Review
Pathology
Ugo Testa, Elvira Pelosi, Germana Castelli
Summary: Primary liver cancer is a significant global health issue, ranking sixth in cancer incidence and fourth in cancer-related death. This review provides an updated analysis on the genetic characterization of liver cancer, including gene mutation profiling, copy number alterations, and gene expression, with the identification of molecular biomarkers and therapeutic targets. These studies contribute to a better understanding of the disease heterogeneity and the discovery of new treatment strategies for HCC patients.
EXPERT REVIEW OF MOLECULAR DIAGNOSTICS
(2022)
Article
Genetics & Heredity
Soojin Park, Se Song Jang, Seungbok Lee, Minsoo Kim, Hyungtai Sim, Hyeongseok Jeon, Sung Eun Hong, Jean Lee, Jeongeun Lee, Eun Young Jeon, Jeongha Lee, Cho-Rong Lee, Soo Yeon Kim, Man Jin Kim, Jihoon G. Yoon, Byung Chan Lim, Woo Joong Kim, Ki Joong Kim, Jung Min Ko, Anna Cho, Jin Sook Lee, Murim Choi, Jong-Hee Chae
Summary: By analyzing the genetic characteristics of 1,180 Korean patients with neurological symptoms, we identified different genetic mechanisms and expression patterns for genes involved in neurodevelopmental disorders.
FRONTIERS IN GENETICS
(2022)
Article
Chemistry, Multidisciplinary
Carmen Suay-Corredera, Maria Rosaria Pricolo, Diana Velazquez-Carreras, Divya Pathak, Neha Nandwani, Carolina Pimenta-Lopes, David Sanchez-Ortiz, Inigo Urrutia-Irazabal, Silvia Vilches, Fernando Dominguez, Giulia Frisso, Lorenzo Monserrat, Pablo Garcia-Pavia, David de Sancho, James A. Spudich, Kathleen M. Ruppel, Elias Herrero-Galan, Jorge Alegre-Cebollada
Summary: Hypertrophic cardiomyopathy (HCM) is a disease caused by mutations in sarcomeric proteins, with many mutations not affecting protein structure or stability. Research shows that these mutations may disrupt the nanomechanics of cMyBP-C, affecting its regulatory role in actomyosin filaments.
Article
Chemistry, Multidisciplinary
Xing Xu, Li Lin, Jian Yang, Weizhou Qian, Rui Su, Xiaoxu Guo, Linfeng Cai, Zirun Zhao, Jia Song, Chaoyong Yang
Summary: This article introduces a nanoliter-scale single-cell multi-omics sample preparation platform called DMF-DR-seq, based on digital microfluidics. DMF-DR-seq demonstrates improved performance compared to current technology, with lower amplification bias, higher genome-wide coverage in DNA sequencing, and better gene detection ability in RNA sequencing. DMF-DR-seq was used to identify genome variation-induced abnormal transcriptome expression, revealing potential essential genes involved in the pathologic progress. The unique flexibility, sensitivity, and accuracy of DMF-DR-seq suggest its potential utility in deeper multi-omics analysis for inheritance mechanism study in single-cell biology.
Article
Biology
Bokang Ko, Jeremy M. Van Raamsdonk
Summary: Gene expression studies provide valuable insights into biological processes, such as aging. This study shows that pooling individual RNA samples before sequencing can yield similar results as sequencing them individually, reducing the cost of experiments. Analysis of gene expression changes across the genome is a powerful and unbiased tool for understanding molecular mechanisms.
