Objective. To investigate the expression of Yin-Yang-1 (YY1) in esophageal carcinoma (ESCA) and its effect on glutamine metabolism in ESCA. Methods. The expression and roles of YY1 in ESCA were investigated using a series of bioinformatics databases and tools. The expression of YY1 between ESCA tissues with the corresponding adjacent tissues was validated using real-time PCR, western blot, and immunohistochemical staining method. Furthermore, the effects of YY1 on ESCC cell proliferation and migration were examined. The correlation between the YY1 and glutamine metabolism was evaluated by western blot. Results. YY1 gene was highly conserved in evolution and upregulated in ESCA tissues and ESCC cell lines (ECA109 and TE-1). In addition, YY1 may affect the level of immune cell infiltration and promote tumor cell immune escape. Functional enrichment analysis found that YY1 involved in many biological processes, such as cell division and glutathione and glutamine metabolism. After siRNA knockdown of YY1 in ECA109 and TE-1, the proliferation and the migration of ECA109 and TE-1 were suppressed. The glutamine consumption and glutamate production were significantly decreased. The protein expression of alanine-, serine-, cysteine-preferring transporter 2 (ASCT2), glutaminase (GLS), and glutamate dehydrogenase (GLUD1) was significantly downregulated. Conclusion. YY1 is highly expressed in ESCA and may promote glutamine metabolism of ESCC cells, indicating it may be as a diagnostic biomarker for ESCA.

Can Luo

Xin Chen

Yuting Bai

Lei Xu

Shuqi Wang

Lihua Yao

Xiaolan Guo

Dongsheng Wang

Xiaowu Zhong

Upregulation of Yin-Yang-1 Associates with Proliferation and Glutamine Metabolism in Esophageal Carcinoma

Non-small-cell lung cancer (NSCLC) is one of the most serious cancers. The circular RNA_0078767 (circ_0078767) expression was decreased in NSCLC tissues. However, the molecular mechanism of circ_0078767 remains unknown. The expression of circ_0078767, microRNA-665 (miR-665), and glutathione peroxidase 3 (GPX3) was detected by quantitative real-time fluorescence polymerase chain reaction (qRT-PCR). Cell proliferation, migration, and invasion were detected by colony formation assay and transwell assay, respectively. The lactate production and glucose consumption were tested by glycolysis. Western blot examined the protein levels of hexokinase-2 (HK2), matrix metalloproteinase-9 (MMP9), and GPX3 cells. Circinteractome predicted the relationship between miR-665 and circ_0078767 or GPX3 and was verified by dual luciferase reporter assays. The xenotransplantation model was established to study the role of circ_0078767 in vivo. The expression of circ_0078767 and GPX3 was decreased in NSCLC tissues, while the expression of miR-665 was increased. Circ_0078767 can sponge miR-665, and GPX3 is the target of miR-665. In vitro complement experiments showed that knockdown of circ_0078767 significantly promoted malignant behavior of NSCLC, while cotransfection of miR-665 inhibitor partially reduced this change. In addition, the GPX3 overexpression decreased the promoting effects of miR-665 upregulation on proliferation, migration, and invasion of NSCLC cells. Mechanically, circ_0078767 regulates the GPX3 expression in NSCLC cells by spongy miR-665. In addition, in vivo studies have shown that downregulation of circ_0078767 promotes tumor growth. Circ_0078767 silencing promotes proliferation, migration, invasion, and glycolysis of NSCLC cells by regulating the miR-665/GPX3 axis, suggesting that circ_0078767/miR-665/GPX3 axis may be a potential regulatory mechanism for the treatment of NSCLC.

