Mixed lineage kinase domain-like protein （Mlkl） was recently found to interact with receptor interacting protein 3 （Rip3） and to be essential for tumor necrosis factor （TNF）-induced programmed ...necrosis （necroptosis） in cultured cell lines. We have generated Mlkl-deficient mice by transcription activator-like effector nucleases （TALENs）-mediated gene disruption and found Mlkl to be dispensable for normal mouse development as well as immune cell develop- ment. Mlkl-deficient mouse embryonic fibroblasts （MEFs） and macrophages both showed resistance to necrotic but not apoptotic stimuli. Mlkl-deficient MEFs and macrophages were indistinguishable from wild-type cells in their abil- ity to activate NF-KB, ERK, JNK, and p38 in response to TNF and lipopolysaccharides （LPS）, respectively. Consis- tently, Mlkl-deficient macrophages and mice exhibited normal interleukin-lp （IL-1β）, IL-6, and TNF production after LPS treatment. Mlkl deficiency protects mice from cerulean-induced acute pancreatitis, a necrosis-related disease, but has no effect on polymicrobial septic shock-induced animal death. Our results provide genetic evidence for the role of Mlkl in necroptosis.
Sorbus sensu stricto (Sorbus s.s.) is a genus with important economical values because of its beautiful leaves, and flowers and especially the colorful fruits. It belongs to the tribe Maleae of the ...family Rosaceae, and comprises about 90 species mainly distributed in China. There is on-going dispute about its infrageneric classification and species delimitation as the species are morphologically similar. With the aim of shedding light on the circumscription of taxa within the genus, phylogenetic analyses were performed using 29 Sorbus s.s. chloroplast (cp) genomes (16 newly sequenced) representing two subgenera and eight sections. The 16 cp genomes newly sequenced range between 159,646 bp and 160,178 bp in length. All the samples examined and 22 taxa re-annotated in Sorbus sensu lato (Sorbus s.l.) contain 113 unique genes with 19 of these duplicated in the inverted repeat (IR). Six hypervariable regions including trnR-atpA, petN-psbM, rpl32-trnL, trnH-psbA, trnT-trnL and ndhC-trnV were screened and 44-53 SSRs and 14-31 dispersed repeats were identified as potential molecular markers. Phylogenetic analyses under ML/BI indicated that Sorbus s.l. is polyphyletic, but Sorbus s.s. and the other five segregate genera, Aria, Chamaemespilus, Cormus, Micromeles and Torminalis are monophyletic. Two major clades and four sub-clades resolved with full-support within Sorbus s.s. are not consistent with the existing infrageneric classification. Two subgenera, subg. Sorbus and subg. Albocarmesinae are supported as monophyletic when S. tianschanica is transferred to subg. Albocarmesinae from subg. Sorbus and S. hupehensis var. paucijuga transferred to subg. Sorbus from subg. Albocarmesinae, respectively. The current classification at sectional level is not supported by analysis of cp genome phylogeny. Phylogenomic analyses of the cp genomes are useful for inferring phylogenetic relationships in Sorbus s.s. Though genome structure is highly conserved in the genus, hypervariable regions and repeat sequences used are the most promising molecule makers for population genetics, species delimitation and phylogenetic studies.
We explored the clinical and pathological impact of epidermal growth factor receptor (EGFR) extracellular domain missense mutations. Retrospective assessment of 260 de novo glioblastoma patients ...revealed a significant reduction in overall survival of patients having tumors with EGFR mutations at alanine 289 (EGFRA289D/T/V). Quantitative multi-parametric magnetic resonance imaging analyses indicated increased tumor invasion for EGFRA289D/T/V mutants, corroborated in mice bearing intracranial tumors expressing EGFRA289V and dependent on ERK-mediated expression of matrix metalloproteinase-1. EGFRA289V tumor growth was attenuated with an antibody against a cryptic epitope, based on in silico simulation. The findings of this study indicate a highly invasive phenotype associated with the EGFRA289V mutation in glioblastoma, postulating EGFRA289V as a molecular marker for responsiveness to therapy with EGFR-targeting antibodies.
