Article
Oncology
Xiangyu Li, Woonghee Kim, Muhammad Arif, Chunxia Gao, Andreas Hober, David Kotol, Linnea Strandberg, Bjorn Forsstrom, Asa Sivertsson, Per Oksvold, Hasan Turkez, Morten Grotli, Yusuke Sato, Haruki Kume, Seishi Ogawa, Jan Boren, Jens Nielsen, Mathias Uhlen, Cheng Zhang, Adil Mardinoglu
Summary: Pyruvate kinase muscle type (PKM) is a key enzyme in glycolysis and plays an important role in cancer. The association between PKM expression and the survival outcome of patients with different cancers is controversial. System biology methods were employed to reveal the prognostic value and potential biological functions of PKM transcripts in different human cancers.
Article
Multidisciplinary Sciences
Jaimie M. Mayner, Evan M. Masutani, Elena Demeester, Aditya Kumar, Gail Macapugay, Pranjali Beri, Valentina Lo Sardo, Adam J. Engler
Summary: 9p21.3 locus polymorphisms show the strongest correlation with coronary artery disease, but the connection is unclear due to its noncoding nature. The lncRNA ANRIL in 9p21.3 may regulate VSMC phenotype to contribute to disease risk. Different subpopulations of risk haplotype cells exhibit variable morphology, proliferation, contraction, and adhesion, suggesting that variable lncRNA penetrance may drive mixed functional outcomes.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Biochemistry & Molecular Biology
Ali Calderon-Aparicio, Bi-Dar Wang
Summary: Prostate cancer is the most frequently diagnosed cancer in American men and often leads to treatment resistance, relapse, and decreased survival rates. Aberrant RNA splicing, which increases proteome diversity, has been linked to prostate cancer development and progression. Targeting aberrant splicing mechanisms through pharmacological and molecular approaches offers potential for improved clinical outcomes in prostate cancer patients.
INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Meng-Han Huang, Gui-Xin Peng, Xue-Ling Mao, Jin-Tao Wang, Jing-Bo Zhou, Jian-Hui Zhang, Meirong Chen, En-Duo Wang, Xiao-Long Zhou
Summary: The study identified different isoforms of METTL8 that play various roles in different cell compartments. The isoforms have distinct localization and show different mechanisms in the modification of mitochondrial tRNA. The interaction between SARS2 and METTL8-Iso1 was found to enhance the modification activity.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Cell Biology
Femke A. Ehlers, Timo Olieslagers, Mathijs Groeneweg, Gerard M. J. Bos, Marcel G. J. Tilanus, Christina E. M. Voorter, Lotte Wieten
Summary: The polymorphisms within HLA-C alleles influence the alternative splicing of HLA-C. Skipping variants of exon 5 were observed in HLA-C*04 and *16, which were co-expressed with the mature transcript. The exon 5 SNP specific to HLA-C*16 altered exonic splicing regulatory elements.
Article
Pharmacology & Pharmacy
Shoshana Buckhalter, Eric Soubeyrand, Sarah A. E. Ferrone, Duncan J. Rasmussen, Joshua D. Manduca, M. Sameer Al-Abdul-Wahid, Jude A. Frie, Jibran Y. Khokhar, Tariq A. Akhtar, Melissa L. Perreault
Summary: Krakom, a traditional herbal medicine used to enhance mood and alleviate pain, has shown increased usage in Europe and North America. The study evaluated the effects of purified alkaloid kratom extract on neuronal oscillatory systems, pain relief, and antidepressant-like behavior, as well as kratom-induced changes in Delta FosB expression. The results suggest that kratom has both antidepressant and analgesic properties, with specific changes in neuronal circuit function, but does not affect the Delta FosB signaling pathway known to be involved in addiction.
