
Xiao-Xiao Liu, Qian-Huan Guo, Wei-Bo Xu, Peng Liu, Kang Yan
Summary: Plants use diverse strategies and complex regulations to adapt to changing environmental conditions. In addition to direct gene transcription regulation, alternative splicing plays a crucial role in coping with various stresses.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Xiaohong Yao, Chaofan Wang, Weiran Yu, Longjie Sun, Zheng Lv, Xiaomei Xie, Shuang Tian, Lu Yan, Hua Zhang, Jiali Liu
Summary: This study found that SRSF1 plays an important role in mouse granulosa cells. Specific knockout of SRSF1 leads to inhibition of follicular development, decreased granulosa cell proliferation, and increased apoptosis.
CELLULAR AND MOLECULAR LIFE SCIENCES
(2023)
Article
Multidisciplinary Sciences
Keita Tomioka, Tatsuo Miyamoto, Silvia Natsuko Akutsu, Hiromi Yanagihara, Kazumasa Fujita, Ekaterina Royba, Hiroshi Tauchi, Takashi Yamamoto, Iemasa Koh, Eiji Hirata, Yoshiki Kudo, Masao Kobayashi, Satoshi Okada, Shinya Matsuura
Summary: Genetic information is protected against genotoxins such as ionizing radiation through DNA double-strand break repair. Studies suggest that variants in DNA repair genes may affect individual differences in chromosomal radiosensitivity. The NBS1 I171V variant was found in a Japanese ovarian cancer patient and may contribute to increased radiosensitivity, as seen in experiments with knock-in HCT116 cells and MEFs.
SCIENTIFIC REPORTS
(2021)
Article
Biochemistry & Molecular Biology
Yulia A. Gladilina, Lylia Bey, Abdullah Hilal, Ekaterina V. Neborak, Varvara G. Blinova, Dmitry D. Zhdanov
Summary: This study highlights the cytoprotective effects of polyamines on normal human CD4(+) T lymphocytes through alternative splicing of RAD51A pre-mRNA, leading to decreased DNA damage and increased cell survival. However, these effects were not observed in cancer cells.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Environmental Sciences
Rupa Rani, Abhidha Kela, Geeta Dhaniya, Kamini Arya, Amit K. Tripathi, Rajesh Ahirwar
Summary: Specific miRNAs have been identified as early warning biomarkers for health effects associated with exposure to PAHs in exposed populations, and they can serve as indicators of early health effects in response to chronic environmental exposure to PAHs.
ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH
(2021)
Article
Plant Sciences
Ibtissam Jabre, Saurabh Chaudhary, Cornelia M. Wilson, Dorothee Staiger, Naeem Syed
Summary: Plants utilize gene regulatory mechanisms to adapt to environmental challenges. This study reveals that stochastic changes in DNA methylation can modulate nucleosome occupancy and alternative splicing (AS) in response to cold stress, thus influencing plant metabolism and stress adaptation.
Article
Reproductive Biology
Xiaohong Yao, Chaofan Wang, Longjie Sun, Lu Yan, Xuexue Chen, Zheng Lv, Xiaomei Xie, Shuang Tian, Wenbo Liu, Lei Li, Hua Zhang, Jiali Liu
Summary: In this study, it was discovered that BCAS2 protein regulates pre-mRNA splicing in granulosa cells, affecting their proliferation and survival. BCAS2 participates in the PRP19 complex to mediate alternative splicing of E2f3 and Flt3l mRNA, thereby inhibiting the cell cycle. These findings reveal the function of BCAS2 in granulosa cells.
JOURNAL OF OVARIAN RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Jinyi Zhou, Lili Gu, Yingying Shi, Ting Huang, Xirui Fan, Xiaowen Bi, Shuai Lu, Juanjuan Liang, Lan Luo, Peng Cao, Zhimin Yin
Summary: The study showed that GSTpi can protect cells from cell death during DNA damage via Ser184 phosphorylation, enhance NBS1 nuclear translocation to activate the ATM-Chk2-p53 signaling pathway, block the cell cycle in the G2/M phase to allow more time for DNA damage repair.
