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Journal articles on the topic 'Liver transcriptome'

Author: Grafiati

Published: 3 June 2025

Last updated: 31 July 2025

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1

Chen, Xinguo, Zhongyang Shen, Xuyi Zhang, et al. "RNA Sequencing Reveals the Suitability of Cardiac Death Livers for Transplantation." BioMed Research International 2018 (November 1, 2018): 1–8. http://dx.doi.org/10.1155/2018/8217486.

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Background. Organ transplantation is considered the best treatment for end-stage organ failure. However, the lack of available organs for transplantation and the increasing number of patients waiting for transplants are primary issues facing the transplant community. Thus, developing strategies to increase the number of donors, especially for liver transplantation, has become a priority. The use of organs acquired from donors who suffered cardiac related deaths has increased the pool of potential liver donors. However, donation after cardiac death (DCD) livers increases the risk of primary gra

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Emami-Khoyi, Arsalan, Rynhardt Le Roux, Matthew G. Adair, et al. "Transcriptomic Diversity in the Livers of South African Sardines Participating in the Annual Sardine Run." Genes 12, no. 3 (2021): 368. http://dx.doi.org/10.3390/genes12030368.

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During austral winter, the southern and eastern coastlines of South Africa witness one of the largest animal migrations on the planet, the KwaZulu-Natal sardine run. Hundreds of millions of temperate sardines, Sardinops sagax, form large shoals that migrate north-east towards the subtropical Indian Ocean. Recent studies have highlighted the role that genetic and environmental factors play in sardine run formation. In the present study, we used massively parallel sequencing to assemble and annotate the first reference transcriptome from the liver cells of South African sardines, and to investig

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Grandt, Josephine, Christian D. Johansen, Anne-Sofie H. Jensen, et al. "The hepatic transcriptome is differentially regulated by a standardized meal in healthy individuals compared to patients with fatty liver disease." PLOS One 20, no. 6 (2025): e0307345. https://doi.org/10.1371/journal.pone.0307345.

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The human liver is dynamic organ with minute to hourly adaptions in response to feeding. Patients with non-alcoholic fatty liver disease (NAFLD) and cirrhosis have altered transcriptomic features compared to controls but how and if food intake affects such is unknown in humans. Our aim was to investigate the hepatic transcriptome at both fasting and postprandial states in patients with NAFLD, cirrhosis, and healthy controls and secondly to develop a browsable resource enabling easy and unrestricted access to such data. We hypothesized that hepatic transcriptome differed between groups, and thi

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Liang, Yan, Nan Wang, Xia Li, et al. "Abstract 4709: Spatial whole transcriptome profiling of human normal liver and HCC uncovers unique insights into metabolic zonation." Cancer Research 83, no. 7_Supplement (2023): 4709. http://dx.doi.org/10.1158/1538-7445.am2023-4709.

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Abstract Understanding the physiology and functions of the liver and cancer requires knowing transcriptional patterns driving biological activities within the functional structures of the tissue, especially the zonated features of the liver metabolic networks. Using the powerful and unique capabilities of GeoMx® Digital Spatial Profiler (DSP) with the Whole Transcriptome Atlas (WTA) panel to resolve functional units within FFPE tissues in situ, here we report the spatial analysis of whole transcriptomes across three micro-dissected zones (pericentral zone 3, intermediate zone 2 and periportal

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Sajed, Sarabandi. "Liver tissue transcriptome data analysis for identification of key miRNAs and genes in sheep (Ovis Aries) with different diets." Medbiotech Journal 7, no. 1 (2023): 55–66. https://doi.org/10.5281/zenodo.7903723.

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Ng, Gavin Yong-Quan, Sung-Wook Kang, Joonki Kim, et al. "Genome-Wide Transcriptome Analysis Reveals Intermittent Fasting-Induced Metabolic Rewiring in the Liver." Dose-Response 17, no. 3 (2019): 155932581987678. http://dx.doi.org/10.1177/1559325819876780.

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Scope: Intermittent fasting (IF) has been extensively reported to promote improved energy homeostasis and metabolic switching. While IF may be a plausible strategy to ameliorate the epidemiological burden of disease in many societies, our understanding of the underlying molecular mechanisms behind such effects is still lacking. The present study has sought to investigate the relationship between IF and changes in gene expression. We focused on the liver, which is highly sensitive to metabolic changes due to energy status. Mice were randomly assigned to ad libitum feeding or IF for 16 hours per

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Teufel, Andreas, Jens U. Marquardt, Frank Staib, and Peter R. Galle. "Snapshot liver transcriptome in hepatocellular carcinoma." Journal of Hepatology 56, no. 4 (2012): 990–92. http://dx.doi.org/10.1016/j.jhep.2011.08.024.

