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1.
Braz. j. biol ; 83: e248911, 2023. tab, graf
Article in English | MEDLINE, LILACS, VETINDEX | ID: biblio-1339362

ABSTRACT

Abstract The telencephalon refers to the most highly developed and anterior part of the forebrain, consisting mainly of the cerebral hemispheres. The study determined Neuroglobin (Ngb) and Hypoxia-inducible factor (HIF-1α) expression in the telencephalon of yak and cattle, and compare the expression and distribution pattern of Ngb and HIF-1α in the two animals. Immunohistochemistry (IHC), quantitative real-time Polymerase Chain Reaction (qRT-PCR), and Western blot (WB) were employed to investigate Ngb and Hif-1α expression in the telencephalon of yak and cattle. mRNA and protein expressions of Ngb and HIF-1α showed positive in different tissues of the yak and cattle telencephalon. Ngb expression in tissues of the yak recorded higher as compare to cattle while HIF-1α expression was found higher in cattle than yak. The HIF-1α expression in some tissues of yak telencephalon was consistent with the cattle. The results documented that HIF-1α may have a direct or indirect synergistic effect on Ngb expression in the yak telencephalon to improve hypoxia adaptation. It is suggested that yak may need more Ngb expression for adaptation, but the expression of HIF-1α seems to be down-regulated during long-term adaptation, and the specific causes of this phenomenon needs to be further verified.


Resumo O telencéfalo refere-se à parte anterior e mais desenvolvida do prosencéfalo, consistindo principalmente dos hemisférios cerebrais. O estudo determinou a expressão de neuroglobina (Ngb) e fator indutível por hipóxia (HIF-1α) no telencéfalo de iaques e bovinos e comparou a expressão e o padrão de distribuição de Ngb e HIF-1α nos dois animais. Imuno-histoquímica (IHC), reação em cadeia da polimerase quantitativa em tempo real (qRT-PCR) e Western blot (WB) foram empregados para investigar a expressão de Ngb e Hif-1α no telencéfalo de iaques e bovinos. As expressões de mRNA e proteínas de Ngb e HIF-1α mostraram-se positivas em diferentes tecidos do telencéfalo de iaque e bovino. A expressão de Ngb nos tecidos do iaque foi registrada mais alta em comparação com o gado, enquanto a expressão do HIF-1α foi encontrada mais alta no gado do que no iaque. A expressão de HIF-1α em alguns tecidos do telencéfalo de iaque foi consistente com o gado. Os resultados documentaram que o HIF-1α pode ter um efeito sinérgico direto ou indireto na expressão de Ngb no telencéfalo de iaque para melhorar a adaptação à hipóxia. É sugerido que o iaque pode precisar de mais expressão de Ngb para adaptação, mas a expressão de HIF-1α parece ser regulada para baixo durante a adaptação de longo prazo, e as causas específicas desse fenômeno precisam ser verificadas.


Subject(s)
Animals , Telencephalon , Hypoxia-Inducible Factor 1, alpha Subunit/genetics , RNA, Messenger/genetics , Cattle , Adaptation, Physiological , Neuroglobin
2.
J Mol Neurosci ; 72(3): 468-481, 2022 Mar.
Article in English | MEDLINE | ID: mdl-34580818

ABSTRACT

Neuropathic pain (NP) involves metabolic processes that are regulated by metabolic genes and their non-coding regulator genes such as microRNAs (miRNAs). Here, we aimed at exploring the key miRNA signatures regulating metabolic genes involved in NP pathogenesis. We downloaded NP-related data from public databases and identified differentially expressed microRNAs (miRNAs) and mRNAs through differential gene expression analysis. The miRNA target prediction was performed, and integration with the differentially expressed metabolic genes (DEMGs) was used for constructing the miRNA-DEMG network. Subsequently, functional enrichment analysis and protein-protein interaction (PPI) analysis were performed to explore the role of DEMGs in the regulatory network. The drug prediction was performed based on the DEMGs in the miRNA-DEMG network. A total of 8251 differentially expressed mRNAs (4193 upregulated and 4058 downregulated), and 959 differentially expressed miRNAs (455 upregulated and 504 downregulated) were identified. Moreover, after target gene prediction, a miRNA-DEMG network composed of 22 miRNAs and 113 mRNAs was constructed. The network was constituted of 135 nodes and 236 edges. We found that DEMGs in the network were mainly enriched in metabolic pathways and metabolic processes. A total of 1200 drugs were predicted as potential therapeutics for NP based on the differentially expressed genes, while 170 drugs were predicted for the DEMGs in the miRNA-DEMG network. Conclusively, our study predicted drugs that may be effective against the metabolic changes induced by miRNA dysregulation in NP. This information will help further reveal the pathological mechanism of NP and provide more treatment options for NP patients.


