Review
Biology
Konstantina Athanasopoulou, Glykeria N. Daneva, Michaela A. Boti, Georgios Dimitroulis, Panagiotis G. Adamopoulos, Andreas Scorilas
Summary: Deciphering the etiopathogenesis of cancer is a complex task that requires a multidimensional approach. The introduction of next- and third-generation sequencing technologies has provided powerful tools for cancer research and has expanded the scope of personalized cancer medicine and pharmacogenomics.
Article
Multidisciplinary Sciences
Haroula Kontaki, Marina Koukaki, Maria Vasilarou, Antonis Giakountis, Elena Deligianni, Xiaolin Luo, Youngsoo Kim, Iannis Talianidis
Summary: Research has shown that targeting Smyd3 with Smyd3-ASO is an efficient approach to reduce tumor burden in a mouse model of HCC, halt the growth of liver tumors, and slow down the growth rates, migration, and xenograft growth capacity of human hepatic cancer cell lines. Smyd3-ASOs also prevent the activation of oncogenic genes and the development of cancer-specific gene expression program, ultimately inhibiting the expansion of hepatic cancer stem cells.
Article
Chemistry, Multidisciplinary
Na Zhao, Jiabao Cao, Jiayue Xu, Beibei Liu, Bin Liu, Dingqiang Chen, Binbin Xia, Liang Chen, Wenhui Zhang, Yuqing Zhang, Xuan Zhang, Zhimei Duan, Kaifei Wang, Fei Xie, Kun Xiao, Wei Yan, Lixin Xie, Hongwei Zhou, Jun Wang
Summary: Utilizing RNA sequencing and third-generation sequencing technology for pathogen identification can improve the ratio of microbial reads and accelerate clinical diagnosis, showing significant potential.
Article
Nanoscience & Nanotechnology
Peng Qi, Ya-ling Zeng, Xu Ye, Ya-mei Li, Feng-jiao Wang, Wang-yang Pu, Rong Zhang, Min Li, Li Xiao, Gang Huang, Sirois Pierre, Jun Chuan, Jingjing Luo, Duan-fang Liao, Hongyan Wen, Kai Li
Summary: In this study, several strategies were tested to limit or abolish self-ligation of next generation sequencing adapters. Experimental data showed that these strategies can significantly reduce or completely eliminate self-ligation. Minimizing or eliminating self-ligation is crucial in improving the sensitivity, efficiency, and reproducibility of enzyme-mediated methylation assays. These strategies may also have applications in other nanotechnologies.
JOURNAL OF BIOMEDICAL NANOTECHNOLOGY
(2023)
Article
Nutrition & Dietetics
Hun Hwan Kim, Sang Eun Ha, Min Yeong Park, Se Hyo Jeong, Pritam Bhagwan Bhosale, Abuyaseer Abusaliya, Chung Kil Won, Jeong Doo Heo, Meejung Ahn, Je Kyung Seong, Hyun Wook Kim, Gon Sup Kim
Summary: Using RNA sequencing, this study identified KYNA as a potential therapeutic target for gastric cancer. KYNA treatment inhibited cancer cell growth and proliferation, while inducing cell death. This research can provide valuable insights for the development of drugs targeting gastric cancer.
Article
Oncology
Federico Pio Fabrizio, Stefano Castellana, Flavia Centra, Angelo Sparaneo, Mario Mastroianno, Tommaso Mazza, Michelina Coco, Domenico Trombetta, Nicola Cingolani, Antonella Centonza, Paolo Graziano, Evaristo Maiello, Vito Michele Fazio, Lucia Anna Muscarella
Summary: DNA methylation is a significant epigenetic mark in cancer cells, and methylation profiles have been suggested as promising biomarkers for cancer. Researchers designed and validated a novel targeted NGS panel for methylation analysis, which can evaluate methylation levels of multiple cancer-related genes simultaneously.
