Prognostic model based on B cell marker genes for NSCLC patients under neoadjuvant immunotherapy by integrated analysis of single-cell and bulk RNA-sequencing data.

BACKGROUND: Neoadjuvant immunotherapy has evolved as an effective option to treat non-small cell lung cancer (NSCLC). B cells play essential roles in the immune system as well as cancer progression. However, the repertoire of B cells and its association with clinical outcomes remains unclear in NSCLC patients receiving neoadjuvant immunotherapy. METHODS: Single-cell RNA sequencing (scRNA-seq) and bulk RNA sequencing data for LUAD samples were accessed from the TCGA and GEO databases. LUAD-related B cell marker genes were confirmed based on comprehensive analysis of scRNA-seq data. We then constructed the B cell marker gene signature (BCMGS) and validated it. In addition, we evaluated the association of BCGMS with tumor immune microenvironment (TIME) characteristics. Furthermore, we validated the efficacy of BCGMS in a cohort of NSCLC patients receiving neoadjuvant immunotherapy. RESULTS: A BCMGS was constructed based on the TCGA cohort and further validated in three independent GSE cohorts. In addition, the BCMGS was proven to be significantly associated with TIME characteristics. Moreover, a relatively higher risk score indicated poor clinical outcomes and a worse immune response among NSCLC patients receiving neoadjuvant immunotherapy. CONCLUSIONS: We constructed an 18-gene prognostic signature derived from B cell marker genes based on scRNA-seq data, which had the potential to predict the prognosis and immune response of NSCLC patients receiving neoadjuvant immunotherapy.

Metabolic heterogeneity in early-stage lung adenocarcinoma revealed by RNA-seq and scRNA-seq.

PURPOSE: Cancer cells maintain cell growth, division, and survival through altered energy metabolism. However, research on metabolic reprogramming in lung adenocarcinoma (LUAD) is limited METHODS: We downloaded TCGA and GEO sequencing data. Consistent clustering with the ConsensusClusterPlus package was employed to detect the scores for four metabolism-related pathways. The LUAD samples in the TCGA dataset were clustered with ConsensusClusterPlus, and the optimal number of clusters was determined according to the cumulative distribution function (CDF). The cell score for each sample in the TCGA dataset was calculated using the MCPcounter estimate function of the MCPcounter package. RESULTS: We identified two subtypes by scoring the samples based on the 4 metabolism-related pathways and cluster dimensionality reduction. The prognosis of cluster B was obviously poorer than that of cluster A in patients with LUAD. The analysis of single-nucleotide variation (SNV) data showed that the top 15 genes in the four metabolic pathways with the most mutations were TKTL2, PGK2, HK3, EHHADH, GLUD2, PKLR, TKTL1, HADHB, CPT1C, HK1, HK2, PFKL, SLC2A3, PFKFB1, and CPT1A. The IFNγ score of cluster B was significantly higher than that of cluster A. The immune T-cell lytic activity score of cluster B was significantly higher than that of cluster A. We further identified 5 immune cell subsets from single-cell sequencing data. The top 5 marker genes of B cells were IGHM, JCHAIN, IGLC3, IGHA1, and IGKC. The C0 subgroup of monocytes had a higher pentose phosphate pathway (PPP) score than the C6 subgroup. CONCLUSIONS: Metabolism-related subtypes could be potential biomarkers in the prognosis prediction and treatment of LUAD.

Differential expression patterns of myogenic regulatory factors in the postnatal longissimus dorsi muscle of Jeju Native Pig and Berkshire breeds along with their co-expression with Pax7

BACKGROUND: Myogenic regulatory factors (MRFs) such as MyoD, Myf6 and Myf5 play a vital role in the growth and development of muscles. Jeju Native Pig (JNP) is the top ranker in Korea amongst the indigenous livestock reared for meat purpose. Few studies covering transcript abundance of the MRFs and related to their co-expression with Pax7 in JNP have been conducted. Despite having better quality pork, JNP does not have a comparative growth rate with respect to western breeds. Therefore, the present study was designed with the objective to study the relative transcript levels of MRFs in the postnatal myogenesis of longissimus dorsi muscles in JNP and Berkshire breeds. RESULTS: Relative transcript levels were analyzed by qRT-PCR and blot expression analysis through Western blotting. Immunocytochemistry was performed to analyze their expressions at cellular levels. ToppCluster aided in the analysis of gene ontology of biological processes. The quantitative transcript levels of MyoD and Pax7 were significantly (P < 0.05) higher in Berkshire than in JNP. Myotube formation was observed under the co-expression of MyoD and Pax7. ToppCluster helped in the understanding of the linking of biological processes of the MRFs with the different signaling pathways. MyBPH had significantly (P < 0.05) high transcript levels during the chosen age groups in JNP than Berkshire. CONCLUSIONS: The current study can be helpful in understanding the genetic basis for myogenesis in postnatal stage. Moreover, it can act as stepping stone for the identification of marker genes related to body growth and meat quality in JNP.