CELLULAR AND MOLECULAR LIFE SCIENCES
(2022)
Article
Plant Sciences
Zhipeng Yu, Xia Huang, Shuhan Wen, Haijuan Cao, Nan Wang, Shihua Shen, Mingquan Ding
Summary: This study reveals that the paper mulberry undergoes a substantial number of alternative splicing events in response to cold stress, with significant enrichment in starch and sucrose metabolism and circadian rhythm pathways. The differential spliced genes also showed differential expression, suggesting a coordinated regulation between gene alternative splicing and expression. Additionally, DNA methylation may play a role in governing gene splicing.
Article
Biochemical Research Methods
Pora Kim, Himansu Kumar, Chengyuan Yang, Ruihan Luo, Jiajia Liu, Xiaobo Zhou
Summary: In this study, researchers systematically investigated the homology sequences around the genomic breakpoints of human fusion genes. Through bioinformatic analysis, they found a relationship between sequence homologies and the immune system. This in-silico study provides valuable knowledge on the sequence homologies around structural variants.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Plant Sciences
Shuai Lu, Cong Gao, Yongzhou Wang, Yingying He, Junrong Du, Moxian Chen, Hua Zhao, Hui Fang, Baohua Wang, Yunying Cao
Summary: This study identified U2AF65A in plant species, conducted phylogenetic and bioinformatic analyses, and studied the localization and stress responses of OsU2AF65A in rice. Using Arabidopsis and rice mutants, the importance of U2AF65A in plant growth and stress responses was demonstrated. These findings provide an overview of the U2AF65 gene family and its role in plant development and stress tolerance.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Gastroenterology & Hepatology
Ni Zhen, Jiabei Zhu, Siwei Mao, Qi Zhang, Song Gu, Ji Ma, Yue Zhang, Minzhi Yin, Haojie Li, Nan Huang, Han Wu, Fenyong Sun, Binwu Ying, Lin Zhou, Qiuhui Pan
Summary: This study reveals aberrant alternative splicing in hepatoblastoma (HB), including the intron retention of long non-coding RNAs from the SNHG family. Furthermore, the interaction between PABPN1 and the splicing machinery in HB is involved in promoting cell proliferation and DNA damage repair via inducing the intron retention of SNHG19. Knockdown of PABPN1 increases the cisplatin sensitivity of HB PDOs.
CELLULAR AND MOLECULAR GASTROENTEROLOGY AND HEPATOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Saurabh Chaudhary, Ibtissam Jabre, Naeem H. Syed
Summary: This study investigates the influence of stable and temperature-dependent variations in DNA methylation and nucleosome occupancy on alternative splicing in plants using an epigenetic Recombinant Inbred Line and the parental ecotype Columbia. The results show significant epigenetic differences between the two lines in response to normal and cold temperatures, affecting gene expression levels and alternative splicing. The patterns of DNA methylation and nucleosome levels around intron-exon boundaries are shown to modulate alternative splicing in Arabidopsis.
