Article
Biochemistry & Molecular Biology
Nikhil Baban Ghate, Sungmin Kim, Roasa Mehmood, Yonghwan Shin, Kyunghwan Kim, Woojin An
Summary: VprBP is an overexpressed kinase in cancer cells that plays a major role in epigenetic gene silencing and tumorigenesis. It has been found to phosphorylate p53 at serine 367 (S367p), leading to attenuation of p53's transcriptional and growth suppressive activities.
Article
Biochemistry & Molecular Biology
Luana Carvalho, Hu Chen, Mark Maienschein-Cline, Elizabeth J. Glover, Subhash C. Pandey, Amy W. Lasek
Summary: It was found that the expression of the gene encoding the splicing factor, PCBP1, was increased in the hippocampus of rats and human subjects with AUD during withdrawal. One gene, Hapln2, showed increased usage of a novel splice site in rats during withdrawal, which was also observed in the hippocampus of AUD subjects. PCBP1 was shown to associate with the splice site near HAPLN2 in rats and human subjects during withdrawal and in AUD. The aberrant splicing of HAPLN2 caused by PCBP1 may lead to loss of protein function and negatively impact hippocampal function in AUD.
MOLECULAR PSYCHIATRY
(2023)
Article
Biochemistry & Molecular Biology
Hyun Jung Oh, Rodrigo Aguilar, Barry Kesner, Hun-Goo Lee, Andrea J. Kriz, Hsueh-Ping Chu, Jeannie T. Lee
Summary: Jpx RNA acts as a determinant of anchor selectivity, influencing CTCF binding and chromosome looping, as well as regulating the expression of Jpx target genes.
Article
Microbiology
Dai-Qing Wu, Qiu-Ying Ding, Na-Na Tao, Ming Tan, Yuan Zhang, Fan Li, Yu-Jiao Zhou, Mei-Ling Dong, Sheng-Tao Cheng, Fang Ren, Juan Chen, Ji-Hua Ren
Summary: This study reveals that SIRT2, a class III histone deacetylase, is significantly upregulated in patients with chronic hepatitis B (CHB), and its protein level is positively correlated with HBV viral load and other clinical indicators. Functional analysis shows that ectopic SIRT2 overexpression promotes HBV transcription and replication, while SIRT2 silencing inhibits HBV transcription and replication. Mechanistically, SIRT2 enhances the activities of transcription factor p53, which affects HBV transcription and replication.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Multidisciplinary Sciences
Hyunyoung Yoon, Kyung Lib Jang
Summary: This study found that HBV X protein and HCV core protein work together to inhibit the expression of E-cadherin in cells, leading to an increased risk of hepatocellular carcinoma. HBV and HCV increase the level and activity of DNA methyl-transferases, resulting in hypermethylation of the E-cadherin promoter. This leads to epithelial-mesenchymal transition and tumor metastasis.
Article
Multidisciplinary Sciences
Magda Rybicka, Eloi R. Verrier, Thomas F. Baumert, Krzysztof Piotr Bielawski
Summary: This study included 284 patients with chronic hepatitis B virus infection and found that certain genetic variations in DIO2, PPARG, GADD45A, and ATF3 were associated with liver fibrosis and cirrhosis in this population. Additionally, a variation in DIO2 was associated with hepatocellular carcinoma.
SCIENTIFIC REPORTS
(2023)
Article
Medicine, General & Internal
Jiali Pan, Yu Tian, Jinghang Xu, Hao Luo, Ning Tan, Yifan Han, Qian Kang, Hongyu Chen, Yuqing Yang, Xiaoyuan Xu
Summary: This study explores the long-term dynamics of serum HBV pgRNA in patients with chronic hepatitis B. The positive rates of HBV pgRNA gradually decline and show biphasic kinetics. Patients treated with entecavir have a later HBV pgRNA seroconversion. Patients who remain positive for HBV pgRNA after 9 years of treatment may have higher viral transcription efficiencies.