Article
Biochemistry & Molecular Biology
Elena Cannone, Valeria Guglielmi, Giulia Marchetto, Chiara Tobia, Barbara Gnutti, Barbara Cisterna, Paola Tonin, Alessandro Barbon, Gaetano Vattemi, Marco Schiavone
Summary: Myofibrillar myopathies (MFMs) are a group of hereditary neuromuscular disorders characterized by myofibrillar derangement, Z-disk disintegration, and protein aggregation. Mutations in genes encoding structural proteins or molecular chaperones are implicated in MFM pathogenesis. In this study, transgenic zebrafish overexpressing mutant MYOT or CRYAB genes showed severe morphological defects and protein aggregation, resembling human myofibrillar myopathy. These findings suggest that zebrafish can serve as a useful model for studying the pathogenesis of MFM and identifying potential therapeutic targets.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Microbiology
David G. Glanville, Caroline Mullineaux-Sanders, Christopher J. Corcoran, Brian T. Burger, Saheed Imam, Timothy J. Donohue, Andrew T. Ulijasz
Summary: Heme is essential for the survival of most life on earth, including bacterial pathogens like Pseudomonas aeruginosa. By using a novel approach called Met-Seq, researchers identified 188 genes that potentially influence intracellular heme levels in P. aeruginosa, shedding light on previously unknown metabolic pathways and potential therapeutic targets.
Article
Oncology
Yaobang Wang, Xi Wang, Xiaoliang Huang, Jie Zhang, Junwen Hu, Yapeng Qi, Bangde Xiang, Qiuyan Wang
Summary: Mutated genes in DPHCC patients are associated with carcinogenesis and immunity. CXCL9 has been identified as a key gene influencing the immune microenvironment and prognosis of DPHCC.
Article
Biotechnology & Applied Microbiology
Alessandro Vinceti, Emre Karakoc, Clare Pacini, Umberto Perron, Riccardo Roberto De Lucia, Mathew J. Garnett, Francesco Iorio
Summary: CRISPR-Cas9 genome-wide screens are crucial for exploring cancer dependencies, with identifying core-fitness genes being essential for assessing therapeutic target safety and understanding tissue-specific genetic diseases. CoRe, an R package, outperforms other tools in identifying reliable and biologically relevant core-fitness genes, aiding in the prioritization of therapeutic targets.
Article
Developmental Biology
Gabriele Lubatti, Marco Stock, Ane Iturbide, Mayra L. Ruiz Tejada Segura, Melina Riepl, Richard C. V. Tyser, Anna Danese, Maria Colome-Tatche, Fabian J. Theis, Shankar Srinivas, Maria-Elena Torres-Padilla, Antonio Scialdone
Summary: A powerful computational tool called CIARA has been developed for the identification of marker genes of rare cell types in single-cell genomics. CIARA outperforms existing methods and can be applied to various types of single-cell omic data.
Article
Medicine, General & Internal
Sana Amanat, Alvaro Gallego-Martinez, Joseph Sollini, Patricia Perez-Carpena, Juan M. Espinosa-Sanchez, Ismael Aran, Andres Soto-Varela, Angel Batuecas-Caletrio, Barbara Canlon, Patrick May, Christopher R. Cederroth, Jose A. Lopez-Escamez
Summary: The study identified specific rare genetic variants associated with severe tinnitus, particularly in genes such as PRUNE2, AKAP9, SORBS1, ITGAX, ANK2, KIF20B, and TSC2. These variants play important roles in biological processes such as membrane trafficking and cytoskeletal protein binding in neurons.
Article
Multidisciplinary Sciences
Saswati Das, Raveen Stephen Stallon Illangeswaran, Smitha Ijee, Sanjay Kumar, Shaji Ramachandran Velayudhan, Poonkuzhali Balasubramanian
Summary: Understanding the mechanisms of acquired chemo-resistance is crucial for improving the survival of patients with acute myeloid leukemia. This article presents a method for identifying epigenetic factors that mediate resistance to a specific chemotherapy drug.
JOVE-JOURNAL OF VISUALIZED EXPERIMENTS
(2022)
Article
Biology
Huifen Cao, Dongyang Xu, Ye Cai, Xueer Han, Lu Tang, Fan Gao, Yao Qi, DingDing Cai, Huifang Wang, Maxim Ri, Denis Antonets, Yuri Vyatkin, Yue Chen, Xiang You, Fang Wang, Estelle Nicolas, Philipp Kapranov
Summary: This study provides strong evidence for the regulatory role of the vlincRNA class of lncRNAs, demonstrating their importance in cellular function regulation and their potential role in maintaining genome stability.