FRONTIERS IN ONCOLOGY
(2022)
Article
Oncology
Mayuko Ichimura-Shimizu, Masami Kojima, Shingo Suzuki, Misaki Miyata, Yui Osaki, Konomi Matsui, Toshiyuki Mizui, Koichi Tsuneyama
Summary: Reduced BDNF expression is associated with weight gain and non-alcoholic steatohepatitis (NASH). BDNF+/- mice show pathological features of NASH, including enhanced fatty acid metabolism and inflammation. Gene expression analysis supports the oxidative stress in BDNF+/- mice. This is the first report demonstrating the role of reduced BDNF expression in the pathogenic mechanism of NASH.
JOURNAL OF PATHOLOGY
(2023)
Article
Genetics & Heredity
Karim Hasanpur, Sevda Hosseinzadeh, Atiye Mirzaaghayi, Sadegh Alijani
Summary: Accurate normalization of gene expression assays using housekeeping genes is crucial, but there is no consensus on the suitable set of housekeeping genes for quantitative real-time PCR analyses of chicken tissues. This study utilized high-throughput gene expression data to identify the most suitable and stable reference genes for 16 chicken tissues. The results revealed tissue-specific sets of reference genes and disproved the suitability of previously widely used housekeeping genes. The newly identified reference genes can contribute to more accurate normalization for future expression analysis of chicken genes.
FRONTIERS IN GENETICS
(2022)
Article
Endocrinology & Metabolism
Yunchen Luo, Zhijian Zhang, Liping Xiang, Bing Zhou, Xuejiao Wang, Yi Lin, Xiaoying Ding, Fang Liu, Yan Lu, Yongde Peng
Summary: The study demonstrates a positive correlation between m6A methylation modifications and NAFLD, with enrichment in lipid metabolism processes. Both high fructose diet and leptin receptor deficiency result in up-regulation of genes related to lipid metabolism pathways, but different regulation of immune inflammatory response genes.
FRONTIERS IN ENDOCRINOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Kseniya Khamina, Andreas B. Diendorfer, Susanna Skalicky, Moritz Weigl, Marianne Pultar, Teresa L. Krammer, Catharine Aquino Fournier, Amy L. Schofield, Carolin Otto, Aaron Thomas Smith, Nina Buchtele, Christian Schoergenhofer, Bernd Jilma, Bernhard J. H. Frank, Jochen G. Hofstaetter, Regina Grillari, Johannes Grillari, Klemens Ruprecht, Christopher E. Goldring, Hubert Rehrauer, Warren E. Glaab, Matthias Hackl
Summary: The plasma levels of tissue-specific microRNAs can serve as diagnostic, disease severity and prognostic biomarkers. Combining diverse microRNAs into biomarker signatures using multivariate statistics is powerful in terms of tissue and condition specific microRNA shedding into the plasma.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Oncology
Nicholas D. Johnson, Xiumei Wu, Christopher D. Still, Xin Chu, Anthony T. Petrick, Glenn S. Gerhard, Karen N. Conneely, Johanna K. DiStefano
Summary: An epigenome-wide analysis of 325 individuals with NAFLD identified 7 CpG sites associated with fibrosis. Gene expression at 288 genes was found to be associated with DNAm at these fibrosis-related CpGs. DNAm-based estimates of cell-type proportions showed changes in natural killer cells and epithelial cell proportions with disease stage. An elastic net regression model predicted fibrosis with a sensitivity of 0.93, suggesting DNAm as a potential biomarker for NAFLD fibrosis.
CLINICAL EPIGENETICS
(2021)
Article
Microbiology
Trinh Thi Bich Tram, Vu Thi Ngoc Ha, Le Pham Tien Trieu, Philip M. Ashton, Emily D. Crawford, Do Dang Anh Thu, Nguyen Le Quang, Guy E. Thwaites, Timothy M. Walker, Catherine Anscombe, Nguyen Thuy Thuong Thuong
Summary: FLASH technique allows for rapid detection of Mycobacterium tuberculosis (Mtb) drug resistance from clinical samples, enabling optimal and timely treatment for tuberculosis (TB) patients.
