Transcriptome analysis uncovers the diagnostic value of miR-192-5p/HNF1A-AS1/VIL1 panel in cervical adenocarcinoma

Xu, Jianrong; Zou, Jian; Wu, Luyao; Lü, Weiguo

doi:10.1038/s41598-020-73523-0

Cited by 15 publications

(16 citation statements)

References 58 publications

(49 reference statements)

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“…In our HeLa cell experiment, the main fragment was 61 nt, which indicates a unique fragment given that we had a maximum read length of 75 nt. Even though the methods used in Tong et al (25) and Xu et al (26, 27) were restricted to a maximum read length of 50 nt, we found traces of this fragment in the pile of fragments with unverifiable length of ≥ 50 nt. It must be emphasized, however, that we tried to validate the 5’ ETS rRF in yet another dataset, Snoek et al (62) (SRA accession: PRJNA413777), but here we failed to detect anything in the 5’ EST region.…”

Section: Discussioncontrasting

confidence: 53%

“…Despite only having read lengths of 50 nt to our disposal (see Results 7.1), where 5’ ETS rRF of Peak 1 was 61 nt, we found clear traces of this rRF (Figure 8J). Furthermore, to explore the clinical relevance of this finding we downloaded the Xu et al dataset (26, 27). Here sRNA was extract from confirmed cervical tumors and samples from normal cervix.…”

Section: Results and Descriptionmentioning

confidence: 99%

“…The Xu et al 2020 (26, 27) (SRA accession PRJNA607023; ENA download: https://www.ebi.ac.uk/ena/browser/view/PRJNA607023) dataset, used for validating the 5’ ETS rRF of the 45S pre-rRNA (NR_146144.1) in clinical samples. We only used the 8 fastq files obtained by sRNA size-fractions.…”

Section: Methodsmentioning

confidence: 99%

“…Figure 8J). Furthermore, to explore the clinical relevance of this finding we downloaded the Xu et al dataset (26,27). Here sRNA was extract from confirmed cervical tumors and samples from normal cervix.…”

Section: Seqpac Example 2: Novel Rrna-derived Srna Affected By Anticamentioning

confidence: 99%

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Seqpac: A New Framework for small RNA analysis in R using Sequence-Based Counts

Skog

Örkenby

Kugelberg

et al. 2021

Preprint

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Small RNA sequencing (sRNA-seq) has become important for studying regulatory mechanisms in many cellular processes. Data analysis remains challenging, mainly because each class of sRNA--such as miRNA, piRNA, tRNA- and rRNA- derived fragments (tRFs/rRFs)--needs special considerations. Analysis therefore involves complex workflows across multiple programming languages, which can produce research bottlenecks and transparency issues. To make analysis of sRNA more accessible and transparent we present seqpac: a tool for advanced group-based analysis of sRNA completely integrated in R. This opens advanced sRNA analysis for Windows users--from adaptor trimming to visualization. Seqpac provides a framework of functions for analyzing a PAC object, which contains 3 standardized tables: sample phenotypic information (P), sequence annotations (A), and a counts table with unique sequences across the experiment (C). By applying a sequence-based counting strategy that maintains the integrity of the fastq sequence, seqpac increases flexibility and transparency compared to other workflows. It also contains an innovative targeting system allowing sequence counts to be summarized and visualized across sample groups and sequence classifications. Reanalyzing published data, we show that seqpac's fastq trimming performs equal to standard software outside R and demonstrate how sequence-based counting detects previously unreported bias. Applying seqpac to new experimental data, we discovered a novel rRF that was down-regulated by RNA pol I inhibition (anticancer treatment), and up-regulated in previously published data from tumor positive patients. Seqpac is available on github (https://github.com/Danis102/seqpac), runs on multiple platforms (Windows/Linux/Mac), and is provided with a step-by-step vignette on how to analyze sRNA-seq data.