Article
Cell Biology
Zhe Liu, Wei Wang, Xinru Li, Xiujuan Zhao, Hongyu Zhao, Wuritu Yang, Yongchun Zuo, Lu Cai, Yongqiang Xing
Summary: Alternative splicing plays an important role in zebrafish embryo development, especially during the maternal-to-zygotic transition process where it is highly abundant and dynamic. Splicing factors are expressed with developmental stage specificity, with a higher expression during the maternal-to-zygotic transition. The inclusion level of alternative splicing events performs well in cluster analysis and can be used as a novel parameter.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Xuena Huang, Hanxi Li, Aibin Zhan
Summary: This study investigates the alternative splicing (AS) response patterns in closely related invasive ascidians, Ciona robusta and Ciona savignyi, under environmental changes. It reveals the factors influencing AS variation and uncovers species-specific and environmentally dependent AS responses to environmental challenges.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Multidisciplinary Sciences
Marina Penova, Shuji Kawaguchi, Jun-ichirou Yasunaga, Takahisa Kawaguchi, Tomoo Sato, Meiko Takahashi, Masakazu Shimizu, Mineki Saito, Kunihiro Tsukasaki, Masanori Nakagawa, Norihiro Takenouchi, Hideo Hara, Eiji Matsuura, Satoshi Nozuma, Hiroshi Takashima, Shuji Izumo, Toshiki Watanabe, Kaoru Uchimaru, Masako Iwanaga, Atae Utsunomiya, Yasuharu Tabara, Richard Paul, Yoshihisa Yamano, Masao Matsuoka, Fumihiko Matsuda
Summary: This study identified strong associations in HLA class I and class II loci with HAM/TSP, with specific alleles like HLAC*07:02, HLA-B*07:02, HLA-DRB1*01:01, and HLA-DQB1*05:01 related to disease risk. Conversely, alleles like HLA-B*40:06, HLA-DRB1*15:01, and HLA-DQB1*06:02 were found to be protective. The amino acid residue DRB1-GB-7-Leu was identified as a genetic risk factor for HAM/TSP development independently of proviral load, serving as a specific marker for disease risk.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Microbiology
Mikiko Izaki, Jun-ichirou Yasunaga, Kisato Nosaka, Kenji Sugata, Hayato Utsunomiya, Youko Suehiro, Takafumi Shichijo, Asami Yamada, Yasuhiko Sugawara, Taizo Hibi, Yukihiro Inomata, Hirofumi Akari, Anat Melamed, Charles Bangham, Masao Matsuoka
Summary: HTLV-1 spreads in vivo through two routes: de novo infection and clonal proliferation of infected cells. Host immune responses play a critical role in maintaining and increasing PVL. Infected clones tend to survive long-term in vivo, with the immune properties of these clones playing an important role in clonal proliferation.
Article
Multidisciplinary Sciences
Guangyong Ma, Jun-ichirou Yasunaga, Kazuya Shimura, Keiko Takemoto, Miho Watanabe, Masayuki Amano, Hirotomo Nakata, Benquan Liu, Xiaorui Zuo, Masao Matsuoka
Summary: Retroviral antisense mRNAs are predominantly localized in the nucleus, functioning as long noncoding RNAs rather than mRNAs, and contributing to viral persistence.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biochemistry & Molecular Biology
Yawara Kawano, Takayuki Sasano, Yuichiro Arima, Saki Kushima, Kenichi Tsujita, Masao Matsuoka, Hiroyuki Hata
Summary: The novel PDK1 inhibitor JX06 effectively inhibited the growth of MM cells and induced apoptosis, reduced metabolites associated with glucose metabolism, and showed a potential combination use with proteasome inhibitors in the clinic, presenting a novel therapeutic strategy in MM.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2022)
Article
Biotechnology & Applied Microbiology
Yasuko Kohda, Shuichi Sakamoto, Maya Umekita, Tomoyuki Kimura, Yumiko Kubota, Rie Arisaka, Yuko Shibuya, Hideyuki Muramatsu, Ryuichi Sawa, Shingo Dan, Manabu Kawada, Masayuki Igarashi
Summary: The newly isolated bispolides C-E exhibit distinct structures from other known bispolides, and show antibacterial and cytotoxic activities against drug-resistant bacteria and tumor cells, indicating potential pharmaceutical value.
JOURNAL OF ANTIBIOTICS
(2022)
Editorial Material
Hematology
Masao Matsuoka
Summary: In this study, Ishio et al identified the crucial genes and the importance of the mTORC1 pathway in the proliferation and survival of adult T-cell leukemia-lymphoma (ATL) cells using whole-genome CRISPR library screening.
