Article
Oncology
E. Pleasance, A. Bohm, L. M. Williamson, J. M. T. Nelson, Y. Shen, M. Bonakdar, E. Titmuss, V Csizmok, K. Wee, S. Hosseinzadeh, C. J. Grisdale, C. Reisle, G. A. Taylor, E. Lewis, M. R. Jones, D. Bleile, S. Sadeghi, W. Zhang, A. Davies, B. Pellegrini, T. Wong, R. Bowlby, S. K. Chan, K. L. Mungall, E. Chuah, A. J. Mungall, R. A. Moore, Y. Zhao, B. Deol, A. Fisic, A. Fok, D. A. Regier, D. Weymann, D. F. Schaeffer, S. Young, S. Yip, K. Schrader, N. Levasseur, S. K. Taylor, X. Feng, A. Tinker, K. J. Savage, S. Chia, K. Gelmon, S. Sun, H. Lim, D. J. Renouf, S. J. M. Jones, M. A. Marra, J. Laskin
Summary: This study demonstrates the importance of comprehensive whole-genome and transcriptome sequencing and analysis in guiding personalized cancer therapy, resulting in positive clinical benefits for a significant proportion of patients.
ANNALS OF ONCOLOGY
(2022)
Article
Genetics & Heredity
Yingying Cao, Shanshan Zhai, Zhuxin Li, Zhengtuan Huang, Liang Liang, Junyu Tao, Jian Xiao, Jing Leng, Haibo Tang
Summary: The tree shrew is a unique experimental animal with small size, high brain-to-body mass ratio, short reproductive cycle and life span, and low maintenance costs. The complete mitochondrial genome of the subspecies Tupaia belangeri yaoshanensis was determined, revealing its length and gene composition.
MITOCHONDRIAL DNA PART B-RESOURCES
(2023)
Article
Oncology
Vaidehi Jobanputra, Kazimierz O. Wrzeszczynski, Reinhard Buttner, Carlos Caldas, Edwin Cuppen, Sean Grimmond, Torsten Haferlach, Charles Mullighan, Anna Schuh, Olivier Elemento
Summary: Whole-genome and transcriptome sequencing (WGTS) provides new opportunities for identifying and reporting a larger number of potentially actionable alterations in clinical tumor samples. However, these comprehensive tests also come with challenges such as the extent and diversity of sequence alterations and the complexity of interpretation.
SEMINARS IN CANCER BIOLOGY
(2022)
Article
Plant Sciences
Hisashi Udagawa, Hiroyuki Ichida, Takanori Takeuchi, Tomoko Abe, Yoshimitsu Takakura
Summary: In this study, a whole-exome sequencing (WES) procedure was developed in tobacco to characterize EMS-induced mutations in a test population, revealing a high number of single nucleotide variants. The amount of mutations detected by WES was 93.5% of those detected by whole-genome sequencing, while requiring significantly less sequencing data, making it a cost-effective tool for high-throughput mutation identification in tobacco.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Biotechnology & Applied Microbiology
Chongqing Wang, Huan Qin, Chun Zhao, Li Yang, Tingting Yu, Yuxin Zhang, Xiang Luo, Qinbo Qin, Shaojun Liu
Summary: The study characterized the ovaries of autotetraploid Carassius auratus (4nRR) and diploid Carassius auratus red var. (RCC) using Illumina sequencing platform, revealing key genes related to oogenesis. Whole-genome re-sequencing showed a large number of SNPs and InDels variations in 4nRR. Genes involved in ubiquitin-mediated proteolysis, calcium transport, and meiosis play crucial roles in oogenesis in 4nRR.
MARINE BIOTECHNOLOGY
(2021)
Article
Medicine, Research & Experimental
Wesley S. van de Geer, Ron H. J. Mathijssen, Job van Riet, Neeltje Steeghs, Mariette Labots, Carla van Herpen, Lot A. Devriese, Vivianne C. G. Tjan-Heijnen, Emile E. Voest, Stefan Sleijfer, John W. M. Martens, Edwin Cuppen, Harmen J. G. van de Werken, Sander Bins
Summary: Drug resistance is a persistent problem in cancer therapy, and alterations in drug transport over the cancer cell membrane can contribute to resistance. This study analyzed the mutational landscape of transporter genes in cancer patients who had received different systemic therapies, and identified potential stressor mechanisms that may be involved in drug resistance.
