Studies of Infection and Experimental Reactivation by Recombinant VZV with Mutations in Virally-Encoded Small Non-Coding RNA

Locked-nucleotide analog antagonists (LNAA) to four varicella zoster virus small non-coding RNA (VZVsncRNA 10-13) derived from the mRNA of the open reading frame (ORF) 61 gene individually reduce VZV replication in epithelial cells and fibroblasts. To study the potential roles VZVsncRNA 10-13 have in neuronal infection we generated two recombinant VZV; one in which 8 nucleotides were changed in VZVsncRNA10 without altering the encoded residues of ORF61 (VZVsnc10MUT) and a second containing a 12-nucleotide deletion of the sequence common to VZVsncRNA12 and 13, located in the ORF61 mRNA leader sequence (VZVsnc12-13DEL). Both were developed from a VZV BAC with a green fluorescent protein (GFP) reporter fused to the N terminal of the capsid protein encoded by ORF23. The growth of both mutant VZV in epithelial cells and fibroblasts was similar to that of the parental recombinant virus. Both mutants established productive infections and experimental latency in neurons derived from human embryonic stem cells (hESC). However, neurons that were latently infected with both VZV mutant viruses showed impaired ability to reactivate when given stimuli that successfully reactivated the parental virus. These results suggest that these VZVsncRNA may have a role in VZV latency maintenance and/or reactivation. The extension of these studies and confirmation of such roles could potentially inform the development of a non-reactivating, live VZV vaccine.

Layered SnS2/porous nickel foil based Schottky junction: An excellent ammonia sensor at room temperature

In recent years, layered materials has gained immense attention in the field of gas sensing owing to their extraordinary electrical, optical and catalytic properties. Their gas sensing performance can further be improved by switching from ohmic to schottky based sensor due to exponential change of conductance in analyte environment. In most of the Schottky based gas sensor, the surface of the sensing material is covered by metal electrode which reduces the sensing performance. Herein, we have fabricated 2D SnS₂ (thickness: 5.62 ± 1.26 nm) based Schottky junction for ammonia detection operated at room temperature using porous nickel foil which allows the analyte molecule to maximize the interaction with the sensing material. We have compared the performance of the Schottky junction sensor with that of SnS₂ based ohmic sensor. The Schottky junction based sensor has 140.7 times higher response than SnS₂ based ohmic sensor at 360 ppm. The response of the sensor exhibits exponential behavior with ammonia concentration which is explained by estimated barrier height modulation from 0.83 eV (in air) to 0.69 eV (at 225 ppm). In addition, the long term stability over six months of the sensor makes it a promising candidate for practical ammonia sensor operated at room temperature.

Threats of climate change and land use patterns enhance the susceptibility of future floods in India

The main objective of this work is the future prediction of the floods in India due to climate and land change. Human activity and related carbon emissions are the primary cause of land use and climate change, which has a substantial impact on extreme weather conditions, such as floods. This study presents high-resolution flood susceptibility maps of different future periods (up to 2100) using a combination of remote sensing data and GIS modelling. To quantify the future flood susceptibility various flood causative factors, Global circulation model (GCM) rainfall and land use and land cover (LULC) data are envisaged. The present flood susceptibility model has been evaluated through receiver operating characteristic (ROC) curve, where area under curve (AUC) value shows the 91.57% accuracy of this flood susceptibility model and it can be used for future flood susceptibility modelling. Based on the projected LULC, rainfall and flood susceptibility, the results of the study indicating maximum monthly rainfall will increase by approximately 40-50 mm in 2100, while the conversion of natural vegetation to agricultural and built-up land is about 0.071 million sq. km. and the severe flood event area will increase by up to 122% (0.15 million sq. km) from now on.

NIR irradiation enhances the apoptotic potentiality of quinacrine-gold hybrid nanoparticles by modulation of HSP-70 in oral cancer stem cells

Cancer stem cells (CSCs) are the tumor cell subpopulations that can self-renew, differentiate, initiate and maintain tumor growth. CSCs are frequently drug-resistant, resulting in tumor recurrence, metastasis, and angiogenesis. Herein, using in vitro oral squamous cell carcinoma (OSCC) CSCs and in vivo xenograft mice model, we have systematically studied the apoptotic potentiality of quinacrine-gold hybrid nanoparticle (QAuNP) and its underlying mechanism after NIR irradiation. QAuNP + NIR caused DNA damage and induced apoptosis in SCC-9-CSCs by deregulating mitochondrial membrane potential (ΔΨm) and activation of ROS. Upregulation of CASPASE-3 and DR-5/DR-4 and reduction of heat shock protein (HSP-70) up to 5-fold were also noticed upon the treatment. The increased expression of DR-5 and CASPASE-3 and decreased expression of HSP-70, CD-44 and Ki-67 were also noted in the xenograft mice treated with QAuNP + NIR + TRAIL. Thus, data suggest that the combined treatment enhances apoptosis in OSCC-CSCs by modulating HSP-70 in the DISC.

Angiographic Localisation of Culprit Vessel in Non ST Elevated Acute Coronary Syndrome

Introduction: Coronary Artery Disease (CAD) is a major cause of mortality and morbidity. Among Acute Coronary Syndrome (ACS), Non-ST Elevated Acute Coronary Syndrome (NSTE-ACS) continues to increase. Unlike ST Elevated Myocardial Infarction (STEMI), association of ischemic changes in Electrocardiogram (ECG) with culprit lesion localisation in NSTE-ACS has not been well reported. Aim: To investigate the association between ECG abnormalities and angiographic localisation of culprit vessel in patients of NSTE-ACS. Materials and Methods: This observational, prospective study was conducted in SCB Medical college and Hospital, Cuttack, Odisha, India, from December 2019 to November 2020. A total of 200 eligible patients of newly diagnosed NSTE- ACS were included. Demographic and risk factor assessment, clinical examination and routine blood investigations were done. All patients had an admission Electrocardiogram (ECG), Echocardiography (Echo) and Coronary Angiography (CAG) done within 72 hours of admission. Admission ECG was associated with CAG to assess predictive value in localisation of culprit vessel. Sensitivity, Specificity, Positive Predictive Value (PPV), Negative Predictive Value (NPV), Likelihood Ratio (LR), pre and post-test odds of individual ECG findings were assessed. Statistical Package for the Social Sciences (SPSS) version 24.0 was used for statistical analysis. results: Sensitivity, specificity, PPV, NPV, LR+, pretest odds and post-test odds of anterior wall, inferior wall, lateral wall and augmented Vector Right (aVR) group ECG changes in predicting Left Anterior Descending (LAD), Right Coronary Artery (RCA), Left Circumflex (LCx) and Left main or Triple Vessel Disease (LM/TVD) as culprit artery were 75.9%, 90.5%, 91.7%, 73.1%, 7.96, 1.38 and 10.98; 69.1%, 91.5%, 87.8%, 76.9%, 8.14, 0.89 and 7.21; 64%, 93%, 87.3%, 77.4%, 9.10, 0.75 and 6.86 and 69.2%, 96.3%, 90%, 86.7%, 18.66, 0.48 and 8.98, respectively. Sensitivity, specificity, PPV and NPV of anterior and lateral, inferior and lateral and anterior and inferior wall ECG changes in predicting LAD and LCx, RCA and LCx and LAD and RCA as culprit vessels were 75.0%, 82.6%, 27.27% and 97.43%; 47.0%, 88.5%, 27.5% and 94.73% and 53.3%, 83.2%, 20.51% and 95.65%, respectively. ECG was normal in 31% of which Myocardial Infarction with Non Obstructive Coronary Artery (MINOCA) (34%) and Single Vessel Disease (SVD) (30.6%) were prevalent. MINOCA were mostly seen in normal ECG pattern. conclusion: ECG is a moderately sensitive but highly specific parameter in predicting LAD, LCx, RCA and LM/TVD as culprit vessels in Non ST Segment Elevation Myocardial Infarction- Acute Coronary Syndromes (NSTE-ACS). Double territory ECG changes have a poor association in predicting culprit vessel. However, a good association was noted for (anterior and lateral) wall ECG changes in predicting LAD and LCx as culprit arteries.

Enhanced superconductivity and ferroelectric quantum criticality in plastically deformed strontium titanate

The properties of quantum materials are commonly tuned using experimental variables such as pressure, magnetic field and doping. Here we explore a different approach using irreversible, plastic deformation of single crystals. We show that compressive plastic deformation induces low-dimensional superconductivity well above the superconducting transition temperature (T_c) of undeformed SrTiO₃, with evidence of possible superconducting correlations at temperatures two orders of magnitude above the bulk T_c. The enhanced superconductivity is correlated with the appearance of self-organized dislocation structures, as revealed by diffuse neutron and X-ray scattering. We also observe deformation-induced signatures of quantum-critical ferroelectric fluctuations and inhomogeneous ferroelectric order using Raman scattering. Our results suggest that strain surrounding the self-organized dislocation structures induces local ferroelectricity and quantum-critical dynamics that strongly influence T_c, consistent with a theory of superconductivity enhanced by soft polar fluctuations. Our results demonstrate the potential of plastic deformation and dislocation engineering for the manipulation of electronic properties of quantum materials.