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Yang, Chao, Xiaoling Zhou, Hong Yang, et al. "Transcriptome analysis reveals liver metabolism programming in kids from nutritional restricted goats during mid-gestation." PeerJ 9 (January 29, 2021): e10593. http://dx.doi.org/10.7717/peerj.10593.

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Background Maternal nutrient restriction during pregnancy causes a metabolic disorder that threatens the offspring’s health in humans and animals. However, the molecular mechanism of how undernutrition affecting hepatic metabolism of fetal or postnatal offspring is still unclear. We aimed to investigate transcriptomic changes of fetal livers in response to maternal malnutrition in goats during mid-gestation and to explore whether these changes would disappear when the nutrition was recovered to normal level during mid-gestation using goats (Capra hircus) as the experimental animals. Methods Fi

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Guo, Jun, Yuan Zhou, Yafen Cheng, et al. "Metformin-Induced Changes of the Coding Transcriptome and Non-Coding RNAs in the Livers of Non-Alcoholic Fatty Liver Disease Mice." Cellular Physiology and Biochemistry 45, no. 4 (2018): 1487–505. http://dx.doi.org/10.1159/000487575.

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Background/Aims: Recent studies have suggested that changes in non-coding mRNA play a key role in the progression of non-alcoholic fatty liver disease (NAFLD). Metformin is now recommended and effective for the treatment of NAFLD. We hope the current analyses of the non-coding mRNA transcriptome will provide a better presentation of the potential roles of mRNAs and long non-coding RNAs (lncRNAs) that underlie NAFLD and metformin intervention. Methods: The present study mainly analysed changes in the coding transcriptome and non-coding RNAs after the application of a five-week metformin interve

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Koglin, Sven, Daronja Trense, Michael Wink, Hedwig Sauer-Gürth, and Dieter Thomas Tietze. "Characterization of a de novo assembled transcriptome of the Common Blackbird (Turdus merula)." PeerJ 5 (December 13, 2017): e4045. http://dx.doi.org/10.7717/peerj.4045.

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Background In recent years, next generation high throughput sequencing technologies have proven to be useful tools for investigations concerning the genomics or transcriptomics also of non-model species. Consequently, ornithologists have adopted these technologies and the respective bioinformatics tools to survey the genomes and transcriptomes of a few avian non-model species. The Common Blackbird is one of the most common bird species living in European cities, which has successfully colonized urban areas and for which no reference genome or transcriptome is publicly available. However, to ta

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Joshi, Vaidehi, Dwayne Carter, Alice E. Chen, et al. "Induction of MASH in three-dimensional bioprinted human liver tissue." PLOS ONE 19, no. 12 (2024): e0312615. https://doi.org/10.1371/journal.pone.0312615.

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Metabolic dysfunction-associated steatohepatitis (MASH), formerly known as nonalcoholic steatohepatitis (MASH), is a major risk factor for cirrhosis and hepatocellular carcinoma (HCC) and a leading cause of liver transplantation. MASH is caused by an accumulation of toxic fat molecules in the hepatocyte which leads to inflammation and fibrosis. Inadequate human “MASH in a dish” models have limited our advances in understanding MASH pathogenesis and in drug discovery. This study uses complex multicellular 3D bioprinting, combining hepatocytes with nonparenchymal cells in physiologically relevan

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Hoyer, Dieter Paul, Sandra Swoboda, Juergen Walter Treckmann, Tamas Benkö, Andreas Paul, and Nahal Brocke-Ahmadinejad. "Transcriptomic profiles of human livers undergoing rewarming machine perfusion before transplantation—first insights." Functional & Integrative Genomics 21, no. 3-4 (2021): 367–76. http://dx.doi.org/10.1007/s10142-021-00781-0.

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AbstractMachine perfusion by controlled oxygenated rewarming (COR) is feasible and safe in clinical application and result in a promising outcome. This study utilizes next-generation sequencing (NGS) to investigate the transcriptome of human liver tissue undergoing COR before liver transplantation. Cold-stored livers were subjected to machine-assisted slow COR for ~120 min before transplantation. Biopsies were taken before (preCOR) and after COR (postCOR) and 1 h after reperfusion (postRep). The samples were sequenced, using RNA-seq to analyze differential transcriptional changes between the d

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Smalling, Rana L., Don A. Delker, Yuxia Zhang, et al. "Genome-wide transcriptome analysis identifies novel gene signatures implicated in human chronic liver disease." American Journal of Physiology-Gastrointestinal and Liver Physiology 305, no. 5 (2013): G364—G374. http://dx.doi.org/10.1152/ajpgi.00077.2013.