BIOMEDICINE & PHARMACOTHERAPY
(2023)
Article
Medicine, General & Internal
Eva Berglund, Gisela Barbany, Christina Orsmark-Pietras, Linda Fogelstrand, Jonas Abrahamsson, Irina Golovleva, Helene Hallbook, Martin Hoglund, Vladimir Lazarevic, Lars-Ake Levin, Jessica Nordlund, Ulrika Noren-Nystrom, Josefine Palle, Tharshini Thangavelu, Lars Palmqvist, Valtteri Wirta, Lucia Cavelier, Thoas Fioretos, Richard Rosenquist, Clinical Genomics Platform SciLifeLab Genomic Med Sweden
Summary: This national multi-center study aims to evaluate the technical feasibility and efficiency of using whole-genome sequencing and whole-transcriptome sequencing as a diagnostic tool for patients with acute lymphoblastic leukemia and acute myeloid leukemia. The study comprises four phases and will involve approximately 700 patients, with endpoints including diagnostic efficiency, clinical feasibility, and health-economic impact.
FRONTIERS IN MEDICINE
(2022)
Article
Medicine, Research & Experimental
Yanan Jiang, Xiuyun Shen, Chaorun Dong, Fengnan Zhi, Yang Gao, Chunpeng Shi, Yuqiu Chao, Jincheng Xu, Desi Shang, Juan Xu, Baofeng Yang, Xia Li, Yunlong Bai
Summary: This study investigates the cardiotoxicity induced by arsenic trioxide (ATO) through whole transcriptome analysis. The results show that ATO alters the coding and noncoding RNA profiles in mouse myocardium and constructs an ATO-related lncRNA-circRNA co-regulation network. Genes in this network may play important roles in ATO-induced cardiotoxicity.
BIOMEDICINE & PHARMACOTHERAPY
(2022)
Article
Oncology
Lirui Zhang, Qiaoshi Xu, Zhien Feng
Summary: This study presents a comprehensive clinical, genomic, and transcriptomic analysis of primary ghost cell odontogenic carcinoma (GCOC). The results provide the first comprehensive molecular atlas for primary GCOC, including previously identified CTNNB1 mutation and novel alterations in MAP3K, EP300, and the 22q11.21 region. The transcriptome analysis reveals significant involvement of cytokine-cytokine receptor interaction and the PI3K-Akt signaling pathway. More GCOC cases should be compared to validate these findings for accurate clinical guidance.
Article
Biochemistry & Molecular Biology
Yunfeng Shi, Baiyang Yu, Shan Cheng, Weiming Hu, Fen Liu
Summary: Through whole-genome bisulfite sequencing and RNA-seq, the potential impact of autophagy in regulating DNA methylation in Arabidopsis and its role in coping with nitrogen deficiency were determined. Differential expression of genes associated with DNA demethylation was observed, suggesting a correlation between DNA demethylation and the ability of Arabidopsis to cope with nitrogen deficiency. Additionally, DNA methylation was found to impact the biosynthesis of salicylic acid, providing insights into how autophagy defects may lead to SA-activated senescence.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Genetics & Heredity
Wenjing Wei, Yuchuan Zhao, Chenchen Zhang, Meiling Yu, Zhuhua Wu, Liuyue Xu, Kehao Peng, Zhilong Wu, Yanxia Li, Xuezhi Wang
Summary: This study explores the mutational pathways of aminoglycoside resistance in Mycobacterium tuberculosis (Mtb) through laboratory evolution and reveals changes in susceptibility to other anti-tuberculosis drugs. Whole-genome sequencing and transcriptional profiling analysis show that Mtb strains harboring rrs A1401G mutation have an evolutionary advantage under aminoglycoside pressure. These findings provide insights into the mechanisms of aminoglycoside resistance.
MICROBIAL GENOMICS
(2023)
Review
Biochemistry & Molecular Biology
Srinithi Purushothaman, Marco Meola, Adrian Egli
Summary: Whole genome sequencing and metagenomic sequencing are rarely combined, but combining them can provide more information critical for patient management, infection control, and pathogen surveillance.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Plant Sciences
Yuan Lin, Bing Hao, Ying Chun Lu, Yang Dong, Ying Li, Guang Hui Zhang, Zi Jiang Yang, Gui Sheng Xiang, Guan Ze Liu, Xue Jiao Li, Qin Zhu, Qing Hui Yang, Xu Zhen Li, Sheng Chao Yang
Summary: The Panax genus is a valuable natural medicinal source that contains high levels of triterpenoid saponins. The PanaxGDB database integrates omics data and information on varieties, providing reliable and comprehensive information on the biology and functions of Panax.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biotechnology & Applied Microbiology
Zhe Xu, Si Cheng, Xin Qiu, Xiaoqi Wang, Qiuwen Hu, Yanfeng Shi, Yang Liu, Jinxi Lin, Jichao Tian, Yongfei Peng, Yong Jiang, Yadong Yang, Jianwei Ye, Yilong Wang, Xia Meng, Zixiao Li, Hao Li, Yongjun Wang
Summary: This study constructed an optimized pipeline and identified applicable fingerprint panels to address the sample tagging problem in whole genome bisulfite sequencing (WGBS) data. By using autosome-wide A/T polymorphic single nucleotide variants (SNVs), a fingerprint panel was designed and genotypes were called from the WGBS data. The capability to tag WGBS data was validated and the lower boundary for the number of fingerprint genetic variants needed for correct sample tagging was determined.