Article
Computer Science, Information Systems
Santos Bringas, Rafael Duque, Alicia Nieto-Reyes, Cristina Tirnauca, Jose Luis Montana
Summary: Collaborative systems require intuitive interaction organization and user awareness information. Usability evaluations in laboratories may be problematic as they restrict the time and place of user interactions. This paper presents a framework based on neural networks to collect human-machine interactions in mobile and ubiquitous contexts and assess system usability.
Article
Genetics & Heredity
Neringa Jurkute, Francesca Cancellieri, Lisa Pohl, Catherina H. Z. Li, Robert A. Heaton, Janine Reurink, James Bellingham, Mathieu Quinodoz, Georgia Yioti, Maria Stefaniotou, Marianna Weener, Theresia Zuleger, Tobias B. Haack, Katarina Stingl, Carel B. Hoyng, Omar A. Mahroo, Iain Hargreaves, F. Lucy Raymond, Michel Michaelides, Carlo Rivolta, Susanne Kohl, Susanne Roosing, Andrew R. Webster, Gavin Arno
Summary: The aim of this study was to investigate the defects in the biosynthesis pathway of coenzyme Q10 (CoQ(10)) in inherited retinal dystrophy. By performing exome or genome sequencing on individuals with inherited retinal dystrophy, patients carrying biallelic variants in CoQ(10) biosynthesis pathway genes were identified. The study provides evidence of CoQ(10) biosynthesis pathway gene defects leading to non-syndromic retinitis pigmentosa in some cases. Intronic variants outside of the canonical splice-sites were shown to be an important cause of the disease.
NPJ GENOMIC MEDICINE
(2022)
Article
Genetics & Heredity
Hane Lee, Alden Y. Huang, Lee-kai Wang, Amanda J. Yoon, Genecee Renteria, Ascia Eskin, Rebecca H. Signer, Naghmeh Dorrani, Shirley Nieves-Rodriguez, Jijun Wan, Emilie D. Douine, Jeremy D. Woods, Esteban C. Dell'Angelica, Brent L. Fogel, Martin G. Martin, Manish J. Butte, Neil H. Parker, Richard T. Wang, Perry B. Shieh, Derek A. Wong, Natalie Gallant, Kathryn E. Singh, Y. Jane Tavyev Asher, Janet S. Sinsheimer, Deborah Krakow, Sandra K. Loo, Patrick Allard, Jeanette C. Papp, Christina G. S. Palmer, Julian A. Martinez-Agosto, Stanley F. Nelson
GENETICS IN MEDICINE
(2020)
Article
Genetics & Heredity
Kathie J. Ngo, Jessica E. Rexach, Hane Lee, Lauren E. Petty, Susan Perlman, Juliana M. Valera, Joshua L. Deignan, Yuanming Mao, Mamdouh Aker, Jennifer E. Posey, Shalini N. Jhangiani, Zeynep H. Coban-Akdemir, Eric Boerwinkle, Donna Muzny, Alexandra B. Nelson, Sharon Hassin-Baer, Gemma Poke, Katherine Neas, Michael D. Geschwind, Wayne W. Grody, Richard Gibbs, Daniel H. Geschwind, James R. Lupski, Jennifer E. Below, Stanley F. Nelson, Brent L. Fogel
Article
Genetics & Heredity
