Subset Of Targets Research Articles

IL-32 and IL-34 in hepatocellular carcinoma.

Hepatocellular carcinoma (HCC) remains a major challenge to clinicians due to its unacceptably high mortality and morbidity. The etiology of HCC is multi-faceted, including viral infection, alcoholism and non-alcoholic fatty liver disease. Dysregulated host immunity contributes to tumorigenesis among these susceptible individuals with pre-existing condition(s). IL-32 and IL-34 are key cytokines driving the development of chronic inflammatory conditions such as rheumatoid arthritis, systemic lupus erythematosus, as well as chronic liver diseases. IL-32 and IL-34 play an important role augmenting the development of HCC, due to their direct influence over host inflammation, however, new roles for these cytokines in HCC are emerging. Here we comprehensively review the latest research for IL-32 and IL-34 in HCC, identifying a subset of potential therapeutic targets for use in precision medicine.

The solution structure of Dead End bound to AU-rich RNA reveals an unusual mode of tandem RRM-RNA recognition required for mRNA regulation

Dead End (DND1) is an RNA-binding protein essential for germline development through its role in post-transcriptional gene regulation. The molecular mechanisms behind selection and regulation of its targets are unknown. Here, we present the solution structure of DND1’s tandem RNA Recognition Motifs (RRMs) bound to AU-rich RNA. The structure reveals how an NYAYUNN element is specifically recognized, reconciling seemingly contradictory sequence motifs discovered in recent genome-wide studies. RRM1 acts as a main binding platform, including atypical extensions to the canonical RRM fold. RRM2 acts cooperatively with RRM1, capping the RNA using an unusual binding pocket, leading to an unusual mode of tandem RRM-RNA recognition. We show that the consensus motif is sufficient to mediate upregulation of a reporter gene in human cells and that this process depends not only on RNA binding by the RRMs, but also on DND1’s double-stranded RNA binding domain (dsRBD), which is dispensable for binding of a subset of targets in cellulo. Our results point to a model where DND1 target selection is mediated by a non-canonical mode of AU-rich RNA recognition by the tandem RRMs and a role for the dsRBD in the recruitment of effector complexes responsible for target regulation.

Mutant Ras and inflammation-driven skin tumorigenesis is suppressed via a JNK-iASPP-AP1 axis.

SummaryConcurrent mutation of a RAS oncogene and the tumor suppressor p53 is common in tumorigenesis, and inflammation can promote RAS-driven tumorigenesis without the need to mutate p53. Here, we show, using a well-established mutant RAS and an inflammation-driven mouse skin tumor model, that loss of the p53 inhibitor iASPP facilitates tumorigenesis. Specifically, iASPP regulates expression of a subset of p63 and AP1 targets, including genes involved in skin differentiation and inflammation, suggesting that loss of iASPP in keratinocytes supports a tumor-promoting inflammatory microenvironment. Mechanistically, JNK-mediated phosphorylation regulates iASPP function and inhibits iASPP binding with AP1 components, such as JUND, via PXXP/SH3 domain-mediated interaction. Our results uncover a JNK-iASPP-AP1 regulatory axis that is crucial for tissue homeostasis. We show that iASPP is a tumor suppressor and an AP1 coregulator.

Best Response Intersection: An Optimal Algorithm for Interdiction Defense

We define the interdiction defense problem as a game over a set of targets with three stages: a first stage where the defender protects a subset of targets, a second stage where the attacker observes the defense decision and attacks a subset of targets, and a third stage where the defender optimizes a system using only the surviving targets. We present a novel algorithm for optimally solving such problems that uses repeated calls to an attacker’s best response oracle. For cases where the defender can defend at most k targets and the attacker can attack at most z targets, we prove that the algorithm makes at most [Formula: see text] calls to the oracle. In application to the direct current optimal power flow problem, we present a new mixed integer programming formulation with bounded big-M values to function as a best response oracle. We use this oracle along with the algorithm to solve a defender-attacker-defender version of the optimal power flow problem. On standard test instances, we find solutions with larger values of k and z than shown in previous studies and with runtimes that are an order of magnitude faster than column and constraint generation. Funding: This work was sponsored in part by the U.S. Department of Energy Office of Electricity’s Advanced Grid Modeling (AGM) program. This work was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory [Contract DE-AC52-07NA27344].

