Editing the nuclear localization signals of E1 and E1Lb enables the production of tropical soybean in temperate growing regions.

Soybean is a typical short-day crop, and most commercial soybean cultivars are restricted to a relatively narrow range of latitudes due to photoperiod sensitivity. Photoperiod sensitivity hinders the utilization of soybean germplasms across geographical regions. When grown in temperate regions, tropical soybean responds to prolonged day length by increasing the vegetative growth phase and delaying flowering and maturity, which often pushes the harvest window past the first frost date. In this study, we used CRISPR/LbCas12a to edit a North American subtropical soybean cultivar named 06KG218440 that belongs to maturity group 5.5. By designing one gRNA to edit the nuclear localization signal (NLS) regions of both E1 and E1Lb, we created a series of new germplasms with shortened flowering time and time to maturity and determined their favourable latitudinal zone for cultivation. The novel partial function alleles successfully achieve yield and early maturity trade-offs and exhibit good agronomic traits and high yields in temperate regions. This work offers a straightforward editing strategy to modify subtropical and tropical soybean cultivars for temperate growing regions, a strategy that could be used to enrich genetic diversity in temperate breeding programmes and facilitate the introduction of important crop traits such as disease tolerance or high yield.

Combination of bulk RNA sequencing and scRNA sequencing uncover the molecular characteristics of MAPK signaling in kidney renal clear cell carcinoma.

The MAPK signaling pathway significantly impacts cancer progression and resistance; however, its functions remain incompletely assessed across various cancers, particularly in kidney renal clear cell carcinoma (KIRC). Therefore, there is an urgent need for comprehensive pan-cancer investigations of MAPK signaling, particularly within the context of KIRC. In this research, we obtained TCGA pan-cancer multi-omics data and conducted a comprehensive analysis of the genomic and transcriptomic characteristics of the MAPK signaling pathway. For in-depth investigation in KIRC, status of MAPK pathway was quantitatively estimated by ssGSEA and Ward algorithm was utilized for cluster analysis. Molecular characteristics and clinical prognoses of KIRC patients with distinct MAPK activities were comprehensively explored using a series of bioinformatics algorithms. Subsequently, a combination of LASSO and COX regression analyses were utilized sequentially to construct a MAPK-related signature to help identify the risk level of each sample. Patients in the C1 subtype exhibited relatively higher levels of MAPK signaling activity, which were associated with abundant immune cell infiltration and favorable clinical outcomes. Single-cell RNA sequencing (scRNA-seq) analysis of KIRC samples identified seven distinct cell types, and endothelial cells in tumor tissues had obviously higher MAPK scores than normal tissues. The immunohistochemistry results indicated the reduced expression levels of PAPSS1, MAP3K11, and SPRED1 in KIRC samples. In conclusion, our study represents the first integration of bulk RNA sequencing and single-cell RNA sequencing to elucidate the molecular characteristics of MAPK signaling in KIRC, providing a solid foundation for precision oncology.

Tumor Vaccines: Unleashing the Power of the Immune System to Fight Cancer.

This comprehensive review delves into the rapidly evolving arena of cancer vaccines. Initially, we examine the intricate constitution of the tumor microenvironment (TME), a dynamic factor that significantly influences tumor heterogeneity. Current research trends focusing on harnessing the TME for effective tumor vaccine treatments are also discussed. We then provide a detailed overview of the current state of research concerning tumor immunity and the mechanisms of tumor vaccines, describing the complex immunological processes involved. Furthermore, we conduct an exhaustive analysis of the contemporary research landscape of tumor vaccines, with a particular focus on peptide vaccines, DNA/RNA-based vaccines, viral-vector-based vaccines, dendritic-cell-based vaccines, and whole-cell-based vaccines. We analyze and summarize these categories of tumor vaccines, highlighting their individual advantages, limitations, and the factors influencing their effectiveness. In our survey of each category, we summarize commonly used tumor vaccines, aiming to provide readers with a more comprehensive understanding of the current state of tumor vaccine research. We then delve into an innovative strategy combining cancer vaccines with other therapies. By studying the effects of combining tumor vaccines with immune checkpoint inhibitors, radiotherapy, chemotherapy, targeted therapy, and oncolytic virotherapy, we establish that this approach can enhance overall treatment efficacy and offset the limitations of single-treatment approaches, offering patients more effective treatment options. Following this, we undertake a meticulous analysis of the entire process of personalized cancer vaccines, elucidating the intricate process from design, through research and production, to clinical application, thus helping readers gain a thorough understanding of its complexities. In conclusion, our exploration of tumor vaccines in this review aims to highlight their promising potential in cancer treatment. As research in this field continues to evolve, it undeniably holds immense promise for improving cancer patient outcomes.