Christine Shieh, Natasha Jones, Brigitte Vanle, Margaret Au, Alden Y. Huang, Ana P. G. Silva, Hane Lee, Emilie D. Douine, Maria G. Otero, Andrew Choi, Katheryn Grand, Ingrid P. Taff, Mauricio R. Delgado, M. J. Hajianpour, Andrea Seeley, Luis Rohena, Hilary Vernon, Karen W. Gripp, Samantha A. Vergano, Sonal Mahida, Sakkubai Naidu, Ana Berta Sousa, Karen E. Wain, Thomas D. Challman, Geoffrey Beek, Donald Basel, Judith Ranells, Rosemarie Smith, Roman Yusupov, Mary-Louise Freckmann, Lisa Ohden, Laura Davis-Keppen, David Chitayat, James J. Dowling, Richard Finkel, Andrew Dauber, Rebecca Spillmann, Loren D. M. Pena, Kay Metcalfe, Miranda Splitt, Katherine Lachlan, Shane A. McKee, Jane Hurst, David R. Fitzpatrick, Jenny E. V. Morton, Helen Cox, Sunita Venkateswaran, Juan I. Young, Eric D. Marsh, Stanley F. Nelson, Julian A. Martinez, John M. Graham, Usha Kini, Joel P. Mackay, Tyler Mark Pierson
GENETICS IN MEDICINE
(2020)
Article
Clinical Neurology
Jeremy D. Woods, Negar Khanlou, Hane Lee, Rebecca Signer, Perry Shieh, Johnathan Chen, Matthew Herzog, Christina Palmer, Julian Martinez-Agosto, Stanley F. Nelson
Article
Biochemistry & Molecular Biology
Xuedong Kang, Yan Zhao, Glen Van Arsdell, Stanley F. Nelson, Marlin Touma
Article
Genetics & Heredity
Yan Zhao, Xuedong Kang, Alexander Barsegian, Jian He, Alejandra Guzman, Ryan P. Lau, Reshma Biniwale, Madhuri Wadhra, Brian Reemtsen, Meena Garg, Nancy Halnon, Fabiola Quintero-Rivera, Wayne W. Grody, Glen Van Arsdell, Stanley F. Nelson, Marlin Touma
JOURNAL OF MOLECULAR MEDICINE-JMM
(2020)
Article
Medicine, General & Internal
Monica Tsai, Timothy J. Thauland, Alden Y. Huang, Chantana Bun, Sean Fitzwater, Paul Krogstad, Emilie D. Douine, Stanley F. Nelson, Hane Lee, Maria I. Garcia-Lloret, Manish J. Butte
NEW ENGLAND JOURNAL OF MEDICINE
(2020)
Review
Infectious Diseases
J. Wes Ulm, Stanley F. Nelson
Summary: Repurposing existing drugs and therapies for COVID-19 shows promise in developing new control strategies. Untested small molecule antivirals previously showed specificity for SARS-CoV or MERS-CoV in vitro but have been largely overlooked in current COVID-19 trials.
TRANSBOUNDARY AND EMERGING DISEASES
(2021)
Article
Genetics & Heredity
Shahram Yazdani, Anish Badjatiya, Naghmeh Dorrani, Hane Lee, Wayne W. Grody, Stanley F. Nelson, Katrina M. Dipple
MOLECULAR GENETICS AND METABOLISM REPORTS
(2020)
Article
Genetics & Heredity
Emily K. Mis, Annalisa G. Sega, Rebecca H. Signer, Tracy Cartwright, Weizhen Ji, Julian A. Martinez-Agosto, Stanley F. Nelson, Christina G. S. Palmer, Hane Lee, Thomas Mitzelfelt, Monica Konstantino, Lauren Jeffries, Mustafa K. Khokha, Elysa Marco, Martin G. Martin, Saquib A. Lakhani
Summary: A novel de novo heterozygous NEUROD2 missense variant was found in an adolescent with developmental delay but without seizures, displaying minimal protein activity in functional testing. Another rare NEUROD2 variant identified in an adolescent with developmental delay showed normal NEUROD2 activity, suggesting that NEUROD2 variants can lead to developmental delay without early-onset seizures.