Ataxin-2, Twenty-four, and Dicer-2 are components of a noncanonical cytoplasmic polyadenylation complex

Cytoplasmic polyadenylation is a mechanism to promote mRNA translation in a wide variety of biological contexts. A canonical complex centered around the conserved RNA-binding protein family CPEB has been shown to be responsible for this process. We have previously reported evidence for an alternative noncanonical, CPEB-independent complex in <i>Drosophila</i>, of which the RNA-interference factor Dicer-2 is a component. Here, we investigate Dicer-2 mRNA targets and protein cofactors in cytoplasmic polyadenylation. Using RIP-Seq analysis, we identify hundreds of potential Dicer-2 target transcripts, ∼60% of which were previously found as targets of the cytoplasmic poly(A) polymerase Wispy, suggesting widespread roles of Dicer-2 in cytoplasmic polyadenylation. Large-scale immunoprecipitation revealed Ataxin-2 and Twenty-four among the high-confidence interactors of Dicer-2. Complex analyses indicated that both factors form an RNA-independent complex with Dicer-2 and mediate interactions of Dicer-2 with Wispy. Functional poly(A)-test analyses showed that Twenty-four and Ataxin-2 are required for cytoplasmic polyadenylation of a subset of Dicer-2 targets. Our results reveal components of a novel cytoplasmic polyadenylation complex that operates during <i>Drosophila</i> early embryogenesis.

The high mobility group protein HMG20A cooperates with the histone reader PHF14 to modulate TGFβ and Hippo pathways.

High mobility group (HMG) proteins are chromatin regulators with essential functions in development, cell differentiation and cell proliferation. The protein HMG20A is predicted by the AlphaFold2 software to contain three distinct structural elements, which we have functionally characterized: i) an amino-terminal, intrinsically disordered domain with transactivation activity; ii) an HMG box with higher binding affinity for double-stranded, four-way-junction DNA than for linear DNA; and iii) a long coiled-coil domain. Our proteomic study followed by a deletion analysis and structural modeling demonstrates that HMG20A forms a complex with the histone reader PHF14, via the establishment of a two-stranded alpha-helical coiled-coil structure. siRNA-mediated knockdown of either PHF14 or HMG20A in MDA-MB-231 cells causes similar defects in cell migration, invasion and homotypic cell–cell adhesion ability, but neither affects proliferation. Transcriptomic analyses demonstrate that PHF14 and HMG20A share a large subset of targets. We show that the PHF14-HMG20A complex modulates the Hippo pathway through a direct interaction with the TEAD1 transcription factor. PHF14 or HMG20A deficiency increases epithelial markers, including E-cadherin and the epithelial master regulator TP63 and impaired normal TGFβ-trigged epithelial-to-mesenchymal transition. Taken together, these data indicate that PHF14 and HMG20A cooperate in regulating several pathways involved in epithelial–mesenchymal plasticity.

Harnessing nucleic acid technologies for human health on earth and in space

Nucleic acid therapeutics are a versatile class of sequence-programmable drugs that offer a robust and clinically viable strategy to modulate expression or correct genetic defects contributing to disease. The majority of drugs currently on the market target proteins; however, proteins only represent a subset of possible disease targets. Nucleic acid therapeutics allow intuitive engagement with genome sequences providing a more direct way to target many diseases at their genetic root cause. Their clinical success depends on platform technologies which can support durable and well tolerated pharmacological activity in a given tissue. Nucleic acid drugs possess a potent combination of target specificity and adaptability required to advance drug development for many diseases. As these therapeutic technologies mature, their clinical applications can also expand access to personalized therapies for patients with rare or solo genetic diseases. Spaceflight crew members exposed to the unique hazards of spaceflight, especially those related to galactic cosmic radiation (GCR) exposure, represent another patient subset who may also benefit from nucleic acid drugs as countermeasures. In this review, we will discuss the various classes of RNA- and DNA-targeted nucleic acid drugs, provide an overview of their present-day clinical applications, and describe major strategies to improve their delivery, safety, and overall efficacy.

