Transcriptome Analysis Reveals Possible Virulence Factors of Paragonimus Proliferus

2020 ◽  
Vol 15 ◽  
Author(s):  
Sheng-hao Li ◽  
Shu-de Li ◽  
Kun-li Wu ◽  
Jun-Yi Li ◽  
Hong-juan Li ◽  
...  
Keyword(s):  
Virulence Factors ◽  
Cathepsin L ◽  
Cysteine Proteases ◽  
Rna Seq ◽  
Hsp 70 ◽  
Illumina Hiseq ◽  
Homology Analysis ◽  
Homologous Genes ◽  
Shock Proteins ◽  
Related Proteins

Objective: To identify the possible virulence factors (VFs) of P. proliferus Methods: By Illumina HiSeq 4000 RNA-Seq platform, transcriptomes of adult P. proliferus worms were sequenced to predict VFs via screening the homologues of traditional VFs of parasites based on the annotations in the functional databases. Homology analysis was also performed to screen homologous genes between P. proliferus and other four Paragonimus species (i.e., P. kellicotti, P. skrjabini, P. miyazakii and P. westermani) whose transcriptomes were downloaded from the National Center for Biotechnology Information (NCBI) database, and then the differential-expressed homologous genes (DEHGs) were screened via comparisons of P. proliferus and P. kellicotti, P. skrjabini, P. miyazakii and P. westermani, respectively. Finally, an overlap of the predicted VFs and DEHGs were performed to identify possible key VFs those do not only belong to the predicted VFs but also DEHGs Results: A total of 1,509 genes of P. proliferus homologous to traditional VFs, including surface antigens (SAGs), secreted proteins (SPs), ATP-Binding Cassette (ABC) Transporters, actin-related proteins (ARPs), aminopeptidases (APases), glycoproteins (GPs), cysteine proteases (CPs), and heat shock proteins (HSPs), were identified. Meanwhile, homology analysis identified 6279 DEHGs among the five species, of which there were 48 DEHGs being mutually differentialexpressed among the four pairs of comparisons, such as MRP, Tuba 3, PI3K, WASF2, ADK, Nop56, DNAH1, PFK- 2/FBPase2, Ppp1r7, SSP7. Furthermore, the overlap between the predicted VFs and DEHGs shew 97 genes of the predicted VFs simultaneously belonged to DEHGs. Strikingly, of these 97 genes, only 26, including Chymotrypsin, Leucine APases, Cathepsin L, HSP 70, and so on, were higher expressed in P. proliferus while all the remaining were lower expressed than in the four other species Conclusions: This work provides a fundamental context for further studies of the pathogenicity of P. proliferus. Most of the predicted VFs which simultaneously belonged to DEHGs were lower expressed in P. proliferus

scholarly journals RNA-seq Characterization of Melanoma Phenotype Switch in 3D Collagen after p38 MAPK Inhibitor Treatment

Biomolecules ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 449
Author(s):  
Vladimír Čermák ◽  
Aneta Škarková ◽  
Ladislav Merta ◽  
Veronika Kolomazníková ◽  
Veronika Palušová ◽  
...  
Keyword(s):  
P38 Mapk ◽  
Rna Seq ◽  
Differentiation Markers ◽  
Illumina Hiseq ◽  
Invasive Phenotype ◽  
Mesenchymal Transition ◽  
Phenotype Switch ◽  
3D Collagen ◽  
Phenotype Plasticity

Melanoma phenotype plasticity underlies tumour dissemination and resistance to therapy, yet its regulation is incompletely understood. In vivo switching between a more differentiated, proliferative phenotype and a dedifferentiated, invasive phenotype is directed by the tumour microenvironment. We found that treatment of partially dedifferentiated, invasive A375M2 cells with two structurally unrelated p38 MAPK inhibitors, SB2021920 and BIRB796, induces a phenotype switch in 3D collagen, as documented by increased expression of melanocyte differentiation markers and a loss of invasive phenotype markers. The phenotype is accompanied by morphological change corresponding to amoeboid–mesenchymal transition. We performed RNA sequencing with an Illumina HiSeq platform to fully characterise transcriptome changes underlying the switch. Gene expression results obtained with RNA-seq were validated by comparing them with RT-qPCR. Transcriptomic data generated in the study will extend the present understanding of phenotype plasticity in melanoma and its contribution to invasion and metastasis.

