Whole transcriptome sequencing reveals drought resistance-related genes in upland cotton

China, especially the Xinjiang cotton area, is facing severe agricultural water shortages, which seriously restrain the development of the cotton industry. Discovering cotton drought resistance genes and cultivating high-quality and drought-resistant cotton materials through molecular breeding methods are of great significance to the development of the cotton industry. In this study, the drought-resistant cotton material Xinluzhong NO.82 and the drought-sensitive cotton material Kexin NO.1 were used to identify a batch of drought-resistant candidate genes through whole transcriptome sequencing. The main research results obtained were as follows: the ceRNA (competing endogenous RNAs) network was constructed using full transcriptional sequencing to screen the core genes in the core pathway; two drought-related candidate genes were obtained. Gohir.A11G156000 was upregulated at 0 h vs 12 h and downregulated at 12 h vs 24 h. Gohir.A07G220600 was downregulated at 0 h vs 12 h and upregulated at 12 h vs 24 h. The results for drought-resistant materials and drought-sensitive materials were similar. Gohir.A11G156000, encoding GABA-T, which is homologous to POP2 in Arabidopsis thaliana, affects the drought resistance of plants by regulating the GABA content. Gohir.A07G220600 encodes L-aspartate oxidase, which is homologous to AO in Arabidopsis thaliana, and is involved in the early steps of NAD biosynthesis and in plant antioxidant reactions. This study confirmed that the use of gene expression regulatory networks can quickly screen reliable drought-resistance genes and can be used for subsequent gene function verification.

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Mammary-type Myofibroblastoma with Leiomyomatous Differentiation: A Rare Variant with Potential Pitfalls

International Journal of Surgical Pathology ◽

10.1177/10668969211031309 ◽

2021 ◽

pp. 106689692110313

Author(s):

Alexander M. Strait ◽

Julia A. Bridge ◽

Anthony J. Iafrate ◽

Marilyn M. Li ◽

Feng Xu ◽

...

Keyword(s):

Adipose Tissue ◽

Transcriptome Sequencing ◽

Smooth Muscle Actin ◽

The Body ◽

Muscle Actin ◽

Mature Adipose Tissue ◽

Spindle Cells ◽

Whole Transcriptome Sequencing ◽

Whole Transcriptome

Myofibroblastoma is a rare, benign stromal tumor with a diverse morphologic spectrum. Mammary-type myofibroblastoma (MTMF) is the extra-mammary counterpart of this neoplasm and its occurrence throughout the body has become increasingly recognized. Similar morphologic variations of MTMF have now been described which mirror those seen in the breast. We describe a case of intra-abdominal MTMF composed of short fascicles of eosinophilic spindle cells admixed with mature adipose tissue. The spindle cells stained diffusely positive for CD34, desmin, smooth muscle actin, and h-caldesmon by immunohistochemistry. Concurrent loss of RB1 (13q14) and 13q34 loci were confirmed by fluorescence in situ hybridization whereas anchored multiplex PCR and whole transcriptome sequencing did not reveal any pathognomonic fusions suggesting an alternative diagnosis. To the best of our knowledge this is the first documented case of leiomyomatous variant of MTMF.

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Comprehensive analysis of the genetic landscape of 21 cases with blastic plasmacytoid dendritic cell neoplasm by whole genome and whole transcriptome sequencing

Leukemia & Lymphoma ◽

10.1080/10428194.2021.1924372 ◽

2021 ◽

pp. 1-4

Author(s):

Isolde Summerer ◽

Wencke Walter ◽

Manja Meggendorfer ◽

Wolfgang Kern ◽

Torsten Haferlach ◽

...

Keyword(s):

Dendritic Cell ◽

Transcriptome Sequencing ◽

Plasmacytoid Dendritic Cell ◽

Comprehensive Analysis ◽

Whole Genome ◽

Cell Neoplasm ◽

Genetic Landscape ◽

Whole Transcriptome Sequencing ◽

Whole Transcriptome

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MA23.09 Fusion Genes Identified from Whole Genome and Whole Transcriptome Sequencing of Malignant Pleural Mesothelioma Tumours

Journal of Thoracic Oncology ◽

10.1016/j.jtho.2019.08.697 ◽

2019 ◽

Vol 14 (10) ◽

pp. S344-S345

Author(s):

T.M. Chee ◽

H. Oey ◽

K. Fong ◽

I. Yang ◽

L. Krause ◽

...

Keyword(s):

Malignant Pleural Mesothelioma ◽

Transcriptome Sequencing ◽

Pleural Mesothelioma ◽

Whole Genome ◽

Fusion Genes ◽

Whole Transcriptome Sequencing ◽

Whole Transcriptome

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The prognosis of gastric adenocarcinoma depends on the crosstalk between immune profiles and tumor genomic alterations.

Journal of Clinical Oncology ◽

10.1200/jco.2021.39.15_suppl.4035 ◽

2021 ◽

Vol 39 (15_suppl) ◽

pp. 4035-4035

Author(s):

Deqiang Wang ◽

Xiaofeng Chen ◽

Yaping Xu ◽

Yuange He ◽

Lifeng Li ◽

...