Abstract P097: Comparative single cell transcriptome profiling of primary tumors, CTCs and metastatic sites from a bladder cancer PDX model

Background: A PDX bladder cancer model, BL0293-F563, grows large subcutaneous tumors, spontaneously metastasizes to the liver and bone, and sheds high numbers of circulating tumor cells (CTCs). This PDX model provides a unique opportunity to explore the relationships between primary tumors, CTCs and metastatic cell subpopulations. Methods: BL0293-F563 tumors (available from the NCI Patient-Derived Models Repository [https://pdmr.cancer.gov/] and originally developed by Jackson Laboratories) were implanted into NSG mice and and primary tumors, metastatic nodules in the liver, and blood were collected at maximal allowable tumor burden. Tumor tissue was dissociated using Miltenyi Tumor Dissociation Kit with OctoDissociator, and Human CTCs were enriched from whole mouse blood through negative selection with anti-mouse CD45 and anti-mouse MHC-1 magnetic beads. Single cell sequencing was done using 10X Genomics 3’ gene expression assay v3.1. Sequencing libraries were prepared using 10X Genomics Chromium and 3’ gene expression kit v3.1. Data processing and analysis was done using 10X Genomics’ Cell Ranger pipeline, Seurat, and consensus non-negative matrix factorization. Results: Using Seurat FindNeighbors, cells in the aggregated dataset were classified into 17 distinct clusters. All clusters were comprised of cells from multiple sites (primary tumor, CTCs, metastases), but three clusters were enriched in CTCs and one cluster was composed of mostly primary tumor cells. All clusters exhibited an epithelial-like gene expression signature score, suggesting that CTC shedding was occurring without prominent epithelial-mesenchymal transition. Consistent with expected differences in oxygenation states, CTC-enriched clusters exhibited a lower hypoxia gene expression score than primary tumor and metastasis-enriched clusters. CTC-enriched clusters also showed higher expression of oxidative phosphorylation genes, suggesting metabolic differences between CTCs and cells from primary tumors and metastases. Based on Human Primary Cell Atlas phenotype prediction, several clusters were associated with stem cell like phenotypes. Additionally, two of three CTC-enriched clusters had elevated expression of mitosis-associated genes, suggesting that at least some populations of CTCs are not quiescent but actively cycling. Conclusions: Utilizing single cell gene expression profiling, we have linked the gene expression profile of CTCs to specific cell subpopulations in primary tumors and metastases. We show that CTC-enriched cell clusters appear to maintain an epithelial phenotype. Subpopulations of CTC cells exhibited enrichment of stemness-associated transcripts and features of active cell cycling.

Citation Format: Tomas Vilimas, Brandie Fullmer, Alyssa Chapman, Li Chen, Ting-Chia Chang, Rini Pauly, Biswajit Das, Chris Karlovich, Yvonne A. Evrard, Howard Stotler, Michelle M. Gottholm-Ahalt, Tara Grinnage-Pulley, Melinda G. Hollingshead, James H. Doroshow, P. Mickey Williams. Comparative single cell transcriptome profiling of primary tumors, CTCs and metastatic sites from a bladder cancer PDX model [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2021 Oct 7-10. Philadelphia (PA): AACR; Mol Cancer Ther 2021;20(12 Suppl):Abstract nr P097.

Ethnobotanical Review of Medicinal Plants Used Against Diarrhea and Dysentery in Northeast India (Assam)

Background:

Since primitive times, plants have been extensively utilized in conventional remedies for primary health care. It is observed that medicinal plants have various bioactive components. It becomes an alternative choice for synthetic medications to treat diarrhea and dysentery, which are the primary waterborne diseases with high mortality rates that bring substantial health threats to global populations.

Objective:

The present review aims to look over the ethnobotanical knowledge for the treatment of diarrhea and dysentery and folklore practices by the people prevailing in Assam.

Methods:

In this perspective, an extensive literature survey was carried out to understand the mechanism, control, and treatment of diarrhea and dysentery in different online academic databases and books. An advanced search was carried out in 'PubMed' and 'Google Scholar' using the term "Phytoconstituents" and "antidiarrheal" along with "Phytoconstituents" and "anti-amoebic".

Results:

Data retrieved from databases were analyzed and interpreted to conclude that in Assam, diarrhea and dysentery are the primary leading causes of mortality among children under five years. It is mainly due to the unhygienic livelihood, unavailability of safe drinking water, unhealthy food, seasonal rainfall, flood, and open defecation. The present investigations reveal that the people of Assam use 39 plant species belonging to 36 families to cure diarrhea and dysentery.

Conclusion:

The present study established the effective use of medicinal plants by various communities in Assam to treat diarrhea and dysentery. Furthermore, it can be used to develop a new therapeutic approach to create new chemical entities (NCE) in drug discovery, which are safe, fruitful, and inexpensive.

An Anti-inflammatory Fe3 O4 -Porphyrin Nanohybrid Capable of Apoptosis through Upregulation of p21 Kinase Inhibitor Having Immunoprotective Properties under Anticancer PDT Conditions

We report the influence of Fe₃ O₄ nanoparticles (NPs) on porphyrins in the development of photosensitizers (PSs) for efficient photodynamic therapy (PDT) and possible post-PDT responses for inflicting cancer cell death. Except for Au, most metal-based nanomaterials are unsuitable for clinical applications. The US Food and Drug Administration and other agencies have approved Feraheme and a few other iron oxide NPs for clinical use, paving the way for novel biocompatible immunoprotective superparamagnetic iron oxide nanohybrids to be developed as nanotherapeutics. A water-soluble nanohybrid, referred to here as E-NP, comprising superparamagnetic Fe₃ O₄ NPs functionalised with tripyridyl porphyrin PS was introduced through a rigid 4-carboxyphenyl linker. As a PDT agent, the efficacy of E-NP toward the AGS cancer cell line showed enhanced photosensitising ability as determined through in vitro photobiological assays. The cellular uptake of E-NPs by AGS cells led to apoptosis by upregulating ROS through cell-cycle arrest and loss of mitochondrial membrane potential. The subcellular localisation of the PSs in mitochondria stimulated apoptosis through upregulation of p21, a proliferation inhibitor capable of preventing tumour development. Under both PDT and non-PDT conditions, this nanohybrid can act as an anti-inflammatory agent by decreasing the production of NO and superoxide ions in murine macrophages, thus minimising collateral damage to healthy cells.

Practice variation in the diagnosis of acute rejection among pediatric heart transplant centers: An analysis of the pediatric heart transplant society (PHTS) registry

BACKGROUND

Freedom from rejection in pediatric heart transplant recipients is highly variable across centers. This study aimed to assess the center variation in methods used to diagnose rejection in the first-year post-transplant and determine the impact of this variation on patient outcomes.

METHODS

The PHTS registry was queried for all rejection episodes in the first-year post-transplant (2010-2019). The primary method for rejection diagnosis was determined for each event as surveillance biopsy, echo diagnosis, or clinical. The percentage of first-year rejection events diagnosed by surveillance biopsy was used to approximate the surveillance strategy across centers. Methods of rejection diagnosis were described and patient outcomes were assessed based on surveillance biopsy utilization among centers.

RESULTS

A total of 3985 patients from 56 centers were included. Of this group, 873 (22%) developed rejection within the first-year post-transplant. Surveillance biopsy was the most common method of rejection diagnosis (71.7%), but practices were highly variable across centers. The majority (73.6%) of first rejection events occurred within 3-months of transplantation. Diagnosis modality in the first-year was not independently associated with freedom from rejection, freedom from rejection with hemodynamic compromise, or overall graft survival.

CONCLUSIONS

Rejection in the first-year after pediatric heart transplant occurs in 22% of patients and most commonly in the first 3 months post-transplant. Significant variation exists across centers in the methods used to diagnose rejection in pediatric heart transplant recipients, however, these variable strategies are not independently associated with freedom from rejection, rejection with hemodynamic compromise, or overall graft survival.