Immune cell infiltration features and related marker genes in lung cancer based on single-cell RNA-seq.

PURPOSE: Immune cells in the immune microenvironment of lung cancer have a great impact on the development of lung cancer. Our purpose was to analyze the immune cell infiltration features and related marker genes for lung cancer. METHODS: Single cell RNA sequencing data of 11,485 lung cancer cells were retrieved from the Gene Expression Omnibus. After quality control and data normalization, cell clustering was performed using the Seurat package. Based on the marker genes of each cell type from the CellMarker database, each cell was divided into G1, G2M, and S phases. Then, differential expression and functional enrichment analyses were performed. CIBERSORT was used to reconstruct immune cell types. RESULTS: Following cell filtering, highly variable genes were identified for all cells. 14 cell types were clustered. Among them, CD4 + T cell, B cell, plasma cell, natural killer cell and cancer stem cell were the top five cell types. Up-regulated genes were mainly enriched in immune-related biological processes and pathways. Using CIBERSORT, we identified the significantly higher fractions of naïve B cell, memory CD4 + T cell, T follicular helper cell, T regulatory helper cell and M1 macrophage in lung cancer tissues compared to normal tissues. Furthermore, the fractions of resting NK cell, monocyte, M0 macrophage, resting mast cell, eosinophil and neutrophil were significantly lower in tumor tissues than normal tissues. CONCLUSION: Our findings dissected the immune cell infiltration features and related marker genes for lung cancer, which might provide novel insights for the immunotherapy of lung cancer.

Expression pattern of drought stress marker genes in soybean roots under two water deficit systems.

The study of tolerance mechanisms for drought stress in soybean is fundamental to the understanding and development of tolerant varieties. Using in silico analysis, four marker genes involved in the classical ABA-dependent and ABA-independent pathways of drought response were identified in the Glycine max genome in the present work. The expression profiles of the marker genes ERD1-like, GmaxRD20A-like, GmaxRD22-like and GmaxRD29B-like were investigated by qPCR in root samples of drought sensitive and tolerant soybean cultivars (BR 16 and Embrapa 48, respectively), submitted to water deficit conditions in hydroponic and pot-based systems. Among the four putative soybean homologs to Arabidopsis genes investigated herein, only GmaxRD29B-like was not regulated by water deficit stress. Distinct expression profiles and different induction levels were observed among the genes, as well as between the two drought-inducing systems. Our results showed contrasting gene expression responses for the GmaxRD20A-like and GmaxRD22-like genes. GmaxRD20A-like was highly induced by continuous drought acclimating conditions, whereas GmaxRD22-like responses decreased after abrupt water deprivation. GmaxERD1-like showed a different expression profile for the cultivars in each system. Conversely, GmaxRD20A-like and GmaxRD22-like genes exhibited similar expression levels in tolerant plants in both systems.

Riscos e benefícios do uso de plantas transgênicas na agricultura / Risks and benefits of transgenic plants to agriculture

O desenvolvimento de técnicas de DNA recombinante possibilitou a produção de plantas transgênicas através da transferência de genes de bactérias, vírus ou animais para as espécies vegetais. Como resultado desta tecnologia, já estão disponíveis ao melhoramento de plantas novas fontes de genes e plantas com resistência a doenças e insetos, tolerância a herbicidas e estresses ambientais e com qualidade superior. O objetivo desta revisão é apontar riscos, benefícios e aspectos importantes no uso de plantas transgênicas na agricultura. Entre as questões que vêm sendo discutidas a respeito de testes a campo de plantas transgênicas, pode-se destacar a segurança dos genes marcadores (especialmente os que conferem resistência a antibióticos ou tolerância a herbicidas) e o fluxo gênico entre espécies vegetais. Apesar dos Estados Unidos da América e a Comunidade Européia possuírem legislações para regulamentar os testes a campo e a liberação de plantas transgênicas em escala comercial, não existe uma legislação internacional que regulamente o uso desses produtos em outras partes do mundo. O impacto da tecnologia do DNA recombinante na produção de novos produtos agrícolas dependerá do entendimento pela sociedade dos riscos e benefícios que essa tecnologia poderá trazer para a agricultura.