Article
Hematology
Takafumi Shichijo, Kisato Nosaka, Hiro Tatetsu, Yusuke Higuchi, Shinya Endo, Yoshitaka Inoue, Kosuke Toyoda, Yoshitaka Kikukawa, Toshiro Kawakita, Jun-ichirou Yasunaga, Masao Matsuoka
Summary: This retrospective study analyzed the clinical outcomes of 39 transplant-ineligible patients with untreated aggressive ATL. The results showed that first-line Mog-containing treatment can significantly improve overall survival compared to chemotherapy alone, even in elderly patients.
BRITISH JOURNAL OF HAEMATOLOGY
(2022)
Article
Hematology
Jun-ichirou Yasunaga
Summary: Adult T-cell leukemia/lymphoma (ATL) is a malignancy caused by human T-cell leukemia virus type I (HTLV-1), which infects mature CD4+ T cells and promotes cell proliferation and evasion of cell death. ATL cells exhibit genetic and transcriptional abnormalities and a regulatory T-cell-like immuno-phenotype, suggesting immune evasion is a critical step in ATL oncogenesis. New therapies that activate anti-ATL/HTLV-1 immunity may be effective in treating and preventing ATL.
INTERNATIONAL JOURNAL OF HEMATOLOGY
(2023)
Article
Oncology
Kosuke Toyoda, Jun-ichirou Yasunaga, Takafumi Shichijo, Yuichiro Arima, Kenichi Tsujita, Azusa Tanaka, Tarig Salah, Wenyi Zhang, Osama Hussein, Miyu Sonoda, Miho Watanabe, Daisuke Kurita, Kazutaka Nakashima, Kyohei Yamada, Hiroaki Miyoshi, Koichi Ohshima, Masao Matsuoka
Summary: Acceleration of glycolysis is a common trait of cancer cells. The viral oncogene HBZ promotes lactate excretion by upregulating TAp73 and lactate transporters MCT1 and MCT4. This mechanism involves HBZ protein binding to EZH2 and reducing its occupancy of the TAp73 promoter, as well as HBZ RNA activating TAp73 transcription via the BATF3-IRF4 machinery. Inactivation of TAp73 leads to intracellular accumulation of lactate, inducing cell death. The TAp73-MCT1/4 pathway may contribute to cancer metabolism.
BLOOD CANCER DISCOVERY
(2023)
Article
Oncology
Tatsuya Morishima, Koichi Takahashi, Desmond Wai Loon Chin, Yuxin Wang, Kenji Tokunaga, Yuichiro Arima, Masao Matsuoka, Toshio Suda, Hitoshi Takizawa
Summary: Genetic mutations in the IDH gene can result in the production of oncometabolite, which is associated with acute myeloid leukemia (AML). Although targeted inhibitors have been developed, refractoriness and resistance are still observed. This study found that aberrant metabolism in IDH mutant cells can persist even after normalization of oncometabolite level. Two signaling pathways, STAT phosphorylation and phospholipid metabolic adaptation, were identified to be important for the growth advantage of IDH2 mutant cells. The release of metabolic adaptation by anti-inflammatory drugs targeting arachidonic acid metabolism sensitized IDH2 mutant cells to apoptosis. These findings have implications for the development of alternative treatments for IDH2 mutant AML patients.
Article
Medicine, Research & Experimental
Tatsuya Yoshinouchi, Keiichi Yamamoto, Mitsuru Migita, Toshiro Yokoyama, Tomofumi Nakamura, Masao Matsuoka
Summary: We present a case of a patient with anorexia nervosa who developed acute pneumonia caused by E. dermatitidis. The fungal etiologic agent was identified using mass spectrometry and genetic analysis. Despite the delayed initiation of antifungal therapy, the pneumonia gradually improved with long-term treatment, highlighting the importance of early diagnosis and effective treatment.