Nectin-4 promotes lymphangiogenesis and lymphatic metastasis in breast cancer by regulating CXCR4-LYVE-1 axis

Tumor-induced lymphangiogenesis promotes tumor progression by generating new lymphatic vessels that helps in tumor dissemination to regional lymph nodes and distant sites. Recently, the role of Nectin-4 in cancer metastasis and angiogenesis has been studied, but its role in lymphangiogenesis is unknown. Here, we systematically delineated the role of Nectin-4 in lymphangiogenesis and its regulation in invasive duct carcinoma (IDC). Nectin-4 expression positively correlated with occurrence risk factors associated with breast cancer (alcohol, smoke, lifestyle habit, etc), CXCR4 expression, and LYVE-1-lymphatic vessel density (LVD). LVD was significantly higher in axillary lymph node (ALN) than primary tumor. Depleting Nectin-4, VEGF-C or both attenuated the important lymphangiogenic marker LYVE-1 expression, tube formation, and migration of ALN derived primary cells. Nectin-4 stimulated the expressions of CXCR4 and CXCL12 under hypoxic conditions in ALN derived primary cells. Further, Nectin-4 augmented expressions of lymphatic metastatic markers (e.g. eNOS, TGF-β, CD-105) and MMPs. Induced expressions of Nectin-4 along with other representative metastatic markers were noted in lymph and blood circulating tumor cells (LCTCs and BCTCs) of local and distant metastatic samples. Thus, Nectin-4 displayed a predominant role in promoting tumor-induced lymphangiogenesis and lymphatic metastasis by modulating CXCR4/CXCL12-LYVE-1- axis.

Indigenous plant protection practices of Tripura, India

BACKGROUND

Traditional plant protection strategies have an integral part of food production system in North Eastern state Tripura, India, which has bestowed with rich heritage and biodiversity. However, there is no comprehensive report on the indigenous plant protection practices (IPPPs) specific to insect and vertebrate pest management, being followed by the inhabitants of the region for centuries. The present study was conducted to investigate, collect, and document the vulnerable IPPP practices followed by the native people from far flung locations of the Tripura.

METHODS

The study aimed to document the IPPP following semi-structured questionnaires, participatory interaction, and direct observations with a total of 200 informants. We have calculated the relative frequencies of citation (RFC) for IPPP and estimated principal component analysis to link the status of IPPP with socio-demographic factors of the informants. The relationship between the field of IPPP used and different covariates (age, education, occupation, gender, location, and house type) was assessed using the Kruskal-Wallis test and Chi-square test. The relationship between adoption level and the respondents' characteristics was analyzed using count regression analysis.

RESULTS

The study found that the status of the IPPP has increased for mitigating pest issues. A total of 39 indigenous practices were recorded specifically to pest management from the ethnic people of Tripura, India. People acquired pretty knowledge about IPPP, and these were inherited from ancestors. The respondents in the study developed notable innovations for the management of many pest issues using locally available resources that warrant cost-effective and eco-friendly. Seed drying before storage to protect grain commodities was the most cited IPPP with a frequency of citation 0.675. In the field of IPPP used, the people primarily practiced agriculture + horticulture + storage category. An important implication from the study is the identification of two IPPP strategies in this region for the first time. Furthermore, the recorded IPPP used field was significantly associated with age, education, occupation, gender, locality, and house type. Likewise, the respondents' socio-demographic variables were coupled considerably with the adoption of specific IPPP.

CONCLUSION

The reported IPPP for alleviating pest problems reflects the wisdom and generosity of the ethnic growers of Tripura, India. The study suggests the IPPP has strong potential in an integrated pest management approach passed down from generation to generation. The vulnerable practices largely remained unexplored due to inadequate scientific scrutiny and authenticity, yet in danger of being lost if not documented systematically. This study provides the first step toward accessing the valuable technology of untapped Tripura in IPPP and could be viable in paving action paradigm for their preservation, diffusion, and application with advanced pest management options.

Locked-nucleotide antagonists to varicella zoster virus small non-coding RNA block viral growth and have potential as an anti-viral therapy

Herpes zoster (HZ) remains a significant health burden with millions of cases in North America and Europe annually. HZ is frequently followed by long-term pain or post-herpetic neuralgia (PHN). Although effective vaccines for HZ are available, currently used nucleotide analogues often have limited effectiveness against HZ and especially PHN, so there remains a need for additional antiviral therapies for HZ. We recently identified a population of small non-coding RNA (sncRNA) encoded by Varicella Zoster Virus (VZV) and showed that single locked-nucleic acid antagonists (LNAA) to some sncRNA can modulate VZV replication in cell culture. In this work, we explored the antiviral effects of combinations of LNAA oligonucleotides targeting VZVsncRNA. Combinations of LNAA targeting three VZVsncRNA encoded in and near a critical viral regulatory gene were additive, achieving 96 % reduction in virus growth in a cell line. VZV growth was also inhibited by more than 90 % in primary human skin fibroblast cultures by individual and combinations of LNAA to VZVsncRNA. The inhibition by VZVsncRNA was specific and not a consequence of innate immune responses since LNAA to a different VZVsncRNA enhanced VZV growth. Targeted VZVsncRNA lack homologous sequences in the human transcriptome suggesting that LNAA to them would have reduced cytotoxicity if used as therapeutics. These results support further development of oligonucleotides targeting VZVsncRNA as a novel treatment for HZ.

Exploration of Benzo[b]carbazole-6,11-diones as anticancer agents: Synthesis and studies of hTopoIIα inhibition and apoptotic effects

Two series of (hetero)arylamino-naphthoquinones and benzo-fused carbazolequinones were considered for study with the rationale that related structural motifs are present in numerous drugs, clinical trial agents, natural products and hTopoIIα inhibitors. Total 42 compounds were synthesized by reactions including dehydrogenative CN and Pd-catalyzed CC bond forming transformations. These compounds were screened against numerous cancer cells including highly metastatic one (MCF-7, MDA-MB-231, H-357 and HEK293T), and normal cells (MCF 10A). Some of the active compounds were evaluated for clonogenic cell survival and apoptotic effects in cancer cells (DAPI nuclear staining, Comet assay, Annexin-V-FITC/PI dual staining, flow cytometry, and western blot analysis with relevant proteins). All compounds were tested for hTopoIIα inhibitory activity. The investigated series compounds showed important properties like significant apoptotic antiproliferation in cancer cells with cell cycle arrest at S-phase and downregulation of NF- κβ signaling cascade, relatively less cytotoxicity to normal cells, and hTopoIIα inhibition with more efficiency compared to an anticancer drug etoposide.

Safety, Antitumor Activity, and Biomarker Analysis in a Phase I Trial of the Once-daily Wee1 Inhibitor Adavosertib (AZD1775) in Patients with Advanced Solid Tumors

PURPOSE

The Wee1 kinase inhibitor adavosertib abrogates cell-cycle arrest, leading to cell death. Prior testing of twice-daily adavosertib in patients with advanced solid tumors determined the recommended phase II dose (RPh2D). Here, we report results for once-daily adavosertib.

PATIENTS AND METHODS

A 3 + 3 dose-escalation design was used, with adavosertib given once daily on days 1 to 5 and 8 to 12 in 21-day cycles. Molecular biomarkers of Wee1 activity, including tyrosine 15-phosphorylated Cdk1/2 (pY15-Cdk), were assessed in paired tumor biopsies. Whole-exome sequencing and RNA sequencing of remaining tumor tissue identified potential predictive biomarkers.

RESULTS

Among the 42 patients enrolled, the most common toxicities were gastrointestinal and hematologic; dose-limiting toxicities were grade 4 hematologic toxicity and grade 3 fatigue. The once-daily RPh2D was 300 mg. Six patients (14%) had confirmed partial responses: four ovarian, two endometrial. Adavosertib plasma exposures were similar to those from twice-daily dosing. On cycle 1 day 8 (pre-dose), tumor pY15-Cdk levels were higher than baseline in four of eight patients, suggesting target rebound during the day 5 to 8 dosing break. One patient who progressed rapidly had a tumor WEE1 mutation and potentially compensatory PKMYT1 overexpression. Baseline CCNE1 overexpression occurred in both of two responding patients, only one of whom had CCNE1 amplification, and in zero of three nonresponding patients.

CONCLUSIONS

We determined the once-daily adavosertib RPh2D and observed activity in patients with ovarian or endometrial carcinoma, including two with baseline CCNE1 mRNA overexpression. Future studies will determine whether CCNE1 overexpression is a predictive biomarker for adavosertib.

