Oncogenic lncRNA downregulates cancer cell antigen presentation and intrinsic tumor suppression.

How tumor cells genetically lose antigenicity and evade immune checkpoints remains largely elusive. We report that tissue-specific expression of the human long noncoding RNA LINK-A in mouse mammary glands initiates metastatic mammary gland tumors, which phenotypically resemble human triple-negative breast cancer (TNBC). LINK-A expression facilitated crosstalk between phosphatidylinositol-(3,4,5)-trisphosphate and inhibitory G-protein-coupled receptor (GPCR) pathways, attenuating protein kinase A-mediated phosphorylation of the E3 ubiquitin ligase TRIM71. Consequently, LINK-A expression enhanced K48-polyubiquitination-mediated degradation of the antigen peptide-loading complex (PLC) and intrinsic tumor suppressors Rb and p53. Treatment with LINK-A locked nucleic acids or GPCR antagonists stabilized the PLC components, Rb and p53, and sensitized mammary gland tumors to immune checkpoint blockers. Patients with programmed ccll death protein-1(PD-1) blockade-resistant TNBC exhibited elevated LINK-A levels and downregulated PLC components. Hence we demonstrate lncRNA-dependent downregulation of antigenicity and intrinsic tumor suppression, which provides the basis for developing combinational immunotherapy treatment regimens and early TNBC prevention.

lncRNA directs cooperative epigenetic regulation downstream of chemokine signals.

lncRNAs are known to regulate a number of different developmental and tumorigenic processes. Here, we report a role for lncRNA BCAR4 in breast cancer metastasis that is mediated by chemokine-induced binding of BCAR4 to two transcription factors with extended regulatory consequences. BCAR4 binding of SNIP1 and PNUTS in response to CCL21 releases the SNIP1's inhibition of p300-dependent histone acetylation, which in turn enables the BCAR4-recruited PNUTS to bind H3K18ac and relieve inhibition of RNA Pol II via activation of the PP1 phosphatase. This mechanism activates a noncanonical Hedgehog/GLI2 transcriptional program that promotes cell migration. BCAR4 expression correlates with advanced breast cancers, and therapeutic delivery of locked nucleic acids (LNAs) targeting BCAR4 strongly suppresses breast cancer metastasis in mouse models. The findings reveal a disease-relevant lncRNA mechanism consisting of both direct coordinated protein recruitment and indirect regulation of transcription factors.

Radiofrequency Ablation of the Infrapatellar Branch of the Saphenous Nerve for the Treatment of Chronic Anterior Inferomedial Knee Pain.

INTRO: Genicular nerve radiofrequency ablation (GNRFA) is an effective treatment for chronic knee pain related to osteoarthritis. It is often utilized when conservative management has failed and patients wish to avoid arthroplasty, are poor surgical candidates due to comorbid medical conditions, or in those suffering from persistent pain after arthroplasty. The classic targets for GNRFA include the superior lateral genicular nerve, superior medial genicular nerve, and inferior medial genicular nerve but multiple anatomic studies have demonstrated additional sensory innervation to the knee. OBJECTIVE: In this research article, we propose an image-guided technique that can safely target the infrapatellar branch of the saphenous nerve which also provides sensory innervation to the anterior capsule. PROPOSAL: The proposed technique includes variations for conventional bipolar radiofrequency ablation, cooled radiofrequency ablation, dual-tined bipolar radiofrequency ablation, and monopolar radiofrequency ablation using a long axis approach. The described technique is based on updated anatomic studies and takes into account safety concerns such as thermal risk to the skin and/or pes anserine tendons and breaching of the synovial cavity. CONCLUSION: Future clinical research should be performed to confirm the safety and effectiveness of this specific approach.

A Stereocontrolled Synthesis of a Phosphorothioate Cyclic Dinucleotide-Based STING Agonist.

We describe a stereodefined synthesis of the newly identified non-natural phosphorothioate cyclic dinucleotide (CDN) STING agonist, BMT-390025. The new route avoids the low-yielding racemic approach using P(III)-based reagents, and the stereospecific assembly of the phosphorothioate linkages are forged via the recently invented P(V)-based platform of the so-called PSI (Ψ) reagent system. This P(V) approach allows for the complete control of chirality of the P-based linkages and enabled conclusive evidence of the absolute configuration. The new approach offers robust procedures for preparing the stereodefined CDN in eight steps starting from advanced nucelosides, with late-stage direct drop isolations and telescoped steps enabling an efficient scale-up that proceeded in an overall 15% yield to produce multigram amounts of the CDN.

