Article
Biology
Holly C. Beale, Jacquelyn M. Roger, Matthew A. Cattle, Liam T. McKay, Drew K. A. Thompson, Katrina Learned, A. Geoffrey Lyle, Ellen T. Kephart, Rob Currie, Du Linh Lam, Lauren Sanders, Jacob Pfeil, John Vivian, Isabel Bjork, Sofie R. Salama, David Haussler, Olena M. Vaske
Summary: The reproducibility of gene expression measured by RNA-Seq is dependent on sequencing depth, with MEND reads being a useful measure for reproducibility. The fraction of reads contributing to reproducibility varies greatly among datasets, suggesting the importance of reporting sequencing depth in MEND reads.
Article
Environmental Sciences
Chao Zhou, Mengyu Liu, Xiang Mei, Qian Li, Wenjuan Zhang, Ping Deng, Zhixin He, Yu Xi, Tong Tong, Huifeng Pi, Yonghui Lu, Chunhai Chen, Lei Zhang, Zhengping Yu, Zhou Zhou, Mindi He
Summary: Exposure to nickel can lead to learning and memory impairment in mice, affect dendrite complexity of neurons, and reduce histone acetylation levels. Treatment with a histone deacetylase inhibitor can alleviate these nickel-induced effects.
SCIENCE OF THE TOTAL ENVIRONMENT
(2021)
Article
Genetics & Heredity
Dalileia A. Santana, Amina Bedrat, Renato D. Puga, Gustavo Turecki, Naguib Mechawar, Tathyane C. Faria, Carolina O. Gigek, Spencer L. M. Payao, Marilia A. C. Smith, Bernardo Lemos, Elizabeth S. Chen
Summary: This study aimed to evaluate H3K9 acetylation and gene expression profiles in three brain regions of Alzheimer's disease (AD) patients and controls, and to identify AD region-specific abnormalities. The results showed hyperacetylation in the cerebellum and slight hypoacetylation in the hippocampus of AD patients. Differentially expressed genes were found in the hippocampus and auditory cortex. Network analysis revealed Rho GTPase-mediated mechanisms. These findings suggest dysregulation of crucial mechanisms in AD patients at the epigenetic and transcriptomic levels, which could contribute to future research on AD pathogenesis.
Article
Biology
Roberto Vera Alvarez, Lorinc Pongor, Leonardo Marino-Ramirez, David Landsman
Summary: PM4NGS is a project management framework for NGS data analysis, providing a standard organizational structure, bioinformatics tool management, and data analysis pipelines. It is easy to install and use on personal computers and laptops, aiming to bridge the gap between researchers in experimental laboratories and data analysis workflows.
Article
Biochemistry & Molecular Biology
Yuchao Jiang, Yuriko Harigaya, Zhaojun Zhang, Hongpan Zhang, Chongzhi Zang, Nancy R. Zhang
Summary: The epigenetic control of gene expression is highly cell-type and context specific, and can be broken down into modular components by a transcription factor activating or repressing the target gene expression. A new nonparametric approach, TRIPOD, is proposed to detect and characterize the relationships between TF, target gene, and TF binding site accessibility using single-cell RNA and ATAC multiomic data.
Article
Biotechnology & Applied Microbiology
Julianne K. David, Sean K. Maden, Mary A. Wood, Reid F. Thompson, Abhinav Nellore
Summary: Short-read tools for detecting intron retention have poor performance and often result in false positives and false negatives, calling into question the completeness and validity of putatively retained introns called by commonly used methods.
Article
Multidisciplinary Sciences
Karolis Ramanauskas, Boris Igic
Summary: kakapo is a Python-based pipeline that allows users to extract and assemble specified genes or gene families. It can flexibly process original RNA-seq reads or GenBank SRA accession inputs without the need for global assembly. The pipeline identifies open reading frames in the gene transcripts and annotates them, and it can also filter out reads from non-target organisms.
Article
Multidisciplinary Sciences
Kai Battenberg, S. Thomas Kelly, Radu Abu Ras, Nicola A. Hetherington, Makoto Hayashi, Aki Minoda
Summary: Single-cell RNA-sequencing analysis has gained popularity, and UniverSC is a universal tool for processing single-cell RNA-seq data on any platform. It provides a command-line tool, docker image, and containerized graphical application for consistent and comprehensive integration, comparison, and evaluation of data from various platforms. Additionally, a cross-platform application with a graphical user interface is available to address the bottleneck of data processing for researchers without bioinformatics expertise.