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The molecular mechanisms behind human liver disease progression to cirrhosis remain elusive. Nuclear receptor small heterodimer partner (SHP/ Nr0b2) is a hepatic tumor suppressor and a critical regulator of liver function. SHP expression is diminished in human cirrhotic livers, suggesting a regulatory role in human liver diseases. The goal of this study was to identify novel SHP-regulated genes that are involved in the development and progression of chronic liver disease. To achieve this, we conducted the first comprehensive RNA sequencing (RNA-seq) analysis of Shp−/− mice, compared the result

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Zhang, Q., Y. Q. Lu, Z. W. Cao, and Y. Z. Yang. "Effects of heat stress on the hepatic transcriptome of yellow-feathered chickens." South African Journal of Animal Science 50, no. 4 (2020): 626–34. http://dx.doi.org/10.4314/sajas.v50i4.14.

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Heat stress is one of the main environmental factors that hamper the efficiency of poultry production. Heat stress is known to be less harmful to yellow-feathered chickens (YFC) than to commercial broilers, especially in its effect on the relative weight of organs. The transcriptome was used to examine the gene expression profile of the livers of YFC that were exposed to heat stress. Mean liver weight (HW) and the hepatic weight index (HWI) of birds in the heat stress group did not differ significantly from those of the control group. A total of 596 genes were differentially expressed in the l

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Xu, Jing, Fei Mao, Yan Lu, Tiemin Liu, Xiaoying Li, and Yao Li. "Hepatic Transcriptomics Reveals Reduced Lipogenesis in High-Salt Diet Mice." Genes 14, no. 5 (2023): 966. http://dx.doi.org/10.3390/genes14050966.

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It has been demonstrated that a high salt diet (HSD) increases the risk of cardiovascular disease and metabolic dysfunction. In particular, the impact and molecular mechanisms of long-term HSD on hepatic metabolism remain largely unknown. To identify differentially expressed genes (DEGs) affecting the metabolism of liver tissues from HSD and control groups, a transcriptome analysis of liver tissues was performed in this study. As a result of the transcriptome analysis, the expression of genes related to lipid and steroid biosynthesis (such as Fasn, Scd1, and Cyp7a1) was significantly reduced i

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Chapple, Richard H., Polyana C. Tizioto, Kevin D. Wells, et al. "Characterization of the rat developmental liver transcriptome." Physiological Genomics 45, no. 8 (2013): 301–11. http://dx.doi.org/10.1152/physiolgenomics.00128.2012.

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Gene regulation and transcriptome studies have been enabled by the development of RNA-Seq applications for high-throughput sequencing platforms. Next generation sequencing is remarkably efficient and avoids many issues inherent in hybridization-based microarray methodologies including the exon-specific dependence of probe design. Biologically relevant transcripts including messenger and regulatory RNAs may now be quantified and annotated regardless of whether they have previously been observed. We used RNA-Seq to investigate global patterns of gene expression in early developing rat liver. Liv

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Reddy, Akhilesh B., Elizabeth S. Maywood, Natasha A. Karp, et al. "Glucocorticoid signaling synchronizes the liver circadian transcriptome." Hepatology 45, no. 6 (2007): 1478–88. http://dx.doi.org/10.1002/hep.21571.

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18

T.A., Dronova, Babyshkina N.N., Kostromitsky D.N., Eremin D.A., and Cherdyntseva N.V. "TRANSCRIPTOME OF METASTATIC COLORECTAL CANCER." CARDIOMETRY, no. 33 (November 25, 2024): 33–35. http://dx.doi.org/10.18137/cardiometry.2024.33.conf.12.

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Colorectal cancer has been one of the leading malignant neoplasms in males and females over many years. The vast majority of patients (70%) with colon lesions develop distant metastases to the liver, which are the main cause of death.

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Poojari, Radhika, and Shibashish Giri. "Whole Transcriptomic Profiling in Metastatic Liver Cancer With Distinct Molecular Signatures." JCO Global Oncology 8, Supplement_1 (2022): 5. http://dx.doi.org/10.1200/go.22.11000.

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PURPOSE Genomics landscape in liver cancer is one of the most revolutionizing platforms in the era of next generation sequencing (NGS). Understanding the intra- and inter-liver cancer heterogeneity has an important role in treatment decision-making. Herein, we present a whole transcriptomic based NGS with distinct molecular signatures in metastatic liver cancer tissues of orthotopic SCID mice. METHODS High throughput whole transcriptome sequencing was carried out using Illumina platform in ex vivo metastatic liver cancer tissues of orthotopic SCID mice. Healthy normal liver tissues were also s

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Luo, Jian-Hua, Silvia Liu, Bao-Guo Ren, and Yan-Ping Yu. "Abstract LB253: Long-read single-cell sequencing of liver cancer." Cancer Research 83, no. 8_Supplement (2023): LB253. http://dx.doi.org/10.1158/1538-7445.am2023-lb253.