Evaluating sustainability impacts of critical mineral extractions: Integration of life cycle sustainability assessment and SDGs frameworks

AbstractThe extraction of critical minerals used in clean technologies has profound impacts on sustainable development goals (SDGs). Life cycle sustainability assessment (LCSA) is used to evaluate the sustainability impacts of products and services, but few frameworks exist to support SDGs assessment for the “green minerals” extraction. Here, we propose a mining‐specific framework identifying linkages between LCSA and SDGs, along with a process to integrate methods and data. As a proof of concept, we assess the LCSA performance and local‐community level SDG impacts of a nickel mining project in Indonesia. Integrating remote sensing, media sources, stakeholder's data, and expert opinion, we find that LCSA encompasses all 17 goals but only a subset of targets and indicators. The study highlights the need to incorporate indigenous people's perspectives in both LCSA and SDG assessments, and points to priority areas for improving life cycle sustainability and SDG outcomes: fighting corruption, protecting cultural heritage, and reducing greenhouse gas emissions. We suggest that this framework can inform corporate social responsibility activities, as well as consumer choices for low‐carbon technologies.

DAP5 drives translation of specific mRNA targets with upstream ORFs in human embryonic stem cells.

Death associated protein 5 (DAP5/eIF4G2/NAT1) is a member of the eIF4G translation initiation factors that has been shown to mediate noncanonical and/or cap-independent translation. It is essential for embryonic development and for differentiation of embryonic stem cells (ESCs), specifically its ability to drive translation of specific target mRNAs. In order to expand the repertoire of DAP5 target mRNAs, we compared ribosome profiles in control and DAP5 knockdown (KD) human ESCs (hESCs) to identify mRNAs with decreased ribosomal occupancy upon DAP5 silencing. A cohort of 68 genes showed decreased translation efficiency in DAP5 KD cells. Mass spectrometry confirmed decreased protein abundance of a significant portion of these targets. Among these was KMT2D, a histone methylase previously shown to be essential for ESC differentiation and embryonic development. We found that nearly half of the cohort of DAP5 target mRNAs displaying reduced translation efficiency of their main coding sequences upon DAP5 KD contained upstream open reading frames (uORFs) that are actively translated independently of DAP5. This is consistent with previously suggested mechanisms by which DAP5 mediates leaky scanning through uORFs and/or reinitiation at the main coding sequence. Crosslinking protein–RNA immunoprecipitation experiments indicated that a significant subset of DAP5 mRNA targets bound DAP5, indicating that direct binding between DAP5 protein and its target mRNAs is a frequent but not absolute requirement for DAP5-dependent translation of the main coding sequence. Thus, we have extended DAP5's function in translation of specific mRNAs in hESCs by a mechanism allowing translation of the main coding sequence following upstream translation of short ORFs.

ABL kinases regulate translation in HER2+ cells through Y-box-binding protein 1 to facilitate colonization of the brain.