FRONTIERS IN PHARMACOLOGY
(2021)
Article
Plant Sciences
Qisheng Wang, Fenfen Qin, Yuxuan Wang, Zijing Wang, Weixin Lin, Zhonghao Li, Qingyang Liu, Xinru Mu, Hui Wang, Shang Lu, Yongwei Jiang, Shengfeng Lu, Qian Wang, Zhigang Lu
Summary: This study found that Compound 511, a traditional Chinese medicine formula, can block the reinstatement of conditioned place preference and locomotor sensitization caused by morphine through epigenetic mechanisms, indicating its potential as a non-opioid treatment for opioid addiction.
Article
Biochemistry & Molecular Biology
Jennifer R. Deuis, Smitha Kumble, Angelo Keramidas, Lotten Ragnarsson, Cas Simons, Lynn Pais, Susan M. White, Irina Vetter
Summary: This study reports a novel missense variant in the SCN9A gene, which causes bilateral lower limb pain in childhood. The mutation alters the activation and inactivation of the sodium channel, indicating a gain-of-function molecular phenotype associated with erythromelalgia.
HUMAN MOLECULAR GENETICS
(2023)
Article
Cell Biology
Ni Zuo, Wei-Zhen Bai, Wan-Qian Wei, Ting-Lu Yuan, Dong Zhang, Yan-Zhang Wang, Wei-Hua Tang
Summary: This study found that a group of CFEM proteins of F. graminearum are required for full virulence in maize stalk infection and that they interact with two secreted maize proteins, ZmLRR5 and ZmWAK17ET. The study also found that ZmWAK17 mediates resistance to stalk rot in maize.
Article
Biochemistry & Molecular Biology
Monikaben Padariya, Robin Fahraeus, Ted Hupp, Umesh Kalathiya
Summary: The study reveals the binding specificity of UPF1 with different mRNA motifs and the impact of insertion on UPF1 catalytic activity. Experimental results demonstrate two structural conformations of UPF1 and enhance understanding of the NMD pathway.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Chemistry, Multidisciplinary
Bojing Jiang, Sin Yen Tan, Shiyu Fang, Xiaohan Feng, Byung Min Park, Hong Kiu Francis Fok, Zhongguang Yang, Ri Wang, Songzi Kou, Angela Ruohao Wu, Fei Sun
Summary: A modular functionalization strategy for recombinant spider silk is presented using SpyTag/SpyCatcher chemistry and AlphaFold2-aided design, enabling the decoration of silk threads with various fusion motifs. Coating the silk with a silica layer using silicatein results in a hybrid inorganic-organic 1D material. The installation of cell-binding ligands on silk threads enhances cell attachment and proliferation, demonstrating a straightforward and powerful approach to 1D protein materials.
ADVANCED FUNCTIONAL MATERIALS
(2023)
Article
Multidisciplinary Sciences
Florian Bernard, Delphine Dargere, Oded Rechavi, Denis Dupuy
Summary: This study used Oxford Nanopore's long-read amplification-free sequencing technology to comprehensively analyze trans-splicing in worms and found evidence of trans-splicing for most genes. However, a subset of genes may only marginally undergo trans-splicing, possibly due to their capacity to generate a 5' terminal hairpin structure mimicking the spliced leader.
NATURE COMMUNICATIONS
(2023)
Article
Oncology
Daisuke Ogiya, Zuzana Chyra, Sigitas J. Verselis, Morgan O'Keefe, Jacquelyn Cobb, Ivane Abiatari, Srikanth Talluri, Anjana Anilkumar Sithara, Teru Hideshima, Michael P. P. Chu, Roman Hajek, David M. Dorfman, Linda M. Pilarski, Kenneth C. Anderson, Sophia Adamia
Summary: This study found that alterations in pre-mRNA splicing (AS) are frequent in multiple myeloma (MM) patients, suggesting the need for innovative treatment strategies. The study also explores how to identify disease-specific alterations in MM and proposes RNA-based therapeutic strategies to eliminate these changes, demonstrating how aberrant HMMR splicing can be inhibited through RNA intervention.