Subject(s)
MicroRNAs , Neuralgia , Computational Biology , Gene Regulatory Networks , Humans , MicroRNAs/genetics , MicroRNAs/metabolism , Neuralgia/drug therapy , Neuralgia/genetics , RNA, Messenger/genetics , RNA, Messenger/metabolism
3.
Methods Mol Biol ; 2418: 95-112, 2022.
Article in English | MEDLINE | ID: mdl-35119662

ABSTRACT

In situ hybridization (ISH) is an excellent method for detecting RNA in histological sections, both to detect gene expression and to assign gene expression to a distinct cell population. Therefore, ISH may be used in basic cell biology to detect the expression of certain genes within a tissue containing various cell populations. Here, we describe the detection and cellular localization of two estrogen receptors, both isoforms of the genomic estrogen receptor (ERα and ERß) in the human testis.


Subject(s)
Estrogen Receptor alpha , Testis , Estrogen Receptor alpha/genetics , Estrogen Receptor alpha/metabolism , Estrogen Receptor beta/genetics , Estrogen Receptor beta/metabolism , Humans , In Situ Hybridization , Male , RNA, Messenger/genetics , Testis/metabolism
4.
Genome Biol ; 23(1): 111, 2022 May 09.
Article in English | MEDLINE | ID: mdl-35534899

ABSTRACT

Recent proteogenomic studies revealed extensive translation outside of annotated protein coding regions, such as non-coding RNAs and untranslated regions of mRNAs. This non-canonical translation is largely due to start codon plurality within the same RNA. This plurality is often due to the failure of some scanning ribosomes to recognize potential start codons leading to initiation downstream-a process termed leaky scanning. Codons other than AUG (non-AUG) are particularly leaky due to their inefficiency. Here we discuss our current understanding of non-AUG initiation. We argue for a near-ubiquitous role of non-AUG initiation in shaping the dynamic composition of mammalian proteomes.


Subject(s)
Mammals , Ribosomes , Animals , Codon , Codon, Initiator/metabolism , Mammals/genetics , Mammals/metabolism , Peptide Chain Initiation, Translational , Protein Biosynthesis , RNA, Messenger/genetics , RNA, Messenger/metabolism , Ribosomes/genetics , Ribosomes/metabolism
5.
Dokl Biochem Biophys ; 503(1): 76-79, 2022 Apr.
Article in English | MEDLINE | ID: mdl-35538282

ABSTRACT

Overexpression of the transcription factor POU2F1 (Oct-1) increases the malignant potential of the tumor and determines the unfavorable prognosis for both solid and hematological cases of the disease in human carcinogenesis. The Oct-1 level determines the rate of development of the disease in acute myelodysplastic leukemia (AML), and a decrease in its expression significantly delays the development of leukemia in mice; however, a complete knockout of Oct-1 leads to the death of the animals. POU2F1 (Oct-1) is expressed as several isoforms transcribed from alternative promoters. They include both ubiquitous and tissue-specific isoforms. It was shown that in Burkitt's lymphoma Namalwa cells 5-azacytidine specifically suppresses the expression of the tissue-specific isoform Oct-1L mRNA (level of Oct-1L is abnormally increased in these cells), while not causing changes in the amount of the ubiquitous isoform Oct-1A mRNA. These results show that it is possible to selectively reduce the transcription level of the Oct-1L isoform aberrantly expressed in human tumor cells.


Subject(s)
Azacitidine , Burkitt Lymphoma , Leukemia , Octamer Transcription Factor-1 , Animals , Azacitidine/pharmacology , Burkitt Lymphoma/metabolism , Burkitt Lymphoma/pathology , Cell Culture Techniques , Mice , Octamer Transcription Factor-1/antagonists & inhibitors , Octamer Transcription Factor-1/genetics , Octamer Transcription Factor-1/metabolism , Protein Isoforms , RNA, Messenger/genetics , RNA, Messenger/metabolism , Tumor Cells, Cultured
6.
BMC Genomics ; 23(1): 358, 2022 May 11.
Article in English | MEDLINE | ID: mdl-35538402