SUMMARYPatients with human epidermal growth factor receptor 2-positive (HER2+/ERBB2) breast cancer often present with brain metastasis. HER2-targeted therapies have not been successful to treat brain metastases in part due to poor blood-brain barrier (BBB) penetrance and emergence of resistance. Here, we report that Abelson (ABL) kinase allosteric inhibitors improve overall survival and impair HER2+ brain metastatic outgrowth in vivo. Mechanistically, ABL kinases phosphorylate the RNA-binding protein Y-box-binding protein 1 (YB-1). ABL kinase inhibition disrupts binding of YB-1 to the ERBB2 mRNA and impairs translation, leading to a profound decrease in HER2 protein levels. ABL-dependent tyrosine phosphorylation of YB-1 promotes HER2 translation. Notably, loss of YB-1 inhibits brain metastatic outgrowth and impairs expression of a subset of ABL-dependent brain metastatic targets. These data support a role for ABL kinases in the translational regulation of brain metastatic targets through YB-1 and offer a therapeutic target for HER2+ brain metastasis patients.

Fixed Parameter Algorithms and Hardness of Approximation Results for the Structural Target Controllability Problem

Recent research has revealed new and unexpected applications of network control science within biomedicine, pharmacology, and medical therapeutics. These new insights and new applications generated in turn a rediscovery of some old, unresolved algorithmic problems. One of these problems is the Structural Target Control optimization problem, known in previous literature also as Structural Output Controllability problem, which is defined as follows. Given a directed network and a target subset of nodes, the task is to select a small (or the smallest) set of nodes from which the target can be independently controlled, i.e., there exists a set of paths from the selected set of nodes (called driver nodes) to the target nodes such that no two paths intersect at the same distance from their targets. Recently, Structural Target Control optimization problem has been shown to be NP-hard, and several heuristic algorithms were introduced and analyzed, both on randomly generated networks, and on biomedical ones. In this paper, we show that the Structural Target Controllability problem is fixed parameter tractable when parameterized by the number of target nodes. We also prove that the problem is hard to approximate at a factor better than O(log n). Taking into consideration the real case formulations of this problem we identify two more parameters which are naturally constrained by smaller bounds: the maximal length of a controlling path and the size of the set of nodes from which the control can start. With these new parameters we provide an approximation algorithm which is of exponential complexity in the size of the set of nodes from which the control can start and polynomial in all the other parameters.

Fixed Parameter Algorithms and Hardness of Approximation Results for the Structural Target Controllability Problem

Recent research has revealed new and unexpected applications of network control science within biomedicine, pharmacology, and medical therapeutics. These new insights and new applications generated in turn a rediscovery of some old, unresolved algorithmic problems. One of these problems is the Structural Target Control optimization problem, known in previous literature also as Structural Output Controllability problem, which is defined as follows. Given a directed network and a target subset of nodes, the task is to select a small (or the smallest) set of nodes from which the target can be independently controlled, i.e., there exists a set of paths from the selected set of nodes (called driver nodes) to the target nodes such that no two paths intersect at the same distance from their targets. Recently, Structural Target Control optimization problem has been shown to be NP-hard, and several heuristic algorithms were introduced and analyzed, both on randomly generated networks, and on biomedical ones. In this paper, we show that the Structural Target Controllability problem is fixed parameter tractable when parameterized by the number of target nodes. We also prove that the problem is hard to approximate at a factor better than O(log n). Taking into consideration the real case formulations of this problem we identify two more parameters which are naturally constrained by smaller bounds: the maximal length of a controlling path and the size of the set of nodes from which the control can start. With these new parameters we provide an approximation algorithm which is of exponential complexity in the size of the set of nodes from which the control can start and polynomial in all the other parameters.

Abstract 162: Identification of novel targets of Serine/arginine-rich protein-specific kinase 2