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Abstract The protein diversity of mammalian cells is determined by arrays of isoforms from genes. Protein mutation is essential in species evolution and cancer development. Accurate Long-read transcriptome sequencing at single-cell level is required to decipher the spectrum of protein expressions in mammalian organisms. In this report, we developed a synthetic long-read single-cell sequencing technology based on LOOPseq technique. We applied this technology to analyze 447 transcriptomes of hepatocellular carcinoma (HCC) and benign liver from an individual. Through Uniform Manifold Approximatio

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Lee, Nikki, Haiyang Wu, Kevin Ng, et al. "Transcriptome Analysis of Acute Phase Liver Graft Injury in Liver Transplantation." Biomedicines 6, no. 2 (2018): 41. http://dx.doi.org/10.3390/biomedicines6020041.

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22

Lillycrop, Karen A., Joanne Rodford, Emma S. Garratt, et al. "Maternal protein restriction with or without folic acid supplementation during pregnancy alters the hepatic transcriptome in adult male rats." British Journal of Nutrition 103, no. 12 (2010): 1711–19. http://dx.doi.org/10.1017/s0007114509993795.

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Feeding pregnant rats a protein-restricted (PR) diet induces altered expression of candidate genes in the liver of the adult offspring, which can be prevented by supplementation of the PR diet with folic acid (PRF). We investigated the effect of maternal nutrition during pregnancy on the liver transcriptome in their adult male offspring. Pregnant rats were fed control, PR or PRF diets. Male offspring were killed on day 84. The liver transcriptome was analysed by microarray (six livers per maternal dietary group) followed by post hoc analysis of relative mRNA levels and gene ontology. These res

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Defour, Merel, Guido J. E. J. Hooiveld, Michel van Weeghel, and Sander Kersten. "Probing metabolic memory in the hepatic response to fasting." Physiological Genomics 52, no. 12 (2020): 602–17. http://dx.doi.org/10.1152/physiolgenomics.00117.2020.

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Tissues may respond differently to a particular stimulus if they have been previously exposed to that same stimulus. Here, we tested the hypothesis that a strong metabolic stimulus such as fasting may influence the hepatic response to a subsequent fast and thus elicit a memory effect. Overnight fasting in mice significantly increased plasma free fatty acids, glycerol, β-hydroxybutyrate, and liver triglycerides, and decreased plasma glucose, plasma triglycerides, and liver glycogen levels. In addition, fasting dramatically changed the liver transcriptome, upregulating genes involved in gluconeo

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Furuya, Shinji, Joseph A. Cichocki, Kranti Konganti, et al. "Histopathological and Molecular Signatures of a Mouse Model of Acute-on-Chronic Alcoholic Liver Injury Demonstrate Concordance With Human Alcoholic Hepatitis." Toxicological Sciences 170, no. 2 (2018): 427–37. http://dx.doi.org/10.1093/toxsci/kfy292.

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Abstract Human alcoholic hepatitis (AH) carries a high mortality rate. AH is an acute-on-chronic form of liver injury characterized by hepatic steatosis, ballooned hepatocytes, neutrophil infiltration, and pericellular fibrosis. We aimed to study the pathogenesis of AH in an animal model which combines chronic hepatic fibrosis with intragastric alcohol administration. Adult male C57BL6/J mice were treated with CCl4 (0.2 ml/kg, 2×weekly by intraperitoneal injections for 6 weeks) to induce chronic liver fibrosis. Then, ethyl alcohol (up to 25 g/kg/day for 3 weeks) was administered continuously t

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Krishna, Yamini, Amelia Acha-Sagredo, Dorota Sabat-Pośpiech, et al. "Transcriptome Profiling Reveals New Insights into the Immune Microenvironment and Upregulation of Novel Biomarkers in Metastatic Uveal Melanoma." Cancers 12, no. 10 (2020): 2832. http://dx.doi.org/10.3390/cancers12102832.

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Metastatic uveal melanoma (mUM) to the liver is incurable. Transcriptome profiling of 40 formalin-fixed paraffin-embedded mUM liver resections and 6 control liver specimens was undertaken. mUMs were assessed for morphology, nuclear BAP1 (nBAP1) expression, and their tumour microenvironments (TME) using an “immunoscore” (absent/altered/high) for tumour-infiltrating lymphocytes (TILs) and macrophages (TAMs). Transcriptomes were compared between mUM and control liver; intersegmental and intratumoural analyses were also undertaken. Most mUM were epithelioid cell-type (75%), amelanotic (55%), and n

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Xu, Zijin, Qiang Zhou, Ying Ying, et al. "Abstract 5091: Exploration of conversion therapies target in pancreatic cancer with liver metastasis in single cell spatial transcriptomic levels." Cancer Research 85, no. 8_Supplement_1 (2025): 5091. https://doi.org/10.1158/1538-7445.am2025-5091.