FRONTIERS IN MEDICINE
(2022)
Article
Cell Biology
Imke K. Mandemaker, Evelyn Fessler, David Corujo, Christiane Kotthoff, Andreas Wegerer, Clement Rouillon, Marcus Buschbeck, Lucas T. Jae, Francesca Mattiroli, Andreas G. Ladurner
Summary: The study reveals that the histone chaperone ANP32B regulates the deposition of macroH2A and stimulates its incorporation into chromatin.
Review
Biochemistry & Molecular Biology
Lung-Yi Mak, Ka-Shing Cheung, James Fung, Wai-Kay Seto, Man-Fung Yuen
Summary: Functional cure, defined by clearance of hepatitis B surface antigen, is not yet achievable with currently approved therapies. Novel treatments in development aim to inhibit viral replication/antigen reduction and restore immune control. However, challenges remain in terms of clinical implications, immunological perturbations, and safety of these compounds.
TRENDS IN MOLECULAR MEDICINE
(2022)
Article
Cell Biology
Alexander Strubel, Philipp Muenick, Oliver Hartmann, Apirat Chaikuad, Birgit Dreier, Jonas V. Schaefer, Jakob Gebel, Christian Osterburg, Marcel Tuppi, Birgit Schaefer, Viktoria Buck, Mathias Rosenfeldt, Stefan Knapp, Andreas Pluckthun, Markus E. Diefenbacher, Volker Doetsch
Summary: p63 and p73, members of the p53 family, regulate transcriptional programs in epithelial tissues and several cell types. In cells expressing both proteins, a p63(2)/p73(2) hetero-tetramer is formed. The level of this hetero-tetramer increases in squamous cell carcinoma.
CELL DEATH & DISEASE
(2023)
Article
Biology
Lei Li, Zhigang Xue, Xiuquan Du
Summary: CircRNA is a non-coding RNA with a circular structure that interacts with RNA-binding proteins through binding sites, playing a key role in various biological activities. Previous studies mainly focused on extracting rich features from multiple views, but the increasing number of views led to redundant information. To address this, we proposed the use of a channel attention mechanism to filter out invalid information and obtain useful multi-view features. Our method outperformed existing methods in detecting RNA binding sites, with an average AUC performance of 93.85%.
COMPUTERS IN BIOLOGY AND MEDICINE
(2023)
Article
Biochemistry & Molecular Biology
Michael G. Mohsen, Matthew K. Midy, Aparaajita Balaji, Ronald R. Breaker
Summary: Researchers have discovered that some engineered aptamers that work well in test tubes may fail to function in cells. To address this issue, they developed the 'Graftamer' approach, using the architecture of a natural riboswitch to improve aptamer selection in vitro and accelerate testing in vivo. The researchers successfully obtained aptamers for quinine, guanine, and caffeine through multiplexed in vitro selection, and these aptamers maintained the structural features of the natural guanine riboswitch aptamer. By grafting the quinine and caffeine aptamers onto a natural guanine riboswitch expression platform, they confirmed their function in cells. They also identified a class of RNA sequences that evaded the selection strategy and gained insight for future improvements.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Anna Barile, Theo Battista, Annarita Fiorillo, Martino Luigi di Salvo, Francesco Malatesta, Angela Tramonti, Andrea Ilari, Roberto Contestabile
Summary: PLP, the active form of vitamin B6, is crucial in metabolism as an enzyme cofactor. In Escherichia coli, PNPO catalyzes PLP formation and is inhibited by the same molecule through allosteric regulation. Crystallographic studies identified the allosteric site of PLP on PNPO, and mutagenesis of the arginine cage can modulate the enzyme's allosteric properties.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2021)
Article
Microbiology
Shiv Kumar, Rohit Verma, Sandhini Saha, Ashish Kumar Agrahari, Shivangi Shukla, Oinam Ningthemmani Singh, Umang Berry, Tushar Kanti Maiti, Shailendra Asthana, C. T. Ranjith-Kumar, Milan Surjit
Summary: Multiple processes exist in a cell to ensure continuous production of essential proteins through different translation processes. Viruses have evolved strategies to use the host translation machinery for their protein synthesis. This study identifies the RNA-protein interactome of the HEV IRESl element and demonstrates the roles of ribosomal protein RPL5 and RNA helicase A (DHX9) in mediating HEV IRESl activity, establishing it as a bona fide internal translation initiation site.
