Dysfunction of GmVPS8a causes compact plant architecture in soybean.

Vacuolar Protein Sorting 8 (Vps8) protein is a specific subunit of the class C core vacuole/endosome tethering (CORVET) complex that plays a key role in endosomal trafficking in yeast (Saccharomyces cerevisiae). However, its functions remain largely unclear in plant vegetative growth. Here, we identified a soybean (Glycine max) T4219 mutant characterized with compact plant architecture. Map-based cloning targeted to a candidate gene GmVPS8a (Glyma.07g049700) and further found that two nucleotides deletion in the first exon of GmVPS8a causes a premature termination of the encoded protein in the T4219 mutant. Its functions were validated by CRISPR/Cas9-engineered mutation in the GmVPS8a gene that recapitulated the T4219 mutant phenotypes. Furthermore, NbVPS8a-silenced tobacco (Nicotiana benthamiana) plants exhibited similar phenotypes to the T4219 mutant, suggesting its conserved roles in plant growth. The GmVPS8a is widely expressed in multiple organs and its protein interacts with GmAra6a and GmRab5a. Combined analysis of transcriptomic and proteomic data revealed that dysfunction of GmVPS8a mainly affects pathways on auxin signal transduction, sugar transport and metabolism, and lipid metabolism. Collectively, our work reveals the function of GmVPS8a in plant architecture, which may extend a new way for genetic improvement of ideal plant-architecture breeding in soybean and other crops.

Unraveling the Diverse Roles of Neglected Genes Containing Domains of Unknown Function (DUFs): Progress and Perspective.

Domain of unknown function (DUF) is a general term for many uncharacterized domains with two distinct features: relatively conservative amino acid sequence and unknown function of the domain. In the Pfam 35.0 database, 4795 (24%) gene families belong to the DUF type, yet, their functions remain to be explored. This review summarizes the characteristics of the DUF protein families and their functions in regulating plant growth and development, generating responses to biotic and abiotic stress, and other regulatory roles in plant life. Though very limited information is available about these proteins yet, by taking advantage of emerging omics and bioinformatic tools, functional studies of DUF proteins could be utilized in future molecular studies.

NAC Transcription Factor GmNAC12 Improved Drought Stress Tolerance in Soybean.

NAC transcription factors (TFs) could regulate drought stresses in plants; however, the function of NAC TFs in soybeans remains unclear. To unravel NAC TF function, we established that GmNAC12, a NAC TF from soybean (Glycine max), was involved in the manipulation of stress tolerance. The expression of GmNAC12 was significantly upregulated more than 10-fold under drought stress and more than threefold under abscisic acid (ABA) and ethylene (ETH) treatment. In order to determine the function of GmNAC12 under drought stress conditions, we generated GmNAC12 overexpression and knockout lines. The present findings showed that under drought stress, the survival rate of GmNAC12 overexpression lines increased by more than 57% compared with wild-type plants, while the survival rate of GmNAC12 knockout lines decreased by at least 46%. Furthermore, a subcellular localisation analysis showed that the GmNAC12 protein is concentrated in the nucleus of the tobacco cell. In addition, we used a yeast two-hybrid assay to identify 185 proteins that interact with GmNAC12. Gene ontology (GO) and KEGG analysis showed that GmNAC12 interaction proteins are related to chitin, chlorophyll, ubiquitin-protein transferase, and peroxidase activity. Hence, we have inferred that GmNAC12, as a key gene, could positively regulate soybean tolerance to drought stress.

Genome-Wide Identification and Expression Analyses of the Chitinase Gene Family in Response to White Mold and Drought Stress in Soybean (Glycine max).

Chitinases are enzymes catalyzing the hydrolysis of chitin that are present on the cell wall of fungal pathogens. Here, we identified and characterized the chitinase gene family in cultivated soybean (Glycine max L.) across the whole genome. A total of 38 chitinase genes were identified in the whole genome of soybean. Phylogenetic analysis of these chitinases classified them into five separate clusters, I-V. From a broader view, the I-V classes of chitinases are basically divided into two mega-groups (X and Y), and these two big groups have evolved independently. In addition, the chitinases were unevenly and randomly distributed in 17 of the total 20 chromosomes of soybean, and the majority of these chitinase genes contained few introns (≤2). Synteny and duplication analysis showed the major role of tandem duplication in the expansion of the chitinase gene family in soybean. Promoter analysis identified multiple cis-regulatory elements involved in the biotic and abiotic stress response in the upstream regions (1.5 kb) of chitinase genes. Furthermore, qRT-PCR analysis showed that pathogenic and drought stress treatment significantly induces the up-regulation of chitinase genes belonging to specific classes at different time intervals, which further verifies their function in the plant stress response. Hence, both in silico and qRT-PCR analysis revealed the important role of the chitinases in multiple plant defense responses. However, there is a need for extensive research efforts to elucidate the detailed function of chitinase in various plant stresses. In conclusion, our investigation is a detailed and systematic report of whole genome characterization of the chitinase family in soybean.