Effects of the quantitative trait locus qPss3 on inhibition of photoperiod sensitivity and resistance to stalk rot disease in maize.

KEY MESSAGE: We identified a quantitative trait locus, qPss3, and fine-mapped the causal locus to a 120-kb interval in maize. This locus inhibits the photoperiod sensitivity caused by ZmCCT9 and ZmCCT10, resulting in earlier flowering by 2 ~ 4 days without reduction in stalk-rot resistance in certain genotypes. Photoperiod sensitivity is a key factor affecting the adaptation of maize (Zea mays L.) to high-latitude growing areas. Although many genes associated with flowering time have been identified in maize, no gene that inhibits photoperiod sensitivity has been reported. In our previous study, we detected large differences in photoperiod sensitivity among maize inbred lines with the same photoperiod-sensitive allele at the ZmCCT10 locus. Here, we used two segregating populations with the same genetic backgrounds but different ZmCCT10 alleles to perform quantitative trait locus (QTL) analysis. We identified a unique QTL, qPss3, on chromosome 3 in the population carrying the sensitive ZmCCT10 allele. After sequential fine-mapping, we eventually delimited qPss3 to an interval of ~ 120 kb. qPss3 behaved as a dominant locus and caused earlier flowering by 2-4 days via inhibiting ZmCCT10-induced photoperiod sensitivity under long-day conditions. qPss3 also inhibited the photoperiod sensitivity induced by another flowering-related gene, ZmCCT9. For application in agriculture, an F1 hybrid heterozygous at both qPss3 and ZmCCT10 loci constitutes an optimal allele combination, showing high resistance to stalk rot without a significant delay in flowering time. Moreover, qPss3 is of great value in regulating the flowering time of tropical maize grown at high-latitude regions.

DICER1-AS1 Promotes the Malignant Behaviors of Colorectal Cancer Cells by Regulating miR-296-5p/STAT3 Axis.

BACKGROUND: Long non-coding RNA (lncRNA) exerts a regulatory role in the occurrence and progression of tumors. This study aimed at probing into the function and mechanism of lncRNA DICER1 antisense RNA 1 (DICER1-AS1) in colorectal cancer (CRC). METHODS: The expressions of DICER1-AS1, miR-296-5p and STAT3 mRNA were tested by quantitative real-time polymerase chain reaction (qRT-PCR). Cell counting kit-8 (CCK-8) assay was employed to detect cell proliferation, and Transwell was used to detect cell migration and invasion. In addition, the expressions of apoptosis-related proteins Bax and Bcl2 were detected by Western blot. Interactions between DICER1-AS1 and miR-296-5p, and miR-296-5p and STAT3 were predicted and determined by bioinformatics analysis, luciferase reporter assay and RNA binding protein immunoprecipitation (RIP) assay. RESULTS: The expressions of DICER1-AS1 and STAT3 mRNA were significantly up-regulated while miR-296-5p expression was remarkably down-regulated in CRC tissues and cell lines. Over-expression of DICER1-AS1 or transfection of miR-296-5p inhibitors could promote the proliferation, migration and invasion and inhibit apoptosis of CRC cells, whereas knockdown of DICER1-AS1 or transfection of miR-296-5p mimics had the opposite effects. Additionally, DICER1-AS1 could down-regulate miR-296-5p expression via sponging it. DICER1-AS1 also enhanced the expression of STAT3, which was identified as a target gene of miR-296-5p. CONCLUSION: DICER1-AS1 acts as an oncogenic lncRNA in CRC via modulating miR-296-5p/STAT3 axis. Our results provide a new direction for the diagnosis and treatment of CRC.

Combined genome-wide association study and transcriptome analysis reveal candidate genes for resistance to Fusarium ear rot in maize.