Abstract Altered metabolism is one of the hallmarks of cancer cells, supporting aberrant proliferation and survival in nutrient scarce and stressful environments. The reprogrammed metabolism supports the acquisition of malignant traits, increasing cellular fitness and providing a selective advantage in tumorigenesis. Multiple signaling cascades converge to regulate cancer cell metabolism to maintain a delicate balance between anabolic and catabolic processes, with the overall goal to fuel ATP production, biosynthesis of macromolecules and maintaining redox balance. Specifically, 70% of human cancers have hyperactivated mechanistic target of rapamycin (mTOR) signaling, the master regulator of cellular metabolism. As an important signaling node, mTOR complex 1(mTORC1) integrates upstream stimuli such as growth factors, amino acids and oxygen levels to regulate a myriad of anabolic processes including protein and nucleotide synthesis, RNA biogenesis and lipid metabolism, thereby promoting cell growth. The highly proliferative state of cancer cells, coupled with a change in energy demands, forces these cells to rewire their cellular metabolism to increase production of cellular building blocks like proteins, lipids and nucleotides. De novo lipogenesis provides lipids which act as an integral component of the plasma membrane as well as functioning as signaling molecules. In addition to promoting various anabolic processes, our lab has demonstrated that mTORC1-activated serine/arginine-rich protein-specific kinase 2 (SRPK2) phosphorylates splicing factors that stabilize lipogenic transcripts, protecting them from nonsense-mediated decay and thereby increasing de novo lipogenesis. This is in contrast to another serine/arginine-rich protein-specific kinase 1 (SRPK1), which is not regulated by mTORC1. Inhibition of the mTORC1-SRPK2 signaling axis blunts de novo lipogenesis and impedes tumor growth in several tumor xenograft models. SRPK2 overexpression is also observed in lung and colon cancers, suggesting SRPK2 may promote the growth of some human tumors. Despite the emerging role for SRPK2 in tumor growth, very few substrates of this kinase are known. We conducted a phospho-proteomics screen to identify novel substrates of SRPK1 and SRPK2. While some of the targets we identified are regulated in an mTORC1-dependent manner, many appear to be regulated independent of mTORC1, such as PTP1B, EGLN1 and EI24. We hypothesize that these mTORC1-independent targets could be SRPK1-dependent revealing potential distinct branches of SRPK signaling. Future studies will focus on not only validating a subset of these novel targets and their role in tumor growth, but also on exploring mTORC1-dependent and independent SRPK signaling. Citation Format: Kripa Shobana Ganesh, Bethany Schaffer, Gina Lee, Jared Johnson, Tomer M. Yaron, Noah Dephoure, Lewis C. Cantley, John Blenis. Identification of novel targets of Serine/arginine-rich protein-specific kinase 2 [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 162.

Abstract 5724: Loss of SWI/SNF chromatin remodeling alters NRF2 signaling in human cancers

Abstract Next-generation sequencing studies of lung cancer has shown a significant number of mutations in two previously unrecognized regulatory pathways. Activating mutations, the NF-E2-related factor 2 (NFE2L2, NRF2) transcription factor induces constitutive expression of cytoprotective and redox maintenance genes. Inactivating mutations in members of the SWI/SNF chromatin-remodeling complex, especially SMARCA4 (BRG1) and ARID1A, lead to changes in nucleosome positioning and gene expression. Here, we show that loss of SWI/SNF complex function activated a subset of NRF2-mediated transcriptional targets. Using a series of isogenic NSCLC lines with reduced or depleted BRG1 and/or BRM expression, we observed significantly increased expression and protein levels of the NRF2-target genes HMOX1 and GSTM4. RNA sequencing of BRG1-proficient and -deficient cell lines confirmed changes in KEAP1-NRF2 target gene expression as well as identified novel targets of the SWI/SNF complex. Importantly, low BRG1 expression levels in primary human NSCLC tumors correlated with increased NRF2-target gene expression. In addition to BRG1 levels, we examined loss of ARID1A across primary human tumors and found ARID1A deficiency was associated with altered NRF2 signaling. The tumors with the highest frequency of altered NRF2 signaling were lung squamous (LUSC) and head and neck squamous (HNSCC), cancers strongly associated with environmental toxicants. Interestingly ARID1A loss depressed NRF2 signaling in LUSC while amplifying it in HNSCC, an observation we are exploring mechanistically in cell line knock out models. Our data demonstrate that loss of SWI/SNF in lung cancer results in activation of the NRF2/KEAP1 pathway and increased expression of a subset of its downstream targets. These data provide an additional molecular explanation for why patients harboring SWI/SNF mutations show a poor prognosis. Our results also potentially link mutations in SWI/SNF complex components, that occur in >20% of human cancers, with exposure to environmental toxicants. A better understanding of these mechanism may yield novel insights into the design of targeted treatment modalities for human lung cancers. Citation Format: Vinh Nguyen, Travis Shranck, Samera Hamad, Bernard Weissman. Loss of SWI/SNF chromatin remodeling alters NRF2 signaling in human cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5724.