Article
Biochemistry & Molecular Biology
Ying Ni, Xudong Liu, Zemenu Mengistie Simeneh, Mengsu Yang, Runsheng Li
Summary: This study evaluates the application of the recently released R10.4 flow cell from Oxford Nanopore Technologies in human cancer genomics and epigenomic research. The results show that R10.4 performs better than R9.4.1 in terms of read accuracy, variant detection, methylation calling, and genome recovery rate. In addition, the study proposes a promising method for high-yield single-cell whole-genome amplification sequencing and provides a possible solution for filtering false positive sites using R10.4 data.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Editorial Material
Pediatrics
Kazuki Iio, Kazuhiro Uda, Hiroshi Hataya, Fumihiko Yasui, Tomoko Honda, Takahiro Sanada, Kenzaburo Yamaji, Michinori Kohara, Masanari Itokawa, Masaru Miura
Article
Multidisciplinary Sciences
Makoto Saito, Yasushi Itoh, Fumihiko Yasui, Tsubasa Munakata, Daisuke Yamane, Makoto Ozawa, Risa Ito, Takayuki Katoh, Hirohito Ishigaki, Misako Nakayama, Shintaro Shichinohe, Kenzaburo Yamaji, Naoki Yamamoto, Ai Ikejiri, Tomoko Honda, Takahiro Sanada, Yoshihiro Sakoda, Hiroshi Kida, Thi Quynh Mai Le, Yoshihiro Kawaoka, Kazumasa Ogasawara, Kyoko Tsukiyama-Kohara, Hiroaki Suga, Michinori Kohara
Summary: Researchers have developed a class of macrocyclic peptides named iHA, which can bind the influenza viral envelope protein hemagglutinin and inhibit virus infection by blocking adsorption and fusion. Particularly, iHA-100 shows powerful efficacy in inhibiting the growth of highly pathogenic influenza viruses and preventing severe pneumonia at later stages of infection in mouse and non-human primate cynomolgus macaque models, indicating its potential as a next-generation, mid-sized biomolecule.
NATURE COMMUNICATIONS
(2021)
Article
Microbiology
Tomoko Honda, Sumiko Gomi, Daisuke Yamane, Fumihiko Yasui, Takuya Yamamoto, Tsubasa Munakata, Yasushi Itoh, Kazumasa Ogasawara, Takahiro Sanada, Kenzaburo Yamaji, Yasuhiro Yasutomi, Kyoko Tsukiyama-Kohara, Michinori Kohara
Summary: NanoLIPS, an improved LIPS assay based on NanoLuciferase (NLuc), is applicable for monitoring HA-specific antibodies in sera from different species. C-NLuc-HA is glycosylated, forming trimeric complexes, and interacts with monoclonal antibodies recognizing conformational epitopes on the HA globular head or stalk domain. This method offers high sensitivity and a broad dynamic range for HA-specific antibody detection in various experimental animal models.
Article
Agriculture, Dairy & Animal Science
Mohammad Enamul Hoque Kayesh, Md Abul Hashem, Kyoko Tsukiyama-Kohara
Summary: Toll-like receptors (TLRs) are evolutionarily conserved pattern recognition receptors that play a crucial role in the innate immunity against microbial pathogens. This study investigated the expression profiles of TLRs in koalas infected with different subtypes of KoRV, revealing variations in TLR expression in koalas infected with exogenous subtypes compared to endogenous subtype, suggesting the importance of TLRs in KoRV infection and providing insights into the koala's immune response to the virus.
Review
Virology
Mohammad Enamul Hoque Kayesh, Takahiro Sanada, Michinori Kohara, Kyoko Tsukiyama-Kohara
Summary: The tree shrew model plays a significant role in understanding human viral infection and pathogenesis, highlighting its potential as a viable viral infection model. Researchers have summarized the latest progress of the tree shrew model in this area.
Review
Microbiology
Mohammad Enamul Hoque Kayesh, Michinori Kohara, Kyoko Tsukiyama-Kohara
Summary: Dengue virus, caused by DENV, is a major threat to human health. The immune system plays a crucial role in fighting against DENV. While there is a partially protective dengue vaccine available, further research is needed to develop a fully protective, durable, and safe vaccine.
