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Drought is one of the most critical abiotic stresses influencing maize yield. Improving maize cultivars with drought tolerance using marker-assisted selection requires a better understanding of its genetic basis. In this study, a doubled haploid (DH) population consisting of 217 lines was created by crossing the inbred lines Han 21 (drought-tolerant) and Ye 478 (drought-sensitive). The population was genotyped with a 6 K SNP assay and 756 SNP (single nucleotide polymorphism) markers were used to construct a linkage map with a length of 1344 cM. Grain yield (GY), ear setting percentage (ESP), and anthesis–silking interval (ASI) were recorded in seven environments under well-watered (WW) and water-stressed (WS) regimes. High phenotypic variation was observed for all traits under both water regimes. Using the LSMEAN (least-squares mean) values from all environments for each trait, 18 QTL were detected, with 9 associated with the WW and 9 with the WS regime. Four chromosome regions, Chr. 3: 219.8–223.7 Mb, Chr. 5: 191.5–194.7 Mb, Chr. 7: 132.2–135.6 Mb, and Chr. 10: 88.2–89.4 Mb, harbored at least 2 QTL in each region, and QTL co-located in a region inherited favorable alleles from the same parent. A set of 64 drought-tolerant BC3F6 lines showed preferential accumulation of the favorable alleles in these four regions, supporting an association between the four regions and maize drought tolerance. QTL-by-environment interaction analysis revealed 28 edQTL (environment-dependent QTL) associated with the WS regime and 22 associated with the WW regime for GY, ESP, and ASI. All WS QTL and 55.6% of WW QTL were located in the edQTL regions. The hotspot genomic regions identified in this work will support further fine mapping and marker-assisted breeding of drought-tolerant maize.

Callus induction in plants is similar to pluripotent stem cell induction in animals and can incite global changes in gene expression. Alternative splicing is considered a key factor underlying functional complexity and function in the induction of pluripotent stem cells in animals. However, the role of alternative splicing in plant callus induction remains unclear. We performed high-throughput RNA sequencing of maize callus induced on a callus induction medium (CIM) at different stages and recorded global alternative splicing changes. At every stage, over 20,000 alternative splicing events were detected, and the numbers slightly increased with callus induction. In total, 648 to 2580 genes were found to exhibit significant alternative splicing changes during callus induction—mainly those that belong to the spliceosome, metabolic pathways, and mRNA surveillance pathways. It was also found that alternative splicing can function alongside transcriptional regulation to contribute to callus induction. Especially, ZmWOX11, whose orthologous gene in Arabidopsis plays a vital role in the first-step cell fate transition of callus induction, was found to exhibit alternative splicing and expression level changes during callus induction. Our results establish a foundation from which researchers can further explore the molecular mechanism of callus induction in maize, especially at alternative splicing level.

In this study, we report that lncRNA SNHG16 is upregulated in non-small cell lung cancer (NSCLC) tissues, and correlates with tumor size, TNM stage and lymph node metastasis. Kaplan-Meier analysis shows that the patients with high SNHG16 expression have poorer disease-free survival (DFS) and overall survival (OS) than the patients with low SNHG16 expression. Multivariate Cox regression analysis reveals that SNHG16 expression could be regarded as an independent predictor for DFS and OS in NSCLC patients. Cell experiments show that SNHG16 promotes NSCLC cell proliferation, migration and invasion. miR-146a is further identified and confirmed to be the target of SNHG16, and SNHG16 functions by targeting miR-146a. Subsequently, MUC5AC, a major mucin in the human respiratory tract correlated with post-operative metastasis and recurrence of NSCLC, is confirmed to be regulated by SNHG16 and miR-146a, and plays a positive role in promoting cell proliferation, migration and invasion, which might be involved in the oncogenic activity of SNHG16-miR-146a axis in NSCLC. Animal experiments also confirm these conclusions. Collectively, these results elucidate a potential mechanism underlying the carcinogenesis role of SNHG16 in NSCLC, and indicate that SNHG16 could act as a novel promising marker for prognosis, and a potential therapeutic target for NSCLC treatment.