The development of recombinant DNA techniques has enabled gene transfer between plants and bacteria, virus or animais to produce transgenic plants. As a result of this technology, there are new genes and plants available to plant breeding for disease and insect resistance, herbicide and environmental stresses tolerance, and for superior quality products. The objectives of this review are topoint out the risks, benefits and importam aspects in using transgenic plants in agriculture. Among the important issues that have been discussed about field tests with transgenic plants, two have received more attention: the safety of marker genes (specially those that confer resistance to antibiotics or herbicides tolerance) and the gene flow between cultivated and wild plant species. Even though the United States of América and the European Community have strict ruies which regulate the field tests and the commercial release of transgenic plants, there are no international laws to regulate the se issues in other parts of the world. The impact of the recombinant DNA technology on the production of new agricultural products will depend on the understanding of their risks and benefits by the society.

Riscos e benefícios do uso de plantas transgênicas na agricultura

The development of recombinant DNA techniques has enabled gene transfer between plants and bacteria, virus or animais to produce transgenic plants. As a result of this technology, there are new genes and plants available to plant breeding for disease and insect resistance, herbicide and environmental stresses tolerance, and for superior quality products. The objectives of this review are topoint out the risks, benefits and importam aspects in using transgenic plants in agriculture. Among the important issues that have been discussed about field tests with transgenic plants, two have received more attention: the safety of marker genes (specially those that confer resistance to antibiotics or herbicides tolerance) and the gene flow between cultivated and wild plant species. Even though the United States of América and the European Community have strict ruies which regulate the field tests and the commercial release of transgenic plants, there are no international laws to regulate the se issues in other parts of the world. The impact of the recombinant DNA technology on the production of new agricultural products will depend on the understanding of their risks and benefits by the society.

O desenvolvimento de técnicas de DNA recombinante possibilitou a produção de plantas transgênicas através da transferência de genes de bactérias, vírus ou animais para as espécies vegetais. Como resultado desta tecnologia, já estão disponíveis ao melhoramento de plantas novas fontes de genes e plantas com resistência a doenças e insetos, tolerância a herbicidas e estresses ambientais e com qualidade superior. O objetivo desta revisão é apontar riscos, benefícios e aspectos importantes no uso de plantas transgênicas na agricultura. Entre as questões que vêm sendo discutidas a respeito de testes a campo de plantas transgênicas, pode-se destacar a segurança dos genes marcadores (especialmente os que conferem resistência a antibióticos ou tolerância a herbicidas) e o fluxo gênico entre espécies vegetais. Apesar dos Estados Unidos da América e a Comunidade Européia possuírem legislações para regulamentar os testes a campo e a liberação de plantas transgênicas em escala comercial, não existe uma legislação internacional que regulamente o uso desses produtos em outras partes do mundo. O impacto da tecnologia do DNA recombinante na produção de novos produtos agrícolas dependerá do entendimento pela sociedade dos riscos e benefícios que essa tecnologia poderá trazer para a agricultura.

Riscos e benefícios do uso de plantas transgênicas na agricultura

The development of recombinant DNA techniques has enabled gene transfer between plants and bacteria, virus or animais to produce transgenic plants. As a result of this technology, there are new genes and plants available to plant breeding for disease and insect resistance, herbicide and environmental stresses tolerance, and for superior quality products. The objectives of this review are topoint out the risks, benefits and importam aspects in using transgenic plants in agriculture. Among the important issues that have been discussed about field tests with transgenic plants, two have received more attention: the safety of marker genes (specially those that confer resistance to antibiotics or herbicides tolerance) and the gene flow between cultivated and wild plant species. Even though the United States of América and the European Community have strict ruies which regulate the field tests and the commercial release of transgenic plants, there are no international laws to regulate the se issues in other parts of the world. The impact of the recombinant DNA technology on the production of new agricultural products will depend on the understanding of their risks and benefits by the society.

O desenvolvimento de técnicas de DNA recombinante possibilitou a produção de plantas transgênicas através da transferência de genes de bactérias, vírus ou animais para as espécies vegetais. Como resultado desta tecnologia, já estão disponíveis ao melhoramento de plantas novas fontes de genes e plantas com resistência a doenças e insetos, tolerância a herbicidas e estresses ambientais e com qualidade superior. O objetivo desta revisão é apontar riscos, benefícios e aspectos importantes no uso de plantas transgênicas na agricultura. Entre as questões que vêm sendo discutidas a respeito de testes a campo de plantas transgênicas, pode-se destacar a segurança dos genes marcadores (especialmente os que conferem resistência a antibióticos ou tolerância a herbicidas) e o fluxo gênico entre espécies vegetais. Apesar dos Estados Unidos da América e a Comunidade Européia possuírem legislações para regulamentar os testes a campo e a liberação de plantas transgênicas em escala comercial, não existe uma legislação internacional que regulamente o uso desses produtos em outras partes do mundo. O impacto da tecnologia do DNA recombinante na produção de novos produtos agrícolas dependerá do entendimento pela sociedade dos riscos e benefícios que essa tecnologia poderá trazer para a agricultura.