ABSTRACT

BACKGROUND AND AIM: Yak estrus is a seasonal phenomenon, probably involving epigenetic regulation of synthesis and secretion of sex hormones as well as growth and development of follicles. N6-methyladenosine (m6A) is the most common internal modification of the eukaryotic mRNA. However, there are no detailed reports on the m6A transcriptome map of yak ovary. Therefore, this study aimed to collected the yak ovarian tissues at three different states of anestrus (YO-A), estrus (YO-F), and pregnancy (YO-P), and obtained the full transcriptome m6A map in yak by MeRIP-seq. RESULTS: The HE staining revealed that the number of growing follicles and mature follicles in the ovary during the estrus period was relatively higher than those in the anestrus period and the pregnancy period. The RT-qPCR showed that the expression of METTL3, METTL14, FTO, YTHDC1 were significantly different across different periods in the ovaries, which suggests that m6A may play a regulatory role in ovarian activity. Next, we identified 20,174, 19,747 and 13,523 m6A peaks in the three ovarian samples of YO-A, YO-F and YO-P using the methylated RNA immunoprecipitation sequencing (MeRIP-seq). The m6A peaks are highly enriched in the coding sequence (CDS) region and 3'untranslated region (3'UTR) as well as the conserved sequence of "RRACH." The GO, KEGG and GSEA analysis revealed the involvement of m6A in many physiological activities of the yak's ovary during reproductive cycle. The association analysis found that some genes such as BNC1, HOMER1, BMP15, BMP6, GPX3, and WNT11 were related to ovarian functions. CONCLUSIONS: The comparison of the distribution patterns of methylation peaks in the ovarian tissues across different periods further explored the m6A markers related to the regulation of ovarian ovulation and follicular development in the yak ovary. This comprehensive map provides a solid foundation for revealing the potential function of the mRNA m6A modification in the yak ovary.


Subject(s)
Ovary , Transcriptome , Adenosine/analogs & derivatives , Adenosine/genetics , Adenosine/metabolism , Animals , Cattle , Epigenesis, Genetic , Female , Ovary/metabolism , Pregnancy , RNA, Messenger/genetics
7.
BMC Infect Dis ; 22(1): 448, 2022 May 10.
Article in English | MEDLINE | ID: mdl-35538443

ABSTRACT

BACKGROUND: The etiopathogenesis of coronavirus disease 2019 (COVID-19) stem partially from the abnormal activation of the innate and adaptive immune systems. Here in the current investigation, the mRNA expression levels of toll-like receptors (TLRs) were evaluated in the nasopharyngeal epithelial cells from COVID-19 patients. METHODS: Epithelial cells were obtained using nasopharyngeal swab samples from 90 COVID-19 patients and 50 controls. COVID-19 cases were classified into those without symptoms, with symptoms but not hospitalized, and with symptoms and hospitalized. To determine the mRNA expression levels of TLRs, first RNA was extracted and cDNA was synthesized, and finally Real-time PCR was exerted. RESULTS: It was seen that the transcript levels of TLR3, TLR7, TLR8, and TLR9 were overexpressed in the COVID-19 patients with clinical symptoms needing hospitalization as well as in those with clinical symptoms without needing for hospitalization compared to controls. Upregulation of TLRs was associated with clinical presentations of the patients. CONCLUSIONS: Modulation of TLR3, TLR7, TLR8, TLR9 in the epithelial cells of COVID-19 cases may estimate the disease severity and requirement for hospitalization.


Subject(s)
COVID-19 , Toll-Like Receptor 3 , Epithelial Cells/metabolism , Humans , Nasopharynx , RNA, Messenger/genetics , Toll-Like Receptor 3/genetics , Toll-Like Receptor 3/metabolism , Toll-Like Receptor 7/genetics , Toll-Like Receptor 8/genetics , Toll-Like Receptor 9/genetics , Toll-Like Receptors/genetics
8.
J Transl Med ; 20(1): 201, 2022 May 10.
Article in English | MEDLINE | ID: mdl-35538537

ABSTRACT

PURPOSE: As a common complication of epithelial ovarian cancer (EOC), malignant ascites contributes to the peritoneal metastasis of EOC. CircRNAs play essential roles in tumor metastasis. However, no circRNAs have been reported to be involved in EOC peritoneal metastasis via ascites. METHODS: Total of 22 samples from 9 EOC patients containing primary lesions (T), tumor cells from ascites (ASC), and metastatic lesions (M) were included for RNA sequencing to identify differentially expressed circRNAs and mRNAs among different tumors. Bioinformatic analyses, including single-sample Gene Set Enrichment Analysis and soft cluster analysis, were performed to find circRNAs potentially correlated with ascitic metastasis. Wound healing and transwell analysis were performed to evaluate tumor cells metastasis in vitro. Quantitative real-time PCR and western-blot were used for gene expression evaluation. RESULTS: According to transcriptomic analysis, ASC showed mesenchymal phenotype while T and M showed epithelial phenotype. 10 circRNAs were differentially expressed among ASC, T, and M. Among them, hsa_circ_0000497 and hsa_circ_0000918 were significantly up-regulated in ASC. Functional analysis showed that both hsa_circ_0000497 and hsa_circ_0000918 promoted metastasis of EOC via epithelial-mesenchymal transition (EMT) in vitro. The regulatory network construction identified 8 miRNAs and 19 mRNAs, and 7 miRNAs and 17 mRNAs as potential downstream target genes of hsa_circ_0000497 and hsa_circ_0000918, respectively, which may play pivotal roles in EOC ascitic metastasis. CONCLUSIONS: circRNAs (hsa_circ_0000497 and hsa_circ_0000918) contribute to metastasis of EOC via ascites by regulating EMT. These circRNAs may serve as novel potential therapeutic targets or prognostic biomarkers for EOC peritoneal metastasis.