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Abstract Objectives: Multidisciplinary treatment drives conversion surgery of pancreatic cancer with liver metastatic clinical cases with unresectable features. The adjuvant regime included AG and FOLFIRINOX and partial cases exhibited no poor response for the treatment. We analyzed single cell spatial transcriptome data to explore biomarkers of therapy. Materials and Methods: The GSE202051 and GSE199102 cohorts derived from GEO database. The quality control, analysis, and plotting of single cell spatial transcriptome rely on the R packages including R packages ISCHIA, robustbase, data.table,

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Ge, Guodong, Jing Ren, Guili Song, Qing Li, and Zongbin Cui. "Transcriptome Analysis Reveals the Molecular Basis of Overfeeding-Induced Diabetes in Zebrafish." International Journal of Molecular Sciences 24, no. 15 (2023): 11994. http://dx.doi.org/10.3390/ijms241511994.

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Diabetes has gradually become a serious disease that threatens human health. It can induce various complications, and the pathogenesis of diabetes is quite complex and not yet fully elucidated. The zebrafish has been widely acknowledged as a useful model for investigating the mechanisms underlying the pathogenesis and therapeutic interventions of diabetes. However, the molecular basis of zebrafish diabetes induced by overfeeding remains unknown. In this study, a zebrafish diabetes model was established by overfeeding, and the molecular basis of zebrafish diabetes induced by overfeeding was exp

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Harvey, Thomas N., Simen R. Sandve, Yang Jin, Jon Olav Vik, and Jacob S. Torgersen. "Liver slice culture as a model for lipid metabolism in fish." PeerJ 7 (September 17, 2019): e7732. http://dx.doi.org/10.7717/peerj.7732.

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Hepatic lipid metabolism is traditionally investigated in vitro using hepatocyte monocultures lacking the complex three-dimensional structure and interacting cell types essential liver function. Precision cut liver slice (PCLS) culture represents an alternative in vitro system, which benefits from retention of tissue architecture. Here, we present the first comprehensive evaluation of the PCLS method in fish (Atlantic salmon, Salmo salar L.) and validate it in the context of lipid metabolism using feeding trials, extensive transcriptomic data, and fatty acid measurements. We observe an initial

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Li, Taotao, Meilin Jin, Xiaojuan Fei, et al. "Transcriptome Comparison Reveals the Difference in Liver Fat Metabolism between Different Sheep Breeds." Animals 12, no. 13 (2022): 1650. http://dx.doi.org/10.3390/ani12131650.

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Hu sheep and Tibetan sheep are two commonly raised local sheep breeds in China, and they have different morphological characteristics, such as tail type and adaptability to extreme environments. A fat tail in sheep is the main adipose depot in sheep, whereas the liver is an important organ for fat metabolism, with the uptake, esterification, oxidation, and secretion of fatty acids (FAs). Meanwhile, adaptations to high-altitude and arid environments also affect liver metabolism. Therefore, in this study, RNA-sequencing (RNA-seq) technology was used to characterize the difference in liver fat me

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Zhao, Xiaodong, Rong Xuan, Aili Wang, et al. "High-Throughput Sequencing Reveals Transcriptome Signature of Early Liver Development in Goat Kids." Genes 13, no. 5 (2022): 833. http://dx.doi.org/10.3390/genes13050833.

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As a vital metabolic and immune organ in animals, the liver plays an important role in protein synthesis, detoxification, metabolism, and immune defense. The primary research purpose of this study was to reveal the effect of breast-feeding, weaning transition, and weaning on the gene expression profile in the goat kid liver and to elucidate the transcriptome-level signatures associated with liver metabolic adaptation. Therefore, transcriptome sequencing was performed on liver tissues, which was collected at 1 day (D1), 2 weeks (W2), 4 weeks (W4), 8 weeks (W8), and 12 weeks (W12) after birth in

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Zhu, Shijia, Naoto Kubota, and Yujin Hoshida. "Transcriptome-Guided Design of Physiological Multilineage Liver Organoids." Trends in Genetics 37, no. 5 (2021): 403–4. http://dx.doi.org/10.1016/j.tig.2021.01.007.

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Wang, Qian, Stuart Brown, David S. Roos, Victor Nussenzweig, and Purnima Bhanot. "Transcriptome of axenic liver stages of Plasmodium yoelii." Molecular and Biochemical Parasitology 137, no. 1 (2004): 161–68. http://dx.doi.org/10.1016/j.molbiopara.2004.06.001.

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Coble, Derrick J., Erin E. Sandford, Tieming Ji, et al. "Impacts ofSalmonella enteritidisinfection on liver transcriptome in broilers." genesis 51, no. 5 (2012): 357–64. http://dx.doi.org/10.1002/dvg.22351.