MICROBIOLOGY SPECTRUM
(2023)
Article
Virology
Andrea Magri, James M. Harris, Valentina D'Arienzo, Rosalba Minisini, Frank Juhling, Peter A. C. Wing, Rachele Rapetti, Monica Leutner, Barbara Testoni, Thomas F. Baumert, Fabien Zoulim, Peter Balfe, Mario Pirisi, Jane A. McKeating
Summary: Chronic hepatitis B virus (HBV) infection is a global health problem that is characterized by interactions between the virus and the host immune system, leading to a spectrum of liver disease. The study investigates the contribution of HBV genomes, including episomal covalently closed circular DNA (cccDNA) and chromosomal integrants, to viral transcripts in chronic hepatitis B (CHB). The results demonstrate that cccDNA-derived transcripts are associated with liver inflammation markers, while integrant-derived transcripts are significantly associated with increasing age but not with inflammatory status.
Article
Surgery
Yvette Chong, Ye-Xin Koh, Jin-Yao Teo, Peng-Chung Cheow, Pierce K. Chow, Alexander Y. Chung, Chung-Yip Chan, Brian K. P. Goh
Summary: The study found that patients with previous non-liver-related abdominal surgery undergoing MILR did not have inferior outcomes compared to patients without previous abdominal surgery. Measures of operative difficulty and complication rates were comparable between the two groups and subgroups.
SURGICAL ENDOSCOPY AND OTHER INTERVENTIONAL TECHNIQUES
(2022)
Article
Surgery
Yun Le Linn, Yuxin Guo, Ye-Xin Koh, Pierce K. H. Chow, Chung-Yip Chan, Alexander Y. F. Chung, London L. P. J. Ooi, Brian K. P. Goh
Summary: This study retrospectively reviewed 25 patients who underwent metastasectomy for intraabdominal EHM from 2003 to 2016. The findings showed that hepatitis B positivity and high tumor grade were significant preoperative predictors of futile surgery. All 7 patients who had both hepatitis B and high tumor grade experienced early recurrence post-metastasectomy.
WORLD JOURNAL OF SURGERY
(2021)
Correction
Multidisciplinary Sciences
Phuong H. D. Nguyen, Siming Ma, Cheryl Z. J. Phua, Neslihan A. Kaya, Hannah L. H. Lai, Chun Jye Lim, Jia Qi Lim, Martin Wasser, Liyun Lai, Wai Leong Tam, Tony K. H. Lim, Wei Keat Wan, Tracy Loh, Wei Qiang Leow, Yin Huei Pang, Chung Yip Chan, Ser Yee Lee, Peng Chung Cheow, Han Chong Toh, Florent Ginhoux, Shridhar Iyer, Alfred W. C. Kow, Yock Young Dan, Alexander Chung, Glen K. Bonney, Brian K. P. Goh, Salvatore Albani, Pierce K. H. Chow, Weiwei Zhai, Valerie Chew
NATURE COMMUNICATIONS
(2021)
Editorial Material
Oncology
Sin Chi Chew, Si Ying Choo, Pierce Kah-Hoe Chow
Summary: A shared immunosuppressive microenvironment was found between foetal liver and hepatocellular carcinoma (HCC), with the re-emergence of specific cells mediated via VEGF-NOTCH signalling. These discoveries suggest novel targets for therapeutic interventions in HCC.
BRITISH JOURNAL OF CANCER
(2021)
Review
Oncology
Sadahisa Ogasawara, Su-Pin Choo, Jiang-Tao Li, Changhoon Yoo, Bruce Wang, Dee Lee, Pierce K. H. Chow
Summary: Systemic therapies like sorafenib and lenvatinib have been standard for advanced HCC treatment, but the approval of atezolizumab in combination with bevacizumab has opened up new possibilities for immunotherapy. As treatment options expand, the challenge in the Asia-Pacific region lies in different drug availability and costs, requiring expert opinions to optimize outcomes for advanced HCC.