Subject(s)
MicroRNAs , Ovarian Neoplasms , Peritoneal Neoplasms , Ascites/genetics , Carcinoma, Ovarian Epithelial/genetics , Female , Humans , MicroRNAs/genetics , MicroRNAs/metabolism , Ovarian Neoplasms/genetics , Peritoneal Neoplasms/genetics , RNA, Circular/genetics , RNA, Messenger/genetics , RNA, Messenger/metabolism
9.
RNA Biol ; 19(1): 609-621, 2022.
Article in English | MEDLINE | ID: mdl-35491909

ABSTRACT

Cells of metazoans respond to internal and external stressors by activating stress response pathways that aim for re-establishing cellular homoeostasis or, if this cannot be achieved, triggering programmed cell death. Problems during translation, arising from defective mRNAs, tRNAs, ribosomes or protein misfolding, can activate stress response pathways as well as mRNA surveillance and ribosome quality control programs. Recently, ribosome collisions have emerged as a central signal for translational stress and shown to elicit different stress responses. Here, we review our current knowledge about the intricate mutual connections between ribosome collisions, stress response pathways and mRNA surveillance. A central factor connecting the sensing of collided ribosomes with degradation of the nascent polypeptides, dissociation of the stalled ribosomes and degradation of the mRNA by no-go or non-stop decay is the E3-ligase ZNF598. We tested whether ZNF598 also plays a role in nonsense-mediated mRNA decay (NMD) but found that it is dispensable for this translation termination-associated mRNA surveillance pathway, which in combination with other recent data argues against stable ribosome stalling at termination codons being the NMD-triggering signal.


Subject(s)
Insurance , Ribosomes , Nonsense Mediated mRNA Decay , Protein Biosynthesis , RNA, Messenger/genetics , RNA, Messenger/metabolism , Ribosomes/metabolism
10.
RNA Biol ; 19(1): 686-702, 2022.
Article in English | MEDLINE | ID: mdl-35491945

ABSTRACT

It has recently been shown that CFIm25, a canonical mRNA 3' processing factor, could play a variety of physiological roles through its molecular function in the regulation of mRNA alternative polyadenylation (APA). Here, we used CRISPR/Cas9-mediated gene editing approach in human embryonic stem cells (hESCs) for CFIm25, and obtained three gene knockdown/mutant cell lines. CFIm25 gene editing resulted in higher proliferation rate and impaired differentiation potential for hESCs, with these effects likely to be directly regulated by the target genes, including the pluripotency factor rex1. Mechanistically, we unexpected found that perturbation in CFIm25 gene expression did not significantly affect cellular mRNA 3' processing efficiency and APA profile. Rather, we provided evidences that CFIm25 may impact RNA polymerase II (RNAPII) occupancy at the body of transcribed genes, and promote the expression level of a group of transcripts associated with cellular proliferation and/or differentiation. Taken together, these results reveal novel mechanisms underlying CFIm25's modulation in determination of cell fate, and provide evidence that the process of mammalian gene transcription may be regulated by an mRNA 3' processing factor.


Subject(s)
Polyadenylation , Stem Cells , Animals , Gene Knockdown Techniques , Humans , Mammals/genetics , RNA, Messenger/genetics , RNA, Messenger/metabolism , mRNA Cleavage and Polyadenylation Factors/metabolism
11.
AAPS J ; 24(3): 64, 2022 05 02.
Article in English | MEDLINE | ID: mdl-35501406

ABSTRACT

Autogene cevumeran is an individualized neoantigen-specific therapy (iNeST) under development for the treatment of various solid tumors. It consists of an RNA-Lipoplex (RNA-LPX) in which the encapsulated mRNA molecule encodes up to ten neoepitopes identified from each individual patient. In association with major histocompatibility complex (MHC) class I and MHC class II, these neoantigens can potentially stimulate and expand neoantigen-specific CD4+ and CD8+ T cells, leading to antitumor responses. As part of the pharmacokinetic (PK) property assessment of Autogene cevumeran in patients, both the lipid and mRNA content in circulation are measured. This work focused on our efforts to establish a sensitive and robust method for the measurement of mRNA levels of RNA-LPX in plasma. Due to the chemical characteristics of mRNA, extra precautions are required in order to effectively preserve mRNA integrity in human plasma during sample collection, handling and storage. To this end, a number of sample collection tubes and storage conditions were evaluated in order to inform the most optimal and operationally feasible conditions by which to preserve mRNA integrity during sample collection and upon freeze-thaw. PAXgene Blood ccfDNA tubes successfully prevented mRNA degradation and were subsequently selected for patient sample collection in the clinical trial. A branched DNA (bDNA)-based mRNA PK assay was developed to achieve the desired assay performance. Here, we discuss the evaluation of various sample collection and processing conditions as well as the optimization of the work flow during bDNA PK method development.