AMERICAN JOURNAL OF MEDICAL GENETICS PART A
(2021)
Article
Biotechnology & Applied Microbiology
Derrick Shih-Wei Chuang, James C. Liao
Summary: This study revealed the important role of phosphoketolase (Xpk) in primary metabolism of cyanobacteria, particularly in energy regulation and dark conditions. Additionally, Xpk is involved in the pathway producing ATP from glycogen to acetate. Deletion of xpk leads to glucose secretion under dark, anaerobic conditions.
METABOLIC ENGINEERING
(2021)
Article
Multidisciplinary Sciences
David P. Bishop, Mika T. Westerhausen, Florian Barthelemy, Thomas Lockwood, Nerida Cole, Elizabeth M. Gibbs, Rachelle H. Crosbie, Stanley F. Nelson, M. Carrie Miceli, Philip A. Doble, Jonathan Wanagat
Summary: This study introduces a novel immuno-mass spectrometry imaging method for quantifying and localizing dystrophin in muscle tissue. The method was validated in mice, human skeletal muscle sections, and DMD patients with different gene mutations, demonstrating its potential for pre-clinical and clinical research in DMD.
SCIENTIFIC REPORTS
(2021)
Article
Genetics & Heredity
Ulrike Hueffmeier, Cornelia Kraus, Miriam S. Reuter, Steffen Uebe, Mary-Alice Abbott, Syed A. Ahmed, Kristyn L. Rawson, Eileen Barr, Hong Li, Ange-Line Bruel, Laurence Faivre, Frederic Tran Mau-Them, Christina Botti, Susan Brooks, Kaitlyn Burns, D. Isum Ward, Marina Dutra-Clarke, Julian A. Martinez-Agosto, Hane Lee, Stanley F. Nelson, Pia Zacher, Rami Abou Jamra, Chiara Kloeckner, Julie McGaughran, Juergen Kohlhase, Sarah Schuhmann, Ellen Moran, John Pappas, Annick Raas-Rothschild, Maria J. Guillen Sacoto, Lindsay B. Henderson, Timothy Blake Palculict, Sureni Mullegama, Houda Zghal Elloumi, Adi Reich, Samantha A. Schrier Vergano, Erica Wahl, Andre Reis, Christiane Zweier
Summary: The study identified an EIF3F variant associated with neurodevelopmental disorder, characterized by intellectual disability, epilepsy, and other symptoms. Patients showed developmental delays, behavioral problems, hearing loss, and short stature, with some also exhibiting microcephaly and reduced sensitivity to pain. A compound heterozygous individual had severe symptoms, suggesting genotype-phenotype correlation.
ORPHANET JOURNAL OF RARE DISEASES
(2021)
Article
Chemistry, Physical
Shanshan Luo, Paul P. Lin, Liang-Yu Nieh, Guan-Bo Liao, Po-Wen Tang, Chi Chen, James C. Liao
Summary: Biological CO2 fixation is the most effective method for large-scale CO2 reduction, accounting for the majority of CO2 fixed on Earth. Cell-free CO2 fixation systems offer an alternative approach, allowing independent control of the fixation rate. By designing an oxygen-insensitive, self-replenishing CO2 fixation system with opto-sensing, the researchers achieved a sustained CO2-fixing rate comparable to or greater than photosynthetic or lithoautotrophic organisms.
Article
Cell Biology
Jing-You Guo, I-Ju Liu, Hsiu-Ting Lin, Mei-Jung Wang, Yu-Ling Chang, Shin-Chang Lin, Mei-Ying Liao, Wei-Chia Hsu, Yi-Ling Lin, James C. Liao, Han-Chung Wu
Summary: By using phage display technology and enzyme-linked immunosorbent assays, 36 enriched peptides were identified in the sera of two COVID-19 patients, with 4 motifs having consensus residues corresponding to two potential B-cell epitopes on SARS-CoV-2 viral proteins. These findings may aid in investigating COVID-19 pathogenesis and advancing the development of epitope-based serological diagnostics and vaccines.
JOURNAL OF BIOMEDICAL SCIENCE
(2021)