FRONTIERS IN MICROBIOLOGY
(2021)
Review
Agriculture, Dairy & Animal Science
Md. Hakimul Haque, Md. Aminul Islam, Md. Rezaul Karim, Mohammad Enamul Hoque Kayesh, Subir Sarker, K. H. M. Nazmul Hussain Nazir, M. Sawkat Anwer
Summary: The COVID-19 pandemic has had detrimental effects on various sectors globally, especially in livestock. Mitigating the negative impacts of COVID-19 on livestock requires implementing current guidelines, as human health and livelihood are closely intertwined with animal health.
Review
Biochemistry & Molecular Biology
Mohammad Enamul Hoque Kayesh, Michinori Kohara, Kyoko Tsukiyama-Kohara
Summary: Chronic hepatitis B virus (HBV) infection is a major global health problem, and the link between Toll-like receptors (TLRs) and chronic HBV infection is being increasingly recognized. TLR agonists have the potential to enhance the host immune response against HBV infection and improve CHB treatment.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Virology
Mohammad Enamul Hoque Kayesh, Michinori Kohara, Kyoko Tsukiyama-Kohara
Summary: The emergence of SARS-CoV-2 and the resulting COVID-19 pandemic have highlighted the importance of understanding the interaction between the virus and host immune responses. Toll-like receptors (TLRs) play a critical role in innate immunity, but their dysregulation may lead to immune-mediated pathology. Utilizing TLR agonists as vaccine adjuvants could enhance the efficacy of COVID-19 vaccines.
Review
Biochemistry & Molecular Biology
Mohammad Enamul Hoque Kayesh, Michinori Kohara, Kyoko Tsukiyama-Kohara
Summary: This review discusses the importance of TLR responses in HCV infection and the mechanisms adopted by HCV to avoid immune surveillance mediated by TLRs.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Infectious Diseases
Md Abul Hashem, Mohammad Enamul Hoque Kayesh, Fumie Maetani, Atsushi Goto, Noriko Nagata, Aki Kasori, Tetsuya Imanishi, Kyoko Tsukiyama-Kohara
Summary: The study investigated the proviral copies and RNA expression in KoRV-infected koalas, revealing variations in viral load based on factors such as age and institution. Different KoRV subtypes were identified in the Japanese zoo koala populations, with additional risk factors like sex and age identified.
INFECTION GENETICS AND EVOLUTION
(2022)
Review
Microbiology
Mohammad Enamul Hoque Kayesh, Md Abul Hashem, Michinori Kohara, Kyoko Tsukiyama-Kohara
Summary: Chronic hepatitis B virus (HBV) infection is a global health problem, and current antiviral therapies are unable to fully cure it. The CRISPR/Cas system shows promise for genome editing and gene therapy, particularly in cleaving HBV DNA. However, the challenge lies in delivering the CRISPR/Cas9 system to target sites in vivo. This review discusses the development of delivery tools, such as adeno-associated virus vectors and lipid nanoparticle-based CRISPR/Cas ribonucleoprotein delivery, to enhance the antiviral efficacy of CRISPR/Cas9 against HBV infection.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Microbiology
Mohammad Enamul Hoque Kayesh, Md Abul Hashem, Fumie Maetani, Atsushi Goto, Noriko Nagata, Aki Kasori, Tetsuya Imanishi, Kyoko Tsukiyama-Kohara
Summary: This study investigated the immune responses of captive koalas infected with multiple KoRV subtypes. The results showed that CD4 and CD8b mRNA expression in koala PBMCs were not significantly affected by different KoRV subtypes. Although there was a slight difference in IFN-gamma mRNA expression in koala PBMCs infected with different subtypes, the difference was not statistically significant. Additionally, IL-6 and IL-10 mRNA expression did not vary significantly in koala PBMCs based on KoRV subtype differences. The study also found significant differential expression of TLR5, 7, 9, 10, and 13 mRNA in koala PBMCs infected with different KoRV subtypes.
Review
Microbiology
Mohammad Enamul Hoque Kayesh, Michinori Kohara, Kyoko Tsukiyama-Kohara
Summary: Hepatotropic viruses can cause acute and chronic liver infections, leading to morbidity and mortality in humans. In Bangladesh, hepatitis A virus (HAV) and hepatitis E virus (HEV) are the main causative agents of acute hepatitis. This review provides an overview of the epidemiology of these hepatotropic viruses in Bangladesh and discusses their transmission modes and control and prevention measures.
Review
Biochemistry & Molecular Biology
Mohammad Enamul Hoque Kayesh, Md Abul Hashem, Kyoko Tsukiyama-Kohara
Summary: Koala populations are declining and facing the threat of KoRV infection, understanding the immune response mechanisms is crucial for prevention and treatment. Vaccines are considered effective measures, while CRISPR/Cas9-based genome editing could be a potential tool for treating KoRV infection.
CURRENT ISSUES IN MOLECULAR BIOLOGY
(2021)