DNA Methylation-Mediated Low Expression of CFTR Stimulates the Progression of Lung Adenocarcinoma.

In recent years, the mortality rate of lung adenocarcinoma (LUAD) is persistently increasing, which has already caused a huge impact on human living standards. Hence, there is an urgent need to probe the molecular mechanism of LUAD progression, so as to disclose prognostic and diagnostic markers for patients with LUAD. Methylation 450 K data and mRNA expression data of LUAD were obtained via bioinformatics analysis to screen methylation-driven genes. The expression of the target gene was detected through qRT-PCR, while the methylation level was evaluated via methylation-specific PCR (MSP). The impact of the gene on cell proliferation, migration, invasion, apoptosis and cell cycle was measured through CCK-8, wound healing, Transwell invasion assay, and flow cytometry. CFTR was defined by bioinformatics analysis as the target gene for this study. qRT-PCR revealed that CFTR was lowly expressed in LUAD cells. MSP displayed that the CFTR promoter region in LUAD cells was hypermethylated, and demethylation could pronouncedly increase the level of CFTR mRNA in LUAD cells. Cell biological functional experiments exhibited that CFTR hindered cell proliferation, migration, and invasion, fostered cell apoptosis of LUAD, and blocked the cell cycle in G2-M phase. CFTR was hypermethylated in LUAD, which mediated the low expression of CFTR in LUAD to stimulate the progression of LUAD.

Etoposide plus cisplatin chemotherapy improves the efficacy and safety of small cell lung cancer.

BACKGROUND: According to the statistical data of GLOBOCAN in 2020, the incidence of lung cancer ranks third worldwide. Approximately 60%-70% of newly diagnosed patients with small cell lung cancer (SCLC) has already progressed to extensive-stage SCLC (ES-SCLC). SCLC is sensitive to chemotherapy and radiotherapy, but prone to secondary drug resistance. At present, chemotherapy is the mainstay of treatment for ES-SCLC. This study is designed to evaluate the efficacy and safety of etoposide plus platinum in the treatment of SCLC. METHODS: A retrospective analysis was performed on 112 patients with SCLC admitted to the China-Japan Union Hospital of Jilin University from 2016 to 2018. According to treatment methods, the patients were divided into an EL group (etoposide plus lobaplatin, n = 53) and an EP group (etoposide plus cisplatin, n = 59). The short-term efficacy (objective response rates and disease control rates) and 2-year survival rates were observed. The two groups were compared in terms of serum levels of pro-gastrin-releasing peptide (ProGRP), neuron-specific enolase (NSE), vascular endothelial growth factor (VEGF) and matrix metalloproteinase-9 (MMP-9) before and after treatment. The incidence of adverse reactions was also compared. The quality of life (QOL) of patients was compared by measuring the Karnofsky Performance Status (KPS) scale. The risk factors affecting treatment efficacy were analyzed by multivariate Logistics analysis. RESULTS: Patients in the EL group had similar objective response rate (ORR) and disease control rate (DCR) to those in the EP group. The 2-year survival prognosis (median survival time) between the two groups was not significantly different. After treatment, serum levels of ProGRP, NSE, VEGF and MMP-9 in both groups decreased remarkably, with no remarkable differences between the two groups. The EL group had a remarkably lower incidence of adverse reactions than the EP group. In the EP group, the KPS scores after 6 cycles of treatment were remarkably higher than those after 2 cycles of treatment. ProGRP, NSE, VEGF and MMP-9 were independent risk factors affecting the efficacy of patients with SCLC. CONCLUSION: With equivalent efficacy, EP regimen is safer than EL regimen in the treatment of SCLC, which suggests that etoposide plus platinum has better clinical application value for SCLC.

Surgical therapy for hemangioma of the azygos vein arch under thoracoscopy: A case report.