JOURNAL OF CLINICAL MICROBIOLOGY
(2023)
Article
Oncology
Tyler Shugg, Reynold C. Ly, Wilberforce Osei, Elizabeth J. Rowe, Caitlin A. Granfield, Ty C. Lynnes, Elizabeth B. Medeiros, Jennelle C. Hodge, Amy M. Breman, Bryan P. Schneider, S. Cenk Sahinalp, Ibrahim Numanagic, Benjamin A. Salisbury, Steven M. Bray, Ryan Ratcliff, Todd C. Skaar
Summary: This study assessed the accuracy of the Aldy computational method in extracting pharmacogenomics genotypes from whole genome sequencing (WGS) and whole exome sequencing (WES) data. The results showed that Aldy achieved over 99% accuracy in calling diplotypes for major pharmacogenes from both WGS and WES data, supporting its importance in clinical applications.
FRONTIERS IN ONCOLOGY
(2023)
Article
Microbiology
Ilayda Akacin, Seymanur Ersoy, Osman Doluca, Mine Gungormusler
Summary: This review provides a comprehensive overview of recent literature on the utilization of TGS and NGS technologies in microbial metagenomics research. It discusses the advantages and limitations of these technologies and presents real-time examples of novel applications in clinical microbiology and public health, food and agriculture, energy and environment, arts and space.
MICROBIOLOGICAL RESEARCH
(2022)
Review
Environmental Sciences
Tessa M. Page, Jonathan W. Lawley
Summary: As we enter the United Nations Decade of Ocean Science for Sustainable Development, efforts to reverse ocean health decline are urgent. Transcriptomic technologies are playing an increasingly important role in marine ecology research, providing researchers with valuable tools to understand genetic variation, cellular processes, and pathways.
FRONTIERS IN MARINE SCIENCE
(2022)
Article
Endocrinology & Metabolism
Hajime Yamakage, Yousuke Konishi, Kazuya Muranaka, Kikuko Hotta, Yoshihiro Miyamoto, Hiroko Morisaki, Takayuki Morisaki, Noriko Satoh-Asahara
Summary: This study aimed to investigate the contribution of PTPN1 polymorphisms on weight reduction and diabetes in obese Japanese patients. The results showed that the SNP rs3787348 in PTPN1 was associated with the effects of weight reduction therapy on BMI and waist circumference among obese Japanese patients.
JOURNAL OF DIABETES INVESTIGATION
(2021)
Review
Biochemistry & Molecular Biology
Takaomi Kessoku, Takashi Kobayashi, Kosuke Tanaka, Atsushi Yamamoto, Kota Takahashi, Michihiro Iwaki, Anna Ozaki, Yuki Kasai, Asako Nogami, Yasushi Honda, Yuji Ogawa, Shingo Kato, Kento Imajo, Takuma Higurashi, Kunihiro Hosono, Masato Yoneda, Haruki Usuda, Koichiro Wada, Satoru Saito, Atsushi Nakajima
Summary: Recent studies have shown a relationship between gut bacteria and NAFLD. Endotoxins produced by Gram-negative bacilli may play a role in the pathogenesis of NAFLD. Treatment strategies can target both intestinal and hepatic factors in NAFLD.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Education & Educational Research
Takaomi Kessoku, Yu Uneno, Yuka Urushibara-Miyachi, Kiyofumi Oya, Akihiko Kusakabe, Atsushi Nakajima, Noritoshi Kobayashi, Yasushi Ichikawa, Mitsunori Miyashita, Manabu Muto, Masanori Mori, Tatsuya Morita
Summary: This study aimed to develop a list of competencies and EPAs necessary for death pronouncement practice. Through anonymous modified Delphi study and non-anonymous web conference, a consensus was reached on a list that includes 11 competencies and 9 EPAs.