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Verhulst, Roskams, Sancho-Bru, and van Grunsven. "Meta-Analysis of Human and Mouse Biliary Epithelial Cell Gene Profiles." Cells 8, no. 10 (2019): 1117. http://dx.doi.org/10.3390/cells8101117.

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Background: Chronic liver diseases are frequently accompanied with activation of biliary epithelial cells (BECs) that can differentiate into hepatocytes and cholangiocytes, providing an endogenous back-up system. Functional studies on BECs often rely on isolations of an BEC cell population from healthy and/or injured livers. However, a consensus on the characterization of these cells has not yet been reached. The aim of this study was to compare the publicly available transcriptome profiles of human and mouse BECs and to establish gene signatures that can identify quiescent and activated human

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Liu, Hui, Yueqin Zhu, Kevin Tak-Pan Ng, Chung-Mau Lo, and Kwan Man. "The Landscape of Aberrant Alternative Splicing Events in Steatotic Liver Graft Post Transplantation via Transcriptome-Wide Analysis." International Journal of Molecular Sciences 24, no. 9 (2023): 8216. http://dx.doi.org/10.3390/ijms24098216.

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The application of steatotic liver graft has been increased significantly due to the severe donor shortage and prevalence of non-alcoholic fatty liver disease. However, steatotic donor livers are vulnerable to acute phase inflammatory injury, which may result in cancer recurrence. Alternative splicing events (ASEs) are critical for diverse transcriptional variants in hepatocellular carcinoma (HCC). Here, we aimed to depict the landscape of ASEs, as well as to identify the differential ASEs in steatotic liver graft and their association with tumor recurrence after transplantation. The overall p

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Frias-Soler, Roberto Carlos, Lilian Villarín Pildaín, Michael Wink, and Franz Bairlein. "A Revised and Improved Version of the Northern Wheatear (Oenanthe oenanthe) Transcriptome." Diversity 13, no. 4 (2021): 151. http://dx.doi.org/10.3390/d13040151.

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This work presents an updated and more complete version of the transcriptome of a long-distance migrant, the Northern Wheatear (Oenanthe oenanthe). The improved transcriptome was produced from the independent mRNA sequencing of adipose tissue, brain, intestines, liver, skin, and muscle tissues sampled during the autumnal migratory season. This new transcriptome has better sequencing coverage and is more representative of the species’ migratory phenotype. We assembled 20,248 transcripts grouped into 16,430 genes, from which 78% were successfully annotated. All the standard assembly quality para

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Fujiwara, Naoto, and Yujin Hoshida. "Hepatocellular Carcinoma Risk Stratification by Genetic Profiling in Patients with Cirrhosis." Seminars in Liver Disease 39, no. 02 (2019): 153–62. http://dx.doi.org/10.1055/s-0039-1681031.

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AbstractPrediction of future hepatocellular carcinoma (HCC) risk in the sizable chronic liver disease population is an urgent unmet need to enable regular HCC screening for early detection. Germline deoxyribonucleic acid polymorphisms likely represent etiology-specific host factors that determine HCC susceptibility, including single nucleotide polymorphisms in EGF, IFNL3, MICA, and TLL1 in hepatitis C with or without active viral infection, and PNPLA3, TM6SF2, and MBOAT7 in metabolic liver diseases. Transcriptome-based prognostic liver signature in diseased liver tissue has been associated wit

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Felizari, Luana D., Sydney M. Bowman, Chiquito J. Crasto, Jhones O. Sarturi, Dale R. Woerner, and Bradley J. Johnson. "Hepatic transcriptome profiling unveils candidate genes in cattle with liver abscesses under the influence of beef genetics in dairy cattle." PLOS One 20, no. 6 (2025): e0324209. https://doi.org/10.1371/journal.pone.0324209.

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Liver abscesses are a significant concern in cattle feeding, linked to visceral condemnation and carcass trimming; however, the molecular mechanism of development and progression of liver abscesses is unknown. This study aimed to evaluate the hepatic transcriptomic profile, immunohistochemistry, and IGF-I circulation in beef × dairy (Angus × Holstein) steers with and without liver abscesses. Samples were collected from twelve steers (final body weight of 719 ± 5.8 kg) originating from the same feedlot and were selected based on liver scores at harvest. The animals were divided into abscessed (

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Miura, Koshiro, and Yasuko Rikihisa. "Liver Transcriptome Profiles Associated with Strain-Specific Ehrlichia chaffeensis-Induced Hepatitis in SCID Mice." Infection and Immunity 77, no. 1 (2008): 245–54. http://dx.doi.org/10.1128/iai.00979-08.