Subject(s)
Liposomes , Neoplasms , CD8-Positive T-Lymphocytes , Humans , Neoplasms/drug therapy , Neoplasms/genetics , RNA , RNA, Messenger/genetics
12.
Methods Mol Biol ; 2477: 71-77, 2022.
Article in English | MEDLINE | ID: mdl-35524112

ABSTRACT

Direct RNA sequencing (dRNA-seq) simultaneously enables the detection of RNA modifications and characterization of full-length transcripts. In principle, full-length native RNA molecule is translocated through the nanopore by a motor protein while a sensor measures ionic current shifts. Then, the current shifts are interpreted by an algorithm that turn out to RNA sequence. Currently, the standard protocol of dRNA-seq provided by Oxford Nanopore Technologies (ONT) allows to directly ligate and sequence only polyadenylated RNA (poly(A) RNA). Here, we describe a method of dRNA-seq that can be applied for both poly(A) RNA and non-poly(A) tailed-RNA.


Subject(s)
Nanopore Sequencing , Nanopores , High-Throughput Nucleotide Sequencing/methods , RNA/genetics , RNA, Messenger/genetics , Sequence Analysis, RNA/methods , Transcriptome
13.
Methods Mol Biol ; 2477: 179-193, 2022.
Article in English | MEDLINE | ID: mdl-35524118

ABSTRACT

Selective Ribosome Profiling (SeRP) is an emerging methodology, developed to capture cotranslational interactions in vivo. To date, SeRP is the only method that can directly capture, in near-codon resolution, ribosomes in action. Thus, SeRP allows us to study the mechanisms of protein synthesis and the network of protein-protein interactions that are formed already during synthesis. Here we report, in detail, the protocol for purification of ribosome- and Nascent-Chain associated factors, followed by isolation of ribosome-protected mRNA footprints, cDNA library generation and subsequent data analysis.


Subject(s)
Protein Biosynthesis , Ribosomes , Codon/metabolism , Gene Library , RNA, Messenger/genetics , RNA, Messenger/metabolism , Ribosomes/metabolism
14.
BMC Bioinformatics ; 23(1): 164, 2022 May 06.
Article in English | MEDLINE | ID: mdl-35524165

ABSTRACT

BACKGROUND: Circular RNAs (circRNAs) are a class of non-coding RNAs formed by pre-mRNA back-splicing, which are widely expressed in animal/plant cells and often play an important role in regulating microRNA (miRNA) activities. While numerous databases have collected a large amount of predicted circRNA candidates and provided the corresponding circRNA-regulated interactions, a stand-alone package for constructing circRNA-miRNA-mRNA interactions based on user-identified circRNAs across species is lacking. RESULTS: We present CircMiMi (circRNA-miRNA-mRNA interactions), a modular, Python-based software to identify circRNA-miRNA-mRNA interactions across 18 species (including 16 animals and 2 plants) with the given coordinates of circRNA junctions. The CircMiMi-constructed circRNA-miRNA-mRNA interactions are derived from circRNA-miRNA and miRNA-mRNA axes with the support of computational predictions and/or experimental data. CircMiMi also allows users to examine alignment ambiguity of back-splice junctions for checking circRNA reliability and examine reverse complementary sequences residing in the sequences flanking the circularized exons for investigating circRNA formation. We further employ CircMiMi to identify circRNA-miRNA-mRNA interactions based on the circRNAs collected in NeuroCirc, a large-scale database of circRNAs in the human brain. We construct circRNA-miRNA-mRNA interactions comprising differentially expressed circRNAs, and miRNAs in autism spectrum disorder (ASD) and cross-species analyze the relevance of the targets to ASD. We thus provide a rich set of ASD-associated circRNA-miRNA-mRNA axes and a useful starting point for investigation of regulatory mechanisms in ASD pathophysiology. CONCLUSIONS: CircMiMi allows users to identify circRNA-mediated interactions in multiple species, shedding light on regulatory roles of circRNAs. The software package and web interface are freely available at https://github.com/TreesLab/CircMiMi and http://circmimi.genomics.sinica.edu.tw/ , respectively.


