Identification and evolution of transcription factors RHR gene family (NFAT and RBPJ) involving lamprey (Lethenteron reissneri) innate immunity

Duan, Xuyuan; Lv, Menggang; Liu, Jessica Aijia; Pang, Yue; Li, Qingwei; Su, Peng; Gou, Meng

doi:10.1016/j.molimm.2021.07.017

Cited by 6 publications

(3 citation statements)

References 56 publications

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“…Due to its unique status in vertebrate evolution, lampreys have become an important animal model in diverse research fields 2 , 30 , such as vertebrate evolutionary and development 8 , 31 , 32 , fundamental aspects of vertebrate neurobiology 31 , 33 , adaptive immunity 34 , 35 , blood clotting 36 , and bioactive compound identification 23 . Metabolomics, as a relatively new member in the “omics” field, provides an additional powerful tool for lamprey studies.…”

Section: Resultsmentioning

confidence: 99%

Spatial Metabolomics Reveals the Multifaceted Nature of Lamprey Buccal Gland and Its Diverse Mechanisms for Blood-Feeding

Gou,

Duan,

et al. 2023

Commun Biol

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Lampreys are blood-sucking vampires in marine environments. From a survival perspective, it is expected that the lamprey buccal gland exhibits a repository of pharmacologically active components to modulate the host’s homeostasis, inflammatory and immune responses. By analyzing the metabolic profiles of 14 different lamprey tissues, we show that two groups of metabolites in the buccal gland of lampreys, prostaglandins and the kynurenine pathway metabolites, can be injected into the host fish to assist lamprey blood feeding. Prostaglandins are well-known blood-sucking-associated metabolites that act as vasodilators and anticoagulants to maintain vascular homeostasis and are involved in inflammatory responses. The vasomotor reactivity test on catfish aortic ring showed that kynurenine can also relax the blood vessels of the host fish, thus improving the blood flow of the host fish at the bite site. Finally, a lamprey spatial metabolomics database (https://www.lampreydb.com) was constructed to assist studies using lampreys as animal model.

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Section: Resultsmentioning

confidence: 99%

Spatial Metabolomics Reveals the Multifaceted Nature of Lamprey Buccal Gland and Its Diverse Mechanisms for Blood-Feeding

Gou,

Duan,

et al. 2023

Commun Biol

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“…Due to its unique status in vertebrate evolution, lampreys have become an important animal model in diverse research fields 2, 33 , such as vertebrate evolutionary and development 7, 34, 35 , fundamental aspects of vertebrate neurobiology 34, 36 , adaptive immunity 37, 38 , blood clogging 39 , and bioactive compound identification 19 . Metabolomics, as a relatively new member in the “omics” field, provides another powerful tool for lamprey studies.…”

Section: Resultsmentioning

confidence: 99%

How do Vampires Suck Blood?

Gou

Duan

et al. 2022

Preprint

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Lampreys are blood-sucking vampires in the marine. From a survival perspective, it is expected that lamprey buccal gland exhibits a repository of pharmacologically active components to modulate the homeostasis of host, inflammatory and immune responses. Several proteins have been found to function as anticoagulants, ion channel blockers, and immune suppressors in lampreys, while small metabolites have never been explored in detail. In this study, by analyzing the metabolic profiles of 14 different lamprey tissues, we have identified two groups of blood-sucking-associated metabolites, i.e., kynurenine pathway metabolites and prostaglandins, in the buccal gland and they can be injected into the host fish to ensure a steady and sustained blood flow to the feeding site. These findings demonstrate the complex nature of lamprey buccal gland and highlight the diversity in the mechanisms utilized for blood-sucking in lampreys. In addition, a lamprey spatial metabolomics database (https://www.lampreydb.com) was constructed to assist studies using lampreys as model animal. The database contains detailed qualitative, quantitative, and spatial distribution information of each detected metabolite, and users can easily query and check their metabolites of interest, and/or identify unknown peaks using the database.

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“…In summary, specific enriched motifs present in HERV sequences (coding and non-coding regions) are implicated in gene expression regulation, with some unique motifs involved in recognizing nuclear receptors within coding regions. Additionally, motifs identified from the full-length sequences also demonstrated enrichment, with those like Rbpjl, vertebrates, Rel homology region (RHR) factors playing roles in immune regulation, development, and inflammation regulation processes in organisms [40][41][42]. (Supplementary Fig.…”

Section: Enrichment and Pathogenicity Analysis Of Motifs In High Alrw...mentioning

confidence: 99%

Enhancing Recognition and Interpretation of Functional Phenotypic Sequences through Fine-Tuning Pre-Trained Genomic Models

Du,

Zhong,

Liu

2023

Preprint

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Decoding high-quality human genomic sequences requires comprehensive analysis of DNA sequence functionality. Through computational and experimental approaches, researchers study the genotype-phenotype relationship and generate important datasets that help unravel complicated genetic blueprints. This study explores the use of deep learning, particularly pre-trained models like DNA_bert_6 and human_gpt2-v1, in interpreting and representing human genome sequences. We meticulously construct multiple datasets linking genotypes and phenotypes to fine-tune pre-trained models for precise DNA sequence classification. Furthermore, we specifically focused on the human endogenous retrovirus (HERV) dataset with commendable classification performance (both binary and multi-classification accuracy and F1 values above 0.935 and 0.888, respectively). We evaluate the influence of sequence length on classification results and analyze the impact of feature extraction in the model’s hidden layers using the HERV dataset. To further understand the phenotype-specific patterns learned by the model, we perform enrichment, pathogenicity and conservation analyzes of specific motifs in the HERV sequence with high average local representation weight (LRAW) scores. Overall, the generated datasets further provide numerous additional genotype-phenotype datasets for evaluating the performance of genomic models. The findings highlight the potential of large models in learning DNA sequence representations, particularly when utilizing the HERV dataset, and provide valuable insights for future research. This work represents an innovative strategy that combines pre-trained model representations with classical omics methods for analyzing the functionality of genome sequences, fostering cross-fertilization between genomics and advanced AI. The source code and data are available athttps://github.com/GeorgeBGM/Genome_Fine-Tuning.

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Identification and evolution of transcription factors RHR gene family (NFAT and RBPJ) involving lamprey (Lethenteron reissneri) innate immunity

Cited by 6 publications

References 56 publications

Spatial Metabolomics Reveals the Multifaceted Nature of Lamprey Buccal Gland and Its Diverse Mechanisms for Blood-Feeding

Spatial Metabolomics Reveals the Multifaceted Nature of Lamprey Buccal Gland and Its Diverse Mechanisms for Blood-Feeding

How do Vampires Suck Blood?

Enhancing Recognition and Interpretation of Functional Phenotypic Sequences through Fine-Tuning Pre-Trained Genomic Models

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