NATURE COMMUNICATIONS
(2022)
Article
Biochemical Research Methods
Malte D. Luecken, M. Buettner, K. Chaichoompu, A. Danese, M. Interlandi, M. F. Mueller, D. C. Strobl, L. Zappia, M. Dugas, M. Colome-Tatche, Fabian J. Theis
Summary: This study benchmarked 68 method and preprocessing combinations on 85 batches of gene expression data, highlighting the importance of highly variable gene selection in improving method performance. When dealing with complex integration tasks, scANVI, Scanorama, scVI, and scGen consistently performed well, while the performance of single-cell ATAC-sequencing integration was strongly influenced by the choice of feature space.
Article
Genetics & Heredity
Zeynab Piryaei, Zahra Salehi, Esmaeil Ebrahimie, Mansour Ebrahimi, Kaveh Kavousi
Summary: This study conducted a meta-analysis of ChIP-seq data from ER+ breast cancer cell lines, identifying new binding sites of ER and revealing new terms and pathways involved in breast cancer development.
BMC MEDICAL GENOMICS
(2023)
Article
Biochemical Research Methods
Tal Ashuach, Mariano I. Gabitto, Rohan V. Koodli, Giuseppe-Antonio Saldi, Michael I. Jordan, Nir Yosef
Summary: Jointly profiling the transcriptome, chromatin accessibility, and other molecular properties of single cells can enhance the study of cellular diversity. MultiVI, a probabilistic model, allows the analysis of multiomic data and enhances single-modality datasets by creating a joint representation. It can be accessed at scvi-tools.org.
Article
Biochemical Research Methods
Yan Wu, Lingfeng Xue, Wen Huang, Minghua Deng, Yihan Lin
Summary: This paper proposes an alternative approach for analyzing transcription factor activities using the expression levels of unmatured mRNAs of target genes. By utilizing this method, researchers can decode the temporal control of transcription factor activities during key biological processes and gain insights into the regulatory principles of dynamic cellular processes. The results also reveal two temporally opposing modules of transcription factors that play important roles in immune responses. Overall, this approach provides a valuable tool for understanding and studying transcription factor activities in dynamic cellular processes.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Biochemical Research Methods
Nikolas Dovrolis, Katerina Kassela, Konstantinos Konstantinidis, Adamantia Kouvela, Stavroula Veletza, Ioannis Karakasiliotis
Summary: The study of viruses' genetic composition is crucial for their identification and classification, especially during times of pandemic turmoil. New technologies in nucleic acid sequencing can introduce artifacts into viral genomes, and this study proposes an algorithm to help remove problematic regions while retaining essential genetic information. This approach aims to improve the accuracy and integrity of viral genomes for novel virus identification and characterization in public databases.
PLOS COMPUTATIONAL BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Mengwei Li, Xiaomeng Zhang, Kok Siong Ang, Jingjing Ling, Raman Sethi, Nicole Yee Shin Lee, Florent Ginhoux, Jinmiao Chen
Summary: DISCO is an integrated database of single-cell omics data, offering an integrated cell atlas and harmonized metadata that users can utilize for comprehensive single-cell data analysis and exploration.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Len Taing, Ariaki Dandawate, Sehi LYi, Nils Gehlenborg, Myles Brown, Clifford A. Meyer
Summary: Cistrome Data Browser is a resource that provides genome-wide location maps of transcription factors, chromatin remodelers, and more in humans and mice. It has a large collection of datasets and diverse search tools, allowing users to find and visualize data effectively.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Endocrinology & Metabolism
Samim Ali Mondal, Roshini Sathiaseelan, Shivani N. Mann, Maria Kamal, Wenyi Luo, Tatiana D. Saccon, Jose V. V. Isola, Frederick F. Peelor III, Tiangang Li, Willard M. Freeman, Benjamin F. Miller, Michael B. Stout
Summary: The naturally occurring diastereomer of 17β-estradiol, 17α-estradiol, can reduce liver fibrosis by suppressing hepatic stellate cell activation and enhancing collagen degradation mechanisms.