Article
Oncology
Mihir Gandhi, Wen-Huan Ling, Chien-Hung Chen, Joon Hyeok Lee, Masatoshi Kudo, Rawisak Chanwat, Simone Strasser, Zhu Xu, Soh-Han Lai, Pierce Kah-Hoe Chow
Summary: The study revealed that the COVID-19 pandemic has significantly impacted the management of HCC among Asia-Pacific countries, leading to delays in diagnosis, changes in treatment modalities, and an increase in video/telephonic consultations. There were considerable variations in changes in HCC management among different countries.
JOURNAL OF HEPATOCELLULAR CARCINOMA
(2021)
Article
Pathology
Indhu-Shree Rajan-Babu, Gui-Ping Phang, Hai-Yang Law, Caroline G. Lee, Samuel S. Chong
Summary: This study presents a rapid, first-tier test based on melting curve analysis for concurrent detection of FMR1 CGG-repeat expansions and their methylation status. The assay showed high sensitivity and specificity and could detect various FMR1 genotypes. The results of this study could aid in fragile X screening and carrier screening of women of reproductive age.
JOURNAL OF MOLECULAR DIAGNOSTICS
(2022)
Article
Rheumatology
Lee Jin Lim, Ashley J. W. Lim, Brandon N. S. Ooi, Justina Wei Lynn Tan, Ee Tzun Koh, Ttsh Rheumatoid Arthritis Study Group, Samuel S. Chong, Chiea Chuen Khor, Lisa Tucker-Kellogg, Caroline G. Lee, Khai Pang Leong
Summary: This study identified sensitive and specific predictors of MTX response in RA patients through a novel strategy combining biologically meaningful genetic feature selection and machine learning. These predictors may facilitate better treatment decision-making in RA management.
Article
Multidisciplinary Sciences
Weiwei Zhai, Hannah Lai, Neslihan Arife Kaya, Jianbin Chen, Hechuan Yang, Bingxin Lu, Jia Qi Lim, Siming Ma, Sin Chi Chew, Khi Pin Chua, Jacob Josiah Santiago Alvarez, Pauline Jieqi Chen, Mei Mei Chang, Lingyan Wu, Brian K. P. Goh, Alexander Yaw-Fui Chung, Chung Yip Chan, Peng Chung Cheow, Ser Yee Lee, Juinn Huar Kam, Alfred Wei-Chieh Kow, Iyer Shridhar Ganpathi, Rawisak Chanwat, Jidapa Thammasiri, Boon Koon Yoong, Diana Bee-Lan Ong, Vanessa H. de Villa, Rouchelle D. Dela Cruz, Tracy Jiezhen Loh, Wei Keat Wan, Zeng Zeng, Anders Jacobsen Skanderup, Yin Huei Pang, Krishnakumar Madhavan, Tony Kiat-Hon Lim, Glenn Bonney, Wei Qiang Leow, Valerie Chew, Yock Young Dan, Wai Leong Tam, Han Chong Toh, Roger Sik-Yin Foo, Pierce Kah-Hoe Chow
Summary: This study investigated intra-tumor heterogeneity in hepatocellular carcinoma (HCC) using a large prospective surgical cohort. The results showed that phenotypic heterogeneity had a different trajectory across stages and diversified rapidly in some patients. Interestingly, phenotypic heterogeneity was found to be more informative in predicting patient survival than genomic heterogeneity, highlighting the importance of studying phenotypic evolution in cancer types.
NATIONAL SCIENCE REVIEW
(2022)
Article
Medicine, General & Internal
Ashley J. W. Lim, Lee Jin Lim, Brandon N. S. Ooi, Ee Tzun Koh, Justina Wei Lynn Tan, Samuel S. Chong, Chiea Chuen Khor, Lisa Tucker-Kellogg, Khai Pang Leong, Caroline G. Lee
Summary: This study proposes a novel approach to predict methotrexate response in rheumatoid arthritis patients by integrating coding haplotypes and machine learning. Through machine learning models, 100 features with good predictive performance were identified, with the majority of predictive pfcHap SNPs predicted to be potentially functional.