scholarly journals Identification of the specific long-noncoding RNAs involved in night-break mediated flowering retardation in Chenopodium quinoa

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Qi Wu ◽  
Yiming Luo ◽  
Xiaoyong Wu ◽  
Xue Bai ◽  
Xueling Ye ◽  
...  
Keyword(s):  
Expression Profiles ◽  
Functional Characterization ◽  
Chenopodium Quinoa ◽  
Noncoding Rnas ◽  
Long Noncoding Rnas ◽  
Rna Seq ◽  
Short Day ◽  
Homologous Genes ◽  
The Relationship ◽  
Encoding Genes

Abstract Background Night-break (NB) has been proven to repress flowering of short-day plants (SDPs). Long-noncoding RNAs (lncRNAs) play key roles in plant flowering. However, investigation of the relationship between lncRNAs and NB responses is still limited, especially in Chenopodium quinoa, an important short-day coarse cereal. Results In this study, we performed strand-specific RNA-seq of leaf samples collected from quinoa seedlings treated by SD and NB. A total of 4914 high-confidence lncRNAs were identified, out of which 91 lncRNAs showed specific responses to SD and NB. Based on the expression profiles, we identified 17 positive- and 7 negative-flowering lncRNAs. Co-expression network analysis indicated that 1653 mRNAs were the common targets of both types of flowering lncRNAs. By mapping these targets to the known flowering pathways in model plants, we found some pivotal flowering homologs, including 2 florigen encoding genes (FT (FLOWERING LOCUS T) and TSF (TWIN SISTER of FT) homologs), 3 circadian clock related genes (EARLY FLOWERING 3 (ELF3), LATE ELONGATED HYPOCOTYL (LHY) and ELONGATED HYPOCOTYL 5 (HY5) homologs), 2 photoreceptor genes (PHYTOCHROME A (PHYA) and CRYPTOCHROME1 (CRY1) homologs), 1 B-BOX type CONSTANS (CO) homolog and 1 RELATED TO ABI3/VP1 (RAV1) homolog, were specifically affected by NB and competed by the positive and negative-flowering lncRNAs. We speculated that these potential flowering lncRNAs may mediate quinoa NB responses by modifying the expression of the floral homologous genes. Conclusions Together, the findings in this study will deepen our understanding of the roles of lncRNAs in NB responses, and provide valuable information for functional characterization in future.

scholarly journals De novo gonad transcriptome analysis of the common littoral shrimp Palaemon serratus: novel insights into sex-related genes

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Inés González-Castellano ◽  
Chiara Manfrin ◽  
Alberto Pallavicini ◽  
Andrés Martínez-Lage
Keyword(s):  
Transcriptome Analysis ◽  
De Novo ◽  
Expression Patterns ◽  
Gonadal Development ◽  
Differentially Expressed ◽  
Rna Seq ◽  
Illumina Hiseq ◽  
Specific Expression ◽  
Development Processes ◽  
The Common

Abstract Background The common littoral shrimp Palaemon serratus is an economically important decapod resource in some European communities. Aquaculture practices prevent the genetic deterioration of wild stocks caused by overfishing and at the same time enhance the production. The biotechnological manipulation of sex-related genes has the proved potential to improve the aquaculture production but the scarcity of genomic data about P. serratus hinders these applications. RNA-Seq analysis has been performed on ovary and testis samples to generate a reference gonadal transcriptome. Differential expression analyses were conducted between three ovary and three testis samples sequenced by Illumina HiSeq 4000 PE100 to reveal sex-related genes with sex-biased or sex-specific expression patterns. Results A total of 224.5 and 281.1 million paired-end reads were produced from ovary and testis samples, respectively. De novo assembly of ovary and testis trimmed reads yielded a transcriptome with 39,186 transcripts. The 29.57% of the transcriptome retrieved at least one annotation and 11,087 differentially expressed genes (DEGs) were detected between ovary and testis replicates. Six thousand two hundred seven genes were up-regulated in ovaries meanwhile 4880 genes were up-regulated in testes. Candidate genes to be involved in sexual development and gonadal development processes were retrieved from the transcriptome. These sex-related genes were discussed taking into account whether they were up-regulated in ovary, up-regulated in testis or not differentially expressed between gonads and in the framework of previous findings in other crustacean species. Conclusions This is the first transcriptome analysis of P. serratus gonads using RNA-Seq technology. Interesting findings about sex-related genes from an evolutionary perspective (such as Dmrt1) and for putative future aquaculture applications (Iag or vitellogenesis genes) are reported here. We provide a valuable dataset that will facilitate further research into the reproductive biology of this shrimp.

scholarly journals Expression of the third member of the serum amyloid A gene family in mouse adipocytes.

