Identification of Differentially Expressed Genes Associated with Litter Size in Berkshire Pig Placenta

Kwon, Seul Gi; Hwang, Jung Hye; Park, Da Hye; Kim, Tae Wan; Kang, Dong Jin; Kang, Kyung Hee; Kim, Il-Suk; Park, Hwa Chun; Na, Chong-Sam; Ha, Ji Hee; Kim, Chul Wook

doi:10.1371/journal.pone.0153311

Cited by 34 publications

(30 citation statements)

References 36 publications

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“…The final libraries were quantified using a KAPA Library Quantification kit (KAPA Biosystems, South Africa) and an Agilent 2100 Bioanalyzer. After qRT-PCR validation, the libraries were subjected to paired-end sequencing with a pair-end 150-base pair reading length on an Illumina HiSeq sequencer (Illumina) [30].…”

Section: Rna Sequencingmentioning

confidence: 99%

Hypo-phosphorylated CD147 promotes migration and invasion of hepatocellular carcinoma cells and predicts a poor prognosis

et al. 2019

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Purpose CD147 is a tumor-associated antigen that plays a key regulatory role in tumor invasion and distant metastasis. However, the exact role of CD147 phosphorylation, which is deregulated during cancer progression, is unknown. Here, the effects of CD147 phosphorylation on the malignant behavior of hepatocellular carcinoma (HCC) cells and its possible underlying mechanisms are explored. Methods An in situ Duolink-proximity ligation assay (PLA) was used to detect CD147 phosphorylation. Tandem mass spectrometry was employed to identify the phosphorylation sites of CD147. The effects of CD147 phosphorylation on the malignant behavior of HCC cells were evaluated using scratch wound healing assays, transwell invasion assays and cell cycle assays. The genes regulated by CD147 phosphorylation were detected by RNA sequencing. Results We identified phosphorylated serine-246 in the C terminus of CD147 in primary HCC tissues, whereas serine to alanine substitution mutation analysis suggested that CD147 is phosphorylated mainly at serine-252 in HCC-derived Huh-7 cells. Recovery expression of S246A/S252A mutants in CD147 knockout cells revealed significantly increased migration and invasion capacities compared to wildtype CD147 expressing cells. Cyclophilin A (CyPA) treatment decreased the phosphorylation level of CD147, whereas NIMA-related kinase 6 (NEK6) increased the CD147 phosphorylation level. Moreover, the CD147 phosphorylation level was found to be dramatically decreased in HCC tissues in patients with distant metastases, and a low phosphorylation level of CD147 was found to be associated with a high serum AFP level, recurrence and a poor overall survival. Conclusions From our data we conclude that hypo-phosphorylated CD147 promotes the migration and invasion of HCC cells and correlates with an unfavorable prognosis in HCC patients, indicating that targeting the aberrantly hypo-phosphorylated form of CD147 may be instrumental for the development of novel therapeutic modalities directed against HCC metastasis.

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Section: Rna Sequencingmentioning

confidence: 99%

Hypo-phosphorylated CD147 promotes migration and invasion of hepatocellular carcinoma cells and predicts a poor prognosis

et al. 2019

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“…Increasing litter size and raising healthy, quality animals are crucial factors in the livestock industry [1].…”

Section: Introductionmentioning

confidence: 99%

“…Understanding the genetic traits controlling the reproductive physiology has become an important research topic in the last decade [1]. Litter size is a complex trait in multiparous mammals.…”

Section: Introductionmentioning

confidence: 99%

Large-Scale Metadata Analysis of Ovary Based Multi-Omics Datasets for Understanding the Genes Regulating Litter Size

Kameshwar¹,

Li²

2020

Preprint

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Background : Litter size is a very important production index in the livestock industry, which is controlled by various complex physiological processes. To understand and reveal the common gene expression patterns involved in controlling prolificacy, we have performed a large-scale metadata analysis of five genome-wide transcriptome datasets of pig and sheep ovary samples obtained from high and low litter groups, respectively. We analyzed separately each transcriptome dataset using GeneSpring v14.8 software by implementing standard, generic analysis pipelines and further compared the list of most significant and differentially expressed genes obtained from each dataset to identify genes that are found to be common and significant across all the studies. Results : We have observed a total of 62 differentially expressed genes common among more than two gene expression datasets. The KEGG pathway analysis of most significant genes has shown that they are involved in metabolism, the biosynthesis of lipids, cholesterol and steroid hormones, immune system, cell growth and death, cancer-related pathways and signal transduction pathways. Of these 62 genes, we further narrowed the list to the 25 most significant genes by focusing on the ones with fold change >1.5 and p<0.05. These genes are CYP11A1, HSD17B2, STAR, SCARB1, IGSF8, MSMB, SERPINA1 , FAM46C, HEXA, PTTG1, TIMP1, FAM167B, CCNG1, FAXDC2, HMGCS1, L2HGDH, Lipin1, MME, MSMO1, PARM1, PTGFR, SLC22A4, SLC35F5, CCNA2, CENPU, CEP55, RASSF2, and SLC16A3 . Conclusions : Interestingly, comparing the list of genes with the list of genes obtained from our literature search analysis, we found only three genes in common. These genes are HEXA, PTTG1, and TIMP1. Our finding points to the potential of a few genes that may be important for ovarian follicular development and oocyte quality. Future studies revealing the function of these genes will further our understanding of how litter size is controlled in the ovary while also providing insight on genetic selection of high litter gilts.