Substituted diaryl ether compounds as retinoic acid-related orphan Receptor-γt (RORγt) agonists.

The discovery of a series of substituted diarylether compounds as retinoic acid related orphan receptor γt (RORγt) agonists is described. Compound 1 was identified from deck mining as a RORγt agonist. Hit-to-lead optimization led to the identification of lead compound 5, which possesses improved potency (10x). Extensive SAR exploration led to the identification of a potent and selective compound 22, that demonstrated an improved pharmacokinetic profile and a dose-dependent pharmacodynamic response. However, when dosed in a MC38 syngeneic tumor model, no evidence of efficacy was observed. ©2020 Elsevier Science Ltd. All rights reserved.

Recognition of synthetic glycopeptides by HIV-1 broadly neutralizing antibodies and their unmutated ancestors.

Current HIV-1 vaccines elicit strain-specific neutralizing antibodies. Broadly neutralizing antibodies (BnAbs) are not induced by current vaccines, but are found in plasma in ∼20% of HIV-1-infected individuals after several years of infection. One strategy for induction of unfavored antibody responses is to produce homogeneous immunogens that selectively express BnAb epitopes but minimally express dominant strain-specific epitopes. Here we report that synthetic, homogeneously glycosylated peptides that bind avidly to variable loop 1/2 (V1V2) BnAbs PG9 and CH01 bind minimally to strain-specific neutralizing V2 antibodies that are targeted to the same envelope polypeptide site. Both oligomannose derivatization and conformational stabilization by disulfide-linked dimer formation of synthetic V1V2 peptides were required for strong binding of V1V2 BnAbs. An HIV-1 vaccine should target BnAb unmutated common ancestor (UCA) B-cell receptors of naïve B cells, but to date no HIV-1 envelope constructs have been found that bind to the UCA of V1V2 BnAb PG9. We demonstrate herein that V1V2 glycopeptide dimers bearing Man5GlcNAc2 glycan units bind with apparent nanomolar affinities to UCAs of V1V2 BnAbs PG9 and CH01 and with micromolar affinity to the UCA of a V2 strain-specific antibody. The higher-affinity binding of these V1V2 glycopeptides to BnAbs and their UCAs renders these glycopeptide constructs particularly attractive immunogens for targeting subdominant HIV-1 envelope V1V2-neutralizing antibody-producing B cells.

LncRNA BCAR4 wires up signaling transduction in breast cancer.

Long noncoding RNAs (lncRNAs) are dysregulated in many cancer types and are believed to play crucial roles in regulating several hallmarks of cancer biology. Currently, most studies support the concept that lncRNAs are involved in either transcriptional or post-transcriptional processes via binding/targeting epigenetic modifiers or hRNP complexes. The discovery of new biological functions of lncRNA and novel RNA binding proteins suggests that lncRNAs may be implicated in a broad spectrum of biological processes such as signal transduction, allosteric regulation of cytoplasmic enzymatic activities, among other potential processes. In a recent report that we have made, based on open-ended lncRNA pulldown technology and a series of systematic analyses, we suggest that lncRNAs also play critical roles in the regulation of noncanonical Hedgehog/GLI 2 signal transduction pathways in cancer cells, which further broadens the scope of known lncRNA functions and aids in the discovery and design of more effective and evidence-based therapeutic targets for the treatment of human cancers and other diseases.

Perioperative Risk Factors for Persistent Postsurgical Pain After Inguinal Hernia Repair: Systematic Review and Meta-Analysis.

Persistent postsurgical pain (PPSP) is one of the most bothersome and disabling long-term complications after inguinal hernia repair surgery. Understanding perioperative risk factors that contribute to PPSP can help identify high-risk patients and develop risk-mitigation approaches. The objective of this study was to systematically review and meta-analyze risk factors that contribute to PPSP after inguinal hernia repair. The literature search resulted in 303 papers included in this review, 140 of which were used for meta-analyses. Our results suggest that younger age, female sex, preoperative pain, recurrent hernia, postoperative complications, and postoperative pain are associated with a higher risk of PPSP. Laparoscopic techniques reduce the PPSP occurrence compared to anterior techniques such as Lichtenstein repair, and tissue-suture techniques such as Shouldice repair. The use of fibrin glue for mesh fixation was consistently associated with lower PPSP rates compared to tacks, staples, and sutures. Considerable variability was observed with PPSP assessment and reporting methodology in terms of study design, follow-up timing, clarity of pain definition, as well as pain intensity or interference threshold. High or moderate risk of bias in at least one domain was noted in >75% of studies. These may limit the generalizability of our results. Future studies should assess and report comprehensive preoperative and perioperative risk factors for PPSP adjusted for confounding factors, and develop risk-prediction models to drive stratified PPSP-mitigation trials and personalized clinical decision-making. PERSPECTIVE: This systematic review and meta-analysis summarizes the current evidence on risk factors for persistent pain after inguinal hernia repair. The findings can help identify patients at risk and test personalized risk-mitigation approaches to prevent pain. PROSPERO REGISTRATION: htttps://www.crd.york.ac.uk/prospero/display_record.php?RecordID=154663.