1989 ◽  
Vol 169 (5) ◽  
pp. 1841-1846 ◽  
Author(s):  
E P Benditt ◽  
R L Meek
Keyword(s):  
Serum Amyloid A ◽  
Cell System ◽  
Serum Amyloid ◽  
Amyloid A ◽  
Differentiated Cells ◽  
Homologous Genes ◽  
Extrahepatic Tissues ◽  
Mouse Adipocytes ◽  
Related Proteins

Three homologous genes that code for three related proteins comprise the serum amyloid A (SAA) family in the mouse. Endotoxin induces equally vigorous expression of mRNAs for the three SAA genes in liver. In extrahepatic tissues SAA1 and/or SAA2 mRNAs have been found only in kidney and intestine, however, SAA3 is expressed in all extrahepatic tissues thus far examined. This observation raised the question: is SAA3 mRNA expressed by a single cell system dispersed throughout all tissues, or by differentiated cells of each tissue? This question was explored in various tissues by in situ hybridization with a single-stranded cRNA probe specific for SAA3 mRNA. We found expression in the liver of SAA3 mRNA by other cells as well as by hepatocytes. A common feature among extrahepatic tissues was SAA3 mRNA expression in adipocytes. SAA3 mRNA was also found in two nonadipose cells, Leydig cells of the testis, and some of the cells located in parafollicular zones of the spleen.

scholarly journals FOXO1 Mitigation of FOXL2C143W/SMAD3 Transcriptomic Landscape in a Model of Granulosa Cell Tumor

2021 ◽  
Vol 5 (Supplement_1) ◽  
pp. A1018-A1019
Author(s):  
Christian Secchi ◽  
Paola Benaglio ◽  
Francesca Mulas ◽  
Martina Belli ◽  
Dwayne Stupack ◽  
...  
Keyword(s):  
Granulosa Cell ◽  
Granulosa Cell Tumor ◽  
Direct Consequence ◽  
Transcript Abundance ◽  
Cell Tumor ◽  
Gene Promoters ◽  
Rna Seq ◽  
Illumina Hiseq ◽  
Rare Type ◽  
Exact Test

Abstract Background: Adult granulosa cell tumor (aGCT) is a rare type of stromal cell malignant cancer of the ovary. Postmenopausal genital bleeding is the main aGCT clinical sign which is attributed to estrogen excess driven by CYP19 upregulation. Typically, aGCTs that are diagnosed at an initial stage can be treated with surgery. However, recurrences are mostly fatal1. Current studies are focused on finding new molecular markers and targets that aim to treat the aGCTs recurrence. Between 95-97% of aGCTs harbor a somatic mutation in the FOXL2 gene, Cys134Trp (c.402C<G)2. A TGF-β pathway protein, SMAD3, was identified as an essential partner in FOXL2C134W transcriptional activity driving CYP19 upregulation3. Recently, the antitumoral FOXO1 gene has been recognized as a potential target for suppressing the FOXL2C134W pathogenic action4. Aim: The objective of this study was to examine whether FOXO1 upregulation affects the FOXL2C143W/SMAD3 transcriptomic landscape. Methods: RNA-seq analysis was performed comparing the effect of FOXL2WT/SMAD3 and FOXL2C143W/SMAD3 overexpression in presence of FOXO1 by transfection of an established human GC line (HGrC1). RNA-seq libraries were prepared using the illumina TrueSeq and sequenced using an illumina HiSeq Platform4000. To quantify transcript abundance for each sample we used salmon (1.1.0) with default parameters, using indexes from hg38. Data was subsequently imported in R using the tximport package and processed with the DESeq2 package. Results: RNA-seq data show that FOXL2C143W/SMAD3 significantly drives 717 genes compared with the WT and enabled us to identify targets (TGFB2, SMARCA4, HSPG2, MKI67, NFKBIA) and neoplastic pathways directly associated with the mutant. To provide evidence that the differences in gene expression were attributed to a direct consequence of FOXL2 binding, we annotated gene promoters with previously published FOXL2 ChIP-seq analysis. The majority (73-40%) of the differential expressed genes (DEGs) between FOXL2C134W and FOXL2WT had a FOXL2 binding site at their promoters, which was a significantly higher proportion than in non-DEGs (Fisher’s exact test, murine: p= 7.9x10-157; human, p= 9.9x10-39). Surprisingly, the number of DEGs between FOXL2C134W + FOXO1 and FOXL2WT was much lower (230) with respect to the number of DEGs between FOXL2C134W and FOXL2WT (717, of which 130 in common; linear regression slope ß = 0 .58), suggesting that the effect of FOXL2C134W compared with FOXL2WT is moderated by the addition of FOXO1. Conclusions: Our transcriptomic study provides the first evidence that FOXO1 can efficiently mitigate 40% of the altered genome-wide effect specifically related to FOXL2C134W in a model of human aGCT.1 Farkkila, A. et al. Ann Med (2017). 2 Jamieson, S. & Fuller, P. J. Endocr Rev (2012). 3 Belli, M. et al. Endocrinology (2018). 4 Belli, M et al. J Endocr Soc (2019).