HER3 expression in metastatic colorectal cancer: Defining the clinicomolecular profile of an emerging target.

3588 Background: The success of tailored systemic therapies in treating distinct molecular subsets of patients (e.g., deficient mismatch repair, BRAF mutant, HER2 amplified) has spurred further exploration of novel targetable subsets within the heterogeneous landscape of metastatic colorectal cancer (mCRC). Human epidermal growth factor receptor 3 [HER3 (ErbB3)], a member of the HER (ErbB) receptor tyrosine kinase family, plays an important role in tumorigenesis and metastases and has emerged as a promising therapeutic target in a diverse array of cancers. For example, patritumab deruxtecan (U3-1402; HER3-DXd) is a HER3-directed antibody drug conjugate that has demonstrated clinically meaningful antitumor activity and acceptable safety profiles in metastatic breast cancer and EGFR-mutated non-small cell lung cancer. There is limited data, however, on the clinicopathological characterization of HER3 expression in mCRC. Methods: Tissue samples (surgical-metastatectomy) (N = 115) were obtained from a clinical cohort of patients (N = 99) with histologically proven mCRC and liver metastases who underwent liver resection with/without perioperative systemic chemotherapy. HER3 expression was analyzed on whole-mount preparations by immunohistochemistry (IHC). Staining was performed and visualized using the HER3 (D22C5) XP Rabbit-mAb (Cell Signaling Technology). Patients were categorized based on membranous intensity score as follows: Low with IHC 0 (absence of staining or staining in < 10% of tumor cells), 1+ (faint/barely perceptible staining in ≥10% of tumor cells) or 2+ (weak to moderate staining in ≥10% of tumor cells), or High with IHC 3+ (strong staining in ≥10% of tumor cells). Clinicomolecular and treatment data, including gender, tumor sidedness, mutational status (RAS or BRAF), and prior chemotherapy were collected by review of patient electronic medical records. Chi-squared (or Fisher’s exact) test were used to determine associations between groups. Overall survival (OS) was calculated using Kaplan-Meier method and compared using log-rank tests. Results: Among 99 analyzed patients, 98 were evaluable for HER3 expression. Of these 25.5%, 26.5%, 40.8% and 7.2% showed HER3 IHC scores of 3+, 2+, 1+ and 0, respectively. No significant association was seen with HER3 expression and clinicopathological variables, mutational status, or prior treatment. Among patients with 2 samples analyzed from the same liver surgery, there was a moderate level of heterogeneity with concordance of 78.5% (kappa 0.43). Patients with high HER3 expression had poorer OS (5-year OS: 52%; median: 90.2 months) compared to low HER3 expression (5-year OS: 85%; median: not reached). Conclusions: In this large cohort of mCRC, HER3 expression was observed in 92.8% of patients and across diverse clinical and molecular features, supporting HER3 as a promising targetable biomarker in a large subset of mCRC.

Insights of clinical significance from solid tumor profiles with FoundationOneCDx.

