There is substantial interest in liquid biopsy approaches for cancer early detection among subjects at risk, using multi-marker panels. CA19-9 is an established circulating biomarker for pancreatic ...cancer; however, its relevance for pancreatic cancer early detection or for monitoring subjects at risk has not been established.
CA19-9 levels were assessed in blinded sera from 175 subjects collected up to 5 years before diagnosis of pancreatic cancer and from 875 matched controls from the Prostate, Lung, Colorectal and Ovarian (PLCO) Cancer Screening Trial. For comparison of performance, CA19-9 was assayed in blinded independent sets of samples collected at diagnosis from 129 subjects with resectable pancreatic cancer and 275 controls (100 healthy subjects; 50 with chronic pancreatitis; and 125 with noncancerous pancreatic cysts). The complementary value of 2 additional protein markers, TIMP1 and LRG1, was determined.
In the PLCO cohort, levels of CA19-9 increased exponentially starting at 2 years before diagnosis with sensitivities reaching 60% at 99% specificity within 0 to 6 months before diagnosis for all cases and 50% at 99% specificity for cases diagnosed with early-stage disease. Performance was comparable for distinguishing newly diagnosed cases with resectable pancreatic cancer from healthy controls (64% sensitivity at 99% specificity). Comparison of resectable pancreatic cancer cases to subjects with chronic pancreatitis yielded 46% sensitivity at 99% specificity and for subjects with noncancerous cysts, 30% sensitivity at 99% specificity. For prediagnostic cases below cutoff value for CA19-9, the combination with LRG1 and TIMP1 yielded an increment of 13.2% in sensitivity at 99% specificity (P = .031) in identifying cases diagnosed within 1 year of blood collection.
CA19-9 can serve as an anchor marker for pancreatic cancer early detection applications.
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•Reduction in lignin content often results in growth inhibition.•Xylem-specific lignin complementation circumvents dwarfism.•Alterations in gene regulation play a role in ...phenylpropanoid homeostasis and its impact on plant growth.•The mechanisms that lead to dwarfism in low-lignin plants remain unknown.
Lignin, a polymer found in the plant secondary cell wall, is a major contributor to biomass’ recalcitrance toward saccharification. Because of this negative impact toward the value of lignocellulosic crops, there is a special interest in modifying the content and composition of this important plant biopolymer. For many years this endeavor has been hindered by the plant growth inhibition that is often associated with manipulations to phenylpropanoid metabolism. Although the actual mechanism by which dwarfism arises remains unknown, recent advances in tissue-specific lignin complementation and better understanding of phenylpropanoid transcriptional regulation has made it possible to disentangle lignin modification from perturbations in plant development.
Activation of the NRF2 pathway through gain-of-function mutations or loss-of-function of its suppressor KEAP1 is a frequent finding in lung cancer. NRF2 activation has been reported to alter the ...tumor microenvironment. Here, we demonstrated that NRF2 alters tryptophan metabolism through the kynurenine pathway that is associated with a tumor-promoting, immune suppressed microenvironment. Specifically, proteomic profiles of 47 lung adenocarcinoma (LUAD) cell lines (11
mutant and 36
wild-type) revealed the tryptophan-kynurenine enzyme kynureninase (KYNU) as a top overexpressed protein associated with activated NRF2. The siRNA-mediated knockdown of
, the gene encoding for NRF2, or activation of the NRF2 pathway through siRNA-mediated knockdown of
or via chemical induction with the NRF2-activator CDDO-Me confirmed that NRF2 is a regulator of KYNU expression in LUAD. Metabolomic analyses confirmed KYNU to be enzymatically functional. Analysis of multiple independent gene expression datasets of LUAD, as well as a LUAD tumor microarray demonstrated that elevated KYNU was associated with immunosuppression, including potent induction of T-regulatory cells, increased levels of PD1 and PD-L1, and resulted in poorer survival. Our findings indicate a novel mechanism of NRF2 tumoral immunosuppression through upregulation of KYNU.