scholarly journals Molecular Characterization of a Novel Cathepsin L in Macrobrachium nipponense and Its Function in Ovary Maturation

2022 ◽  
Vol 12 ◽  
Author(s):  
Sufei Jiang ◽  
Yiwei Xiong ◽  
Wenyi Zhang ◽  
Junpeng Zhu ◽  
Dan Cheng ◽  
...  
Keyword(s):  
Cathepsin L ◽  
Cysteine Proteases ◽  
Macrobrachium Nipponense ◽  
Reading Frame ◽  
Physiological Processes ◽  
Gonad Somatic Index ◽  
Oriental River Prawn ◽  
Ovary Maturation

Cathepsin L genes, which belonged to cysteine proteases, were a series of multifunctional protease and played important roles in a lot of pathological and physiological processes. In this study, we analyzed the characteristics a cathepsin L (named Mn-CL2) in the female oriental river prawn, Macrobrachium nipponense which was involved in ovary maturation. The Mn-CL2 was1,582 bp in length, including a 978 bp open reading frame that encoded 326 amino acids. The Mn-CL2 was classified into the cathepsin L group by phylogenetic analysis. Real-time PCR (qPCR) analysis indicated that Mn-CL2 was highly expressed in the hepatopancreas and ovaries of female prawns. During the different ovarian stages, Mn-CL2 expression in the hepatopancreas and ovaries peaked before ovarian maturation. In situ hybridization studies revealed that Mn-CL2 was localized in the oocyte of the ovary. Injection of Mn-CL2 dsRNA significantly reduced the expression of vitellogenin. Changes in the gonad somatic index also confirmed the inhibitory effects of Mn-CL2 dsRNA on ovary maturation. These results suggest that Mn-CL2 has a key role in promoting ovary maturation.

scholarly journals YeATS - a tool suite for analyzing RNA-seq derived transcriptome identifies a highly transcribed putative extensin in heartwood/sapwood transition zone in black walnut

F1000Research ◽  
2015 ◽  
Vol 4 ◽  
pp. 155 ◽  
Author(s):  
Sandeep Chakraborty ◽  
Monica Britton ◽  
Jill Wegrzyn ◽  
Timothy Butterfield ◽  
Pedro José Martínez-García ◽  
...  
Keyword(s):  
Transition Zone ◽  
Transcript Abundance ◽  
Black Walnut ◽  
Open Reading Frames ◽  
Rna Seq ◽  
Reading Frame ◽  
Homologous Genes ◽  
Associated Proteins ◽  
Molecular Components ◽  
Reading Frames