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“…To find the quantitative trait loci (QTL) and causal genes for these traits, several studies for linkages [11-13] and candidate genes ([14-17] have been conducted by using modern molecular information. Many of the major genes involved in the prolificacy of pig, such as ESR , FSHB , RBP4 , PRLR , MTNR1A , OPN , BMP families, and GDF9 genes have been characterized [18, 19].…”

Section: Introductionmentioning

confidence: 99%

“…Genetic studies have revealed an increasing number of associated QTLs and candidate genes involved in pig litter size [20-22]. Recently, several studies of the transcriptome for reproductive organs reveals differentially expressed genes affecting reproduction and candidate genes for litter size in European pig breeds [9, 15, 17] and Chinese indigenous pig breeds [14, 23]. Although QTLs and candidate genes have been reported to affect the litter size in many pig breeds, however, the studies were only focused on specific species or breeds and the findings cannot elucidate the marked differences of the reproductive traits between Asian and European pig breeds and the variations of litter size between pigs.…”

Section: Introductionmentioning

confidence: 99%

Changes in Ovary Transcriptome and Alternative splicing at estrus from Xiang pigs with Large and Small Litter Size

Zhang

Tang

Ran

et al. 2019

Preprint

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29 30 2 1 2 Abstract 3 Background/Aims: Litter size is one of the most important reproductive traits in pig breeding, which is affected by 4 multiple genes and the environment. Ovaries are the most important reproductive organs and have a profound impact 5 on the reproduction efficiency. Therefore, genetic differences in the ovaries may contribute to the observed 6 differences in litter size. Although QTLs and candidate genes have been reported to affect the litter size in many pig 7 breeds, however, the findings cannot elucidate the marked differences of the reproductive traits between breeds. The 8 aim of present work is to elucidate the mechanisms of the differences for the reproductive traits and identify 9 candidate genes associated with litter size in Xiang pig breed. Methods: The changes in ovary transcriptome and 10 alternative splicing were investigated at estrus between Xiang pigs with large and small litter size by RNA-seq 11 technology. The RNA-seq results were confirmed by RT-qPCR method. Results: We detected 16,219 -16,285 expressed 12 genes and 12 types of alternative splicing (AS) events in Xiang pig samples. A total of 762 differentially expressed genes 13 were identified by XL (Xiang pig group with larger litter size) vs XS (Xiang pig group with small litter size) sample 14 comparisons. A total of 34 genes were upregulated and 728 genes were downregulated in XL ovary samples compared 15 with the XS samples. Alternative splicing (AS) rates in XL samples were slightly lower than that observed in XS samples. 16 Most of differentially expressed genes were differentially regulated on AS level. Eleven candidate genes were 17 potentially identified to be related to Xiang pig fecundity and litter size, which may be closely related to the gonad 18 development, oocyte maturation or embryo quality. Conclusion: The significant changes in the expression of the 19 protein-coding genes and the level of alternative splicing in estrus ovarian transcriptome between XL and XS groups 20 probably are the molecular mechanisms of phenotypic variation in litter size. 21 22

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Identification of Differentially Expressed Genes Associated with Litter Size in Berkshire Pig Placenta

Cited by 34 publications

References 36 publications

Hypo-phosphorylated CD147 promotes migration and invasion of hepatocellular carcinoma cells and predicts a poor prognosis

Hypo-phosphorylated CD147 promotes migration and invasion of hepatocellular carcinoma cells and predicts a poor prognosis

Large-Scale Metadata Analysis of Ovary Based Multi-Omics Datasets for Understanding the Genes Regulating Litter Size

Changes in Ovary Transcriptome and Alternative splicing at estrus from Xiang pigs with Large and Small Litter Size

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