Callus induction is a dedifferentiation process that accompanies a cell fate transition, and epigenetic regulation plays a crucial role in the process. N6‐methyladenosine (m6A) methylation is an important mechanism in post‐transcriptional epigenetic regulation and functions in cell reprogramming. However, the function of m6A methylation during callus induction is still unknown. Here, we performed transcriptome‐wide m6A‐seq on immature maize embryos after culturing for 2, 4, or 8 days with or without the auxin analogue 2,4‐D. A total of 26,794 unique m6A peaks were detected from 17,456 maize genes; and 2,338 specific, 2,4‐D‐induced m6A peaks (D‐specific m6A) were detected only in embryos cultured with 2,4‐D. Furthermore, a positive correlation between m6A methylation and mRNA abundance was discovered in the genes with D‐specific m6A deposition, especially at the beginning of callus induction. Key genes involved in callus induction, i.e. BABY BOOM and LBD transcription factors, underwent m6A methylation, increasing their transcript levels, thus improving callus induction. These results revealed the importance of m6A methylation during the early stage of callus induction and provided new insights into the molecular mechanism of callus induction at an epitranscriptomic level.

CD146 was originally identified as a melanoma cell adhesion molecule (MCAM) and highly expressed in many tumors and endothelial cells. However, the evidence that CD146 acts as an adhesion molecule to mediate a homophilic adhesion through the direct interactions between CD146 and itself is still lacking. Recent evidence revealed that CD146 is not merely an adhesion molecule, but also a cellular surface receptor of miscellaneous ligands, including some growth factors and extracellular matrixes. Through the bidirectional interactions with its ligands, CD146 is actively involved in numerous physiological and pathological processes of cells. Overexpression of CD146 can be observed in most of malignancies and is implicated in nearly every step of the development and progression of cancers, especially vascular and lymphatic metastasis. Thus, immunotherapy against CD146 would provide a promising strategy to inhibit metastasis, which accounts for the majority of cancer-associated deaths. Therefore, to deepen the understanding of CD146, we review the reports describing the newly identified ligands of CD146 and discuss the implications of these findings in establishing novel strategies for cancer therapy.

A massively parallel array of monoclonal antibodies enables rapid antibody development and target discovery across species., Antibodies are essential for elucidating gene function. However, affordable technology for proteome-scale antibody generation does not exist. To address this, we developed Proteome Epitope Tag Antibody Library (PETAL) and its array. PETAL consists of 62,208 monoclonal antibodies (mAbs) against 15,199 peptides from diverse proteomes. PETAL harbors binders for a great multitude of proteins in nature due to antibody multispecificity, an intrinsic antibody feature. Distinctive combinations of 10,000 to 20,000 mAbs were found to target specific proteomes by array screening. Phenotype-specific mAb-protein pairs were found for maize and zebrafish samples. Immunofluorescence and flow cytometry mAbs for membrane proteins and chromatin immunoprecipitation–sequencing mAbs for transcription factors were identified from respective proteome-binding PETAL mAbs. Differential screening of cell surface proteomes of tumor and normal tissues identified internalizing tumor antigens for antibody-drug conjugates. By finding high-affinity mAbs at a fraction of current time and cost, PETAL enables proteome-scale antibody generation and target discovery.