Subject(s)
Autism Spectrum Disorder , MicroRNAs , Animals , Gene Regulatory Networks , MicroRNAs/genetics , RNA, Circular , RNA, Messenger/genetics , Reproducibility of Results , Software
15.
BMC Cancer ; 22(1): 499, 2022 May 06.
Article in English | MEDLINE | ID: mdl-35524230

ABSTRACT

BACKGROUND: Atypical teratoid/rhabdoid tumor (AT/RT) is a malignant pediatric tumor of the central nervous system (CNS) with high recurrence and low survival rates that is often misdiagnosed. MicroRNAs (miRNAs) are involved in the tumorigenesis of numerous pediatric cancers, but their roles in AT/RT remain unclear. METHODS: In this study, we used miRNA sequencing and gene expression microarrays from patient tissue to study both the miRNAome and transcriptome traits of AT/RT. RESULTS: Our findings demonstrate that 5 miRNAs were up-regulated, 16 miRNAs were down-regulated, 179 mRNAs were up-regulated and 402 mRNAs were down-regulated in AT/RT. qPCR revealed that hsa-miR-17-5p and MAP7 mRNA were the most significantly differentially expressed miRNA and mRNA in AT/RT tissues. Furthermore, the results from analyses using the miRTarBase database identified MAP7 mRNA as a target gene of hsa-miR-17-5p. CONCLUSIONS: Our findings suggest that the dysregulation of hsa-miR-17-5p may be a pivotal event in AT/RT and miRNAs that may represent potential therapeutic targets and diagnostic biomarkers.


Subject(s)
Central Nervous System Neoplasms , MicroRNAs , Rhabdoid Tumor , Central Nervous System Neoplasms/genetics , Child , Gene Expression Profiling , Gene Regulatory Networks , Humans , MicroRNAs/genetics , MicroRNAs/metabolism , RNA, Messenger/genetics , Rhabdoid Tumor/genetics
16.
BMC Vet Res ; 18(1): 167, 2022 May 06.
Article in English | MEDLINE | ID: mdl-35524260

ABSTRACT

BACKGROUND: Among the world's finest natural fiber composites is derived from the secondary hair follicles (SHFs) of cashmere goats yield one of the world's best natural fibres. Their development and cycling are characterized by photoperiodism with diverse, well-orchestrated stimulatory and inhibitory signals. Long non-coding RNA (lncRNAs) and mRNAs play important roles in hair follicle (HF) development. However, not many studies have explored their specific functions in cashmere development and cycling. This study detected mRNAs and lncRNAs with their candidate genes and related pathways in SHF development and cycling of cashmere goat. We utilized RNA sequencing (RNA-Seq) and bioinformatics analysis on lncRNA and mRNA expressions in goat hair follicles to discover candidate genes and metabolic pathways that could affect development and cycling (anagen, catagen, and telogen). RESULTS: We identified 228 differentially expressed (DE) mRNAs and 256 DE lncRNA. For mRNAs, catagen and anagen had 16 upregulated and 35 downregulated DEGs, catagen and telogen had 18 upregulated and 9 downregulated DEGs and telogen and anagen had 52 upregulated and 98 downregulated DEGs. LncRNA witnessed 22 upregulated and 39 downregulated DEGs for catagen and anagen, 36 upregulated and 29 downregulated DEGs for catagen and telogen as well as 66 upregulated and 97 downregulated DEGs for telogen and anagen. Several key genes, including MSTRG.5451.2, MSTRG.45465.3, MSTRG.11609.2, CHST1, SH3BP4, CDKN1A, GAREM1, GSK-3ß, DEFB103A KRTAP9-2, YAP1, S100A7A, FA2H, LOC102190037, LOC102179090, LOC102173866, KRT2, KRT39, FAM167A, FAT4 and EGFL6 were shown to be potentially important in hair follicle development and cycling. They were related to, WNT/ß-catenin, mTORC1, ERK/MAPK, Hedgehog, TGFß, NFkB/p38MAPK, caspase-1, and interleukin (IL)-1a signaling pathways. CONCLUSION: This work adds to existing understanding of the regulation of HF development and cycling in cashmere goats via lncRNAs and mRNAs. It also serves as theoretical foundation for future SHF research in cashmere goats.


Subject(s)
RNA, Long Noncoding , Animals , Gene Expression Profiling/veterinary , Glycogen Synthase Kinase 3 beta , Goats/metabolism , Hair Follicle/metabolism , RNA, Long Noncoding/genetics , RNA, Messenger/genetics , RNA, Messenger/metabolism , RNA-Seq/veterinary
17.
J Immunol Res ; 2022: 9284204, 2022.
Article in English | MEDLINE | ID: mdl-35528619