The transcriptome provides a functional footprint of the genome by enumerating the molecular components of cells and tissues. The field of transcript discovery has been revolutionized through high-throughput mRNA sequencing (RNA-seq). Here, we present a methodology that replicates and improves existing methodologies, and implements a workflow for error estimation and correction followed by genome annotation and transcript abundance estimation for RNA-seq derived transcriptome sequences (YeATS - Yet Another Tool Suite for analyzing RNA-seq derived transcriptome). A unique feature of YeATS is the upfront determination of the errors in the sequencing or transcript assembly process by analyzing open reading frames of transcripts. YeATS identifies transcripts that have not been merged, result in broken open reading frames or contain long repeats as erroneous transcripts. We present the YeATS workflow using a representative sample of the transcriptome from the tissue at the heartwood/sapwood transition zone in black walnut. A novel feature of the transcriptome that emerged from our analysis was the identification of a highly abundant transcript that had no known homologous genes (GenBank accession: KT023102). The amino acid composition of the longest open reading frame of this gene classifies this as a putative extensin. Also, we corroborated the transcriptional abundance of proline-rich proteins, dehydrins, senescence-associated proteins, and the DNAJ family of chaperone proteins. Thus, YeATS presents a workflow for analyzing RNA-seq data with several innovative features that differentiate it from existing software.

A possible alternative mechanism of kinin generation in vivo by cathepsin L

2005 ◽  
Vol 386 (7) ◽  
pp. 699-704 ◽  
Author(s):  
Luciano Puzer ◽  
Juliana Vercesi ◽  
Marcio F.M. Alves ◽  
Nilana M.T. Barros ◽  
Mariana S. Araujo ◽  
...  
Keyword(s):  
Blood Pressure ◽  
Enzyme Inhibitor ◽  
Alternative Pathway ◽  
Cathepsin L ◽  
Specific Inhibitor ◽  
Cysteine Proteases ◽  
Hypotensive Effect ◽  
Alternative Mechanism

Abstract We investigated the ability of cathepsin L to induce a hypotensive effect after intravenous injection in rats and correlated this decrease in blood pressure with kinin generation. Simultaneously with blood pressure decrease, we detected plasma kininogen depletion in the treated rats. The effect observed in vivo was abolished by pre-incubation of cathepsin L with the cysteine peptidase-specific inhibitor E-64 (1 μM) or by previous administration of the bradykinin B2 receptor antagonist JE049 (4 mg/kg). A potentiation of the hypotensive effect caused by cathepsin L was observed by previous administration of the angiotensin I-converting enzyme inhibitor captopril (5 mg/kg). In vitro studies indicated that cathepsin L excised bradykinin from the synthetic fluorogenic peptide Abz-MTSVIRRPPGFSPFRAPRV-NH2, based on the Met375–Val393 sequence of rat kininogen (Abz=o-aminobenzoic acid). In conclusion, our data indicate that in vivo cathepsin L releases a kinin-related peptide, and in vitro experiments suggest that the kinin generated is bradykinin. Although it is well known that cysteine proteases are strongly inhibited by kininogen, cathepsin L could represent an alternative pathway for kinin production in pathological processes.

Morphological and molecular modifications induced by heat shock in Drosophila melanogaster embryos

Development ◽  
1983 ◽  
Vol 77 (1) ◽  
pp. 167-182
Author(s):  
Giorgio Graziosi ◽  
Franco de Cristini ◽  
Angelo di Marcotullio ◽  
Roberto Marzari ◽  
Fulvio Micali ◽  
...  
Keyword(s):  
Drosophila Melanogaster ◽  
Heat Shock ◽  
Dna Synthesis ◽  
Histological Analysis ◽  
Developmental Stages ◽  
Early Embryo ◽  
Direct Relation ◽  
Hsp 70 ◽  
Survival Pattern ◽  
Shock Proteins

The early embryo of Drosophila melanogaster did not survive treatment at 37 °C (heat shock) for 25 min. The histological analysis of eggs treated in this way showed that the heat shock caused disintegration of nuclei and of cytoplasmic islands, displacement and swelling of nuclei and blocked mitoses. These effects were not observed in embryos treatedafter blastoderm formation. After this stage, we noticed that development was slowed down. The heat shock proteins (hsp 83,70 and 68) were, under shock, synthesized at all developmental stages. There was little or no synthesis of hsp 70 and 68 in unfertilized eggs, but synthesis increased in proportion to the number of nuclei present. Most probably, hsp 70 synthesis was directed by zygotic mRNA. DNA synthesis was not blocked by the heat shock though the overall incorporation of [3H]thymidine was substantially reduced, presumably because of the block of mitoses. We did not find a direct relation between survival pattern and hsp synthesis. We concluded that some, at least, of the heat shock genes can be activated at all developmental stages and that heat shock could be used for synchronizing mitoses.

Sign in / Sign up

Export Citation Format

Share Document