Abstract 3012: Patient-derived models of rare cancers in the National Cancer Institute's patient-derived models repository

There is an unmet need for preclinical models of rare cancers and rare disease sub-types. The National Cancer Institute's Patient-Derived Models Repository (NCI PDMR; https://pdmr.cancer.gov) is developing quality-controlled, early-passage, clinically-annotated patient-derived tumor xenografts (PDXs), in vitro tumor cell cultures (PDCs), cancer associated fibroblasts (CAFs), and patient-derived organoids (PDOrg) and has focused on addressing unmet needs in the preclinical model space including developing models from adult and pediatric patients with rare cancers. To date, NCI has created and molecularly characterized over 150 preclinical models of rare cancer including indications such as Hurthle cell carcinoma, osteosarcomas, Merkel cell carcinomas, salivary gland cancers, synovial sarcomas, and carcinosarcomas. Rare cancer models developed to date will be reviewed and their histopathologic and molecular characteristics compared to that reported in the clinical setting. A pipeline to identify fusion proteins in these rare cancers such as the Ewing sarcoma EWSR1-FLI1 fusion and NAB2-STAT6 fusions in solitary fibrous tumors (SFT) has been implemented. Four malignant peripheral nerve sheath tumors (MPNST) PDX models are available for researches; these models were developed from patients diagnosed between the ages of 37-68. At the time of model development, two patients were treatment naïve and two had prior radiotherapy. Two of the MPNST PDX models have NF1 oncogenic mutations, three have deep deletions in CDKN2A/B, and three have a mutation in either EED or SUZ12 consistent with the reported molecular characteristics of patients with MPNST. Also of clinical relevance, of two mesothelioma models available, one carries an NF2 driver mutation and the other BAP1 and LATS2 and a PDX model for Hurthle cell carcinoma has wide-spread loss of heterozygosity (LOH 80%). Models for other rare cancers are in development, including four cholangiocarcinoma PDXs with histopathologic confirmation that are currently being expanded for molecular characterization and distribution. Funded by NCI Contract No. HHSN261200800001E

Citation Format: Cindy R. Timme, Sergio Y. Alcoser, Devynn Breen, John Carter, Ting-Chia Chang, Alice Chen, Li Chen, Kristen Cooley, Biswajit Das, Emily Delaney, Michelle A. Eugeni, Michelle M. Gottholm-Ahalt, Tara Grinnage-Polley, Jenna Hull, Chris Karlovich, Kimberly Klarmann, Shahanawaz Jiwani, Candace Mallow, Chelsea McGlynn, Justine Mills, Malorie Morris, Michael Mullendore, Dianne Newton, Tia Shearer, Jesse Stottlemyer, Shannon Uzelac, Thomas Walsh, P. Mickey Williams, Yvonne A. Evrard, Melinda G. Hollingshead, James H. Doroshow. Patient-derived models of rare cancers in the National Cancer Institute's patient-derived models repository [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 3012.

Abstract 3010: Single agent response comparisons in a large-scale, preclinical trial of rare cancer PDXs by the National Cancer Institute's patient-derived models repository

The National Cancer Institute's Patient-Derived Models Repository (NCI PDMR; https://pdmr.cancer.gov) is performing a large-scale preclinical study with 39 patient-derived xenograft (PDX) models of rare cancers (including mesothelioma, MPNST, osteosarcoma, Merkel cell carcinoma) treated with 56 novel therapeutic combinations (targeted and cytotoxic agents) in an exploratory, n-of-4 arm, study design. Drug combinations with additive activity may undergo clinical evaluation in patients with rare cancers. PDX tumors are treated with a set of 8 combinations plus relevant vehicle controls while in parallel enough PDXs are serially passaged for the next passage and drug set. Every serial passage undergoes several quality control assessments that serve as go/no-go criteria. Combinations that show promising responses (e.g., regression or durable tumor growth inhibition) are repeated along with the single agent arms to determine if the response is driven by the combination or only one of the agents. We are currently at the half-way point in the overall study and here report interim results for the early combination agents that have single agent data for comparison. In a combination of a VEGFi and EGFRi, 6/37 models achieved a partial regression (30% shrinkage for more than one consecutive time point) and 17/37 had tumor growth inhibition while drug was on board. Single agent studies have been completed for 17/37 models with this combination and 7/9 responses were due to at least an additive effect of the combination. In contrast, while an HDACi + nucleoside analog combination had 16/36 responsive models, response in most of the single agent studies was due to only one of the agents. As part of this study, 3 models have been identified that have responded to at least 50% of the combinations tested possibly indicating a hypersensitive phenotype: two Merkel cell carcinomas (n=28 and 32) and one Neuroendocrine carcinoma (n=27). There is no immediate link between mechanism of action of the agents in the combinations, and the two Merkel cell carcinoma responses only had a moderate overlap. Finally, two Rhabdomyosarcoma models in the study have been the least responsive models to date. Funded by NCI Contract No. HHSN261200800001E

Citation Format: Yvonne A. Evrard, Sergio Y. Alcoser, Suzanne Borgel, Devynn Breen, John Carter, Tiffanie Chase, Alice Chen, Li Chen, Kristen Cooley, Biswajit Das, Emily Delaney, Lyndsay Dutko, Shannon Ecker, Thomas Forbes, Kyle Georgius, Michelle M. Gottholm-Ahalt, Tara Grinnage-Pulley, Sierra Hoffman, Chris Karlovich, Kimberly Klarmann, Shahanawaz Jiwani, Justine Mills, Malorie Morris, Michael Mullendore, Dianne Newton, Gloryvee Rivera, Howard Stotler, Jesse Stottlemyer, Savanna Styers, Cindy R. Timme, Debbie Trail, Shannon Uzelac, Tomas Vilimas, Thomas Walsh, Nikki Walters, P. Mickey Williams, Melinda G. Hollingshead, James H. Doroshow. Single agent response comparisons in a large-scale, preclinical trial of rare cancer PDXs by the National Cancer Institute's patient-derived models repository [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 3010.

Abstract 3015: Applications of immunohistochemistry in characterization of patient derived xenograft models

Background: Well characterized patient derived xenograft models (PDX) are becoming the preferred pre-clinical tool in translational cancer research for biologic understanding of the disease, development of new treatments, and identifying potential therapy predictive and resistant biomarkers. Characterization of PDX models using a multi-omic approach is most desirable, however such efforts can be expensive and technically demanding. Immunohistochemistry (IHC) has become an indispensable ancillary tool in the accurate classification of tumor types, determination of cell of origin, identification of biologic properties like growth and metastatic potential, and evaluation for the presence/absence of therapeutic or prognostic biomarkers.

Methods: 43 IHC assays were validated on the Leica Bond RX automated staining platform to identify common inconsistencies in PDX development including markers for classifying carcinomas, lymphomas, sarcomas, murine tumors, and theragnostic biomarkers. Rabbit antibodies are used rather than mouse antibodies to prevent non-specific staining of murine tissue.

Results: 1. IHC evaluation of models within NCI's Patient Derived Models Repository (pdmr.cancer.gov) led to re-classification or sub-classification of 12 tumor models in accordance with WHO guidelines. 2. IHC evaluation of theragnostic markers in 8 breast cancer PDX models showed concordant results throughout passaging, suggesting stability of these biomarkers in our models. 3. We observe malignant transformation of murine or transplanted benign human tissue at a rate of 2.5%. On IHC analysis, 52% were human lymphomas, 20% were murine lymphomas, and 28% were other murine tumors.

Conclusions: IHC is a rapid, cost-effective tool that can be used for accurate tumor classification, identifying subclonal outgrowth and tumor evolution, assessing stability of biomarkers and identifying malignant transformation of benign tissue. Funded by NCI Contract No. HHSN261200800001E

ANTIBODYCLONEVENDORANTIBODYCLONEVENDORAndrogen Receptor[EPR1535(2)]abcamGATA3[EPR16651]abcamB-Catenin[E247]abcamGCDFP-15[EPR1582Y]abcamCD19polyclonalabcamGFAPpolyclonalDAKO/AgilentCD3polyclonalabcamHER2 ErbB2[SP3]abcamCD20[SP32]abcamKi-67[D2H10]Cell SignalingCD34[EP373Y]abcamKu80[EPR3468]abcamCD45polyclonalabcamMGMTMT3.1MilliporeCD56 (NCAM1)[EPR2566]abcamMitochondria Marker (Biotin)MTC02abcamCD68[EPR20545]abcamMyogenin[EPR4789]abcamCDX2[EPR2764Y]abcamNAPSIN A[EPR6252]abcamChromogranin A[SP12]abcamp63polyclonalGeneTexCK7 (purified)[EPR1619Y]abcamPD-1[EPR4877(2)]abcamCK19[EPR1580Y]abcamPD-L1 (CD274)RBT-PDL1LifeSpan BiosciencesCK20[EPR1622Y]abcamProgesterone Receptor[SP2]abcamCytokeratin wide spectrumpolyclonalabcamProstate Specific Antigen (PSA)[EP1588Y]abcamDesmin[Y66]abcamS100[EPR19013]abcamEBV LMP1[D24-G]abcamSmooth Muscle Actin (SMA)polyclonalabcamERG[EPR3864]abcamSynaptophysin[SP11]abcamEstrogen Receptor[SP1]abcamTTF1[SP141]abcamFOXP1monoclonalLifeSpan BiosciencesVimentin[EPR3776]abcamFOXP3(5H10L18)Invitrogen

Citation Format: Lindsay Dutko, Gloryvee Rivera, Erin Cantu, Vishnuprabha Rahulkannan, Kelly Benauer, Tiffanie Chase, Emily Delaney, Jesse Stottlemyer, Chelsea McGlynn, Howard Stotler, John Carter, Suzanne Borgel, Michelle M. Gottholm Ahalt, Michelle Eugeni, Melinda Hollingshead, Yvonne Evrard, Chris Karlovich, Biswajit Das, Mickey Williams, James H. Doroshow, Shahanawaz Jiwani. Applications of immunohistochemistry in characterization of patient derived xenograft models [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 3015.