BACKGROUND: Azygos vein aneurysms are extremely rare, and their pathogenesis is not clear. The overwhelming majority of patients have no obvious clinical symptoms and are found to have the disease by physical examination or by chance. There are few reports on the diagnosis of and treatment strategy for this disease. Moreover, the choice of therapeutic schedule and the treatment window are controversial. CASE SUMMARY: We report a case of azygos vein arch aneurysm in a 53-year-old woman. The patient had symptoms of back pain, chest tightness, and choking. Enhanced chest computed tomography showed a soft-tissue mass in the right posterior mediastinum, which was connected to the superior vena cava. The enhancement degree in the venous phase was the same as that of the superior vena cava. The patient received video-assisted thoracoscopic surgery. After the operation, her back pain disappeared, and her dysphagia and chest tightness were also significantly relieved. The postoperative pathology confirmed hemangioma. The patient was discharged on the seventh day after surgery without any comp-lications. CONCLUSION: Some patients with hemangioma of the azygos vein arch may experience dysphagia and chest tightness caused by the tumor compressing the esophagus and trachea. Enhanced computed tomography scanning is vital for the diagnosis of azygos vein aneurysms. In addition, despite the difficulty and risk of surgery, thoracoscopic surgery for azygos vein aneurysms is completely feasible.

Exploring genetic architecture for pod-related traits in soybean using image-based phenotyping.

Mature pod color (PC) and pod size (PS) served as important characteristics are used in the soybean breeding programs. However, manual phenotyping of such complex traits is time-consuming, laborious, and expensive for breeders. Here, we collected pod images from two different populations, namely, a soybean association panel (SAP) consisting of 187 accessions and an inter-specific recombinant inbred line (RIL) population containing 284 RILs. An image-based phenotyping method was developed and used to extract the pod color- and size-related parameters from images. Genome-wide association study (GWAS) and linkage mapping were performed to decipher the genetic control of pod color- and size-related traits across 2 successive years. Both populations exhibited wide phenotypic variations and continuous distribution in pod color- and size-related traits, indicating quantitative polygenic inheritance of these traits. GWAS and linkage mapping approaches identified the two major quantitative trait loci (QTL) underlying the pod color parameters, i.e., qPC3 and qPC19, located to chromosomes 3 and 19, respectively, and 12 stable QTLs for pod size-related traits across nine chromosomes. Several genes residing within the genomic region of stable QTL were identified as potential candidates underlying these pod-related traits based on the gene annotation and expression profiling data. Our results provide the useful information for fine-mapping/map-based cloning of QTL and marker-assisted selection of elite varieties with desirable pod traits. Supplementary Information: The online version contains supplementary material available at 10.1007/s11032-021-01223-2.

Long Non-Coding RNA GATA6-AS1 Sponges miR-324-5p to Inhibit Lung Cancer Cell Proliferation and Invasion.

BACKGROUND: Long non-coding RNAs (lncRNAs), which are key regulators of gene expression, are involved in lung cancer progression. Although numerous differentially expressed lncRNAs have been reported, merely a limited number of studies have been performed to verify their functions in lung cancer. METHODS: RNA sequencing data were re-analyzed to investigate the GATA6-AS1 expression in lung cancer. RT-qPCR was performed to verify the expression of GATA6-AS1 in collected tissue samples and cell lines. CCK-8 and transwell assays were carried out to evaluate the role of GATA6-AS1 in lung cancer cells. Dual-luciferase reporter assay and bioinformatic analysis were used to explore the miRNA which can be sponged by GATA6-AS1 in lung cancer cells. RESULTS: Currently, we focused on exploring the role and mechanisms of GATA6-AS1 in lung cancer. Expression of GATA6-AS1 was decreased in lung cancer based on the analysis of RNA sequencing dataset, TCGA data and RT-qPCR of clinical tissue samples. Via overexpression of GATA6-AS1, it was revealed that GATA6-AS1 inhibited lung cancer cell proliferation and invasion. Oncogene miR-324-5p was predicted to interact with GATA6-AS1. RT-qPCR and dual-luciferase reporter assay verified the regulation of miR-324-5p by GATG6-AS1 in lung cancer cells. Overexpression of GATA6-AS1 increased the expression of FBXO11 and SP1, two target genes of miR-324-5p. We further showed that miR-324-5p mimic reversed the effect of GATA6-AS1 overexpression in lung cancer cells. CONCLUSION: Overall, our findings demonstrated GATA6-AS1 as a novel tumor suppressor in lung cancer.