AMERICAN JOURNAL OF PHYSIOLOGY-ENDOCRINOLOGY AND METABOLISM
(2023)
Article
Multidisciplinary Sciences
Yiran A. Shen, Bhuwan K. Khatri, Santosh J. Rananaware, Danmeng Q. Li, David Ostrov, Piyush Jain, Christopher Lessard, Cuong Nguyen
Summary: COVID-19 is caused by SARS-CoV-2 and its severity is influenced by various known and unknown risk factors. A genome-wide association study identified genetic loci associated with COVID-19 susceptibility, particularly in individuals of European ancestry. Additionally, the study explored the linkage between HLA and COVID-19 severity and found differential presentation of viral peptides in different ancestral origins. These findings contribute to a better understanding of the disease's pathogenesis and potential clinical treatments.
Article
Neurosciences
Sarah R. Ocanas, Victor A. Ansere, Collyn M. Kellogg, Jose V. V. Isola, Ana J. Chucair-Elliott, Willard M. Freeman
Summary: Biological sex influences neurodegenerative diseases through genetic and hormonal mechanisms. Microglial reactivity and the pro-inflammatory environment of the aging brain are influenced by sex, age, and disease state. Further research is needed to understand the regulation of microglial sex effects and develop sex-informed prevention and treatment strategies for brain diseases.
BRAIN RESEARCH BULLETIN
(2023)
Article
Oncology
Sabira Mohammed, Nidheesh Thadathil, Phoebe Ohene-Marfo, Albert L. Tran, Michael Van Der Veldt, Constantin Georgescu, Sangphil Oh, Evan H. Nicklas, Dawei Wang, Nair Hariprasad Haritha, Wenyi Luo, Ralf Janknecht, Benjamin F. Miller, Jonathan D. Wren, Willard M. Freeman, Sathyaseelan S. Deepa
Summary: Blocking necroptosis reduces inflammation and hepatocellular carcinoma (HCC) in a mouse model of diet-induced HCC, particularly in male mice, suggesting necroptosis as a potential therapeutic target for NAFLD-mediated HCC.
MOLECULAR CANCER RESEARCH
(2023)
Article
Cardiac & Cardiovascular Systems
Kausik Umanath, Ruicong She, Clare Hassett, Indra Adrianto, Albert M. Levin, Gina Savickas, Jerry Yee, Pablo Ortiz
Summary: In this study, the transcriptome analysis of cells shed in first-morning urine samples from patients with difficult-to-control hypertension revealed the gene expression profile associated with renal inflammation, providing insights into the underlying mechanisms of this condition.
JOURNAL OF THE AMERICAN HEART ASSOCIATION
(2023)
Article
Multidisciplinary Sciences
Sarah R. Ocanas, Jose V. V. Isola, Tatiana D. Saccon, Kevin D. Pham, Ana J. Chucair-Elliott, Augusto Schneider, Willard M. Freeman, Michael B. Stout
Summary: Assessing cell-type-specific epigenomic and transcriptomic changes are key to understanding ovarian aging. The optimization of TRAP and INTACT methods were performed using a transgenic NuTRAP mouse model to study the ovarian transcriptome and epigenome in specific cell types.
JOVE-JOURNAL OF VISUALIZED EXPERIMENTS
(2023)
Article
Geriatrics & Gerontology
Michael B. B. Stout, Kelli L. L. Vaughan, Jose V. V. Isola, Shivani N. N. Mann, Bayli Wellman, Jessica M. M. Hoffman, Hunter L. L. Porter, Willard M. M. Freeman, Julie A. A. Mattison
Summary: Recent studies have shown that 17 alpha-estradiol can extend the healthspan and lifespan of male mice through multiple mechanisms, making it a potential candidate for translation into humans. However, there is currently no established dosing paradigm for the treatment of aging and chronic disease in humans. This study aimed to assess the tolerability of 17 alpha-estradiol treatment and evaluate metabolic and endocrine responses in male rhesus macaque monkeys during a short treatment period. The results showed that the dosing regimens were well-tolerated and had mild benefits on metabolic parameters, but significant feminization effects were observed.
Article
Dermatology
Jesse Veenstra, David Ozog, Ian Loveless, Indra Adrianto, Peter Dimitrion, Kalpana Subedi, Ben J. Friedman, Li Zhou, Qing-Sheng Mi
Summary: Differentiating between keratoacanthoma (KA) and well-differentiated cutaneous squamous cell carcinoma (cSCC) is challenging due to overlapping clinical and histological features. This study used RNA sequencing and imaging mass cytometry to identify key differences in transcriptomes and cellular characteristics between KA and cSCC, revealing distinct keratinocyte populations and immunosuppressive environments.