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•EGFRA289D/T/V-mutated GBM tumors have distinct in vivo imaging characteristics•EGFRA289D/T/V-associated decrease in OS is driven by tumor proliferation and invasion•EGFRA289V leads to phosphorylation of Erk followed by increased MMP1 secretion•Targeting of EGFRA289V via mAb806 can reduce tumor growth and increase survival
Binder et al. show that glioblastoma (GBM) expressing EGFR A289 mutants exhibit invasive features and are associated with shorter survival in patients and mice. GBM cells expressing EGFRA289V increase ERK-dependent MMP1 expression but are sensitive to an EGFR monoclonal antibody being clinically developed.
The root tissues play important roles in water and nutrient acquisition, environmental adaptation, and plant development. In this study, a diversity panel of 388 wheat accessions was collected to ...investigate nine root system architecture (RSA) traits at the three-leaf stage under two growing environments: outdoor pot culture (OPC) and indoor pot culture (IPC). Phenotypic analysis revealed that root development was faster under OPC than that under IPC and a significant correlation was observed between the nine RSA traits. The 660K single-nucleotide polymorphism (SNP) chip was used for a genome-wide association study (GWAS). Significant SNPs with a threshold of -log
(
-value) ≥ 4 were considered. Thus, 36 quantitative trait loci (QTLs), including 13 QTL clusters that were associated with more than one trait, were detected, and 31 QTLs were first identified. The QTL clusters on chromosomes 3D and 5B were associated with four and five RSA traits, respectively. Two candidate genes,
and
, were found to be associated with more than one RSA trait using haplotype analysis, and preferentially expressed in the root tissues. These favourable alleles for RSA traits identified in this study may be useful to optimise the root system in wheat.
Although aerobic glycolysis (the Warburg effect) is a hallmark of cancer, key questions, including when, how, and why cancer cells become highly glycolytic, remain less clear. For a largely unknown ...regulatory mechanism, a rate-limiting glycolytic enzyme pyruvate kinase M2 (PKM2) isoform is exclusively expressed in embryonic, proliferating, and tumor cells, and plays an essential role in tumor metabolism and growth. Because the receptor tyrosine kinase/PI3K/AKT/mammalian target of rapamycin (RTK/PI3K/AKT/mTOR) signaling cascade is a frequently altered pathway in cancer, we explored its potential role in cancer metabolism. We identified mTOR as a central activator of the Warburg effect by inducing PKM2 and other glycolytic enzymes under normoxic conditions. PKM2 level was augmented in mouse kidney tumors due to deficiency of tuberous sclerosis complex 2 and consequent mTOR activation, and was reduced in human cancer cells by mTOR suppression. mTOR up-regulation of PKM2 expression was through hypoxia-inducible factor 1α (HIF1α)-mediated transcription activation, and c-Myc-heterogeneous nuclear ribonucleoproteins (hnRNPs)-dependent regulation of PKM2 gene splicing. Disruption of PKM2 suppressed oncogenic mTOR-mediated tumorigenesis. Unlike normal cells, mTOR hyperactive cells were more sensitive to inhibition of mTOR or glycolysis. Dual suppression of mTOR and glycolysis synergistically blunted the proliferation and tumor development of mTOR hyperactive cells. Even though aerobic glycolysis is not required for breach of senescence for immortalization and transformation, the frequently deregulated mTOR signaling during multistep oncogenic processes could contribute to the development of the Warburg effect in many cancers. Components of the mTOR/HIF1α/Myc-hnRNPs/PKM2 glycolysis signaling network could be targeted for the treatment of cancer caused by an aberrant RTK/PI3K/AKT/mTOR signaling pathway.