BackgroundCitrulline post-translational modification of proteins is mediated by protein arginine deiminase (PADI) family members and has been associated with autoimmune diseases. The role of ...PADI-citrullinome in immune response in cancer has not been evaluated. We hypothesized that PADI-mediated citrullinome is a source of neoantigens in cancer that induces immune response.MethodsProtein expression of PADI family members was evaluated in 196 cancer cell lines by means of indepth proteomic profiling. Gene expression was assessed using messenger RNA data sets from The Cancer Genome Atlas. Immunohistochemical analysis of PADI2 and peptidyl-citrulline was performed using breast cancer tissue sections. Citrullinated 12–34-mer peptides in the putative Major Histocompatibility Complex-II (MHC-II) binding range were profiled in breast cancer cell lines to investigate the relationship between protein citrullination and antigen presentation. We further evaluated immunoglobulin-bound citrullinome by mass spectrometry using 156 patients with breast cancer and 113 cancer-free controls.ResultsProteomic and gene expression analyses revealed PADI2 to be highly expressed in several cancer types including breast cancer. Immunohistochemical analysis of 422 breast tumor tissues revealed increased expression of PADI2 in ER− tumors (p<0.0001); PADI2 protein expression was positively correlated (p<0.0001) with peptidyl-citrulline staining. PADI2 expression exhibited strong positive correlations with a B cell immune signature and with MHC-II-bound citrullinated peptides. Increased circulating citrullinated antigen–antibody complexes occurred among newly diagnosed breast cancer cases relative to controls (p=0.0012).ConclusionsAn immune response associated with citrullinome is a rich source of neoantigens in breast cancer with a potential for diagnostic and therapeutic applications.
Using a combination of mass-spectrometry and aptamer array-based proteomics, we characterized the protein features of circulating extracellular vesicles (EVs) in the context of lung (LUAD) and ...pancreatic ductal (PDAC) adenocarcinomas. We profiled EVs isolated from conditioned media of LUAD and PDAC cell lines to identify EV-associated protein cargoes released by these cancer cell types. Analysis of the resulting data identified LUAD and PDAC specific and pan-adenocarcinoma EV protein signatures. Bioinformatic analyses confirmed enrichment of proteins annotated to vesicle-associated processes and intracellular compartments, as well as representation of cancer hallmark functions and processes. Analysis of upstream regulator networks indicated significant enrichment of TP53, MYC, TGFB1 and KRAS-driven network effectors (
= 1.69 × 10
-2.93 × 10
) manifest in the adenocarcinoma sEV protein cargoes. We extended these findings by profiling the proteome of EVs isolated from lung (
= 15) and pancreatic ductal (
= 6) adenocarcinoma patient plasmas obtained at time of diagnosis, along with EVs derived from matched healthy controls (
= 21). Exploration of these proteomic data revealed abundant protein features in the plasma EVs with capacity to distinguish LUAD and PDAC cases from controls, including features yielding higher performance in the plasma EV isolates relative to unfractionated plasmas.
Small-cell-lung cancer (SCLC) is associated with overexpression of oncogenes including Myc family genes and YAP1 and inactivation of tumor suppressor genes. We performed in-depth proteomic profiling ...of plasmas collected from 15 individuals with newly diagnosed early stage SCLC and from 15 individuals before the diagnosis of SCLC and compared findings with plasma proteomic profiles of 30 matched controls to determine the occurrence of signatures that reflect disease pathogenesis. A total of 272 proteins were elevated (area under the receiver operating characteristic curve (AUC) ≥ 0.60) among newly diagnosed cases compared to matched controls of which 31 proteins were also elevated (AUC ≥ 0.60) in case plasmas collected within one year prior to diagnosis. Ingenuity Pathway analyses of SCLC-associated proteins revealed enrichment of signatures of oncogenic MYC and YAP1. Intersection of proteins elevated in case plasmas with proteomic profiles of conditioned medium from 17 SCLC cell lines yielded 52 overlapping proteins characterized by YAP1-associated signatures of cytoskeletal re-arrangement and epithelial-to-mesenchymal transition. Among samples collected more than one year prior to diagnosis there was a predominance of inflammatory markers. Our integrated analyses identified novel circulating protein features in early stage SCLC associated with oncogenic drivers.
Abstract
Mediator is a multisubunit transcriptional co-regulator that is involved in the regulation of an array of processes including plant metabolism. The pathways regulated by Mediator-dependent ...processes include those for the synthesis of phenylpropanoids (MED5), cellulose (MED16), lipids (MED15 and CDK8), and the regulation of iron homeostasis (MED16 and MED25). Traditional genetic and biochemical approaches laid the foundation for our understanding of Mediator function, but recent transcriptomic and metabolomic studies have provided deeper insights into how specific subunits cooperate in the regulation of plant metabolism. In this review, we highlight recent developments in the investigation of Mediator and plant metabolism, with particular emphasis on the large-scale biology studies of med mutants.
