Article
Immunology
Chenxi Liu, Songxin Yan, Haizhen Chen, Ziyan Wu, Liubing Li, Linlin Cheng, Haolong Li, Yongzhe Li
Summary: This study found that the GTF2I rs117026326 and rs73366469 SNPs were strongly associated with SSc in the Chinese Han population, while NFKB1 rs1599961 showed a suggestive association with SSc. However, TYK2 rs2304256 was not significantly associated with SSc in this particular population.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Julia P. A. S. Tormin, Bruno R. Nascimento, Craig A. Sable, Jose Luiz P. da Silva, Camilo Brandao-de-Resende, Luiz Paulo C. Rocha, Cecilia H. R. Pinto, Eula Graciele A. Neves, Frederico V. B. Macedo, Clara L. Fraga, Kaciane K. B. Oliveira, Adriana C. Diamantino, Antonio Luiz P. Ribeiro, Andrea Z. Beaton, Maria Carmo P. Nunes, Walderez O. Dutra
Summary: Inflammation associated with rheumatic heart disease is influenced by gene polymorphisms and inflammatory cytokines. Serum levels of cytokines were found to be higher in clinical RHD patients compared to latent RHD patients, with IL-4, IL-8, and IL-1RA emerging as the best predictors of clinical disease. Gene polymorphisms in IL2, IL4, IL6, and IL10 were associated with clinical RHD, suggesting a potential role in discriminating between latent and clinical RHD.
Article
Rheumatology
Kristina Elizabeth Neergaard Clark, Corrado Campochiaro, Eszter Csomor, Adam Taylor, Katherine Nevin, Nicholas Galwey, Mary A. Morse, Jennifer Singh, Yee Voan Teo, Voon H. Ong, Emma Derrett-Smith, Nicolas Wisniacki, Shaun M. Flint, Christopher P. Denton
Summary: Clinical heterogeneity is a key feature of systemic sclerosis (SSc), with hallmark SSc autoantibodies playing a central role in diagnosis and associating with distinct patterns of complications. This study used high-dimensional transcriptional and proteomic analysis to reveal a molecular spectrum of SSc based on skin gene expression and serum protein analysis, showing differences in fibrosis markers and gene expression profiles between different autoantibody specificities. Individual patient pathway analysis identified overlapping and distinct disease processes within SSc subgroups.
ANNALS OF THE RHEUMATIC DISEASES
(2021)
Article
Rheumatology
Yasser B. M. Ali, Basima A. El-Akhras, R. El-Shazly, Iman H. Bassyouni
Summary: Cytokine polymorphisms are associated with SLE pathogenicity, including the important cytokine IL-27. A study on Egyptian population showed that the TG genotype and G allele of the IL-27p28 gene may be risk factors for SLE susceptibility.
CLINICAL RHEUMATOLOGY
(2021)
Article
Genetics & Heredity
Jie Wei, Huan Zhang, Xiaoya Ma, Yujie Li, Wenqian Zhou, Jinping Guo, Tianbo Jin, Mingjun Hu
Summary: This study investigated the association between single nucleotide polymorphisms (SNPs) of the OR51E1 gene and glioma susceptibility in the Chinese Han population. The results showed that polymorphisms rs10768148, rs7102992, and rs10500608 were associated with glioma risk in the overall sample. Stratified analyses based on gender and age revealed specific SNP-glioma associations. Additionally, synergistic and redundant relationships between certain SNPs were identified. Overall, this study provides a basis for assessing glioma risk-associated variants in the Chinese Han population.
Article
Multidisciplinary Sciences
Mohamed Jahromi, Torki Al-Otaibi, Osama Ashry Gheith, Nashwa Farouk Othman, Tarek Mahmoud, Parasad Nair, Medhat A-Halim, Parul Aggarwal, Grace Messenger, Philip Chu, Sacha A. De Serres, Jamil R. Azzi
Summary: New Onset Diabetes After Transplantation (NODAT) is a serious metabolic complication post kidney transplant, and studies have found an association between gene polymorphisms like interferon gamma and NODAT.
SCIENTIFIC REPORTS
(2021)
Article
Rheumatology
Chenxi Liu, Songxin Yan, Haizhen Chen, Ziyan Wu, Liubing Li, Yongzhe Li
Summary: In the Chinese Han population, ARID3A rs10415976, ARID3A rs350146, and CXCR5 rs77871618 were suggestively associated with SSc, while TNFSF8 rs1555457 was strongly associated with SSc.
CLINICAL RHEUMATOLOGY
(2023)
Review
Immunology
Maheswari Muruganandam, Angie Ariza-Hutchinson, Rosemina A. Patel, Wilmer L. Sibbitt
Summary: Systemic sclerosis is a complex autoimmune disease characterized by vascular damage, inflammation, and fibrosis. Biomarkers play an important role in understanding the disease process and potential therapeutic targets. Anti-nuclear antibodies are classical biomarkers, while other proteins and pathways are also implicated. The use of biomarker panels combined with advanced analysis techniques can help determine disease activity and treatment response.