Fusarium ear rot, caused by Fusarium verticillioides, is a devastating fungal disease in maize that reduces yield and quality; moreover, F. verticillioides produces fumonisin mycotoxins, which pose serious threats to human and animal health. Here, we performed a genome-wide association study (GWAS) under three environmental conditions and identified 34 single-nucleotide polymorphisms (SNPs) that were significantly associated with Fusarium ear rot resistance. With reference to the maize B73 genome, 69 genes that overlapped with or were adjacent to the significant SNPs were identified as potential resistance genes to Fusarium ear rot. Comparing transcriptomes of the most resistant and most susceptible lines during the very early response to Fusarium ear rot, we detected many differentially expressed genes enriched for pathways related to plant immune responses, such as plant hormone signal transduction, phenylpropanoid biosynthesis, and cytochrome P450 metabolism. More than one-fourth of the potential resistance genes detected in the GWAS were differentially expressed in the transcriptome analysis, which allowed us to predict numbers of candidate genes for maize resistance to ear rot, including genes related to plant hormones, a MAP kinase, a PR5-like receptor kinase, and heat shock proteins. We propose that maize plants initiate early immune responses to Fusarium ear rot mainly by regulating the growth-defense balance and promoting biosynthesis of defense compounds.

Construction and analysis of circular RNA molecular regulatory networks in clear cell renal cell carcinoma.

Increasing evidence has indicated that circular (circ)RNAs participate in carcinogenesis; however, the specific regulatory mechanisms underlying the effects of circRNAs, microRNAs (miRNAs/miRs) and genes on the development of clear cell renal cell carcinoma (CCRCC) remain unclear. In the present study, RNA microarray data from CCRCC tissues and control samples were downloaded from the Gene Expression Omnibus and The Cancer Genome Atlas, in order to identify significantly dysregulated circRNAs, miRNAs and genes. The Cancer­Specific circRNA Database was used to explore the interactions between miRNAs and circRNAs, whereas TargetScan and miRDB were employed to predict the mRNA targets of miRNAs. Functional enrichment and prognostic analyses were conducted in R. The results revealed that 324 circRNAs were downregulated, whereas 218 circRNAs were upregulated in cancer. In addition, a circRNA­miRNA­mRNA interaction network was constructed. Gene Ontology analysis of the upregulated genes revealed that these genes were enriched in biological processes, including 'flavonoid metabolic process', 'cellular glucuronidation' and 'T cell activation'. The downregulated genes were mainly enriched in biological processes, such as 'nephron development', 'kidney development' and 'renal system development'. The hub genes, including membrane palmitoylated protein 7, aldehyde dehydrogenase 6 family member A1, transcription factor AP­2α, collagen type IV α 4 chain, nuclear receptor subfamily 3 group C member 2, plasminogen, Holliday junction recognition protein, claudin 10, kinesin family member 18B and thyroid hormone receptor ß, and the hub miRNAs, including miR­21­3p, miR­155­3p, miR­144­3p, miR­142­5p, miR­875­3p, miR­885­3p, miR­3941, miR­224­3p, miR­584­3p and miR­138­1­3p, were significantly associated with CCRCC survival. In conclusion, these results suggested that the significantly dysregulated circRNAs, miRNAs and genes identified in this study may be considered potential biomarkers of the carcinogenesis of CCRCC and the survival of patients with this disease.

PELP1 is a novel oncogene in gastric tumorigenesis and negatively regulated by miR-15 family microRNAs.

BACKGROUD: Gastric cancer (GC) is one of the leading causes of cancer-related death in East Asia and some South American countries, but its mechanism has not been clarified clearly. Proline-, glutamic acid-, and leucine-rich protein-1 (PELP1), a co-regulatory molecule of estrogen receptor α (ER α), is up-regulated in series of cancers such as endometrial carcinoma, ovarian cancer, colorectal cancer, breast cancer, and non-small cell lung cancer. However, PELP1's role in GC is still obscure, and its aberrant expression in cancers also remains to be explained. METHODS: Immunohistochemical staining and Real-time PCR were used to compare the expression level of PELP1 in GC tissues and adjacent tissues. Western blot was used to detect the expression of PELP1 in cell lines. Kaplan-meier analysis and chi-square test were applied to evaluate the potential of PELP1 to function as a cancer biomarker. RNA interference was used to inhibit PELP1 expression in GC cells, followed by detecting cell proliferation, apoptosis, migration and invasion. Luciferase assay was conducted to validate whether miR-15 family members can directly target PELP1. RESULTS: In this study, we validated that PELP1 was significantly up-regulated in GC samples and cell lines. It was also demonstrated that the up-regulation of PELP1 was associated with several clinicopathologic features such as tumor diameter (P< 0.001), serum CEA level (P= 0.034), and lymphatic metastasis (P= 0.0009) of GC patients, and its high expression was correlated with shorter disease-free survival and overall survival of the patients. Knockdown of PELP1 remarkably arrested the proliferationï» migration and invasion, while promoted apoptosis. We also confirmed that miR-15 family microRNAs, most of which were down-regulated and tumor suppressor in cancers, were posttranscriptional regulators of PELP1. CONCLUSION: In conclusion, we demonstrated that PELP1 was an oncogene of GC associated with patients' prognosis and miR-15 family members contributed to its aberrant expression in cancers.