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ABSTRACT Infection of humans with Ehrlichia chaffeensis, the etiologic agent of human monocytic ehrlichiosis, can cause hepatitis of various levels of severity. When the three human isolates of E. chaffeensis, each belonging to a different genogroup, are inoculated into severe combined immunodeficiency mice, the order of severity of clinical signs and bacterial burden detected in the liver is as follows (from greatest to least severity and highest to lowest burden): strain Wakulla, followed by strain Liberty, followed by strain Arkansas. In this article, we used microarray analysis to define t

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Minkah, Nana K., Laura Reynolds, Vera Okolo, and Stefan Kappe. "Type I Interferon remodels intrahepatocytic signaling to promote T cell dysfunction during liver stage Plasmodium infection." Journal of Immunology 208, no. 1_Supplement (2022): 170.36. http://dx.doi.org/10.4049/jimmunol.208.supp.170.36.

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Abstract Malaria is caused by Plasmodium parasites and accounted for 627,000 deaths in 2021. Upon deposition into the dermis, Plasmodium parasites traffic to, infect, and develop within hepatocytes before egressing to cause symptomatic erythrocytic infection. We recently reported that liver stage Plasmodium replication induces type I Interferon (IFN-I) signaling that compromises anti-malaria T cells. We now show that this IFN-I-mediated, inferior T cell response is mostly limited to hepatic CD8 T cells and is characterized by diminished cytokine production, impaired homeostatic CD8 T cell surv

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Boylan, Joan M., Jennifer A. Sanders, and Philip A. Gruppuso. "Regulation of fetal liver growth in a model of diet restriction in the pregnant rat." American Journal of Physiology-Regulatory, Integrative and Comparative Physiology 311, no. 3 (2016): R478—R488. http://dx.doi.org/10.1152/ajpregu.00138.2016.

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Limited nutrient availability is a cause of intrauterine growth restriction (IUGR), a condition that has important implications for the well being of the offspring. Using the established IUGR model of maternal fasting in the rat, we investigated mechanisms that control gene expression and mRNA translation in late-gestation fetal liver. Maternal fasting for 48 h during the last one-third of gestation was associated with a 10–15% reduction in fetal body weight and a disproportionate one-third reduction in total fetal liver protein. The fetal liver transcriptome showed only subtle changes consist

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Ilgisonis, Ekaterina V., Elena A. Ponomarenko, Svetlana N. Tarbeeva, et al. "Gene-centric coverage of the human liver transcriptome: QPCR, Illumina, and Oxford Nanopore RNA-Seq." Frontiers in Molecular Biosciences 9 (December 5, 2022). http://dx.doi.org/10.3389/fmolb.2022.944639.

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It has been shown that the best coverage of the HepG2 cell line transcriptome encoded by genes of a single chromosome, chromosome 18, is achieved by a combination of two sequencing platforms, Illumina RNA-Seq and Oxford Nanopore Technologies (ONT), using cut-off levels of FPKM &gt; 0 and TPM &gt; 0, respectively. In this study, we investigated the extent to which the combination of these transcriptomic analysis methods makes it possible to achieve a high coverage of the transcriptome encoded by the genes of other human chromosomes. A comparative analysis of transcriptome coverage for v

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Zhang, Youwen, Ioulia Chatzistamou, and Hippokratis Kiaris. "Transcriptomic coordination at hepatic steatosis indicates robust immune cell engagement prior to inflammation." BMC Genomics 22, no. 1 (2021). http://dx.doi.org/10.1186/s12864-021-07784-y.

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Abstract Background Deregulation in lipid metabolism leads to the onset of hepatic steatosis while at subsequent stages of disease development, the induction of inflammation, marks the transition of steatosis to non-alcoholic steatohepatitis. While differential gene expression unveils individual genes that are deregulated at different stages of disease development, how the whole transcriptome is deregulated in steatosis remains unclear. Methods Using outbred deer mice fed with high fat as a model, we assessed the correlation of each transcript with every other transcript in the transcriptome.

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Yu, Shizhe, Haoren Wang, Lingpeng Yang, et al. "Spatial transcriptome profiling of normal human liver." Scientific Data 9, no. 1 (2022). http://dx.doi.org/10.1038/s41597-022-01676-w.

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AbstractThe comprehensive study of the spatial-cellular anatomy of the human liver is critical to addressing the cellular origins of liver disease. Here we conducted spatial transcriptomics on normal human liver tissue sections, providing detailed information of liver zonation at the transcriptional level. We present 6581 high-quality spots from normal livers of two human donors. In this dataset, cells were mainly hepatocytes, and we classified them into four sub-groups. Collectively, these data provide a reliable reference for studies on spatial heterogeneity of liver lobules.

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Sung, Inyoung, Sangseon Lee, Dongmin Bang, Jungseob Yi, Sunho Lee, and Sun Kim. "MDTR: a knowledge-guided interpretable representation for quantifying liver toxicity at transcriptomic level." Frontiers in Pharmacology 15 (January 24, 2025). https://doi.org/10.3389/fphar.2024.1398370.