Background
Despite the effectiveness of chemotherapy and targeted therapy for colorectal cancer, drug resistance drives therapy failure and tumor relapse. Increasing evidence has suggested that ...cancer cells can enter a reversible drug-tolerant persister state to survive chemotherapy or targeted agents. However, the traits and treatable vulnerabilities of anti-colorectal cancer drug-tolerant persister cells is not yet known.
Methods
In this study, we established 5-fluorouracil and AZ628-tolerant persister cell models in two colorectal cancer cell lines, namely HCT116 and SW620, and revealed the characteristics of colorectal cancer persister cells by cell viability assay and flow cytometry. We investigated the efficacy and mechanism of ferroptosis inducers RSL3 and FIN56 on persister cells, which are glutathione peroxidase 4 inhibitors. In the xenograft mouse model, we further evaluated the inhibitory effect of RSL3 on tumor regrowth.
Results
Colorectal cancer persister cells, which were enriched in the residual cancer cell population, exhibited reduced drug sensitivity, were largely quiescent and expressed high levels of stem cell-related genes and mesenchymal markers but not epithelial markers. The persister cells were more sensitive and underwent ferroptosis induced by glutathione peroxidase 4 inhibitors. Mechanistically, glutathione peroxidase 4 and ferrous iron, which are pivotal ferroptosis regulators, were upregulated in residual cells or tumors, and were hence potential therapeutic targets of persister cells. In the xenograft model, we confirmed that inhibition of glutathione peroxidase 4 restrained tumor regrowth after discontinuation of anti-cancer drug treatment. Moreover, biopsies obtained from patients with colorectal cancer undergoing neoadjuvant chemoradiotherapy revealed upregulated glutathione peroxidase 4 and ferritin heavy chain 1. High glutathione peroxidase 4 expression correlates with a worse prognosis in colorectal cancer patients.
Conclusions
Our work reveals that the upregulated glutathione peroxidase 4 and ferrous iron in anti-colorectal cancer drug-tolerant persister cells were potential therapeutic targets. Glutathione peroxidase 4 inhibition combined with chemotherapy or targeted therapy may be a promising therapy for colorectal cancer.
Zinc (Zn) deficiency causes serious diseases in people who rely on cereals as their main food source. However, the grain zinc concentration (GZnC) in wheat is low. Biofortification is a sustainable ...strategy for reducing human Zn deficiency.
In this study, we constructed a population of 382 wheat accessions and determined their GZnC in three field environments. Phenotype data was used for a genome-wide association study (GWAS) using a 660K single nucleotide polymorphism (SNP) array, and haplotype analysis identified an important candidate gene for GZnC.
We found that GZnC of the wheat accessions showed an increasing trend with their released years, indicating that the dominant allele of GZnC was not lost during the breeding process. Nine stable quantitative trait loci (QTLs) for GZnC were identified on chromosomes 3A, 4A, 5B, 6D, and 7A. And an important candidate gene for GZnC, namely, TraesCS6D01G234600, and GZnC between the haplotypes of this gene showed, significant difference (P ≤ 0.05) in three environments.
A novel QTL was first identified on chromosome 6D, this finding enriches our understanding of the genetic basis of GZnC in wheat. This study provides new insights into valuable markers and candidate genes for wheat biofortification to improve GZnC.
Purpose
Radiation therapy treatment planning is a trial‐and‐error, often time‐consuming process. An approximately optimal dose distribution corresponding to a specific patient's anatomy can be ...predicted by using pre‐trained deep learning (DL) models. However, dose distributions are often optimized based not only on patient‐specific anatomy but also on physicians’ preferred trade‐offs between planning target volume (PTV) coverage and organ at risk (OAR) sparing or among different OARs. Therefore, it is desirable to allow physicians to fine‐tune the dose distribution predicted based on patient anatomy. In this work, we developed a DL model to predict the individualized 3D dose distributions by using not only the patient's anatomy but also the desired PTV/OAR trade‐offs, as represented by a dose volume histogram (DVH), as inputs.