Chemical synthesis of highly congested gp120 V1V2 N-glycopeptide antigens for potential HIV-1-directed vaccines.

Critical to the search for an effective HIV-1 vaccine is the development of immunogens capable of inducing broadly neutralizing antibodies (BnAbs). A key first step in this process is to design immunogens that can be recognized by known BnAbs. The monoclonal antibody PG9 is a BnAb that neutralizes diverse strains of HIV-1 by targeting a conserved carbohydrate-protein epitope in the variable 1 and 2 (V1V2) region of the viral envelope. Important for recognition are two closely spaced N-glycans at Asn(160) and Asn(156). Glycopeptides containing this synthetically challenging bis-N-glycosylated motif were prepared by convergent assembly, and were shown to be antigenic for PG9. Synthetic glycopeptides such as these may be useful for the development of HIV-1 vaccines based on the envelope V1V2 BnAb epitope.

Expanding the limits of isonitrile-mediated amidations: on the remarkable stereosubtleties of macrolactam formation from synthetic seco-cyclosporins.

The scope of isonitrile-mediated amide bond-forming reactions is further explored in this second-generation synthetic approach to cyclosporine (cyclosporin A). Both type I and type II amidations are utilized in this effort, allowing access to epimeric cyclosporins A and H from a single precursor by variation of the coupling reagents. This work lends deeper insight into the relative acylating ability of the formimidate carboxylate mixed anhydride (FCMA) intermediate, while shedding light on the far-reaching impact of remote stereochemical changes on the effective preorganization of seco-cyclosporins.

A fascinating journey into history: exploration of the world of isonitriles en route to complex amides.

We describe herein our recent explorations in the field of isonitrile chemistry. An array of broadly useful coupling methodologies has been developed for the formation of peptidyl and glycopeptidyl amide bonds. We further describe the application of these methods to the syntheses of complex systems, including the cyclic peptide cyclosporine A, constrained peptide systems, and heterocycles.

On the synthesis of conformationally modified peptides through isonitrile chemistry: implications for dealing with polypeptide aggregation.

A method for introducing a dimethyleneoxy constraint joining the N atoms of two consecutive amino acids in the context of a polypeptide has been developed. This constraint can profoundly affect the tendency of a polypeptide to suffer aggregation and desolubilization, and it can be readily removed under mild conditions.

Synthetic studies toward (+)-cortistatin A.

We describe herein the synthesis of a late-stage intermediate en route to cortistatin A. Key transformations included a Snieckus-like cascade sequence culminating in a 6π-electrocyclization, an alkylative dearomatization, and the stereoselective functionalization of the cortistatin A-ring. While the total synthesis we sought was not accomplished, the work sets the stage for several approaches to the preparation of novel analogs via diverted total synthesis.

IMRT planning parameter optimization for spine stereotactic radiosurgery.

Spine stereotactic radiosurgery (SSRS) is a noninvasive treatment for metastatic spine lesions. MD Anderson Cancer Center reports a quality assurance (QA) failure rate approaching 15% for SSRS cases, which we hypothesized is due to difficulties in accurately calculating dose resulting from a large number of small-area segments. Clinical plans typically use 9 beams with an average of 10 segments per beam and minimum segment area of 2-3 cm2. The purpose of this study was to identify a set of intensity-modulated radiation therapy (IMRT) planning parameters that attempts to optimize the balance among QA passing rate, plan quality, dose calculation accuracy, and delivery time for SSRS plans. Using Pinnacle version 9.10, we evaluated the effects of 2 IMRT parameters: maximum number of segments and minimum segment area. Initial evaluation of the data revealed that 5 segments per beam along with minimum segment area of 4 cm2 and 4 monitor units (MU) per segment (5-4-4 plans) was the most promising. IMRT QA was performed using a PTW OCTAVIUS 4D phantom with a 2D detector array. Our data showed no significant plan quality change with decreased number of segments and increased minimum segment area. The average coverage of GTV and CTV was 82.5 ± 13% (clinical) vs 82.5 ± 13% (5-4-4) and 92.3 ± 8% (clinical) vs 91.5 ± 8% (5-4-4). Maximum point dose to cord was 11.4 ± 3.5 Gy (clinical) vs 11.0 ± 4.0 Gy (5-4-4). Total plan delivery time was decreased by an average of 11.3% for the 5-4-4 plans. For IMRT QA, the gamma index passing rate (distance to agreement: 2.5 mm, local dose difference: 4%) for the original plans vs the 5-4-4 plans averaged 90.3% and 91.9%, respectively. In conclusion, IMRT parameters of 5 segments per beam and 4 cm2 minimum segment areas provided a better balance of plan quality, delivery efficiency, and plan dose calculation accuracy for SSRS.