The black layer (BL) is traditionally used as an indicator for kernel harvesting in maize, as it turns visibly dark when the kernel reaches physiological maturity. However, the molecular roles of BL in kernel development have not been fully elucidated. In this work, microscopy images showed that BL began to appear at a growth stage earlier than 10 days after pollination (DAP), and its color gradually deepened to become dark as the development period progressed. Scanning electron microscopy observations revealed that BL is a tissue structure composed of several layers of cells that are gradually squeezed and compressed during kernel development. Laser-capture microdissection (LCM) was used to sample BL and its neighboring inner tissue, basal endosperm transfer layer (BETL), and outer tissue, inner epidermis (IEP), from 20 DAP of kernels. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry profiling (MALDI-TOF MS profiling) detected 41, 104, and 120 proteins from LCM-sampled BL, BETL, and IEP, respectively. Gene ontology (GO) analysis indicated that the 41 BL proteins were primarily involved in the response to stress and stimuli. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis found that the BL proteins were enriched in several defense pathways, such as the ascorbate and aldarate metabolic pathways. Among the 41 BL proteins, six were BL-specific proteins that were only detected from BL. Annotations of five BL-specific proteins were related to stress responses. During kernel development, transcriptional expression of most BL proteins showed an increase, followed by a decrease, and reached a maximum zero to 20 DAP. These results suggest a role for BL in stress responses for protecting filial tissue against threats from maternal sides, which helps to elucidate the biological functions of BL.

Maize transformation is highly based on the formation of embryonic callus, which is mainly derived from scutellum cells of the immature maize embryo. However, only a few genes involved in callus induction have been identified in maize. To reveal the potential genes involved in the callus induction of maize, we carried out a high-throughput RNA sequencing on embryos that were cultured for 0, 1, 2, 4, 6, and 8 days, respectively, on a medium containing or lacking 2,4-dichlorophenoxyacetic acid. In total, 7,525 genes were found to be induced by 2,4-dichlorophenoxyacetic acid and categorized into eight clusters, with clusters 2 and 3 showing an increasing trend related to signal transmission, signal transduction, iron ion binding, and heme binding. Among the induced genes, 659 transcription factors belong to 51 families. An AP2 transcription factors, ZmBBM2, was dramatically and rapidly induced by auxin and further characterization showed that overexpression of ZmBBM2 can promote callus induction and proliferation in three inbred maize lines. Therefore, our comprehensive analyses provide some insight into the early molecular regulations during callus induction and are useful for further identification of the regulators governing callus formation.

Hybrid breeding of Chinese jujube (Ziziphus jujube) is limited by embryo abortion. Improving the success of embryogenic progeny and immature embryo culture techniques could increase the breeding ef...

Inflammatory myofibroblastic tumor (IMT) is a distinctive neoplasm composed of myofibroblastic and fibroblastic spindle cells, accompanied by the inflammatory infiltration of plasma cells, lymphocytes and/or eosinophils. Epithelioid inflammatory myofibroblastic sarcoma (EIMS), which primarily consists of cells with a round or epithelioid morphology, is associated with a poor prognosis and rapid development of local recurrence, and has been recognized to be a variant of IMT. Diagnosis of EIMS is difficult owing to its close resemblance to malignant mesothelioma, anaplastic large cell lymphoma, gastrointestinal stromal tumor and other malignant diseases. In the present study, a case of this rare tumor was evaluated in a 26-year-old male who was admitted to hospital after experiencing abdominal pain for ~18 days and abdominal distention for 1 week. The patient's tumor was examined by imaging, gross examination, histology, immunohistochemistry and fluorescence in situ hybridization (FISH). The magnetic resonance imaging enhanced-scanning image revealed that the morphology of the tumor was irregular, and signal was medley consisting of high and low hybrid reinforcement. Tumors were located in the bladder and rectal pit, in the lower part of the lower abdomen, indicating the presence of malignancy and involvement of the small intestine and rectum. Enhanced-scanning imaging revealed notable inhomogeneous enhancement. Gross examination revealed that the tumor was solid and had a variegated appearance with alternating fleshy and mucoid areas in the cut surface. Microscopically, the tumors were dominated by sheets of epithelioid-to-round cells with a prominent inflammatory infiltrate. The majority of the stroma was myxoid. Immunohistochemically, the tumor cells exhibited diffuse strong staining for ALK receptor tyrosine kinase (hereafter ALK), vimentin, tumor protein P53, desmin, Wilms' tumor 1 and programmed death-ligand 1. FISH analysis also revealed the existence of ALK rearrangement. The expression of PD-L1 in EIMS indicates that the immune checkpoint blockade could represent a novel therapy for the treatment of EIMS.