ABSTRACT

Objective: To investigate the potential diagnostic and predictive significance of immune-related genes in IgA nephropathy (IgAN) and discover the abnormal glomerular inflammation in IgAN. Methods: GSE116626 was used as a training set to identify different immune-related genes (DIRGs) and establish machine learning models for the diagnosis of IgAN; then, a nomogram model was generated based on GSE116626, and GSE115857 was used as a test set to evaluate its clinical value. Short Time-Series Expression Miner (STEM) analysis was also performed to explore the changing trend of DIRGs with the progression of IgAN lesions. GSE141344 was used with DIRGs to establish the ceRNA network associated with IgAN progression. Finally, ssGSEA analysis was performed on the GSE141295 dataset to discover the abnormal inflammation in IgAN. Results: Machine learning (ML) performed excellently in diagnosing IgAN using six DIRGs. A nomogram model was constructed to predict IgAN based on the six DIRGs. Three trends related to IgAN lesions were identified using STEM analysis. A ceRNA network associated with IgAN progression which contained 8 miRNAs, 14 lncRNAs, and 3 mRNAs was established. A higher macrophage ratio and lower CD4+ T cell ratio in IgAN compared to controls were observed, and the correlation between macrophages and monocytes in the glomeruli of IgAN patients was inverse compared to controls. Conclusion: This study reveals the diagnostic and predictive significance of DIRGs in IgAN and finds that the imbalance between macrophages and CD4+ immune cells may be an important pathomechanism of IgAN. These results provide potential directions for the treatment and prevention of IgAN.


Subject(s)
Glomerulonephritis, IGA , Female , Glomerulonephritis, IGA/diagnosis , Glomerulonephritis, IGA/genetics , Humans , Inflammation/pathology , Kidney Glomerulus/pathology , Macrophages/pathology , Male , RNA, Messenger/genetics
18.
Comput Math Methods Med ; 2022: 8504441, 2022.
Article in English | MEDLINE | ID: mdl-35529267

ABSTRACT

Clear cell renal carcinoma (ccRCC) is one of the most common renal carcinomas worldwide, which has worse prognosis compared with other subtypes of tumors. We propose a potential RNA regulatory mechanism associated with ccRCC progression. Accordingly, we screened out clinical factors and the expression of RNAs and miRNAs of ccRCC from the TCGA database. 9 lncRNAs (FGF12-AS2, WT1-AS, TRIM36-IT1, AC009093.1, LINC00443, TCL6, COL18A1-AS1, AC110619.1, HOTTIP), 2 miRNAs (mir-155 and mir-21), and 3 mRNAs (COL4A4, ERMP1, PRELID2) were selected from differential expression RNAs and built predictive survival models. The survival models performed very well in predicting prognosis and were found to be highly correlated with tumor stage. In addition, the survival-related lncRNA-miRNA-mRNA (ceRNA) network was constructed by 18 RNAs including 12 mRNAs, 2 miRNAs, and 4 lncRNAs. It is found that the "ECM-receptor interaction," "Pathways in cancer," and "Chemokine signaling pathway" as the main pathways in KEGG pathway analysis. Overall, we established predictive survival model and ceRNA network based on multivariate Cox regression analysis. It may open a new approach and potential biomarkers for clinical prognosis and treatment of ccRCC patients.


Subject(s)
Carcinoma, Renal Cell , Kidney Neoplasms , MicroRNAs , RNA, Long Noncoding , Biomarkers, Tumor/genetics , Carcinoma, Renal Cell/genetics , Female , Fibroblast Growth Factors/genetics , Fibroblast Growth Factors/metabolism , Gene Expression Regulation, Neoplastic , Gene Regulatory Networks , Humans , Kaplan-Meier Estimate , Kidney Neoplasms/genetics , Male , MicroRNAs/genetics , MicroRNAs/metabolism , Prognosis , RNA, Long Noncoding/genetics , RNA, Long Noncoding/metabolism , RNA, Messenger/genetics , RNA, Messenger/metabolism
19.
Clin Transl Med ; 12(5): e738, 2022 May.
Article in English | MEDLINE | ID: mdl-35522942