PTEN-induced partial epithelial-mesenchymal transition drives diabetic kidney disease.

Epithelial-mesenchymal transition (EMT) contributes significantly to interstitial matrix deposition in diabetic kidney disease (DKD). However, detection of EMT in kidney tissue is impracticable, and anti-EMT therapies have long been hindered. We reported that phosphatase and tensin homolog (PTEN) promoted transforming growth factor beta 1 (TGF-ß), sonic hedgehog (SHH), connective tissue growth factor (CTGF), interleukin 6 (IL-6), and hyperglycemia-induced EMT when PTEN was modified by a MEX3C-catalyzed K27-linked polyubiquitination at lysine 80 (referred to as PTENK27-polyUb). Genetic inhibition of PTENK27-polyUb alleviated Col4a3 knockout-, folic acid-, and streptozotocin-induced (STZ-induced) kidney injury. Serum and urine PTENK27-polyUb concentrations were negatively correlated with glomerular filtration rate (GFR) for diabetic patients. Mechanistically, PTENK27-polyUb facilitated dephosphorylation and protein stabilization of TWIST, SNAI1, and YAP in renal epithelial cells, leading to enhanced EMT. We identified that a small molecule, triptolide, inhibited MEX3C-catalyzed PTENK27-polyUb and EMT of renal epithelial cells. Treatment with triptolide reduced TWIST, SNAI1, and YAP concurrently and improved kidney health in Col4a3 knockout-, folic acid-injured disease models and STZ-induced, BTBR ob/ob diabetic nephropathy models. Hence, we demonstrated the important role of PTENK27-polyUb in DKD and a promising therapeutic strategy that inhibited the progression of DKD.

LncRNAs-directed PTEN enzymatic switch governs epithelial-mesenchymal transition.

Despite the structural conservation of PTEN with dual-specificity phosphatases, there have been no reports regarding the regulatory mechanisms that underlie this potential dual-phosphatase activity. Here, we report that K27-linked polyubiquitination of PTEN at lysines 66 and 80 switches its phosphoinositide/protein tyrosine phosphatase activity to protein serine/threonine phosphatase activity. Mechanistically, high glucose, TGF-ß, CTGF, SHH, and IL-6 induce the expression of a long non-coding RNA, GAEA (Glucose Aroused for EMT Activation), which associates with an RNA-binding E3 ligase, MEX3C, and enhances its enzymatic activity, leading to the K27-linked polyubiquitination of PTEN. The MEX3C-catalyzed PTENK27-polyUb activates its protein serine/threonine phosphatase activity and inhibits its phosphatidylinositol/protein tyrosine phosphatase activity. With this altered enzymatic activity, PTENK27-polyUb dephosphorylates the phosphoserine/threonine residues of TWIST1, SNAI1, and YAP1, leading to accumulation of these master regulators of EMT. Animals with genetic inhibition of PTENK27-polyUb, by a single nucleotide mutation generated using CRISPR/Cas9 (PtenK80R/K80R), exhibit inhibition of EMT markers during mammary gland morphogenesis in pregnancy/lactation and during cutaneous wound healing processes. Our findings illustrate an unexpected paradigm in which the lncRNA-dependent switch in PTEN protein serine/threonine phosphatase activity is important for physiological homeostasis and disease development.

IMRT planning parameter optimization for spine stereotactic radiosurgery.