Background Tobacco smoke is by far the greatest risk factor for non-small-cell lung cancer (NSCLC). Nicotine, an active alkaloid in tobacco, is unable to initiate tumorigenesis in humans and rodents, but can promote the growth and metastasis of various tumors, including NSCLC, initiated by tobacco carcinogens. Recently, cigarette smoke is reported to downregulate 24 miRNAs more than 3-fold in the lungs of rats, and most of these downregulated miRNAs are associated with NSCLC initiation and development. Nicotine as the major tobacco component might be associated with the expression changes of some miRNAs. Methods qRT-PCR was performed to determine the miRNA and mRNA expression, and western blot was conducted to measure protein expression. MTT assay was used to detect cell proliferation. Results The effects of nicotine on the expression of 24 miRNAs in NSCLC cell lines were determined, and the results showed that nicotine treatment decreased miR-99b and miR-192 expression. Cell proliferation and epithelial-to-mesenchymal transition (EMT) detection showed that nicotine promoted NSCLC cell proliferation and EMT, and restoration of miR-99b or miR-192 expression relieved the effects of nicotine on NSCLC cell proliferation and EMT. Subsequently, fibroblast growth factor receptor 3 (FGFR3) and retinoblastoma 1 (RB1) were confirmed to be the targets of miR-99b and miR-192, respectively, and were upregulated by nicotine in NSCLC cells. In addition, FGFR3 or RB1 knockdown inhibited NSCLC cell proliferation and EMT. Conclusion This study, for the first time, elucidates nicotine-miR-99b/miR-192-FGFR3/RB1 regulatory network that nicotine promotes NSCLC cell proliferation and EMT by downregulating miR-99b and miR-192, and upregulating their targets FGFR3 and RB1. These findings offer novel insights into the understanding of underlying molecular mechanisms of NSCLC related with the nicotine effects.

In this study, we report that long non-coding RNA (lncRNA) SNHG16 is upregulated in non-small cell lung cancer (NSCLC) tissues, and is correlated with tumor size, TNM stage and lymph node metastasis. Kaplan-Meier analysis shows that the patients with high SNHG16 expression have poorer disease-free survival (DFS) and overall survival (OS) than the patients with low SNHG16 expression. Multivariate Cox regression analysis reveals that SNHG16 expression could be regarded as an independent predictor for DFS and OS in NSCLC patients. In vitro experiments show that SNHG16 knockdown inhibits NSCLC cell proliferation, migration and invasion, and SNHG16 overexpression promotes NSCLC cell proliferation, migration and invasion. We further identify and confirm that miR-146a is the target of SNHG16, and SNHG16 functions by targeting miR-146a. Subsequently, MUC5AC, a major mucin in the human respiratory tract correlated with post-operative metastasis and recurrence of NSCLC, is confirmed to be regulated by SNHG16 and miR-146a, and might be involved in the oncogenic activity of SNHG16-miR-146a axis in NSCLC. In vivo experiments also confirm these conclusions. Taken together, the present results elucidate a potential mechanism underlying the carcinogenesis role of SNHG16 in NSCLC, and indicate that SNHG16 could act as a novel promising marker for prognosis, and a potential therapeutic target for NSCLC treatment in the future.

Metastasis is the leading cause of death in breast cancer patients. However, the mechanisms underlying metastasis are not well understood and there is no effective treatment in the clinic. Here, we demonstrate that in MMTV-PyMT, a highly malignant spontaneous breast tumor model, IL-25 (also called IL-17E) was expressed by tumor-infiltrating CD4+ T cells and macrophages. An IL-25 neutralization antibody, while not affecting primary tumor growth, substantially reduced lung metastasis. Inhibition of IL-25 resulted in decreased type 2 T cells and macrophages in the primary tumor microenvironments, both reported to enhance breast tumor invasion and subsequent metastasis to the lung. Taken together, our data suggest IL-25 blockade as a novel treatment for metastatic breast tumor. Electronic supplementary material The online version of this article (doi:10.1007/s13238-016-0345-7) contains supplementary material, which is available to authorized users.