BLOOD CANCER JOURNAL
(2023)
Article
Microbiology
Adeline Goulet, Jennifer Mahony, Christian Cambillau, Douwe van Sinderen
Summary: Bacteriophages, known as phages, are the most abundant biological entities on Earth. They possess molecular nanodevices to package and store their genome, and to introduce it into the cytoplasm of their bacterial hosts. The adhesion devices of phages infecting Gram-positive bacteria are diverse and not well understood. The protein structure prediction program AlphaFold2 is able to predict the structure and function of these molecular machineries. In this study, the structure predictions of adhesion devices from P335 phages infecting Lactococcus spp. were presented, showing the diverse topology of these devices. The adhesion devices of certain phages were found to share a similar topology with Skunavirus p2, suggesting a common activation mechanism.
Article
Biotechnology & Applied Microbiology
Ashwini M. Darshetkar, Swaranjali S. Patil, Anupama A. Pable, Altafhusain B. Nadaf, Vitthal T. Barvkar
Summary: In this study, the complete mitochondrial genome of a halophyte species Pandanus odorifer (Forssk.) Kuntze (Pandanaceae) was reported. The genome is circular with a length of 330,962 bp and contains 33 protein coding genes, 3 rRNAs, and 6 tRNAs. Analysis revealed the pseudogenization of important respiratory genes in the mitochondrial genome, but nuclear encoded copies were recovered. Phylogenetic analysis placed P. odorifer sister to P. tectorius.
PLANT BIOTECHNOLOGY REPORTS
(2023)
Article
Oncology
Yi Hu, Chun Yang, Tania Amorim, Mohsin Maqbool, Jenny Lin, Chen Li, Chuanfeng Fang, Li Xue, Ariel Kwart, Hua Fang, Mei Yin, Allison J. Janocha, Daisuke Tsuchimoto, Yusaku Nakabeppu, Xiaofeng Jiang, Alex Mejia-Garcia, Faiz Anwer, Jack Khouri, Xin Qi, Qing Y. Zheng, Jennifer S. Yu, Shan Yan, Thomas LaFramboise, Kenneth C. Anderson, Leal C. Herlitz, Nikhil C. Munshi, Jianhong Lin, Jianjun Zhao
Summary: This study identified APE2 as a critical molecule upregulated in the kidney following cisplatin treatment, leading to MYH9 dysfunction in mitochondria and potential development of AKI. Knockout of APE2 attenuated cisplatin-induced kidney injury, suggesting a novel target for prophylactic treatment of AKI.
Article
Multidisciplinary Sciences
Hiroki Sakamoto, Koji Miyanishi, Shingo Tanaka, Ryo Ito, Kota Hamaguchi, Akira Sakurada, Masanori Sato, Tomohiro Kubo, Takahiro Osuga, Kazuyuki Murase, Kohichi Takada, Yusaku Nakabeppu, Masayoshi Kobune, Junji Kato
Summary: The study found that MUTYH deficiency is associated with the development of liver tumors in NASH-related conditions. In mouse experiments, MUTYH-null mice fed a high-fat high-cholesterol+high-iron diet were more likely to develop liver tumors and showed higher accumulation of oxidative stress markers. Gene expression analysis also indicated involvement of the Wnt/beta-catenin signaling pathway and increased c-Myc expression in MUTYH-null liver tissues.
SCIENTIFIC REPORTS
(2021)
Article
Multidisciplinary Sciences
Sugako Oka, Julio Leon, Kunihiko Sakumi, Nona Abolhassani, Zijing Sheng, Daisuke Tsuchimoto, Frank M. LaFerla, Yusaku Nakabeppu
Summary: 8-Oxoguanine accumulates in Alzheimer's disease brains, and deficiency of MTH1 and OGG1 can increase its accumulation, leading to microglial activation and neuronal loss. Minocycline can inhibit microglial activation and reduce neuroinflammation, providing a potential new approach for preventing and treating AD.