TPM, FPKM, or Normalized Counts? A Comparative Study of Quantification Measures for the Analysis of RNA-seq Data from the NCI Patient-Derived Models Repository

Background

In order to correctly decode phenotypic information from RNA-sequencing (RNA-seq) data, careful selection of the RNA-seq quantification measure is critical for inter-sample comparisons and for downstream analyses, such as differential gene expression between two or more conditions. Several methods have been proposed and continue to be used. However, a consensus has not been reached regarding the best gene expression quantification method for RNA-seq data analysis.

Methods

In the present study, we used replicate samples from each of 20 patient-derived xenograft (PDX) models spanning 15 tumor types, for a total of 61 human tumor xenograft samples available through the NCI patient-derived model repository (PDMR). We compared the reproducibility across replicate samples based on TPM (transcripts per million), FPKM (fragments per kilobase of transcript per million fragments mapped), and normalized counts using coefficient of variation, intraclass correlation coefficient, and cluster analysis.

Results

Our results revealed that hierarchical clustering on normalized count data tended to group replicate samples from the same PDX model together more accurately than TPM and FPKM data. Furthermore, normalized count data were observed to have the lowest median coefficient of variation (CV), and highest intraclass correlation (ICC) values across all replicate samples from the same model and for the same gene across all PDX models compared to TPM and FPKM data.

Conclusion

We provided compelling evidence for a preferred quantification measure to conduct downstream analyses of PDX RNA-seq data. To our knowledge, this is the first comparative study of RNA-seq data quantification measures conducted on PDX models, which are known to be inherently more variable than cell line models. Our findings are consistent with what others have shown for human tumors and cell lines and add further support to the thesis that normalized counts are the best choice for the analysis of RNA-seq data across samples.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12967-021-02936-w.

Hetero-Trifunctional Malonate-Based Nanotheranostic System for Targeted Breast Cancer Therapy

Designing multifunctional linkers is crucial for tricomponent theranostic targeted nanomedicine development as they are essential to enrich polymeric systems with different functional moieties. Herein, we have obtained a hetero-trifunctional linker from malonic acid and demonstrated its implication as an amphiphilic targeted nanotheranostic system (CB DX UN PG FL). We synthesized it with varying hydrophilic segment to fine-tune the hydrophobic/hydrophilic ratio to optimize its self-assembly. pH-responsive hydrazone-linked doxorubicin was conjugated to the backbone (UN PG FL) containing folate as a targeting ligand. Cobalt carbonyl complex was used for T₂-weighted magnetic resonance imaging (MRI). Electron micrographs of optimized molecule CB DX UN PG_(4 kDa) FL in an aqueous system have demonstrated about 50-60 nm-sized uniform micelles. The relaxivity study and the one-dimensional (1D) imaging experiments clearly revealed the effect of the nanotheranostics system on transverse relaxation (T₂) of water molecules, which validated the system as a T₂-weighted MRI contrast agent. The detailed in vitro biological studies validated the targeted delivery and anticancer potential of CB DX UN PG_(4 kDa) FL. Combining the data on transverse relaxation, folate mediated uptake, and anticancer activity, the designed molecule will have a significant impact on the development of targeted theranostic.

Profiling 523 cancer associated genes in circulating tumor DNA of children with CNS tumors

3023

Background: Pediatric central nervous system (CNS) cancers often pose unique challenges including tumor ‘invisibility’, where surgical resection is restricted due to the sensitive tumor location and tissue biopsy is not always feasible. Detecting cancer associated mutations and copy number variations (CNV) at diagnosis is increasingly important, as the WHO classification of pediatric CNS cancers has incorporated molecular signatures with tumor grade. To achieve CNS tumor molecular ‘visibility’, we previously established a liquid biopsy platform for detecting single nucleotide variants in circulating tumor DNA (ctDNA). However, our method was limited by the restricted number of genes that can be monitored and the inability to detect genomic events including CNVs. To address this, we developed a deep sequencing liquid biopsy approach to profile alterations across selected genes. Our platform provides an opportunity for multi-gene monitoring, to assess tumor subclonal evolution and response to treatment in the absence of repeat tissue biopsies. Methods: We tested the performance of our platform using paired tissue, CSF, and plasma/serum from 10 children with diffuse midline glioma (DMG). ctDNA was analyzed using the TruSight Oncology 500 (TSO500) ctDNA targeted panel covering 523 genes. Matched tumor, CSF, and blood were assessed for concordance and sequencing results were compared to digital droplet PCR (ddPCR) detection of H3K27M mutation. Results: The median exons with ³500X coverage was 96% for 7 CSF samples with optimal input (³60ng), 0.01% for 3 CSF samples with < 5ng input, and 74.5% for plasma/serum samples. ctDNA was more readily detectable in CSF, yet concordance between paired tumor, CSF and plasma/serum was observed. DMG associated mutations in genes including H3F3A, HIST1H3B, TP53, and ACVR1 were detected in ctDNA. Of 9 H3K27M mutations identified in tumor, 8 were present in CSF and 3 in plasma/serum, for a positive percent agreement of 89% and 33%, respectively, with the tumor results. Among CSF samples, H3.3K27M was detected in 6/6 cases, and H3.1K27M in 2/3 cases, with variant allele frequencies comparable to ddPCR results. CNVs including PDGFRA/B and MDM4 amplifications were present in CSF and confirmed by analysis of paired tumor. Additional events, including PIK3CA p.E545Q, PPM1D truncation, and KRAS amplification, were detected in CSF but absent from paired tumor, indicating tissue heterogeneity. Strategies to optimize ctDNA detection, including optimization of ctDNA isolation and adjustment of library QC metrics, were identified. Conclusions: This proof-of-concept study demonstrates the feasibility of our high depth, targeted sequencing approach for detecting clinically relevant mutations in ctDNA from children with CNS tumors. This approach may aid in diagnosis of CNS tumor molecular subtype, and monitoring of tumor evolution and response to therapy in serially collected ctDNA.

NCI protocol 10250: A phase II study of temozolomide and olaparib for the treatment of advanced uterine leiomyosarcoma

11506

Background: Uterine leiomyosarcoma (uLMS) is an aggressive sarcoma subtype with frequent metastatic relapse. After failure of front-line chemotherapy, remaining options provide limited benefit (trabectedin: ORR 11%, mPFS 4.0 mos; pazopanib: ORR 11%, median PFS 2.9 mos; dacarbazine: ORR 9%, mPFS 1.5 mos). Recent molecular studies suggest uLMS harbors characteristic defects in the homologous recombination (HR) DNA repair pathway, including somatic biallelic BRCA2 deletion in 10%, implicating potential sensitivity to PARP-inhibitor based treatment approaches. In preclinical uLMS models in which temozolomide (T, an oral equivalent to dacarbazine) or the PARP inhibitor olaparib (O) showed limited single agent activity, the combination of T + O was highly effective in inhibiting uLMS tumor growth and promoting apoptosis. Methods: NCI protocol #10250 is a single-arm, open-label, multi-center phase II study evaluating T + O in advanced uLMS. Pts had progression on ≥ 1 prior line and ECOG PS ≤ 2. Pts received T 75 mg/m2 PO daily + O 200 mg PO BID days 1-7 in 21-day cycles. Primary endpoint was ORR. A one-stage binomial design was used. If ≥ 5/22 responded, the treatment was considered promising (95% power; α = 0.06). All pts underwent paired tumor biopsies. Correlative assays to evaluate for HR deficiency (whole exome sequencing/RNAseq, RAD51 foci formation) and for intrinsic PARP inhibitor resistance (SLFN11 expression) will be correlated with response. Results: 22 patients were evaluable (median age 55, median prior treatment lines 3). Median follow-up was 10.8 mos. Primary endpoint, ORR within 6 mos of initiating treatment, was 23% (5/22). Overall ORR was 27% (6/22). Median PFS was 6.9 mos (95% CI: 5.4 mos – not estimable (NE)). Median duration of response (DOR) was 12.0 mos (95% CI: 9.5 mos – NE). Hematologic toxicity was common (grade 3/4 neutropenia, 77%; thrombocytopenia 32%) but manageable with dose modification. Correlative assays are ongoing with plans to present at the meeting. An immunohistochemical assay for RAD51 foci has been adapted for uLMS samples and clearly distinguishes BRCA2- deleted and wild-type tumors. Conclusions: NCI 10250 met the prespecified primary efficacy endpoint of ORR in a population of patients with heavily pre-treated uLMS. Responses are durable (median DOR 12 mos). Correlative assays are being completed to evaluate whether uLMS tumors with HR deficiency or with preserved SLFN11 expression are most sensitive to T + O and may underlie durable responses. A randomized study of the combination is planned. Clinical trial information: NCT03880019.