Article
Medical Laboratory Technology
Mulias Lian, Chanin Limwongse, Chui-Sheun Yoon, Caroline G. Lee, Hai-Yang Law, Samuel S. Chong
Summary: This study presents a simplified single-tube assay that can simultaneously screen for CAG repeat expansion in the genes responsible for SCAs 1, 2, 3, 6, 7, 12, and dentatorubral-pallidoluysian atrophy. The method uses differentially labeled locus-specific primers and a common triplet-primed primer to distinguish amplified products from each locus. Blinded evaluation of the assay on 60 genotype-known DNA samples correctly detected repeat expansion in the expected SCA repeat locus for all samples.
CLINICAL CHEMISTRY
(2022)
Article
Multidisciplinary Sciences
Sock Hoai Chan, Yasmin Bylstra, Jing Xian Teo, Jyn Ling Kuan, Nicolas Bertin, Mar Gonzalez-Porta, Maxime Hebrard, Roberto Tirado-Magallanes, Joanna Hui Juan Tan, Justin Jeyakani, Zhihui Li, Jin Fang Chai, Yap Seng Chong, Sonia Davila, Liuh Ling Goh, Eng Sing Lee, Eleanor Wong, Tien Yin Wong, Shyam Prabhakar, Jianjun Liu, Ching-Yu Cheng, Birgit Eisenhaber, Neerja Karnani, Khai Pang Leong, Xueling Sim, Khung Keong Yeo, John C. Chambers, E-Shyong Tai, Patrick Tan, Saumya S. Jamuar, Joanne Ngeow, Weng Khong Lim
Summary: This study characterizes the clinically significant genetic variation in Asian populations and reveals the diverse genetic risk burden attributable to ancestry-specific variants. It also identifies individuals with variants discordant to their self-reported ethnicity, possibly due to cryptic admixture. Additionally, the study highlights the presence of pharmaceutical genetic variants in a significant proportion of Asians.
NATURE COMMUNICATIONS
(2022)
Article
Medicine, Research & Experimental
Ashley J. W. Lim, C. Tera Tyniana, Lee Jin Lim, Justina Wei Lynn Tan, Ee Tzun Koh, Samuel S. Chong, Chiea Chuen Khor, Khai Pang G. Leong, Caroline G. Lee
Summary: This study utilizes machine-learning optimized polygenic risk score (PRS) to complement the limitations of genome-wide association studies (GWAS) in disease/trait outcome prediction. By predicting rheumatoid arthritis (RA), 9 SNPs were found to have excellent predictive performance and a RA ML-PRS calculator was developed for individualized clinical application.
JOURNAL OF TRANSLATIONAL MEDICINE
(2023)
Article
Medical Laboratory Technology
Vivienne J. Tan, Timing Liu, Zainul Arifin, Beatrice Pak, Arnold S. C. Tan, Simin Wong, Chiea-Chuen Khor, Henry Yang, Caroline G. Lee, Zhongwei Huang, Mahesh A. Choolani, Samuel S. Chong
Summary: This study explored the suitability of third-generation single-molecule sequencing as a screening platform for preimplantation genetic testing for aneuploidy or structural rearrangements (PGT-A/SR). The results showed that Nanopore-based PGT-A could accurately identify cells with segmental imbalance or aneuploidy, with high concordance compared to commercial kits.
CLINICAL CHEMISTRY
(2023)
Article
Oncology
Josephine Yu Yan Yap, Laura Shih Hui Goh, Ashley Jun Wei Lim, Samuel S. S. Chong, Lee Jin Lim, Caroline G. G. Lee
Summary: Hepatocellular carcinoma (HCC) is the third leading cause of cancer-related death worldwide. This study used artificial intelligence methods to identify a signature of exosomal RNAs that can predict HCC. Nine exosomal RNAs, mainly in the immune, platelet/neutrophil and cytoskeletal pathways, were identified and showed potential to be clinically useful minimally invasive biomarkers for HCC with an accuracy of about 85%.