Xiting Liu

Ze Chen

Yuqiang Wu

Feng Gu

Dong Yan

Lei Yang

Qin Ma

Caihong Fu

Circ_0078767 Inhibits the Progression of Non-Small-Cell Lung Cancer by Regulating the GPX3 Expression by Adsorbing miR-665

Shaker-type K+ channels are critical for plant K+ acquisition and translocation that play key roles during plant growth and development. However, molecular mechanisms towards K+ channels are extremely rare in fruit trees, especially in peach. In this study, we identified 7 putative shaker-type K+ channel genes from peach, which were unevenly distributed on 5 chromosomes. The peach shaker K+ channel proteins were classified into 5 subfamilies, I-V, and were tightly clustered with pear homologs in the phylogenetic tree. Various cis-acting regulatory elements were detected in the promoter region of the shaker-type K+ channel genes, including phytohormone-responsive, abiotic stress-responsive, and development regulatory elements. The peach shaker K+ channel genes were expressed differentially in distinct tissues, and PpSPIK was specifically expressed in the full-bloom flowers; PpKAT1 and PpGORK were predominantly expressed in the leaves, while PpAKT1, PpKC1, and PpSKOR were majorly expressed in the roots. The peach shaker K+ channel genes were differentially regulated by abiotic stresses in that K+ deficiency, and ABA treatment mainly increased the shaker K+ channel gene expression throughout the whole seedling, whereas NaCl and PEG treatment reduced the shaker K+ channel gene expression, especially in the roots. Moreover, electrophysiological analysis demonstrated that PpSKOR is a typical voltage-dependent outwardly rectifying K+ channel in peach. This study lays a molecular basis for further functional studies of the shaker-type K+ channel genes in peach and provides a theoretical foundation for K+ nutrition and balance research in fruit trees.

Yong Yang

Jinlong Han

Yue Zhang

Shizhuo Lin

Meixia Liang

Lizi Zhao

Zhizhong Song

Genome-Wide Identification and Characterization of the Shaker-Type K+ Channel Genes in Prunus persica (L.) Batsch

The availability of comprehensive genomic datasets across patient populations enables the application of novel methods for reconstructing tumor evolution within individual patients. To this end, we propose studying autosomal broad copy number alterations (CNAs) as a framework to better understand early tumor evolution. We compared the broad CNAs and somatic mutations of patients with 1 to 10 autosomal broad CNAs against the full set of patients, using data from The Cancer Genome Atlas breast cancer project. We reveal here that the frequency of a chromosome arm obtaining a broad CNA and a genome acquiring somatic mutations changes as autosomal broad CNAs accumulate. Therefore, we propose that the number of autosomal broad CNAs is an important characteristic of breast tumors that needs to be taken into consideration when studying breast tumors. To investigate this idea more in-depth, we next studied the frequency that specific chromosome arms acquire broad CNAs in patients with 1 to 10 broad CNAs. With this process, we identified the broad CNAs that exhibit the fastest rates of accumulation across all patients. This finding suggests a likely order of occurrence of these alterations in patients, which is apparent when we consider a subset of patients with few broad CNAs. Here, we lay the foundation for future studies to build upon our findings and use autosomal broad CNAs as a method to monitor breast tumor progression in vivo to further our understanding of how early tumor evolution unfolds.

Joseph R. Larsen

Peter Kuhn

James B. Hicks

Early Breast Cancer Evolution by Autosomal Broad Copy Number Alterations

The fruiting bodies or mycelia of Hericium coralloides (H. coralloides) contain many physiologically active compounds that are used to treat various diseases, including cardiovascular disorders and cancers. However, the genome of H. coralloides has not been sequenced, which hinders further investigations into aspects, such as bioactivity or evolutionary events. The present study is aimed at (i) performing de novo sequencing of the assembled genome; (ii) mapping the reads from PE400 DNA into the assembled genome; (iii) identifying the full length of all the repeated sequences; and (iv) annotating protein-coding genes using GO, eggNOG, and KEGG databases. The assembled genome comprised 5,59,05,675&#x2009;bp, including 307 contigs. The mapping rate of reads obtained from PE400 DNA in the assembled genome was 92.46&#x0025;. We identified 2,525 repeated sequences of 14,23,274&#x2009;bp length. We predicted ncRNAs of 48,895&#x2009;bp and 11,736 genes encoding proteins that were annotated in the GO, eggNOG, and KEGG databases. We are the first to sequence the entire H. coralloides genome (NCBI; Assembly: ASM367540v1), which will serve as a reference for studying the evolutionary diversification of edible and medicinal mushrooms and facilitate the application of bioactivity in H. coralloides.