Abstract
Mediator is a multisubunit transcriptional co-regulator that is involved in the regulation of an array of processes including plant metabolism. The pathways regulated by Mediator-dependent ...processes include those for the synthesis of phenylpropanoids (MED5), cellulose (MED16), lipids (MED15 and CDK8), and the regulation of iron homeostasis (MED16 and MED25). Traditional genetic and biochemical approaches laid the foundation for our understanding of Mediator function, but recent transcriptomic and metabolomic studies have provided deeper insights into how specific subunits cooperate in the regulation of plant metabolism. In this review, we highlight recent developments in the investigation of Mediator and plant metabolism, with particular emphasis on the large-scale biology studies of med mutants.
Abstract
Mediator is a multisubunit transcriptional co-regulator that is involved in the regulation of an array of processes including plant metabolism. The pathways regulated by Mediator-dependent ...processes include those for the synthesis of phenylpropanoids (MED5), cellulose (MED16), lipids (MED15 and CDK8), and the regulation of iron homeostasis (MED16 and MED25). Traditional genetic and biochemical approaches laid the foundation for our understanding of Mediator function, but recent transcriptomic and metabolomic studies have provided deeper insights into how specific subunits cooperate in the regulation of plant metabolism. In this review, we highlight recent developments in the investigation of Mediator and plant metabolism, with particular emphasis on the large-scale biology studies of med mutants.
Plant metabolic networks are precisely regulated by the spatial and temporal expression of suites of genes. Among the various transcription (co)factors, a multi‐protein complex, Mediator has been ...identified as a hub for transcription regulation. The core Mediator complex, comprising the head, middle and tail domains, functions as a bridge between transcription factors and basal transcription machinery, whereas the CDK8 kinase module plays a repressive regulatory role. It is still unclear, however, how the kinase module represses target genes especially in planta. Using a forward genetic screen, our lab determined that MED5, an Arabidopsis Mediator tail subunit, is required for maintaining phenylpropanoid homeostasis. A semi‐dominant mutant (ref4‐3) characterized by a single amino acid substitution in MED5a (G383S) was isolated as a strong suppressor of phenylpropanoid pathway, indicated by decreased soluble phenylpropanoid metabolite accumulation, reduced lignin content and dwarfism. In contrast, knocking out MED5a and MED5b (med5a/5b) results in the accumulation of increased levels of phenylpropanoid pathway derivatives. Considering that the CDK8 kinase module is a repressive module in Mediator, we tested the hypothesis that Arabidopsis MED5 represses phenylpropanoid pathway by interacting with CDK8.
To test this hypothesis, CDK8 knockout lines (cdk8‐1) were crossed with ref4‐3, and the phenylpropanoid content of the resulting double mutants was evaluated. In ref4‐3 cdk8‐1 plants, the concentration of sinapate esters and total lignin content are as low as they are in ref4‐3, yet the growth defect in ref4‐3 is largely rescued. To further determine the genes targeted by MED5 and CDK8 in maintaining proper plant growth, we performed an RNA‐seq analysis which showed that a majority of the genes involved in salicylic acid (SA) biosynthesis and signaling are up‐regulated in ref4‐3 compared to wild type and ref4‐3 cdk8‐1. Consistent with this observation, both free and total SA, both of which have been previously implicated in dwarfing in lignin‐modified plants, are accumulated to elevated levels in ref4‐3 but not in wild type and ref4‐3 cdk8‐1. Nevertheless, blocking SA biosynthesis is not sufficient to restore the growth deficiency of ref4‐3, suggesting that the hyperaccumulation of SA is more likely to be an effect rather than a cause for its dwarf phenotype.
At the molecular level, to elucidate how ref4‐3 regulates downstream gene targets in either a CDK8‐dependent manner, we performed RNA polymerase II (Pol II) ChIP‐seq analysis in wild type, ref4‐3, cdk8‐1 and ref4‐3 cdk8‐1. The Pol II ChIP‐seq data may provide additional information for us to identify the genes that are causative for the dwarfism of ref4‐3.
Taken together, this study identifies the genetic interaction between MED5 and CDK8 in Arabidopsis, which enhances our understanding in the function of Mediator in plant metabolism and its role in lignin‐modification‐induced dwarfism.
Support or Funding Information
Department of Energy; Global Climate and Energy Project
This is from the Experimental Biology 2018 Meeting. There is no full text article associated with this published in The FASEB Journal.
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