ABSTRACT

BACKGROUND: Dysregulation of the epitranscriptome causes abnormal expression of oncogenes in the tumorigenic process. Previous studies have shown that NAT10 can regulate mRNA translation efficiency through RNA acetylation. However, the role of NAT10-mediated acetylation modification in bladder cancer remains elusive. METHODS: The clinical value of NAT10 was estimated according to NAT10 expression pattern based on TCGA data set and the tumor tissue array. Acetylated RNA immunoprecipitation sequencing was utilized to explore the role of NAT10 in mRNA ac4C modification. Translation efficiency and mRNA stability assay were applied to study the effect of NAT10-deletion on target genes. The nude mouse model and genetically engineered mice were conducted to further verify the characteristics of NAT10 in promoting BLCA progression and regulating downstream targets. RESULTS: NAT10 was essential for the proliferation, migration, invasion, survival and the stem-cell-like properties of bladder cancer cell lines. NAT10 was responsible for mRNA ac4C modification in BLCA cells, including BCL9L, SOX4 and AKT1. Deficient NAT10 in both xenograft and transgenic mouse models of bladder cancer reduced the tumor burden. Furthermore, acetylated RNA immunoprecipitation sequencing data and RNA immunoprecipitation qPCR results revealed that NAT10 is responsible for a set of ac4C mRNA modifications in bladder cancer cells. Inhibition of NAT10 led to a loss of ac4C peaks in these transcripts and represses the mRNA's stability and protein expression. Mechanistically, the ac4C reduction modification in specific regions of mRNAs resulting from NAT10 downregulation impaired the translation efficiency of BCL9L, SOX4 and AKT1 as well as the stability of BCL9L, SOX4. CONCLUSIONS: In summary, these findings provide new insights into the dynamic characteristics of mRNA's post-transcriptional modification via NAT10-dependent acetylation and predict a role for NAT10 as a therapeutic target in bladder cancer. HIGHLIGHTS: NAT10 is highly expressed in BLCA patients and its abnormal level predicts bladder cancer progression and low overall survival rate. NAT10 is necessary and sufficient for BLCA tumourigenic properties. NAT10 is responsible for ac4C modification of target transcripts, including BCL9L, SOX4 and AKT1. NAT10 may serve as an effective and novel therapeutic target for BLCA.


Subject(s)
N-Terminal Acetyltransferases , Urinary Bladder Neoplasms , Animals , Cytidine/analogs & derivatives , Cytidine/genetics , Humans , Mice , N-Terminal Acetyltransferases/metabolism , RNA/metabolism , RNA, Messenger/genetics , RNA, Messenger/metabolism , SOXC Transcription Factors , Urinary Bladder Neoplasms/genetics
20.
Clin Transl Med ; 12(5): e778, 2022 May.
Article in English | MEDLINE | ID: mdl-35522946

ABSTRACT

BACKGROUND: Solute carrier family 7 member 11 (SLC7A11) is overexpressed in multiple human tumours and functions as a transporter importing cystine for glutathione biosynthesis. It promotes tumour development in part by suppressing ferroptosis, a newly identified form of cell death that plays a pivotal role in the suppression of tumorigenesis. However, the role and underlying mechanisms of SLC7A11-mediated ferroptosis in hepatoblastoma (HB) remain largely unknown. METHODS: Reverse transcription quantitative real-time PCR (RT-qPCR) and western blotting were used to measure SLC7A11 levels. Cell proliferation, colony formation, lipid reactive oxygen species (ROS), MDA concentration, 4-HNE, GSH/GSSG ratio and cell death assays as well as subcutaneous xenograft experiments were used to elucidate the effects of SLC7A11 in HB cell proliferation and ferroptosis. Furthermore, MeRIP-qPCR, dual luciferase reporter, RNA pulldown, RNA immunoprecipitation (RIP) and RACE-PAT assays were performed to elucidate the underlying mechanism through which SLC7A11 was regulated by the m6A modification in HB. RESULTS: SLC7A11 expression was highly upregulated in HB. SLC7A11 upregulation promoted HB cell proliferation in vitro and in vivo, inhibiting HB cell ferroptosis. Mechanistically, SLC7A11 mRNA exhibited abnormal METTL3-mediated m6A modification, which enhanced its stability and expression. IGF2 mRNA-binding protein 1 (IGF2BP1) was identified as the m6A reader of SLC7A11, enhancing SLC7A11 mRNA stability and expression by inhibiting SLC7A11 mRNA deadenylation in an m6A-dependent manner. Moreover, IGF2BP1 was found to block BTG2/CCR4-NOT complex recruitment via competitively binding to PABPC1, thereby suppressing SLC7A11 mRNA deadenylation. CONCLUSIONS: Our findings demonstrated that the METTL3-mediated SLC7A11 m6A modification enhances HB ferroptosis resistance. The METTL3/IGF2BP1/m6A modification promotes SLC7A11 mRNA stability and upregulates its expression by inhibiting the deadenylation process. Our study highlights a critical role of the m6A modification in SLC7A11-mediated ferroptosis, providing a potential strategy for HB therapy through blockade of the m6A-SLC7A11 axis.


Subject(s)
Amino Acid Transport System y+ , Ferroptosis , Hepatoblastoma , Immediate-Early Proteins , Liver Neoplasms , Adenosine/analogs & derivatives , Adenosine/pharmacology , Amino Acid Transport System y+/genetics , Amino Acid Transport System y+/metabolism , Animals , Ferroptosis/genetics , Hepatoblastoma/genetics , Humans , Immediate-Early Proteins/metabolism , Liver Neoplasms/genetics , Liver Neoplasms/metabolism , Liver Neoplasms/pathology , Methyltransferases/genetics , Methyltransferases/metabolism , RNA, Messenger/genetics , Tumor Suppressor Proteins/metabolism
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