SCIENTIFIC REPORTS
(2021)
Article
Cell Biology
Guianfranco Mazzei, Ryohei Ikegami, Nona Abolhassani, Naoki Haruyama, Kunihiko Sakumi, Takashi Saito, Takaomi C. Saido, Yusaku Nakabeppu
Summary: The study found that high-fat diet caused cognitive impairment, increased A beta deposition, and microgliosis in transgenic mouse models of Alzheimer's disease, accompanied by insulin resistance in the hippocampus.
Article
Biochemistry & Molecular Biology
Teruya Nakamura, Kohtaro Okabe, Shogo Hirayama, Mami Chirifu, Shinji Ikemizu, Hiroshi Morioka, Yusaku Nakabeppu, Yuriko Yamagata
Summary: MUTYH is a crucial DNA repair enzyme, and mutations associated with colorectal cancer can lead to MAP disease. Studies have shown that MUTYH participates in base excision repair with PCNA during DNA replication and contains a binding motif related to proteins involved in DNA damage response.
NUCLEIC ACIDS RESEARCH
(2021)
Correction
Multidisciplinary Sciences
Erika Castillo, Julio Leon, Guianfranco Mazzei, Nona Abolhassani, Naoki Haruyama, Takashi Saito, Takaomi Saido, Masaaki Hokama, Toru Iwaki, Tomoyuki Ohara, Toshiharu Ninomiya, Yutaka Kiyohara, Kunihiko Sakumi, Frank M. LaFerla, Yusaku Nakabeppu
SCIENTIFIC REPORTS
(2021)
Article
Clinical Neurology
Yukino Miyachi, Takayuki Fujii, Ryo Yamasaki, Daisuke Tsuchimoto, Kyoko Iinuma, Ayako Sakoda, Shoko Fukumoto, Takuya Matsushita, Katsuhisa Masaki, Noriko Isobe, Yusaku Nakabeppu, Jun-ichi Kira
Summary: This study aimed to investigate the impact of serum anti-oligodendrocyte antibodies on the clinical features of MS patients and validate whether these antibodies could serve as biomarkers for CNS tissue damage in MS patients. Results showed that anti-oligodendrocyte antibodies were positive in PPMS and SPMS patients, while absent in RRMS, NMOSD, OIND patients, and healthy controls.
FRONTIERS IN NEUROLOGY
(2021)
Article
Biochemistry & Molecular Biology
Jingwen Chen, Xin Wu, Yanyi Wang, Yunfeng Pan, Yan Ren, Yusaku Nakabeppu, Yimei Fan, Yaping Wang
Summary: This study demonstrates that Mutyh deficiency can lead to changes in mitochondrial structure and impair mitochondrial function through downregulation of Mfn2 and alteration of the ratio of L-Opa1/S-Opa1, accompanied by a reduction in alpha-ketoglutaric acid (alpha-KG). Further analysis reveals that Mutyh deficiency may cause downregulation of histone demethylases and DNA demethylases and inhibition of Mfn2 transcription. Interestingly, supplementation of alpha-KG can alleviate the damage associated with Mutyh deficiency, restore Mfn2 expression, and prevent degradation of L-Opa1.
FREE RADICAL RESEARCH
(2022)
Article
Neurosciences
Yuri Mizuno, Nona Abolhassani, Guianfranco Mazzei, Takashi Saito, Takaomi C. Saido, Ryo Yamasaki, Jun-ichi Kira, Yusaku Nakabeppu
Summary: Oxidative stress is a major risk factor for Alzheimer's disease, characterized by the accumulation of 8-oxoG in the brain. Deficiency of MTH1 and OGG1 accelerates the accumulation of 8-oxoG in DNA and leads to reduced anxiety-related behavior in 6-month-old mice.