BMC MEDICAL EDUCATION
(2022)
Article
Gastroenterology & Hepatology
Suguru Kurokawa, Masato Yoneda, Yuji Ogawa, Yasushi Honda, Takaomi Kessoku, Kento Imajo, Satoru Saito, Atsushi Nakajima, Kikuko Hotta
Summary: In this study, two differentially methylated region networks were examined in viral hepatitis and hepatocellular carcinoma. One network was associated with fibrosis and tumorigenesis in both NAFLD and viral hepatitis, while the other network was specifically associated with NAFLD progression. FABP1, SGK2, and HNF4A were identified as potential candidate targets for the prevention and treatment of HCC.
BMC GASTROENTEROLOGY
(2022)
Article
Gastroenterology & Hepatology
Yuki Kasai, Takaomi Kessoku, Kosuke Tanaka, Atsushi Yamamoto, Kota Takahashi, Takashi Kobayashi, Michihiro Iwaki, Anna Ozaki, Asako Nogami, Yasushi Honda, Yuji Ogawa, Shingo Kato, Kento Imajo, Takuma Higurashi, Kunihiro Hosono, Masato Yoneda, Haruki Usuda, Koichiro Wada, Miwa Kawanaka, Takumi Kawaguchi, Takuji Torimura, Masayoshi Kage, Hideyuki Hyogo, Hirokazu Takahashi, Yuichiro Eguchi, Shinichi Aishima, Noritoshi Kobayashi, Yoshio Sumida, Akira Honda, Shunsuke Oyamada, Satoru Shinoda, Satoru Saito, Atsushi Nakajima
Summary: The study found that the concentrations of fecal and serum BAs were significantly higher in patients with NAFLD as fibrosis worsened, indicating the involvement of abnormal BA metabolism in the progression of fibrosis in NAFLD. Abnormalities in BA metabolism may be a potential therapeutic target in NAFLD with fibrosis.
CLINICAL AND TRANSLATIONAL GASTROENTEROLOGY
(2022)
Article
Oncology
Anna Ozaki, Takaomi Kessoku, Kosuke Tanaka, Atsushi Yamamoto, Kota Takahashi, Yuma Takeda, Yuki Kasai, Michihiro Iwaki, Takashi Kobayashi, Tsutomu Yoshihara, Takayuki Kato, Akihiro Suzuki, Yasushi Honda, Yuji Ogawa, Akiko Fuyuki, Kento Imajo, Takuma Higurashi, Masato Yoneda, Masataka Taguri, Hiroto Ishiki, Noritoshi Kobayashi, Satoru Saito, Yasushi Ichikawa, Atsushi Nakajima
Summary: Opioids are commonly used in cancer pain management, but can cause constipation as a side effect. Traditional laxatives may not be effective in preventing opioid-induced constipation. However, a new drug called naldemedine has been found to safely and effectively treat this constipation without affecting pain relief. This study compared the effectiveness of magnesium oxide and naldemedine in preventing opioid-induced constipation, and found that naldemedine significantly prevented deterioration in constipation-specific quality of life and reduced gastrointestinal adverse effects compared to magnesium oxide.
Article
Multidisciplinary Sciences
Aya Kitamoto, Takuya Kitamoto
Summary: The changes in lipid profile during the differentiation and maturation of cultured human subcutaneous white preadipocytes into mature adipocytes were described. Different stages of cells were clearly separated based on lipid extraction and mass spectrometry analysis. A total of 145 lipid species were identified to have statistical significance.
Article
Medicine, General & Internal
Michihiro Iwaki, Takaomi Kessoku, Kosuke Tanaka, Anna Ozaki, Yuki Kasai, Atsushi Yamamoto, Kota Takahashi, Takashi Kobayashi, Asako Nogami, Yasushi Honda, Yuji Ogawa, Kento Imajo, Masato Yoneda, Noritoshi Kobayashi, Satoru Saito, Atsushi Nakajima
Summary: Non-alcoholic fatty liver disease (NAFLD) is a liver disease associated with metabolic abnormalities. Currently, there is no consensus on the efficacy and safety of drugs used to treat NAFLD. Guanabenz acetate is a potential treatment for improving NAFLD and metabolic abnormalities. This study aims to evaluate the efficacy and safety of guanabenz acetate treatment in NAFLD patients.