JOURNAL OF INFLAMMATION RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Ivan Sammir Aranda-Uribe, Juan Carlos Lopez-Vazquez, Rosa Elda Barbosa-Cobos, Julian Ramirez-Bello
Summary: The study investigated the association between TLR4 and TLR9 gene polymorphisms with rheumatoid arthritis and systemic lupus erythematosus in Mexican patients, and found that these variants are not risk factors for RA or SLE in this population.
MOLECULAR BIOLOGY REPORTS
(2021)
Review
Biochemistry & Molecular Biology
Wenwen Wei, Xin Wang, Yuanzhong Zhou, Xuejun Shang, Hongsong Yu
Summary: Pregnancy-induced hypertension (PIH) is a severe pregnancy complication that can lead to maternal mortality. Various genetic factors have been shown to play an important role in the occurrence and development of PIH. This review summarizes the genetic risk factors involved in the renin-angiotensin system, endothelin system, inflammatory factors, oxidative stress, and other functional networks that may contribute to the pathogenesis of PIH.
Article
Oncology
Nannan Tang, Junbin Huang, Chun Chen, Xiaojun Wu, Honggui Xu, Guohua Chen, Hongman Xue
Summary: The study found that the A allele frequencies of IL2RA rs2104286 and IL10 rs1800896, and the C allele frequency of IL10 rs1800872 were significantly higher in children with EBV-associated hemophagocytic lymphohistiocytosis (EBV-HLH). The AA genotype of IL2RA rs2104286 and IL10 rs1800896, and the CC genotype of IL10 rs1800872 may be associated with a significantly higher risk of developing EBV-HLH. Additionally, certain haplotypes of IL2RA and IL10 were also found to be associated with an increased risk of EBV-HLH.
PEDIATRIC BLOOD & CANCER
(2021)
Article
Genetics & Heredity
Lulin Ma, Yan Huang, Shiqian Huang, Feng Xu, Yafeng Wang, Shuai Zhao, Daling Deng, Yuanyuan Ding, Tianhao Zhang, Wenjing Zhao, Xiangdong Chen
Summary: This study aimed to explore the molecular mechanisms of individual differences in etomidate anesthesia and identified several single nucleotide polymorphisms (SNPs) associated with the effectiveness of etomidate anesthesia. This provides theoretical evidence for future use of etomidate anesthesia.
FRONTIERS IN GENETICS
(2022)
Article
Pharmacology & Pharmacy
Rong-Hong Guo, Hao Cheng, Xiao-Ying Zhang, Zhen Yu, Guang-Hui Wang, Shu-Ya Hao, Xiao-Peng Gao, Hong-Yan Wen
Summary: This study aimed to investigate the changes in absolute numbers of T-lymphocyte subsets and serum cytokines in patients with systemic sclerosis (SSc). The study found that patients with SSc had lower numbers of Th2 and Treg cells compared to healthy controls, which led to significantly increased ratios of Th1/Th2 and Th17/Treg. Additionally, the levels of certain cytokines were significantly higher in SSc patients. The findings contribute to a better understanding of the pathogenesis of SSc and provide a basis for the development of novel therapeutic interventions targeting these cells and cytokines.
FRONTIERS IN PHARMACOLOGY
(2022)
Review
Chemistry, Medicinal
Przemyslaw Kotyla, Olga Gumkowska-Sroka, Bartosz Wnuk, Kacper Kotyla
Summary: Systemic sclerosis and systemic lupus erythematosus are two distinct autoimmune diseases belonging to connective tissue disorders, with no groundbreaking therapeutic approaches developed yet. The discovery of JAK kinases may offer a new therapeutic potential for previously untreatable diseases.
Article
Rheumatology
Tatiana Nevskaya, Janet E. Pope, Matthew A. Turk, Jenny Shu, April Marquardt, Frank van den Hoogen, Dinesh Khanna, Jaap Fransen, Marco Matucci-Cerinic, Murray Baron, Christopher P. Denton, Sindhu R. Johnson
Summary: Research findings suggest that systemic sclerosis (SSc) subset classification systems are primarily based on the extent of skin involvement and/or SSc-specific autoantibodies, nailfold capillary patterns, and molecular, genomic, and cellular patterns. While some classification systems have prognostic value for clinical phenotype, severity, and mortality, only subsetting by gene expression signatures in tissue samples has been linked to response to therapy.