JOURNAL OF INVESTIGATIVE DERMATOLOGY
(2023)
Article
Immunology
Sarah R. Ocanas, Kevin D. Pham, Jillian E. J. Cox, Alex W. Keck, Sunghwan Ko, Felix A. Ampadu, Hunter L. Porter, Victor A. Ansere, Adam Kulpa, Collyn M. Kellogg, Adeline H. Machalinski, Manu A. Thomas, Zsabre Wright, Ana J. Chucair-Elliott, Willard M. Freeman
Summary: This study compared the transcriptome and translatome of hippocampal microglia between young and old mice and found sex differences in microglial gene expression. In old age, these differences were primarily female-biased and enriched in markers of senescence and disease. These findings may explain the differences in susceptibility and disease progression in Alzheimer's disease between males and females. Further studies are needed to explore the role of sex differences in microglial heterogeneity and the involvement of sex-specific regulators in response to Alzheimer's pathology.
JOURNAL OF NEUROINFLAMMATION
(2023)
Review
Geriatrics & Gerontology
Victor A. Ansere, Matthew P. Bubak, Benjamin F. Miller, Willard M. Freeman
Summary: Experimental approaches like Heterochronic Plasma Transfer (HPT) are important tools for studying aging, but they have limitations and design challenges. This review provides insights into the considerations and caveats of HPT as a research tool, including plasma preparation, administration route, dosing regimen, and appropriate controls, to assist investigators in achieving their experimental goals.
REJUVENATION RESEARCH
(2023)
Article
Geriatrics & Gerontology
Collyn M. Kellogg, Kevin Pham, Adeline H. Machalinski, Hunter L. Porter, Harris E. Blankenship, Kyla B. Tooley, Michael B. Stout, Heather C. Rice, Amanda L. Sharpe, Michael J. Beckstead, Ana J. Chucair-Elliott, Sarah R. Ocanas, Willard M. Freeman
Summary: This study reveals that microglia are the primary source of MHC-I in mice and humans, with its expression increasing with aging and in Alzheimer's disease. The expression of Lilrs and Pilrs, MHC-I binding receptor families, also increases with aging and AD. These findings suggest the possibility of cell-autonomous MHC-I signaling in regulating microglial reactivation and neurodegeneration.
Letter
Immunology
Peter Dimitrion, Iltefat Hamzavi, Congcong Yin, Jugmohit Toor, Kalpana Subedi, Namir Khalasawi, Angela Miller, Richard Huggins, Indra Adrianto, Jesse Veenstra, Gautham Vellaichamy, Aakash Hans, Steven Daveluy, Mohammad Athar, Wilson Liao, Henry Lim, David Ozog, Li Zhou, Qing-Sheng Mi
CELLULAR & MOLECULAR IMMUNOLOGY
(2023)
Article
Biochemical Research Methods
Jonathan D. Ogata, Wancen Mu, Eric S. Davis, Bingjie Xue, J. Chuck Harrell, Nathan C. Sheffield, Douglas H. Phanstiel, Michael Love, Mikhail G. Dozmorov
Summary: Exclusion regions are abnormal sections of reference genomes where short sequencing reads pile up. Removing reads overlapping these regions improves biological signal, particularly in differential analysis. Multiple exclusion region sets have been created by labs, primarily available through ENCODE and Github, causing uncertainty in which sets to use. Additionally, gap regions like centromeres, telomeres, and short arms pose further considerations when generating exclusion sets.
Article
Geriatrics & Gerontology
Ramasamy Selvarani, Hoang Van Michelle Nguyen, Nidheesh Thadathil, Roman F. Wolf, Willard M. Freeman, Christopher D. Wiley, Sathyaseelan S. Deepa, Arlan Richardson
Summary: This study utilized knockin mouse models to investigate the impact of necroptosis-induced chronic inflammation on aging and age-related diseases. The findings revealed a significant association between increased necroptosis, inflammation, and various age-related pathological changes.
Article
Respiratory System
Albert M. Levin, Ruicong She, Yalei Chen, Indra Adrianto, Indrani Datta, Ian M. Loveless, Lori Garman, Courtney G. Montgomery, Jia Li, Michael C. Iannuzzi, Benjamin A. Rybicki
Summary: This study found that environmental exposure risk profiles for sarcoidosis differ between African Americans and European Americans, with exposure to metals, especially aluminum, being the highest risk factor. These differences may partially explain the racially disparate incidence rates of sarcoidosis, which are associated with genetic variation.
ANNALS OF THE AMERICAN THORACIC SOCIETY
(2023)