MEDICAL MYCOLOGY CASE REPORTS
(2023)
Article
Oncology
Asami Yamada, Jun-ichirou Yasunaga, Lihan Liang, Wenyi Zhang, Junya Sunagawa, Shinji Nakaoka, Shingo Iwami, Yasunori Kogure, Yuta Ito, Keisuke Kataoka, Masanori Nakagawa, Masako Iwanaga, Atae Utsunomiya, Ki-Ryang Koh, Toshiki Watanabe, Kisato Nosaka, Masao Matsuoka
Summary: This study demonstrates that profiling the humoral immunity to HTLV-1 antigens and measuring proviral load can be used to classify disease status and predict the development of HTLV-1-associated diseases. The study also highlights the importance of anti-Gag proteins in disease prognosis.
Article
Chemistry, Multidisciplinary
Ryohei Kajino, Shuichi Sakamoto, Yoshihito Ueno
Summary: In this study, the synthesis of (S)-5'-C-aminopropyl-2'-O-methyladenosine and (S)-5'-C-aminopropyl-2'-O-methylguanosine phosphoramidites was reported, and the properties of small interfering RNAs (siRNAs) containing four (S)-5'-C-aminopropyl-2'-O-methylnucleosides were investigated. The results showed that siRNAs containing (S)-5'-C-aminopropyl-nucleosides at the 3'- and 5'-regions of the passenger strand exhibited good tolerance for RNA interference (RNAi) activity, while the (S)-5'-C-aminopropyl modification in the central region of the passenger strand decreased the RNAi activity. Furthermore, siRNAs containing three or four consecutive (S)-5'-C-aminopropyl-2'-O-methylnucleosides at the 3'- and 5'-regions of the passenger strand showed RNAi activity similar to that of the corresponding 2'-O-methyl-modified siRNAs. Finally, it was observed that (S)-5'-C-aminopropyl modifications effectively improved the serum stability of the siRNAs compared with 2'-O-methyl modifications.
Article
Hematology
Yasunori Kogure, Takuro Kameda, Junji Koya, Makoto Yoshimitsu, Kisato Nosaka, Jun-ichirou Yasunaga, Yoshitaka Imaizumi, Mizuki Watanabe, Yuki Saito, Yuta Ito, Marni B. McClure, Mariko Tabata, Sumito Shingaki, Kota Yoshifuji, Kenichi Chiba, Ai Okada, Nobuyuki Kakiuchi, Yasuhito Nannya, Ayako Kamiunten, Yuki Tahira, Keiichi Akizuki, Masaaki Sekine, Kotaro Shide, Tomonori Hidaka, Yoko Kubuki, Akira Kitanaka, Michihiro Hidaka, Nobuaki Nakano, Atae Utsunomiya, R. Alejandro Sica, Ana Acuna-Villaorduna, Murali Janakiram, Urvi Shah, Juan Carlos Ramos, Tatsuhiro Shibata, Kengo Takeuchi, Akifumi Takaori-Kondo, Yasushi Miyazaki, Masao Matsuoka, Kenji Ishitsuka, Yuichi Shiraishi, Satoru Miyano, Seishi Ogawa, B. Hilda Ye, Kazuya Shimoda, Keisuke Kataoka
Summary: Through whole-genome sequencing of 150 ATL cases, we identified the genetic landscape of ATL. We found frequent loss-of-function alterations in the CIC gene, which were previously overlooked. Truncations of the REL gene were also common and found in diffuse large B-cell lymphoma. Recurrent mutations in non-coding regions of driver genes were identified. By combining analyses of coding and noncoding mutations, structural variations, and copy number alterations, we discovered 56 recurrently altered driver genes, including 11 novel ones. ATL cases were classified into 2 molecular groups based on their driver alteration profile.
Letter
Biophysics
Kosuke Toyoda, Jun-ichirou Yasunaga, Ilseung Choi, Youko Suehiro, Naokuni Uike, Jun Okamura, Masao Matsuoka
BONE MARROW TRANSPLANTATION
(2021)