3126 Background: FoundationOne CDx (F1CDx) is a US FDA-approved companion diagnostic test to identify patients who may benefit from treatment in accordance with the approved therapeutic product labeling for 28 drug therapies. Tumor profiling with F1CDx detects genomic findings with evidence of additional clinical significance. This study analyzes the breadth and impact of clinical decision insights from F1CDx clinical reports across solid tumors. Methods: F1CDx consecutive reports (n = 109,695) were retrospectively analyzed for the type and frequency of clinically significant predictive, prognostic, and diagnostic genomic alterations and signatures in common cancer types and across solid tumors. Predictive markers were defined as therapeutically relevant markers in drug labels or NCCN guidelines or targets of ESCAT evidence Tier I/II (Mateo et al., 2018; PMID: 30137196). Prognostic and diagnostic markers were determined in accordance with NCCN, ESMO, or WHO guidelines. We also describe the frequency and targets of interventional clinical trials with targeted therapies or immune checkpoint inhibitors that were matched to tumor profiles based on clinical or strong preclinical evidence. Results: Predictive genomic findings of clinical significance were identified in more than half of non-small cell lung cancer (NSCLC), colorectal cancer (CRC), breast cancer (BC), and melanoma (MEL) tissue samples; over a third of ovarian cancer (OC), urothelial carcinoma (UC), and head and neck squamous cell carcinoma (HNSCC); approximately a fourth of prostate cancer (PC), gastro-esophageal adenocarcinoma (GEA), cholangiocarcinoma (CA), and glioma (GL) samples; and one in 18 pancreatic adenocarcinoma (PA) samples (Table). Prognostic markers were reported for patients with NSCLC (18%), CRC (10%), BC (16%), PC (25%), CA (8.1%), MEL (24%), GL (74%), or HNSCC (7.1%). Diagnostic markers were frequently detected for patients with GL and noted for patients with BC, GEA, or MEL (Table). Interventional clinical trials were evidence-matched to most F1CDx tumor profiles (89%, range 82% in PC to 99% in PA), with the targets of approved therapies accounting for a small subset of targets in clinical development. Conclusions: F1CDx reports support clinical decision making by interpreting predictive, prognostic, and diagnostic markers according to professional guidelines as well as investigational markers for the enrollment in clinical trials. [Table: see text]

Signatures of plant defense response specificity mediated by herbivore-associated molecular patterns in legumes.

Chewing herbivores activate plant defense responses through a combination of mechanical wounding and elicitation by herbivore-associated molecular patterns (HAMPs). HAMPs are wound response amplifiers; however, specific defense outputs may also exist that strictly require HAMP-mediated defense signaling. To investigate HAMP-mediated signaling and defense responses, we characterized cowpea (Vigna unguiculata) transcriptome changes following elicitation by inceptin, a peptide HAMP common in Lepidoptera larvae oral secretions. Following inceptin treatment, we observed large-scale reprogramming of the transcriptome consistent with three different response categories: (i) amplification of mechanical wound responses, (ii) temporal extension through accelerated or prolonged responses, and (iii) examples of inceptin-specific elicitation and suppression. At both early and late timepoints, namely 1 and 6 h, large sets of transcripts specifically accumulated following inceptin elicitation. Further early inceptin-regulated transcripts were classified as reversing changes induced by wounding alone. Within key signaling- and defense-related gene families, inceptin-elicited responses included target subsets of wound-induced transcripts. Transcripts displaying the largest inceptin-elicited fold changes included transcripts encoding terpene synthases (TPSs) and peroxidases (POXs) that correspond with induced volatile production and increased POX activity in cowpea. Characterization of inceptin-elicited cowpea defenses via heterologous expression in Nicotiana benthamiana demonstrated that specific cowpea TPSs and POXs were able to confer terpene emission and the reduced growth of beet armyworm (Spodoptera exigua) herbivores, respectively. Collectively, our present findings in cowpea support a model where HAMP elicitation both amplifies concurrent wound responses and specifically contributes to the activation of selective outputs associated with direct and indirect antiherbivore defenses.

Cell-cell adhesions in embryonic stem cells regulate the stability and transcriptional activity of β-catenin.