Characterization of phytohormone and transcriptome reprogramming profiles during maize early kernel development.

BACKGROUND: During maize early kernel development, the dramatic transcriptional reprogramming determines the rate of developmental progression, and phytohormone plays critical role in these important processes. To investigate the phytohormone levels and transcriptome reprogramming profiles during maize early kernel development, two maize inbreds with similar genetic background but different mature kernel sizes (ILa and ILb) were used. RESULTS: The levels of indole-3-acetic acid (IAA) were increased continuously in maize kernels from 5 days after pollination (DAP) to 10 DAP. ILa had smaller mature kernels than ILb, and ILa kernels had significantly lower IAA levels and significantly higher SA levels than ILb at 10 DAP. The different phytohormone profiles correlated with different transcriptional reprogramming in the two kernels. The global transcriptomes in ILa and ILb kernels were strikingly different at 5 DAP, and their differences peaked at 8 DAP. Functional analysis showed that the biggest transcriptome difference between the two kernels is those response to biotic and abiotic stresses. Further analyses indicated that the start of dramatic transcriptional reprogramming and the onset of significantly enriched functional categories, especially the "plant hormone signal transduction" and "starch and sucrose metabolism", was earlier in ILa than in ILb, whereas more significant enrichment of those functional categories occurred at later stage of kernel development in ILb. CONCLUSIONS: These results indicate that later onset of the significantly enriched functional categories, coincide with their stronger activities at a later developmental stage and higher IAA level, are necessary for young kernels to undergo longer mitotic activity and finally develop a larger kernel size. The different onset times and complex interactions of the important functional categories, especially phytohormone signal, and carbohydrate metabolism, form the most important molecular regulators mediating maize early kernel development.

The Auxin-Regulated Protein ZmAuxRP1 Coordinates the Balance between Root Growth and Stalk Rot Disease Resistance in Maize.

To optimize fitness, plants must efficiently allocate their resources between growth and defense. Although phytohormone crosstalk has emerged as a major player in balancing growth and defense, the genetic basis by which plants manage this balance remains elusive. We previously identified a quantitative disease-resistance locus, qRfg2, in maize (Zea mays) that protects against the fungal disease Gibberella stalk rot. Here, through map-based cloning, we demonstrate that the causal gene at qRfg2 is ZmAuxRP1, which encodes a plastid stroma-localized auxin-regulated protein. ZmAuxRP1 responded quickly to pathogen challenge with a rapid yet transient reduction in expression that led to arrested root growth but enhanced resistance to Gibberella stalk rot and Fusarium ear rot. ZmAuxRP1 was shown to promote the biosynthesis of indole-3-acetic acid (IAA), while suppressing the formation of benzoxazinoid defense compounds. ZmAuxRP1 presumably acts as a resource regulator modulating indole-3-glycerol phosphate and/or indole flux at the branch point between the IAA and benzoxazinoid biosynthetic pathways. The concerted interplay between IAA and benzoxazinoids can regulate the growth-defense balance in a timely and efficient manner to optimize plant fitness.

Metformin promotes the proliferation and differentiation of murine preosteoblast by regulating the expression of sirt6 and oct4.