Methods
In this work, we developed a modified U‐Net network to predict the 3D dose distribution by using patient PTV/OAR masks and the desired DVH as inputs. The desired DVH, fine‐tuned by physicians from the initially predicted DVH, is first projected onto the Pareto surface, then converted into a vector, and then concatenated with feature maps encoded from the PTV/OAR masks. The network output for training is the dose distribution corresponding to the Pareto optimal DVH. The training/validation datasets contain 77 prostate cancer patients, and the testing dataset has 20 patients.
Results
The trained model can predict a 3D dose distribution that is approximately Pareto optimal while having the DVH closest to the input desired DVH. We calculated the difference between the predicted dose distribution and the optimized dose distribution that has a DVH closest to the desired one for the PTV and for all OARs as a quantitative evaluation. The largest absolute error in mean dose was about 3.6% of the prescription dose, and the largest absolute error in the maximum dose was about 2.0% of the prescription dose.
Conclusions
In this feasibility study, we have developed a 3D U‐Net model with the patient's anatomy and the desired DVH curves as inputs to predict an individualized 3D dose distribution that is approximately Pareto optimal while having the DVH closest to the desired one. The predicted dose distributions can be used as references for dosimetrists and physicians to rapidly develop a clinically acceptable treatment plan.
Previous transcriptome profiling studies have investigated the molecular mechanisms of pollen and anther development, and identified many genes involved in these processes. However, only 51 anther ...ESTs of Upland cotton (Gossypium hirsutum) were found in NCBI and there have been no reports of transcriptome profiling analyzing anther development in Upland cotton, a major fiber crop in the word.
Ninety-eight hundred and ninety-six high quality ESTs were sequenced from their 3'-ends and assembled into 6,643 unigenes from a normalized, full-length anther cDNA library of Upland cotton. Combined with previous sequenced anther-related ESTs, 12,244 unigenes were generated as the reference genes for digital gene expression (DGE) analysis. The DGE was conducted on anthers that were isolated at tetrad pollen (TTP), uninucleate pollen (UNP), binucleate pollen (BNP) and mature pollen (MTP) periods along with four other tissues, i.e., roots (RO), stems (ST), leaves (LV) and embryos (EB). Through transcriptome profiling analysis, we identified 1,165 genes that were enriched at certain anther development periods, and many of them were involved in starch and sucrose metabolism, pentose and glucuronate interconversion, flavonoid biosynthesis, and ascorbate and aldarate metabolism.
We first generated a normalized, full-length cDNA library from anthers and performed transcriptome profiling analysis of anther development in Upland cotton. From these results, 10,178 anther expressed genes were identified, among which 1,165 genes were stage-enriched in anthers. And many of these stage-enriched genes were involved in some important processes regulating anther development.
Glioblastoma (GBM) is the most lethal type of human brain cancer, where deletions and mutations in the tumour suppressor gene PTEN (phosphatase and tensin homolog) are frequent events and are ...associated with therapeutic resistance. Herein, we report a novel chromatin-associated function of PTEN in complex with the histone chaperone DAXX and the histone variant H3.3. We show that PTEN interacts with DAXX and, in turn PTEN directly regulates oncogene expression by modulating DAXX-H3.3 association on the chromatin, independently of PTEN enzymatic activity. Furthermore, DAXX inhibition specifically suppresses tumour growth and improves the survival of orthotopically engrafted mice implanted with human PTEN-deficient glioma samples, associated with global H3.3 genomic distribution changes leading to upregulation of tumour suppressor genes and downregulation of oncogenes. Moreover, DAXX expression anti-correlates with PTEN expression in GBM patient samples. Since loss of chromosome 10 and PTEN are common events in cancer, this synthetic growth defect mediated by DAXX suppression represents a therapeutic opportunity to inhibit tumorigenesis specifically in the context of PTEN deletion.
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