Caixia Zhang

Lijun Xu

Jian Li

Jiansong Chen

Manjun Yang

Genome Sequencing of Hericium coralloides by a Combination of PacBio RS II and Next-Generation Sequencing Platforms

Phenomics and chlorophyll fluorescence can help us to understand the various stresses a plant may undergo. In this research work, we observe the image-based morphological changes in the wheat canopy. These changes are monitored by capturing the maximum area of wheat canopy image that has maximum photosynthetic activity (chlorophyll fluorescence signals). The proposed algorithm presented here has three stages: (i) first, derivation of dynamic threshold value by curve fitting of data to eliminate the pixels of low-intensity value, (ii) second, extraction and segmentation of thresholded region by application of histogram-based <svg xmlns:xlink="http://www.w3.org/1999/xlink" xmlns="http://www.w3.org/2000/svg" style="vertical-align:-0.0498209pt" id="M2" height="8.68572pt" version="1.1" viewBox="-0.0498162 -8.6359 9.95144 8.68572" width="9.95144pt"><g transform="matrix(.013,0,0,-0.013,0,0)"><use xlink:href="#g113-76"/></g></svg>-means algorithm iteratively (this scheme of the algorithm is referred to as the curve fit <svg xmlns:xlink="http://www.w3.org/1999/xlink" xmlns="http://www.w3.org/2000/svg" style="vertical-align:-0.0498209pt" id="M3" height="8.68572pt" version="1.1" viewBox="-0.0498162 -8.6359 9.95144 8.68572" width="9.95144pt"><g transform="matrix(.013,0,0,-0.013,0,0)"><use xlink:href="#g113-76"/></g></svg>-means (CfitK-means) algorithm); and (iii) third, computation of 23 grey level cooccurrence matrix (GLCM) texture features (traits) from the wheat images has been done. These features help to do statistical analysis and infer agronomical insights. The analysis consists of correlation, factor, and agglomerative clustering to identify water stress indicators. A public repository of wheat canopy images was used that had normal and water stress response chlorophyll fluorescence images. The analysis of the feature dataset shows that all 23 features are proved fruitful in studying the changes in the shape and structure of wheat canopy due to water stress. The best segmentation algorithm was confirmed by doing exhaustive comparisons of seven segmentation algorithms. The comparisons showed that the best algorithm is CfitK-means as it has a maximum IoU score value of 95.75.

Ankita Gupta

Lakhwinder Kaur

Gurmeet Kaur

Inferring Agronomical Insights for Wheat Canopy Using Image-Based Curve Fit <svg xmlns:xlink="http://www.w3.org/1999/xlink" xmlns="http://www.w3.org/2000/svg" style="vertical-align:-0.0498209pt" height="8.68572pt" version="1.1" viewBox="-0.0498162 -8.6359 9.95144 8.68572" width="9.95144pt"><g transform="matrix(.013,0,0,-0.013,0,0)"><path id="g113-76" d="M743 650H503L496 622L527 618C563 613 564 603 532 573C449 495 371 431 323 392C301 374 272 355 246 346L280 522C297 609 300 614 379 622L385 650H135L129 622C209 614 215 609 198 522L124 133C106 39 99 35 23 28L17 0H271L277 28C193 35 192 39 208 133L239 316C264 328 280 325 303 288C368 183 435 90 502 0H652L659 28C602 34 584 43 543 94C495 154 403 283 347 369L574 554C634 603 659 612 735 624L743 650Z" /></g></svg>-Means Segmentation Algorithm and Statistical Analysis