Keyword(s):

Gastric Adenocarcinoma ◽

Transcriptome Sequencing ◽

Clonal Expansion ◽

Genomic Alterations ◽

M1 Macrophages ◽

Mutual Correlation ◽

Cell Counts ◽

M1 Macrophage ◽

Whole Transcriptome Sequencing ◽

Whole Transcriptome

4035 Background: Gastric adenocarcinoma (GAC) is with a complex microenvironment of tumor cells. A better understanding of the immune landscape of GACs may lead to the improved treatment strategies with ICIs. Methods: To determine whether the molecular characteristics can serve in prognostic stratification of GACs, tumor tissue and blood samples were collected from 231 GAC patients. The median follow-up time was 34 months. The TCR profile was determined by TCR-β CDR3 sequencing while mutation and gene expression profiles were determined by whole exon and whole transcriptome sequencing, respectively. Tumour-infiltrating immune cells were characterized using immunofluorescence (IF) staining. Results: The results showed the OS of patients with high levels of TCR clonality (TCR clonal expansion) was significantly improved compared with patients with low levels (HR = 1.80 and 2.22, p = 0.022 and 0.008, respectively) in the whole group and in the subgroup of patients with stages IB to III disease. Furthermore, low local clonality was an independent risk factor for OS (adjusted-HR = 1.68 and 1.95, p = 0.049 and 0.029, respectively). Thus, TCR clonal expansion in tumour tissue had a strong prognostic value for GAC patients, independent of clinicopathological factors. Based on whole exon and whole transcriptome sequencing, RNF43/FBXW7/ARID2 mutations and local TCR clonality jointly impacted prognosis (p < 0.001), and functional changes in corresponding Wnt pathway/Notch pathway/SWI/SNF complex characterized a GAC subset with enhanced tumour immunogenicity and TCR clonal expansion. TCR CDR3 sequence similarity comparisons yielded clusters of TCR clones of likely similar functions. The most expansive TCR clusters negatively correlated with the percentage of subclonal mutations (Pearson r = -0.8183, p < 0.001), indicating that tumors with less genomic heterogeneity might induce a greater immune response. By IF staining and mutual correlation analysis, only M1 macrophages showed a significant positive correlation with local TCR clonality for epithelia, stroma, and total cell counts. Tumors were categorized according to the density of M1 macrophages, M1 macrophage infiltrated subtype was associated with favorable OS (p = 0.040 and 0.043) and its combination with the local TCR clonality improved prognosis stratification (p < 0.001). Finally, the scoring by local TCR clonality, RNF43/FBXW7/ARID2 mutations and M1 infiltration determined the best prognosis (p < 0.001). Conclusions: TCR profiles were associated with genomic alterations and may serve as a prognostic biomarker for GACs. A multi-omic model including TCR profiles might produce an improved stratification for treatments and outcomes.

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PD57-01 WHOLE-TRANSCRIPTOME SEQUENCING IDENTIFIED GENE EXPRESSION SIGNATURES ASSOCIATED WITH AGGRESSIVE CLEAR CELL RENAL CELL CARCINOMA

The Journal of Urology ◽

10.1016/j.juro.2018.02.2645 ◽

2018 ◽

Vol 199 (4S) ◽

Author(s):

Ken Batai ◽

Elliot Imler ◽

Michael Phung ◽

Robert Bell ◽

Aye Lwin ◽

...

Keyword(s):

Gene Expression ◽

Renal Cell Carcinoma ◽

Cell Carcinoma ◽

Renal Cell ◽

Transcriptome Sequencing ◽

Clear Cell ◽

Cell Renal Cell Carcinoma ◽

Gene Expression Signatures ◽

Whole Transcriptome Sequencing ◽

Whole Transcriptome

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Analysis of mRNAs and ncRNAs and Prediction Competing Endogenous RNA Networks in Colorectal Cancer Chemo-Resistance by Whole-Transcriptome Sequencing

10.21203/rs.3.rs-38686/v1 ◽

2020 ◽

Author(s):

Fei Yao ◽

Chuanren Zhou ◽

Qiyou Huang ◽

Xiaoying Huang ◽

Jie Chen ◽

...

Keyword(s):

Colorectal Cancer ◽

Drug Resistance ◽

Cell Lines ◽

Transcriptome Sequencing ◽

Regulatory Networks ◽

Parental Cell ◽

Resistant Cell ◽

Competing Endogenous Rna ◽

Whole Transcriptome Sequencing ◽

Whole Transcriptome

Abstract Background: Chemo-resistance is a major clinical obstacle to the treatment of colorectal cancer (CRC), mRNAs and non-coding RNAs (ncRNAs) have been reported to modulate the development of chemo-resistance. However, the profiles of mRNAs and ncRNAs as well as competing endogenous RNA (ceRNA) networks in CRC chemo-resistance are still unclear, and whether different drug resistance of CRC have the same mechanisms also needs to be explored. This study aims to uncover the expression of mRNAs and ncRNAs in parental cell lines and different chemo-resistant cell lines, and construct ceRNA regulatory networks by whole-transcriptome sequencing.Methods: The expression of mRNAs and ncRNAs in parental cell lines and drug-resistant cell lines were identified by whole-transcriptome sequencing and bioinformatics methods.Results: A total of 1779 mRNAs, 64 miRNAs, 11 circRNAs and 295 lncRNAs were common differentially expressed in two different chemo-resistant cell lines when compared with the control. In addition, 5,767 lncRNA-miRNA-mRNA relationship pairs and 47 circRNA-miRNA-mRNA pathways were constructed according to ceRNA regulatory rules, in which AC109322.2-hsa-miR-371a-5p-BTNL3 and hsacirc_027876-hsa-miR-582-3p-FREM1 were identified as the most potential ceRNA networks involved in drug resistance to CRC. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of two ceRNA regulatory networks showed that the TNF signaling pathway may be crucial in the process of CRC drug resistance.Conclusions: A large number of mRNAs and ncRNAs in chemo-resistant cell lines were different expressed, which may play pivotal roles in development of drug resistance through the ceRNA regulatory network. This study may improve our understanding of the underlying mechanisms and provide a promising therapeutic strategy for CRC chemo-resistance.

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