JOURNAL OF RHEUMATOLOGY
(2021)
Article
Biochemical Research Methods
Joseph D. Romano, Trang T. Le, William La Cava, John T. Gregg, Daniel J. Goldberg, Praneel Chakraborty, Natasha L. Ray, Daniel Himmelstein, Weixuan Fu, Jason H. Moore
Summary: This article introduces the latest release of PMLB, which provides the largest collection of diverse, public benchmark datasets for evaluating new machine learning and data science methods. Version 1.0 introduces several critical improvements developed following discussions with the open-source community.
Review
Genetics & Heredity
Elisabetta Manduchi, Joseph D. Romano, Jason H. Moore
Summary: Parametric statistical methods have traditionally been used in genetic analysis of complex traits, but machine learning methods are better suited for detecting and modeling patterns in complex genetic architectures. The goal of AutoML is to eliminate guesswork by automatically identifying the right algorithms and hyperparameters for optimization. This review discusses the promises and challenges of AutoML in genetic analysis and emphasizes the potential for developing novel AutoML methods and software in the field of genetics and genomics.
Article
Genetics & Heredity
Alexandra J. Lee, Dallas L. Mould, Jake Crawford, Dongbo Hu, Rani K. Powers, Georgia Doing, James C. Costello, Deborah A. Hogan, Casey S. Greene
Summary: Genome-wide transcriptome profiling identifies genes prone to differential expression and those specifically changed in experimental manipulation. A novel approach called SOPHIE is introduced to distinguish between common and specific transcriptional patterns, allowing efficient prediction of genes specific to a biological process. SOPHIE successfully identifies common DEGs and highly specific but low-magnitude transcriptional changes, complementing traditional DE analyses.
GENOMICS PROTEOMICS & BIOINFORMATICS
(2022)
Article
Microbiology
Georgia Doing, Alexandra J. J. Lee, Samuel L. Neff, Taylor Reiter, Jacob D. Holt, Bruce A. Stanton, Casey S. Greene, Deborah A. Hogan
Summary: In this study, thousands of Pseudomonas aeruginosa RNA sequencing gene expression profiles were reanalyzed to create a powerful tool for hypothesis generation and testing. Raw sequence data were uniformly processed and validated using the Salmon pseudoaligner. Filtering criteria were developed to exclude samples with aberrant gene expression and normalization steps greatly improved gene expression correlations. The resulting compendia and algorithm for incorporating new data provide useful tools for P. aeruginosa RNA-seq analysis.
Article
Microbiology
Alexandra J. J. Lee, Georgia Doing, Samuel L. L. Neff, Taylor Reiter, Deborah A. A. Hogan, Casey S. S. Greene
Summary: This article studies the genomic heterogeneity of Pseudomonas aeruginosa strains, compares the expression patterns of core genes and accessory genes between PAO1 and PA14 strains, and finds differences in the expression patterns of some core genes among different strains.
Article
Biology
Gabriel Dias Rodrigues, Angelica Carandina, Costanza Scata, Chiara Bellocchi, Lorenzo Beretta, Pedro Paulo da Silva Soares, Eleonora Tobaldini, Nicola Montano
Summary: Systemic sclerosis (SSc) patients often experience cardiovascular autonomic dysfunction, leading to arrhythmic complications and mortality. This study aimed to evaluate the progression of cardiac autonomic impairment over time in different subsets of SSc patients. The results showed that the worsening of cardiac autonomic dysfunction was associated with the diffuse cutaneous (dcSSc) subset, which had a more extent of skin and internal organs fibrosis.
Article
Biochemical Research Methods
Jineta Banerjee, Jaclyn N. Taroni, Robert J. Allaway, Deepashree Venkatesh Prasad, Justin Guinney, Casey Greene
Summary: High-throughput profiling methods have made molecular characterization routine, and machine learning can be used to extract disease-relevant patterns. However, machine learning for rare diseases faces challenges due to limited clinical cases and few samples.
Article
Biochemistry & Molecular Biology
Ricardo Avila, Vincent Rubinetti, Xinghua Zhou, Dongbo Hu, Zhongchao Qian, Marco Alvarado Cano, Everaldo Rodolpho, Ginger Tsueng, Casey Greene, Chunlei Wu
Summary: MyGeneset.info provides an API for integrated annotations for gene sets, allowing users to import gene sets from commonly-used resources and create their own sets. It offers a means for managing and utilizing gene sets in a more FAIR manner.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemical Research Methods
Benjamin Heil, Jake Crawford, Casey Greene
Summary: This study evaluates the performance of complex non-linear models and simple linear models in a series of prediction tasks. The results show that linear models perform just as well as non-linear models in tissue prediction and metadata-derived sex prediction. However, it is also found that only non-linear models can utilize predictive signals in the data. Therefore, considering both linear models and non-linear models is critical when building predictive models from gene expression data.