NEUROSCIENCE RESEARCH
(2022)
Article
Cell Biology
Md Akram Hossain, Yunfeng Lin, Garrett Driscoll, Jia Li, Anne McMahon, Joshua Matos, Haichao Zhao, Daisuke Tsuchimoto, Yusaku Nakabeppu, Jianjun Zhao, Shan Yan
Summary: APE2 is essential for activating the ATR DDR pathway in response to various stressful conditions in Xenopus laevis egg extracts and human pancreatic cancer cells. Inhibition of APE2 leads to increased DNA damage and sensitizes cancer cells to chemotherapy drugs, indicating its crucial role in maintaining genome integrity.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Cell Biology
Chukwuemeka George Anene-Nzelu, Peter Yiqing Li, Tuan Danh Anh Luu, Shi Ling Ng, Zenia Tiang, Bangfen Pan, Wilson Lek Wen Tan, Matthew Ackers-Johnson, Ching Kit Chen, Yee Phong Lim, Rina Wang Miao Qin, Wee Woon Chua, Lim Xin Yi, Roger Sik-Yin Foo, Yusaku Nakabeppu
Summary: Doxorubicin, commonly used for cancer treatment, can cause cardiotoxicity. This study demonstrates that deficiency of OGG1 gene exacerbates doxorubicin-induced cardiac dysfunction and increases mortality in mice. Transcriptomic analysis reveals dysregulation of genes related to inflammation in the hearts of Ogg1 knockout mice.
OXIDATIVE MEDICINE AND CELLULAR LONGEVITY
(2022)
Article
Psychiatry
Kazuya Matsuo, Yasuharu Shinoda, Nona Abolhassani, Yusaku Nakabeppu, Kohji Fukunaga
Summary: This study explored molecular alterations in the hippocampus of rats with autism spectrum disorder (ASD) and the effects of chronic administration of intranasal oxytocin (OXT). The results revealed that prenatal valproic acid (VPA) exposure altered gene expression in the hippocampus, with some of these genes suggested as candidates for ASD and involved in memory, developmental processes, and epilepsy. OXT treatment partly improved the expression of these genes, which interacted with genes involved in social behaviors and hippocampal-dependent memory.
FRONTIERS IN PSYCHIATRY
(2022)
Article
Biochemistry & Molecular Biology
Teruya Nakamura, Yukari Koga-Ogawa, Kana Fujimiya, Mami Chirifu, Masataka Goto, Shinji Ikemizu, Yusaku Nakabeppu, Yuriko Yamagata
Summary: The human MTH1 protein recognizes substrates through the exchange of protonation states, and the protonation state change is related to its substrate binding ability.
Article
Neurosciences
Sayaka Okuzono, Fumihiko Fujii, Yuki Matsushita, Daiki Setoyama, Yohei Shinmyo, Ryoji Taira, Kousuke Yonemoto, Satoshi Akamine, Yoshitomo Motomura, Masafumi Sanefuji, Takeshi Sakurai, Hiroshi Kawasaki, Kihoon Han, Takahiro A. Kato, Hiroyuki Torisu, Dongchon Kang, Yusaku Nakabeppu, Yasunari Sakai, Shouichi Ohga
Summary: Epileptic seizures are common comorbidities in children with autism spectrum disorder (ASD), but little is known about the genes involved and their role in regulating neuronal excitability. This study found that Shank3, an ASD-associated gene, plays a unique role in protecting thalamocortical neurons from hyperexcitability during the early postnatal period. These findings have important implications for understanding the mechanisms underlying seizures in children with autism.
NEUROSCIENCE RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Xu Zheng, Wenhe Zhang, Yinchao Hu, Zhexuan Zhao, Jiaxin Wu, Xiaoqing Zhang, Fengqi Hao, Jinling Han, Jing Xu, Wenjing Hao, Ruoxi Wang, Meihong Tian, Zsolt Radak, Yusaku Nakabeppu, Istvan Boldogh, Xueqing Ba
Summary: Exercise-induced generation of 8-oxoG promotes muscle remodeling and adaptation by activating the Ras-MEK-MyoD signal pathway. This study reveals the signaling role of DNA repair metabolite 8-oxoG in muscle remodeling and adaptation, and suggests its potential therapeutic application in muscle damage-related disorders.