Review
Nutrition & Dietetics
Takashi Kobayashi, Michihiro Iwaki, Asako Nogami, Yasushi Honda, Yuji Ogawa, Kento Imajo, Satoru Saito, Atsushi Nakajima, Masato Yoneda
Summary: The increasing prevalence of NAFLD and NASH, along with changes in global lifestyle, necessitates further research to understand the mechanisms and develop new treatment strategies. Furthermore, the association between periodontal disease and systemic conditions suggests the need for exploration in this area. This review provides a summary of recent studies on the link between periodontal disease and NAFLD, the concept of the mouth-gut-liver axis, oral and intestinal microbiota, and liver disease, as well as proposing new directions for research and treatment.
Article
Multidisciplinary Sciences
Takuya Kitamoto, Aya Kitamoto
Summary: In this study, changes in lipid and protein profiles during the differentiation and maturation of adipocytes were reported using cultured adipocyte cell lines. It was found that numerous proteins were significantly altered during the differentiation and maturation of adipocytes, involving multiple pathways.
Article
Health Care Sciences & Services
Akiko Abe, Koji Amano, Tatsuya Morita, Tomofumi Miura, Naoharu Mori, Ryohei Tatara, Takaomi Kessoku, Yoshinobu Matsuda, Keita Tagami, Hiroyuki Otani, Masanori Mori, Tomohiko Taniyama, Nobuhisa Nakajima, Erika Nakanishi, Jun Kako, Daisuke Kiuchi, Hiroto Ishiki, Hiromichi Matsuoka, Eriko Satomi, Mitsunori Miyashita
Summary: Beliefs and perceptions of parenteral nutrition and hydration (PNH) among advanced cancer patients have not been clarified. However, more than half of the patients believe that PNH is beneficial and a standard medical practice, but many patients feel that they have not received sufficient explanation.
PALLIATIVE MEDICINE REPORTS
(2022)
Article
Medicine, Research & Experimental
Atsushi Yamamoto, Takaomi Kessoku, Kosuke Tanaka, Kota Takahashi, Yuki Kasai, Anna Ozaki, Michihiro Iwaki, Takashi Kobayashi, Tsutomu Yoshihara, Noboru Misawa, Kanji Ohkuma, Akiko Fuyuki, Takuma Higurashi, Kunihiro Hosono, Masato Yoneda, Tomoyuki Iwasaki, Takeo Kurihashi, Machiko Nakatogawa, Ayao Suzuki, Masataka Taguri, Shunsuke Oyamada, Keisuke Ariyoshi, Noritoshi Kobayashi, Yasushi Ichikawa, Atsushi Nakajima
Summary: This study aims to investigate the improvement of loss of defecation desire in patients with chronic constipation after 4 weeks of Elobixibat treatment.
CONTEMPORARY CLINICAL TRIALS COMMUNICATIONS
(2022)
Article
Health Care Sciences & Services
Yusuke Hiratsuka, Mitsunori Miyashita, Yu Uneno, Kiyohumi Oya, Soichiro Okamoto, Takaomi Kessoku, Hironori Mawatari, Shunsuke Oyamada, Junko Nozato, Keita Tagami, Akira Inoue
Summary: This study developed a scale, DPBS-oncol, to evaluate the burden experienced by clinicians related to death pronouncement. The scale was validated and shown to have sufficient reliability. Furthermore, the total score of DPBS-oncol was moderately correlated with other scales measuring clinicians' attitudes towards end-of-life care.
PALLIATIVE MEDICINE REPORTS
(2022)