PLOS COMPUTATIONAL BIOLOGY
(2023)
Review
Microbiology
Halie M. Rando, Ronan Lordan, Likhitha Kolla, Elizabeth Sell, Alexandra J. Lee, Nils Wellhausen, Amruta Naik, Jeremy P. Kamil, Anthony S. Gitter, Casey Greene
Summary: The SARS-CoV-2 pandemic has caused significant damage worldwide, leading to increased demands for vaccine development. Developing, producing, and distributing vaccines are crucial in saving lives and mitigating the impact of the COVID-19 pandemic.
Review
Microbiology
Halie M. M. Rando, Ronan Lordan, Alexandra J. J. Lee, Amruta Naik, Nils Wellhausen, Elizabeth Sell, Likhitha Kolla, Anthony Gitter, Casey S. S. Greene
Summary: Vaccines have revolutionized the relationship between people and diseases over the past 150 years. During the COVID-19 pandemic, mRNA vaccines have gained attention, but traditional vaccine development platforms have also played a significant role. Different approaches, such as whole-virus vaccines and subunit vaccines, have been used to develop COVID-19 vaccines.
Review
Medicine, General & Internal
Marvin J. Fritzler, Chelsea Bentow, Lorenzo Beretta, Boaz Palterer, Janire Perurena-Prieto, Maria Teresa Sanz-Martinez, Alfredo Guillen-Del-Castillo, Ana Marin, Vicent Fonollosa-Pla, Eduardo Callejas-Moraga, Carmen Pilar Simeon-Aznar, Michael Mahler
Summary: Anti-nuclear (ANA) are important biomarkers in supporting the diagnosis and prognosis of systemic sclerosis (SSc). In addition to the well-known SSc autoantibodies, such as anti-centromere, anti-topoisomerase I (Scl-70), anti-RNA polymerase III, other autoantibodies like anti-U11/U12 ribonucleoprotein (RNP) antibodies have been associated with specific SSc phenotypes and malignancy. The U11/U12 RNP macromolecular complex is involved in alternative mRNA splicing and its antibodies have been linked to severe pulmonary fibrosis and gastrointestinal dysmotility. This literature review aims to summarize the knowledge of anti-U11/U12/RNPC-3 antibodies in SSc.
Article
Biology
Steven M. Foltz, Casey S. Greene, Jaclyn N. Taroni
Summary: By employing supervised and unsupervised machine learning evaluations, we identified the best normalization methods, including quantile and Training Distribution Matching normalization, for combining microarray and RNA-seq data. Nonparanormal normalization and z-scores were also found to be appropriate for certain applications. Our study demonstrates the possibility of effective cross-platform normalization using existing methods for machine learning applications.
COMMUNICATIONS BIOLOGY
(2023)
Review
Computer Science, Artificial Intelligence
Ryan T. Scott, Lauren M. Sanders, Erik L. Antonsen, Jaden J. A. Hastings, Seung-min Park, Graham Mackintosh, Robert J. Reynolds, Adrienne L. Hoarfrost, Aenor Sawyer, Casey S. Greene, Benjamin S. Glicksberg, Corey A. Theriot, Daniel C. Berrios, Jack Miller, Joel Babdor, Richard Barker, Sergio E. Baranzini, Afshin Beheshti, Stuart Chalk, Guillermo M. Delgado-Aparicio, Melissa Haendel, Arif A. Hamid, Philip Heller, Daniel Jamieson, Katelyn J. Jarvis, John Kalantari, Kia Khezeli, Svetlana V. Komarova, Matthieu Komorowski, Prachi Kothiyal, Ashish Mahabal, Uri Manor, Hector Garcia Martin, Christopher E. Mason, Mona Matar, George I. Mias, Jerry G. Myers Jr, Charlotte Nelson, Jonathan Oribello, Patricia Parsons-Wingerter, R. K. Prabhu, Amina Ann Qutub, Jon Rask, Amanda Saravia-Butler, Suchi Saria, Nitin Kumar Singh, Michael Snyder, Frank Soboczenski, Karthik Soman, David Van Valen, Kasthuri Venkateswaran, Liz Warren, Liz Worthey, Jason H. Yang, Marinka Zitnik, Sylvain V. Costes
Summary: Deep-space exploration requires new technologies for astronaut health systems and autonomous biomonitoring. This article discusses the vision for precision space health based on the findings from a NASA workshop on artificial intelligence and machine learning.
NATURE MACHINE INTELLIGENCE
(2023)
Article
Biochemical Research Methods
Hyunjun Choi, Jay Moran, Nicholas Matsumoto, Miguel E. Hernandez, Jason H. Moore
Summary: Aliro is an open-source software package that automates machine learning analysis through a clean web interface. By leveraging the power of large language models, users can interact with their data and quickly discover new insights. It also includes a pre-trained machine learning recommendation system for automated algorithm and hyperparameter selection, as well as visualization of the evaluated model and data.