Gastric cancer (GC) is a malignant tumor with high mortality and poor prognosis. Immunotherapies, especially immune checkpoint inhibitors (ICI), are widely used in various tumors, but patients with GC do not benefit much from immunotherapies. Therefore, effective predictive biomarkers are urgently needed for GC patients to realize the benefits of immunotherapy. Recent studies have indicated that long noncoding RNAs (lncRNAs) could be used as biomarkers in the immune landscape of multiple tumors. In this study, we constructed a novel immune-related lncRNA (irlncRNA) risk model to predict the survival and immune landscape of GC patients. First, we identified differentially expressed irlncRNAs (DEirlncRNAs) from RNA-Seq data of The Cancer Genome Atlas (TCGA). By using various algorithms, we constructed a risk model with 11 DEirlncRNA pairs. We then tested the accuracy of the risk model, demonstrating that the risk model has good efficiency in predicting the prognosis of GC patients. Inner validation sets were further used to confirm the effectiveness of the risk model. In addition, our risk model has a preferable performance in predicting the immune infiltration status of tumors, immune checkpoint status of the patients, and immunotherapy score. In conclusion, our risk model may provide insights into the prognosis of and immunotherapy strategy for GC.

Xiaolong Liang

Lang Zha

Gangfeng Yu

Xiong Guo

Chuan Qin

Anqi Cheng

Ziwei Wang

Construction and Comprehensive Prognostic Analysis of a Novel Immune-Related lncRNA Signature and Immune Landscape in Gastric Cancer

We identified the key genes controlling the late maturation of the Japonica cultivar Isehikari, which was found at Ise Jingu Shrine and matures 6 days later than Koshihikari. We conducted a genetics-based approach through this study. First, the latest mature plants, which flowered later than Isehikari, were segregated in the F2 and F3 generations of Koshihikari&#x00D7;Isehikari. Next, the linkage relationship of a single late-maturing gene with the SSR markers on the long arm of chromosome 3 was inferred by using late-maturing homozygous F2 segregants. Moreover, genetic analyses of late maturity were conducted through the process of six times of continuous backcross with Koshihikari as a recurrent parent by using the late-maturing homozygous F3 line as a nonrecurrent parent, thus developing a late-maturing isogenic Koshihikari (BC6F2). As a result, we elucidated a single late-maturing gene with incomplete dominance that caused the 14-day maturation delay of Koshihikari. The whole-genome sequencing was conducted on both of Koshihikari and the late-maturing isogenic Koshihikari. Then, the SNP call was conducted as the reference genome of Koshihikari. Finally, a single SNP was identified in the key gene Hd16 of the late-maturing isogenic Koshihikari.

Motonori Tomita

Ryotaro Tokuyama

Shosuke Matsumoto

Kazuo Ishii

Whole-Genome Sequencing Revealed a Late-Maturing Isogenic Rice Koshihikari Integrated with Hd16 Gene Derived from an Ise Shrine Mutant

About this journal

International Journal of Genomics publishes papers in all areas of genome-scale analysis, including bioinformatics, clinical and disease genomics, epigenomics, evolutionary and functional genomics, genome engineering, and synthetic genomics.

Journal profile

Meet the editorial board

International Journal of Genomics maintains an Editorial Board of practicing researchers from around the world, to ensure manuscripts are handled by editors who are experts in the field of study.

Editor spotlight

Submit your proposal

Do you think there is an emerging area of research that really needs to be highlighted? Or an existing research area that has been overlooked or would benefit from deeper investigation? Raise the profile of a research area by leading a Special Issue.

Special Issues

Author guidelines

Editorial board

Databases and indexing

International Journal of Genomics - Table of contents 2022

International Journal of Genomics | Hindawi

title

International Journal of Genomics publishes papers in all areas of genome-scale analysis, including bioinformatics, clinical and disease genomics, epigenomics, evolutionary and functional genomics, genome engineering, and synthetic genomics.

International Journal of Genomics