A critical review of biogas production and usage with legislations framework across the globe

This review showcases a comprehensive analysis of studies that highlight the different conversion procedures attempted across the globe. The resources of biogas production along with treatment methods are presented. The effect of different governing parameters like feedstock types, pretreatment approaches, process development, and yield to enhance the biogas productivity is highlighted. Biogas applications, for example, in heating, electricity production, and transportation with their global share based on national and international statistics are emphasized. Reviewing the world research progress in the past 10 years shows an increase of ~ 90% in biogas industry (120 GW in 2019 compared to 65 GW in 2010). Europe (e.g., in 2017) contributed to over 70% of the world biogas generation representing 64 TWh. Finally, different regulations that manage the biogas market are presented. Management of biogas market includes the processes of exploration, production, treatment, and environmental impact assessment, till the marketing and safe disposal of wastes associated with biogas handling. A brief overview of some safety rules and proposed policy based on the world regulations is provided. The effect of these regulations and policies on marketing and promoting biogas is highlighted for different countries. The results from such studies show that Europe has the highest promotion rate, while nowadays in China and India the consumption rate is maximum as a result of applying up-to-date policies and procedures.

On the Role of Magnesium Ions in the DNA-Scissoring Activity of the Restriction Endonuclease ApaI: Stochastic Kinetics from a Single Molecule to Mesoscopic Paradigm

Biochemical reactions occurring inside cells have significant stochastic signatures due to the low copy number of reacting species. Kinetics of DNA cleavage by restriction endonucleases are no exception as established by single-molecule experiments. Here, we propose a simple reaction scheme to understand the role of the cofactor magnesium ion in the action of the endonuclease ApaI. The methodology is based on the waiting time distribution of cleavage product formation that enables us to determine the corresponding rate both analytically and numerically. The theory is developed at the single-molecule level and then generalized to the biologically relevant case of a population of DNA-endonuclease complexes present inside a cell. The theoretical rate versus cofactor concentration curve is matched with relevant single-molecule experimental data that reveals positive cooperativity of cofactor binding and provides a reliable estimate of model parameters. Furthermore, a parameter range is identified where the dispersion of the waiting time, measured using the coefficient of variation, is significantly lower than the Poisson limit and becomes minimum at the in vivo magnesium ion concentration level. Such low dispersion can play a role in the robust DNA-scissoring activity of ApaI under in vivo conditions.

Anti-Cancer Stem Cells Potentiality of an Anti-Malarial Agent Quinacrine: An Old Wine in a New Bottle

Quinacrine (QC) is a tricyclic compound and a derivative of 9-aminoacridine. It has been widely used to treat malaria and other parasitic diseases since the last century. Interestingly, studies have revealed that it also displays anti-cancer activities. Here, we have discussed the anti-cancer mechanism of QC along with its potentiality to specifically target cancer stem cells. The anti-cancer action of this drug includes DNA intercalation, inhibition of DNA repair mechanism, prevention of cellular growth, cell cycle arrest, inhibition of DNA and RNA polymerase activity, induction of autophagy, promotion of apoptosis, deregulation of cell signaling in cancer cells and cancer stem cells, inhibition of metastasis and angiogenesis. In addition, we have also emphasized on the synergistic effect of this drug with other potent chemotherapeutic agents and mentioned its different applications in anti-cancer therapy.

Molecular Profiling-Based Assignment of Cancer Therapy (NCI-MPACT): A Randomized Multicenter Phase II Trial

This trial assessed the utility of applying tumor DNA sequencing to treatment selection for patients with advanced, refractory cancer and somatic mutations in one of four signaling pathways by comparing the efficacy of four study regimens that were either matched to the patient's aberrant pathway (experimental arm) or not matched to that pathway (control arm).

MATERIALS AND METHODS

Adult patients with an actionable mutation of interest were randomly assigned 2:1 to receive either (1) a study regimen identified to target the aberrant pathway found in their tumor (veliparib with temozolomide or adavosertib with carboplatin [DNA repair pathway], everolimus [PI3K pathway], or trametinib [RAS/RAF/MEK pathway]), or (2) one of the same four regimens, but chosen from among those not targeting that pathway.

RESULTS

Among 49 patients treated in the experimental arm, the objective response rate was 2% (95% CI, 0% to 10.9%). One of 20 patients (5%) in the experimental trametinib cohort had a partial response. There were no responses in the other cohorts. Although patients and physicians were blinded to the sequencing and random assignment results, a higher pretreatment dropout rate was observed in the control arm (22%) compared with the experimental arm (6%; P = .038), suggesting that some patients may have had prior tumor mutation profiling performed that led to a lack of participation in the control arm.

CONCLUSION

Further investigation, better annotation of predictive biomarkers, and the development of more effective agents are necessary to inform treatment decisions in an era of precision cancer medicine. Increasing prevalence of tumor mutation profiling and preference for targeted therapy make it difficult to use a randomized phase II design to evaluate targeted therapy efficacy in an advanced disease setting.

Scanning of a Double-Sided Germanium Strip Detector

This work presents the results from the characterization of a Position-Sensitive Planar Germanium (PSPGe) detector. The PSPGe detector is a double-sided orthogonal strip detector consisting of 10x10 electrical segmentation along the horizontal and vertical directions. The characterization was performed using the coincidence setup between the PSPGe detector and the well-characterized scanning system employing the positron annihilation correlation principle. The scanning system consists of a Position Sensitive Detector (PSD) and 22Na positron source. The main objective of this study is to deploy PSPGe detector for future decay experiments at the Facility for Antiproton and Ion Research (FAIR), Germany. The measurements have been performed to find the depth of gamma-ray interaction in the planar segmented detector. The 2-Dimensional image obtained from the PSD has been used to find the depth of gamma-ray interaction in the planar strip detector using pulse shape analysis. In addition, the sensitivity of PSPGe detector has been investigated by calculating the rise-time from pulse shapes for the front and back strips of the detector.

Development of a position-sensitive fast scintillator (LaBr3(Ce)) detector setup for gamma-ray imaging application

We have characterized a Cerium doped Lanthanum Bromide (LaBr3(Ce) ) crystal coupled with the position-sensitive photo-multiplier system for the gamma-ray imaging application. One can use this detector set-up for the scanning of high purity germanium detectors for pulse shape analysis in gamma-ray spectroscopy experiments and the image formation of an object by Compton back-scattering . The sensor has been tested for energy, timing and position information of the gamma-rays interacting within the detector crystal. The GEANT4 simulation results are consistent with the experimental results. We have reconstructed the image of irradiation spots in different positions throughout the detector crystal. Position resolution is found to be around 3.5 mm with the 2 mm collimated gamma-rays. The 2-d image of hexagonal Bismuth Germanate (BGO) crystal and a cylindrical LaBr3(Ce) crystal have been reconstructed in coincidence technique. The performance of the detector for imaging application has been investigated by coincidence technique in GEANT4 simulation and compared with the experimental data. We have reconstructed the 2-d images of objects with various geometrical shapes by Compton back-scattered events of the gamma-rays. This position-sensitive detector can be used as an absorber of a Compton camera for the image reconstruction of an extended radioactive source. One can also use this kind of set-up as in radiation imaging and many other applications where the energy and source position of the gamma-ray is the main interest.

Activation of TRPV4 by mechanical, osmotic or pharmaceutical stimulation is anti-inflammatory blocking IL-1β mediated articular cartilage matrix destruction

OBJECTIVE

Cartilage health is maintained in response to a range of mechanical stimuli including compressive, shear and tensile strains and associated alterations in osmolality. The osmotic-sensitive ion channel Transient Receptor Potential Vanilloid 4 (TRPV4) is required for mechanotransduction. Mechanical stimuli inhibit interleukin-1β (IL-1β) mediated inflammatory signalling, however the mechanism is unclear. This study aims to clarify the role of TRPV4 in this response.

DESIGN

TRPV4 activity was modulated glycogen synthase kinase (GSK205 antagonist or GSK1016790 A (GSK101) agonist) in articular chondrocytes and cartilage explants in the presence or absence of IL-1β, mechanical (10% cyclic tensile strain (CTS), 0.33 Hz, 24hrs) or osmotic loading (200mOsm, 24hrs). Nitric oxide (NO), prostaglandin E₂ (PGE₂) and sulphated glycosaminoglycan (sGAG) release and cartilage biomechanics were analysed. Alterations in post-translational tubulin modifications and primary cilia length regulation were examined.