E-cadherin (CDH1) is involved in maintaining cell-cell adhesions in embryonic stem cells (ESCs). However, its function in the context of cell fate decisions is largely unknown. Using mouse ESCs (mESCs), we demonstrate that E-cadherin and β-catenin interact at the membrane and continue to do so upon internalization within the cell. Cdh1-/- mESCs failed to form tight colonies, with altered differentiation, marker expression and retention of pluripotency factors during differentiation. Interestingly, Cdh1-/- mESCs showed dramatically reduced β-catenin levels. Transcriptional profiling of Cdh1-/- mESCs displayed a significant alteration in the expression of a subset of β-catenin targets in a cell state- and GSK3β-dependent manner. Our findings hint at hitherto unknown roles played by E-cadherin in regulating the activity of β-catenin in ESCs.

Loss of RNA binding protein HuD facilitates the production of the senescence-associated secretory phenotype

HuD, an RNA binding protein, plays a role in the regulation of gene expression in certain types of cells, including neuronal cells and pancreatic β-cells, via RNA metabolism. Its aberrant expression is associated with the pathogenesis of several human diseases. To explore HuD-mediated gene regulation, stable cells expressing short hairpin RNA against HuD were established using mouse neuroblastoma Neuro2a (N2a) cells, which displayed enhanced phenotypic characteristics of cellular senescence. Two approaches, RNA immunoprecipitation (RNA IP)-NanoString profiling and cytokine array, were used to subsequently identify a subset of putative HuD targets that act as senescence-associated secretory phenotype (SASP), including C-C motif ligand 2 (CCL2), CCL20, C-X-C motif chemokine ligand 2 (CXCL2), and interleukin-6 (IL-6). Here, we further demonstrated that HuD regulates the expression of CCL2, a SASP candidate upregulated in cells following HuD knockdown, by binding to the 3′-untranslated region (UTR) of Ccl2 mRNA. Downregulation of HuD increased the level of CCL2 in N2a cells and the brain tissues of HuD knockout (KO) mice. Exposure to γ-irradiation induced cellular senescence in N2a cells and HuD knockdown facilitated stress-induced cellular senescence. Our results reveal that HuD acts as a novel regulator of CCL2 expression, and its aberrant expression may contribute to cellular senescence by regulating SASP production.

Autoantibodies Against Proteins Previously Associated With Autoimmunity in Adult and Pediatric Patients With COVID-19 and Children With MIS-C.

The antibody profile against autoantigens previously associated with autoimmune diseases and other human proteins in patients with COVID-19 or multisystem inflammatory syndrome in children (MIS-C) remains poorly defined. Here we show that 30% of adults with COVID-19 had autoantibodies against the lung antigen KCNRG, and 34% had antibodies to the SLE-associated Smith-D3 protein. Children with COVID-19 rarely had autoantibodies; one of 59 children had GAD65 autoantibodies associated with acute onset of insulin-dependent diabetes. While autoantibodies associated with SLE/Sjögren’s syndrome (Ro52, Ro60, and La) and/or autoimmune gastritis (gastric ATPase) were detected in 74% (40/54) of MIS-C patients, further analysis of these patients and of children with Kawasaki disease (KD), showed that the administration of intravenous immunoglobulin (IVIG) was largely responsible for detection of these autoantibodies in both groups of patients. Monitoring in vivo decay of the autoantibodies in MIS-C children showed that the IVIG-derived Ro52, Ro60, and La autoantibodies declined to undetectable levels by 45-60 days, but gastric ATPase autoantibodies declined more slowly requiring >100 days until undetectable. Further testing of IgG and/or IgA antibodies against a subset of potential targets identified by published autoantigen array studies of MIS-C failed to detect autoantibodies against most (16/18) of these proteins in patients with MIS-C who had not received IVIG. However, Troponin C2 and KLHL12 autoantibodies were detected in 2 of 20 and 1 of 20 patients with MIS-C, respectively. Overall, these results suggest that IVIG therapy may be a confounding factor in autoantibody measurements in MIS-C and that antibodies against antigens associated with autoimmune diseases or other human proteins are uncommon in MIS-C.