Osteopenia, osteoporosis and bone salt metabolism disorder are common diseases in the aged and diabetics. From case reports of patients with T2DM, we have observed that metformin can decrease risk of bone fracture and promote bone formation. However, the underlying mechanism of metformin's effect on bone metabolism remains unknown. In our research, we show that metformin can promote proliferation of murine preosteoblast by regulating AMPK-mTORC2 and AKT-mTORC1 signaling axis. Furthermore, we have observed that metformin can promote SIRT6 expression before and during differentiation of murine preosteoblast. The interaction between SIRT6 and NF-κB is highly important in osteoblast differentiation just as the relationship between OPG and RANKL in the process of bone formation. During differentiation, we show that SIRT6 inhibits phosphorylation of NF-κB and that OPG increases while RANKL decrease in HG groups. In addition, ablation of sirt6 in mice causes phosphorylation of NF-κB at high-levels and RANKL increases slightly in femur bone cells. However, other bone formation marker proteins such as RUNX2, OSTERIX and OPG appear at low-levels in sirt6 KO mice. It has been confirmed that downregulation of OCT4 is critical incident in the differentiation of embryonic stem cells. Fortunately, we observe that SIRT6 can suppress OCT4 expression in murine preosteoblast and the expression of OCT4 is at high-level in sirt6 KO mice. Taken together, this study's results illuminate metformin's effect on bone metabolism under HG condition and help to elucidate why metformin can promote bone fracture healing of patients with T2DM.

qRfg3, a novel quantitative resistance locus against Gibberella stalk rot in maize.

KEY MESSAGE: A quantitative trait locus  qRfg3 imparts recessive resistance to maize Gibberella stalk rot. qRfg3 has been mapped into a 350-kb interval and could reduce the disease severity index by ~26.6%. Gibberella stalk rot, caused by the fungal pathogen Fusarium graminearum, severely affects maize yield and grain quality worldwide. To identify more resistance quantitative trait loci (QTLs) against this disease, we analyzed a recombinant inbred line (RIL) population derived from a cross between resistant H127R and susceptible C7-2 inbred lines. Within this population, maize resistance to Gibberella stalk rot had high broad-sense heritability. A major QTL, qRfg3, on chromosome 3 was consistently detected across three field trials, accounting for 10.7-19.4% of the total phenotypic variation. Using a progeny-based sequential fine-mapping strategy, we narrowed qRfg3 down to an interval of ~350 kb. We further demonstrated that qRfg3 is a recessive resistance locus to Gibberella stalk rot that reduced the disease severity index by ~26.6%. Both the gene location and recessive genetic mode distinguish qRfg3 from other stalk rot resistance loci. Hence, qRfg3 is valuable as a complement to existing resistance QTLs to improve maize resistance to Gibberella stalk rot.

Transcriptome analysis of maize resistance to Fusarium graminearum.

BACKGROUND: Gibberella stalk rot caused by Fusarium graminearum is one of the most destructive soil-borne diseases of maize (Zea mays L.). Chemical means of controlling Gibberella stalk rot are not very effective; development of highly resistant hybrids is the best choice for disease control. Hence, understanding of the molecular basis underlying maize resistance against Gibberella stalk rot would undoubtedly facilitate the resistance breeding for stalk rot. RESULTS: Two quantitative trait loci (QTL), qRfg1 and qRfg2, conferring resistance to Gibberella stalk rot were detected in our previous study. Three near-isogenic lines (NILs) of maize with either qRfg1 (NIL1) or qRfg2 (NIL2), or neither (NIL3) were generated and subjected to RNA sequencing to study the transcriptional changes after F. graminearum inoculation at 0 (control), 6, and 18 h post-inoculation (hpi). In total, 536,184,652 clean reads were generated, and gene expression levels were calculated using FPKM (fragments per kilobase of exon model per million mapped reads). A total of 7252 differentially expressed genes (DEGs) were found in the three NILs after F. graminearum inoculation. As many as 2499 DEGs were detected between NIL1 and NIL3 at 0 hpi, of which 884 DEGs were more abundant in NIL1 and enriched in defense responses. After F. graminearum inoculation, 1070 and 751 genes were exclusively up- and downregulated, respectively, in NIL1 as compared to NIL3. The 1070 upregulated DEGs were enriched in growth/development, photosynthesis/biogenesis, and defense-related responses. Genes encoding putative auxin-induced proteins and GH3 family proteins in auxin signaling pathway were highly induced and lasted longer in NIL3. Genes involved in polar auxin transport (PAT) were more abundant in NIL3 as compared with NIL2. CONCLUSIONS: The qRfg1 confers its resistance to Gibberella stalk rot through both constitutive and induced high expression of defense-related genes; while qRfg2 enhances maize resistance to the disease via relatively lower induction of auxin signaling and repression of PAT. The defense-related transcriptional changes underlying each QTL will undoubtedly facilitate our understanding of the resistance mechanism and resistance breeding for maize stalk rot.