Spine stereotactic radiosurgery (SSRS) is a noninvasive treatment for metastatic spine lesions. MD Anderson Cancer Center reports a quality assurance (QA) failure rate approaching 15% for SSRS cases, which we hypothesized is due to difficulties in accurately calculating dose resulting from a large number of small-area segments. Clinical plans typically use 9 beams with an average of 10 segments per beam and minimum segment area of 2 to 3 cm2. The purpose of this study was to identify a set of intensity-modulated radiation therapy (IMRT) planning parameters that attempts to optimize the balance among QA passing rate, plan quality, dose calculation accuracy, and delivery time for SSRS plans. Using Pinnacle version 9.10, we evaluated the effects of 2 IMRT parameters: maximum number of segments and minimum segment area. Initial evaluation of the data revealed that 5 segments per beam along with minimum segment area of 4 cm2 and 4 minimum Monitor Units (MU) per segment (544 plans) was the most promising. IMRT QA was performed using an OCTAVIUS 4D phantom with a 2D detector array. Our data showed no significant plan quality change with decreased number of segments and increased minimum segment area. The average coverage of GTV and CTV was 82.5 ± 13% (clinical) vs 82.5 ± 13% (544) and 92.3 ± 8% (clinical) vs 91.5 ± 8% (544). Maximum point dose to cord was 11.4 ± 3.5 Gy (clinical) vs 11.0 ± 4.0 Gy (544). Total plan delivery time was decreased by an average of 11.3% for the 544 plans. In addition, the QA passing rate for the original plan vs the 544 plan averaged 90.3% and 91.9%, respectively. In conclusion, IMRT parameters of 5 segments per beam and 4 cm2 minimum segment area provided a better balance of plan quality, delivery efficiency, and plan dose calculation accuracy for SSRS.

The Genomic Landscape and Pharmacogenomic Interactions of Clock Genes in Cancer Chronotherapy.

Cancer chronotherapy, treatment at specific times during circadian rhythms, endeavors to optimize anti-tumor effects and to lower toxicity. However, comprehensive characterization of clock genes and their clinical relevance in cancer is lacking. We systematically characterized the alterations of clock genes across 32 cancer types by analyzing data from The Cancer Genome Atlas, Cancer Therapeutics Response Portal, and The Genomics of Drug Sensitivity in Cancer databases. Expression alterations of clock genes are associated with key oncogenic pathways, patient survival, tumor stage, and subtype in multiple cancer types. Correlations between expression of clock genes and of other genes in the genome were altered in cancerous versus normal tissues. We identified interactions between clock genes and clinically actionable genes by analyzing co-expression, protein-protein interaction, and chromatin immunoprecipitation sequencing data and also found that clock gene expression is correlated to anti-cancer drug sensitivity in cancer cell lines. Our study provides a comprehensive analysis of the circadian clock across different cancer types and highlights potential clinical utility of cancer chronotherapy.

Expression of Long Noncoding RNA YIYA Promotes Glycolysis in Breast Cancer.

Long noncoding RNA (lncRNA) is yet to be linked to cancer metabolism. Here, we report that upregulation of the lncRNA LINC00538 (YIYA) promotes glycolysis, cell proliferation, and tumor growth in breast cancer. YIYA is associated with the cytosolic cyclin-dependent kinase CDK6 and regulated CDK6-dependent phosphorylation of the fructose bisphosphatase PFK2 (PFKFB3) in a cell-cycle-independent manner. In breast cancer cells, these events promoted catalysis of glucose 6-phosphate to fructose-2,6-bisphosphate/fructose-1,6-bisphosphate. CRISPR/Cas9-mediated deletion of YIYA or CDK6 silencing impaired glycolysis and tumor growth in vivo In clinical specimens of breast cancer, YIYA was expressed in approximately 40% of cases where it correlated with CDK6 expression and unfavorable survival outcomes. Our results define a functional role for lncRNA in metabolic reprogramming in cancer, with potential clinical implications for its therapeutic targeting.Significance: These findings offer a first glimpse into how a long-coding RNA influences cancer metabolism to drive tumor growth. Cancer Res; 78(16); 4524-32. ©2018 AACR.

A Pan-cancer Analysis of the Expression and Clinical Relevance of Small Nucleolar RNAs in Human Cancer.

Increasing evidence has demonstrated that small nucleolar RNAs (snoRNAs) play important roles in tumorigenesis. We systematically investigated the expression landscape and clinical relevance of snoRNAs in >10,000 samples across 31 cancer types from The Cancer Genome Atlas. We observed overall elevated expression of snoRNAs and their ribonucleoproteins in multiple cancer types. We showed complex regulation of snoRNA expression by their host genes, copy number variation, and DNA methylation. Unsupervised clustering revealed that the snoRNA expression subtype is highly concordant with other molecular/clinical subtypes. We further identified 46 clinically relevant snoRNAs and experimentally demonstrated functional roles of SNORD46 in promoting cell proliferation, migration, and invasion. We developed a user-friendly data portal, SNORic, to benefit the research community. Our study highlights the significant roles of snoRNAs in the development and implementation of biomarkers or therapeutic targets for cancer and provides a valuable resource for cancer research.