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Section: Discussioncontrasting

confidence: 53%

Section: Results and Descriptionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Seqpac Example 2: Novel Rrna-derived Srna Affected By Anticamentioning

confidence: 99%

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Seqpac: A New Framework for small RNA analysis in R using Sequence-Based Counts

Skog

Örkenby

Kugelberg

et al. 2021

Preprint

View full text Add to dashboard Cite

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“…To independently evaluate and define the LINC01016 gene structure, RNA-Seq datasets (20)(21)(22) were obtained, and splice events were determined based on de novo predictions for LINC01016 in the testis (Fig. 4A) and cervix (Fig.…”

Section: De Novo Prediction Of Splice Events Expression and Isoform Identification In Testis And Cervixmentioning

confidence: 99%

Gene structure, differential exon usage, and expression of the testis long intergenic non-protein coding RNA 1016 in humans reveals isoform-specific roles in controlling biological processes

Yang

et al. 2021

Preprint

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Long noncoding RNAs (lncRNAs) have emerged as critical regulators of biological processes. The constant expansion of newly-identified lncRNA genes requires that each one be comprehensively annotated to understand its molecular functions. Here, we describe a detailed characterization of the gene which encodes long intergenic non-protein coding RNA 01016 (LINC01016, a.k.a., LncRNA1195) with a focus on its structure, exon usage, and expression in human and macaque tissues. In this study, we show that it is exclusively conserved among non-human primates, suggesting its recent evolution and is expressed and processed into 12 distinct RNAs in testis, cervix, and uterus tissues. Further, we integrate de novo annotation of expressed LINC01016 transcripts and isoform-dependent gene expression analyses to show that human LINC01016 is a multi-exon gene, processed through differential exon usage with isoform-specific functions. Furthermore, in gynecological cancers, such as cervical squamous cell carcinoma and uterine corpus endometrial carcinoma, LINC01016 is downregulated; however, its higher expression is predictive of relapse-free survival in these cancers. Collectively, these analyses reveal that, unlike coding RNAs, lncRNA isoforms are differentially regulated and precisely processed in specific tissues to perform distinct biological roles.

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Tumor suppressor miR‐192‐5p targets TRPM7 and inhibits proliferation and invasion in cervical cancer

Dong

Zhuang

Wang

et al. 2021

The Kaohsiung J of Med Scie

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Cervical cancer is the fourth highest mortality cancer among women worldwide.Many researchers have discovered the major anticancer role of miR-192-5p.However, no study has revealed the effect of miR-192-5p on cervical cancer and its molecular mechanism. Therefore, in this study, we aimed to explore the role of miR-192-5p in proliferation, invasion of cervical cancer, and its regulatory mechanism. Firstly, the expression level of miR-192-5p was examined by real-time quantitative polymerase chain reaction. Cell counting kit-8 analysis was applied to detect the proliferation of transfected Caski and SiHa cells. Flow cytometry assay was applied to detect the apoptosis of transfected Caski and SiHa cells. Our result showed that miR-192-5p restrained cervical cancer cell proliferation and induced apoptosis. Then we employed wound healing and transwell assays to analyze the migration and invasion abilities of Caski and SiHa cells in vitro. The results showed that miR-192-5p had an inhibitory effect on cervical cancer migration and invasion. The results of in vivo experiment demonstrated that miR-192-5p also inhibited tumor development in nude mice. We further detected that the binding of transient receptor potential melastatin-subfamily member 7 (TRPM7) to miR-192-5p using bioinformatic methods and dual-luciferase reporter assay. Finally, we found that TRPM7 overexpression reversed the inhibitory effects of miR-192-5p on proliferation, migration, and invasion on cervical cancer cells. In conclusion, the findings of the present study revealed that miR-192-5p performs an inhibitory role in cervical cancer proliferation and invasion by targeting TRPM7.

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Transcriptome analysis uncovers the diagnostic value of miR-192-5p/HNF1A-AS1/VIL1 panel in cervical adenocarcinoma

Cited by 15 publications

References 58 publications

Seqpac: A New Framework for small RNA analysis in R using Sequence-Based Counts

Seqpac: A New Framework for small RNA analysis in R using Sequence-Based Counts

Gene structure, differential exon usage, and expression of the testis long intergenic non-protein coding RNA 1016 in humans reveals isoform-specific roles in controlling biological processes

Tumor suppressor miR‐192‐5p targets TRPM7 and inhibits proliferation and invasion in cervical cancer

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