RESULTS

In isolated chondrocytes, mechanical loading inhibited IL-1β mediated NO and PGE₂ release. This response was inhibited by GSK205. Similarly, osmotic loading was anti-inflammatory in cells and explants, this response was abrogated by TRPV4 inhibition. In explants, GSK101 inhibited IL-1β mediated NO release and prevented cartilage degradation and loss of mechanical properties. Upon activation, TRPV4 cilia localisation was increased resulting in histone deacetylase 6 (HDAC6)-dependent modulation of soluble tubulin and altered cilia length regulation.

CONCLUSION

Mechanical, osmotic or pharmaceutical activation of TRPV4 regulates HDAC6-dependent modulation of ciliary tubulin and is anti-inflammatory. This study reveals for the first time, the potential of TRPV4 manipulation as a novel therapeutic mechanism to supress pro-inflammatory signalling and cartilage degradation.

Cross-Site Concordance Evaluation of Tumor DNA and RNA Sequencing Platforms for the CIMAC-CIDC Network

PURPOSE

Whole-exome (WES) and RNA sequencing (RNA-seq) are key components of cancer immunogenomic analyses. To evaluate the consistency of tumor WES and RNA-seq profiling platforms across different centers, the Cancer Immune Monitoring and Analysis Centers (CIMAC) and the Cancer Immunologic Data Commons (CIDC) conducted a systematic harmonization study.

EXPERIMENTAL DESIGN

DNA and RNA were centrally extracted from fresh frozen and formalin-fixed paraffin-embedded non-small cell lung carcinoma tumors and distributed to three centers for WES and RNA-seq profiling. In addition, two 10-plex HapMap cell line pools with known mutations were used to evaluate the accuracy of the WES platforms.

RESULTS

The WES platforms achieved high precision (> 0.98) and recall (> 0.87) on the HapMap pools when evaluated on loci using > 50× common coverage. Nonsynonymous mutations clustered by tumor sample, achieving an index of specific agreement above 0.67 among replicates, centers, and sample processing. A DV200 > 24% for RNA, as a putative presequencing RNA quality control (QC) metric, was found to be a reliable threshold for generating consistent expression readouts in RNA-seq and NanoString data. MedTIN > 30 was likewise assessed as a reliable RNA-seq QC metric, above which samples from the same tumor across replicates, centers, and sample processing runs could be robustly clustered and HLA typing, immune infiltration, and immune repertoire inference could be performed.

CONCLUSIONS

The CIMAC collaborating laboratory platforms effectively generated consistent WES and RNA-seq data and enable robust cross-trial comparisons and meta-analyses of highly complex immuno-oncology biomarker data across the NCI CIMAC-CIDC Network.

Genetic characterization of foot-and-mouth disease virus serotype O isolates collected during 2014-2018 revealed dominance of O/ME-SA/Ind2001e and the emergence of a novel lineage in India

Foot-and-mouth disease (FMD) is endemic in India with a preponderance of outbreaks caused by FMD virus (FMDV) serotype O. Out of the 11 global topotypes of serotype O, only ME-SA topotype has been reported in the country so far. Lineage O/ME-SA/Ind2001 and O/ME-SA/PanAsia are documented as the most dominant ones in terms of the number of outbreaks caused by them. To understand the distribution of topotype/lineages in India and their antigenic behaviour during the year 2014-2018, a total of 286 FMDV serotype O viral isolates were sequence determined at the VP1 region, and 109 isolates were characterized antigenically. All the isolates grouped in the ME-SA topotype, being distributed in lineage O/ME-SA/Ind2001 (within sub-lineages O/ME-SA/Ind2001d and O/ME-SA/Ind2001e), and a new group designated here as O/ME-SA/2018 cluster. The sub-lineage O/ME-SA/Ind2001e reported for the first time in India during the year 2015, replaced sub-lineage O/ME-SA/Ind2001d gradually, which was dominating since 2008. During the years 2014-2018, the sub-lineage O/ME-SA/Ind2001e was found to be the most predominant one whose mean evolutionary rate was observed to be faster than that of the sub-lineage O/ME-SA/Ind2001d. The codon sites 45 and 85 of VP1 were found to be under diversifying selection in a large proportion of trees. The common ancestor predicted for sub-lineages O/ME-SA/Ind2001e and O/ME-SA/2018 dates back to 2012 and 2016, respectively. The sustenance and spread of the new O/ME-SA/2018 cluster need to be assessed by continued surveillance. The Indian vaccine strain O/INDR2/1975 was found to provide adequate antigenic coverage to the emerging and prevalent serotype O lineages. The trait association tests showed frequent virus exchange among different states, which could be an important confounder in the region-specific assessment of effectiveness of FMD control programme.

Escherichia coli, a common constituent of benign prostate hyperplasia-associated microbiota induces inflammation and DNA damage in prostate epithelial cells

BACKGROUND

The role of microbiota in the pathophysiology of benign prostate hyperplasia (BPH), especially in creating an inflammatory milieu may not be avoided. The major objectives of this study were to investigate the microbial composition of BPH tissues, its association with inflammation and check the effect of clinically isolated bacteria on prostate epithelial cells.

METHODS

The study includes 36 patients with a pathological diagnosis of BPH. Following strict aseptic measures, tissues were collected after transurethral resection of prostate, multiple pieces of the resected tissues were subjected to histopathological analysis, bacterial culture and genomic DNA extraction. Microbial composition was analyzed by culture and/or next-generation sequencing methods. Annotation of operational taxonomy unit has been done with an in-house algorithm. The extent of inflammation was scored through histological evaluation of tissue sections. The effect of clinical isolates on nuclear factor-κB (NF-κB) activity and induction of DNA-damage in the prostate epithelial cells were evaluated.

RESULTS

Histopathological analysis of the BPH tissues showed the presence of inflammation in almost all the tissues with a varied level at different regions of the same tissue section and the level of overall inflammation was different from patients to patients. Microbial culture of tissue samples showed the presence of live bacteria in 55.5% (20 out of 36) of the patient tissues. Majority of the isolates were coagulase-positive Staphylococcus, E. coli and Micrococcus spp. Further, V3 16S rRNA sequencing of the DNA isolated from BPH tissues showed the presence of multiple bacteria and the most common phylum in the BPH tissues were found to be Proteobacteria, Actinobacteria, Firmicutes, and Bacteroidetes. The E. coli, isolated from one of the tissue was able to activate NF-κB and induce DNA damage in prostate epithelial cells. Phospho-histone γH2A.X staining confirmed the presence of cells with damaged DNA lesion in BPH tissues and also correlated with the severity of inflammation.

CONCLUSION

Our study has shown that the BPH tissues do have a divergent microbial composition including the commonly found E. coli (phylum Proteobacteria), and these bacteria might contribute to the BPH-associated inflammation and/or tissue damage. The BPH-associated E. coli induced NF-κB signaling and DNA damage in prostate epithelial cells in vitro.

Immunological and functional aspects of MAGEA3 cancer/testis antigen

Identification of ectopic gene activation in cancer cells serves as a basis for both gene signature-guided tumor targeting and unearthing of oncogenic mechanisms to expand the understanding of tumor biology/oncogenic process. Proteins expressed only in germ cells of testis and/or placenta (immunoprivileged organs) and in malignancies are called cancer testis antigens; they are antigenic because of the lack of antigen presentation by those specific cell types (germ cells), which limits the exposure of the proteins to the immune cells. Since the Cancer Testis Antigens (CTAs) are immunogenic and expressed in a wide variety of cancer types, CT antigens have become interesting target for immunotherapy against cancer. Among CT antigens MAGEA family is reported to have 12 members (MAGEA1 to MAGEA12). The current review highlights the studies on MAGEA3 which is a CT antigen and reported in almost all types of cancer. MAGEA3 is well tried for cancer immunotherapy. Recent advances on its functional and immunological aspect warranted much deliberation on effective therapeutic approach, thus making it a more interesting target for cancer therapy.

COMPARATIVE ANALYSIS OF CARBOXYMETHYL CELLULOSE AND PARTIALLY HYDROLYZED POLYACRYLAMIDE – LOW-SOLID NONDISPERSED DRILLING MUD WITH RESPECT TO PROPER-TY ENHANCEMENT AND SHALE INHIBITION

During drilling, different problems are encountered that can interfere with smooth drilling processes, including the accumulation of cuttings, reduced penetration rates, pipe sticking, loss of wellbore stability, and loss of circulation. These problems are generally encountered with conventional drilling mud, such as the bentonite–barite mud system. Formation damage is the most common problem encountered in bentonite mud systems with high solid content. In this work, we aimed to formulate two low-solid nondispersed (LSND) muds: carboxymethyl cellulose (CMC)–LSND mud and partially hydrolyzed polyacrylamide (PHPA)–LSND mud. A comparative analysis was performed to evaluate their property enhancements. LSND muds aid in maintaining hole stability and proper cutting removal. The results of this work show that the addition of both CMC and PHPA helps to improve drilling fluid properties; however, the PHPA–LSND mud was found to be superior. Shale swelling is a major concern in the petroleum industry, as it causes various other problems, such as pipe sticking, low penetration rates, and bit wear. The effect of these two LSND polymer muds in inhibiting shale swelling was analyzed using shale collected from the Champhai district of Mizoram, India.