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IntroductionDrug-induced liver injury (DILI) has been investigated at the patient level. Analysis of gene perturbation at the cellular level can help better characterize biological mechanisms of hepatotoxicity. Despite accumulating drug-induced transcriptome data such as LINCS, analyzing such transcriptome data upon drug treatment is a challenging task because the perturbation of expression is dose and time dependent. In addition, the mechanisms of drug toxicity are known only as literature information, not in a computable form.MethodsTo address these challenges, we propose a Multi-Dimensional

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Lin, Yan, Ying Li, Guangyu Liang, et al. "Single‐cell transcriptome analysis of aging mouse liver." FASEB Journal 38, no. 4 (2024). http://dx.doi.org/10.1096/fj.202302282r.

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AbstractAging has a great impact on the liver, which causes a loss of physiological integrity and an increase in susceptibility to injury, but many of the underlying molecular and cellular processes remain unclear. Here, we performed a comprehensive single‐cell transcriptional profiling of the liver during aging. Our data showed that aging affected the cellular composition of the liver. The increase in inflammatory cells including neutrophils and monocyte‐derived macrophages, as well as in inflammatory cytokines, could indicate an inflammatory tissue microenvironment in aged livers. Moreover,

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Liu, Xi, Frédéric Hérault, Christian Diot, and Erwan Corre. "Development of a relevant strategy using de novo transcriptome assembly method for transcriptome comparisons between Muscovy and common duck species and their reciprocal inter-specific mule and hinny hybrids fed ad libitum and overfed." BMC Genomics 21, no. 1 (2020). http://dx.doi.org/10.1186/s12864-020-07099-4.

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Abstract Background Common Pekin and Muscovy ducks and their intergeneric hinny and mule hybrids have different abilities for fatty liver production. RNA-Seq analyses from the liver of these different genetic types fed ad libitum or overfed would help to identify genes with different response to overfeeding between them. However RNA-seq analyses from different species and comparison is challenging. The goal of this study was develop a relevant strategy for transcriptome analysis and comparison between different species. Results Transcriptomes were first assembled with a reference-based approac

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Jonsson, William O., Agnieszka K. Borowik, Atul Pranay, et al. "Kinetic proteomics identifies targeted changes in liver metabolism and the ribo-interactome by dietary sulfur amino acid restriction." GeroScience, March 28, 2023. http://dx.doi.org/10.1007/s11357-023-00758-w.

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AbstractDietary sulfur amino acid restriction (SAAR) protects against diet-induced obesity, extends healthspan, and coincides with an overall reduction in hepatic protein synthesis. To explore the underpinnings of SAAR-induced slowed growth and its impact on liver metabolism and proteostasis, we resolved changes in hepatic mRNA and protein abundances and compared synthesis rates of individual liver proteins. To achieve this, adult male mice were provided deuterium-labeled drinking water while freely consuming either a regular-fat or high-fat diet that was SAA restricted. Livers from these mice

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Kelly, Amy C., Fredrick Rosario, Jeannie Chan, Laura A. Cox, Theresa L. Powell, and Thomas Jansson. "Transcriptomic Responses are Sex-Dependent in the Skeletal Muscle and Liver in Offspring of Obese Mice." American Journal of Physiology-Endocrinology and Metabolism, July 20, 2022. http://dx.doi.org/10.1152/ajpendo.00263.2021.

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Infants born to obese mothers are more likely to develop metabolic disease, including glucose intolerance and hepatic steatosis, in adult life. We examined the effects of maternal obesity on the transcriptome of skeletal muscle and liver tissues of the near-term fetus and 3-month-old offspring in mice born to dams fed a high fat and sugar diet. Previously, we have shown that male, but not female, offspring develop glucose intolerance, insulin resistance, and liver steatosis at 3-months-old. Female C57BL6/J mice were fed normal chow or an obesogenic high-calorie diet before mating and throughou

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Wei, Rongxue, Yongqiang Teng, Chunchun Han, et al. "Multi-omics reveals goose fatty liver formation from metabolic reprogramming." Frontiers in Veterinary Science 11 (January 29, 2024). http://dx.doi.org/10.3389/fvets.2024.1122904.

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To comprehensively provide insight into goose fatty liver formation, we performed an integrative analysis of the liver transcriptome, lipidome, and amino acid metabolome, as well as peripheral adipose tissue transcriptome analysis using samples collected from the overfed geese and normally fed geese. Transcriptome analysis showed that liver metabolism pathways were mainly enriched in glucolipid metabolism, amino acid metabolism, inflammation response, and cell cycle; peripheral adipose tissue and the liver cooperatively regulated liver lipid accumulation during overfeeding. Liver lipidome patt

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