Abstract 3916: Patient-derived organoid and cell culture models from the NCI Patient-Derived Models Repository (NCI PDMR) preserve genomic stability and heterogeneity of patient tumor specimens

Background: The National Cancer Institute (NCI) has developed a Patient-Derived Models Repository (PDMR; https://pdmr.cancer.gov) of preclinical models including patient-derived xenografts (PDX), organoids (PDOrg) and patient-derived cell cultures (PDC). Extensive clinical annotation and genomic datasets are available for these preclinical models. However, it is unclear if the molecular profiles of the corresponding patient tumors are stably propagated in these models. We have previously demonstrated that PDX models from the NCI PDMR faithfully represent the patient tumors both in terms of genomic stability and tumor heterogeneity. Here, we conduct an in-depth investigation of genomic representation of patient tumors in the PDOrgs and PDCs.

Methods: PDOrgs (n=64) and PDCs (n=94) were established from tumor fragments (i.e., initiator specimens) obtained either from patient specimens or from PDX specimens of early passage. For some models (n=19), both PDOrgs and PDCs were generated from the same tumor tissue; in fewer cases (n=4), PDCs were established from organoids derived from patient specimens. Whole Exome Sequencing and RNA-Seq were performed on all PDCs and PDOrgs, and data were compared with patient specimens or early passage PDXs.

Results: A majority of the PDOrgs and PDCs have stably inherited the genome of the corresponding patient specimens based on the following observations: (1) &gt;87% of PDOrgs and PDCs maintained similar copy number alteration profiles compared with the initiator specimens of the preclinical model; (2) the variant allele frequency (VAF) of clinically relevant mutations remained consistent between the PDOrgs, PDCs, and the initiator specimens, with none of the PDCs or PDOrgs deviating by &gt;15% VAF; and (3) clinically relevant biomarkers (e.g., MSI, LOH, mutational signatures etc.) are concordant amongst the PDOrgs, PDCs, and the initiator specimens. We observed that the majority of SNVs and indels present in the initiator specimens were also found in the PDOrgs and PDCs, suggesting almost all the tumor heterogeneity was preserved in these preclinical models.

Conclusions: This large and histologically diverse set of PDOrgs and PDCs from the NCI PDMR exhibited genomic stability and faithfully represented the tumor heterogeneity observed in corresponding patient specimens. These preclinical models thus represent a valuable resource for researchers interested in pre-clinical drug or other studies.

Citation Format: Biswajit Das, Yvonne A. Evrard, Li Chen, Rajesh Patidar, Tomas Vilimas, Justine N. McCutcheon, Amanda L. Peach, Nikitha V. Nair, Thomas D. Forbes, Brandie A. Fullmer, Anna J. Lee Fong, Luis E. Romero, Alyssa K. Chapman, Kelsey A. Conley, Robin D. Harrington, Shahanawaz S. Jiwani, Peng Wang, Michelle M. Gottholm-Ahalt, Erin N. Cantu, Gloryvee Rivera, Lindsay M. Dutko, Kelly M. Benauer, Vishnuprabha R. Kannan, Carrie A. Bonomi, Kelly M. Dougherty, Joseph P. Geraghty, Marion V. Gibson, Savanna S. Styers, Abigail J. Walke, Jenna E. Moyer, Anna Wade, Mariah L. Baldwin, Kaitlyn A. Arthur, Kevin J. Plater, Luke Stockwin, Matthew R. Murphy, Michael E. Mullendore, Dianne L. Newton, Melinda G. Hollingshead, Chris A. Karlovich, Paul M. Williams, James H. Doroshow. Patient-derived organoid and cell culture models from the NCI Patient-Derived Models Repository (NCI PDMR) preserve genomic stability and heterogeneity of patient tumor specimens [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 3916.

Abstract 3554: Genomic landscape of acquired uniparental disomy in NCI PDMR patient derived xenograft models

Background: Acquired Uniparental Disomy (aUPD) is relatively common in cancer. Occurrence of aUPD is more frequent in some tumor histologies (e.g., serous ovarian, colorectal) and may be relevant for choice of therapy. The Patient-Derived Models Repository (PDMR; https://pdmr.cancer.gov) developed by The National Cancer Institute (NCI) includes patient-derived xenograft (PDX) models from multiple tumor histologies with different passages and lineages. The associated clinical annotation and genomic data make it possible to assess the prevalence of aUPD in the PDMR cohort and the stability of aUPD in different passages and lineages within a PDX model.

Methods: High tumor purity in the PDX specimens (after removal of mouse reads representing the stroma) enabled highly accurate assessment of loss of heterozygosity (LOH). Variants called by GATK Haplotype caller from whole exome sequencing (WES) data were used to identify segments of homozygosity using BCFtools/RoH (runs of homozygosity). The RoH segments were then intersected with the bed file for chromosome arms to get %LOH at the arm level. If %LOH on a chromosome arm was &gt;90%, we considered the sample to have aUPD at the arm level. WES was also used to look for associations between DNA damage repair (DDR) pathway alterations and aUPD.

Results: We made the following observations: a) aUPD was observed most frequently in chr18q (75/427, 17.6%) and chr3p (69/427, 16%) of PDX models; b) aUPD was observed more frequently in certain tumor histologies, e.g., clear cell renal cell carcinoma (6/8), small cell lung cancer (3/4) and non-small cell lung cancer (25/38); c) extensive aUPD was observed in 4 PDMR models (&gt;50% of evaluated chromosome arms in these models have aUPD); d) aUPD was not observed in some tumor histologies, i.e., synovial sarcoma, uterine endometrioid carcinoma; e) in the vast majority of PDMR models (&gt;90%), aUPD is maintained faithfully across lineages and through multiple passaging; f) subclonal aUPD events were observed in some models across different lineages; g) significant enrichment of double strand DNA break repair (DSBR) pathway alterations was observed in PDMR models without aUPD (p=0.0007, Fisher's exact test) suggesting defects in DSBR are not associated with aUPD; and h) aUPD was rarely observed in MSI-high models (1/30) suggesting mutual exclusivity of mismatch repair (MMR) pathway defects and aUPD.

Conclusion: We observed a relatively high frequency of UPD in the PDMR models (at least 1 arm of a chromosome). UPD was more frequently observed in specific chromosomal arms. The frequency of aUPD was higher in some tumor histologies and absent in others. aUPD was stably maintained across passages and lineages, although some heterogeneity was observed. Our data suggest aUPD is not associated with defects in DSBR and MMR pathways. Preclinical drug studies using NCI PDMR models may suggest appropriate therapeutic options for cancers with aUPD.

Citation Format: Rajesh Patidar, Li Chen, Chris A. Karlovich, Biswajit Das, Yvonne A. Evrard, Tomas Vilimas, Justine N. McCutcheon, Amanda L. Peach, Nikitha V. Nair, Thomas D. Forbes, Brandie A. Fullmer, Anna J. Lee Fong, Luis E. Romero, Alyssa K. Chapman, Kelsey A. Conley, Robin D. Harrington, Shahanawaz S. Jiwani, Peng Wang, Michelle M. Gottholm Ahalt, Erin N. Cantu, Gloryvee Rivera, Lindsay M. Dutko, Kelly M. Benauer, Vishnuprabha R. Kannan, Suzanne D. Borgel, John P. Carter, Jesse M. Stottlemyer, Tiffanie L. Miner, Devynn R. Breen, Emily T. Delaney, Chelsea A. McGlynn, Candace N. Mallow, Marianne Radzyminski, Shannon N. Uzelac, Sergio Y. Alcoser, Tara L. Grinnage-Pulley, Michelle A. Eugeni, Dianne L. Newton, Melinda G. Hollingshead, Paul M. Williams, James H. Doroshow. Genomic landscape of acquired uniparental disomy in NCI PDMR patient derived xenograft models [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 3554.

Abstract 5056: Quality control efforts in a large-scale, preclinical trial of rare cancer PDXs by the National Cancer Institute's patient-derived models repository (NCI PDMR)

The National Cancer Institute's Patient-Derived Models Repository (NCI PDMR; https://pdmr.cancer.gov) is performing a large-scale multi-year preclinical study with 39 PDX models of rare cancers (mesothelioma, MPNST, osteosarcoma, Merkel cell carcinoma, etc) treated with 56 novel therapeutic combinations in an exploratory, n-of-4 arm, study design. Combinations that show promising responses (e.g., regression or durable inhibition of tumor growth) will be repeated along with the single agent arms to determine if the response is driven by the combination or only one of the agents. In order to do this in a timely fashion, relatively speaking, the PDX tumors are serially passaged and each passage is treated with a set of 8 combinations plus relevant vehicle control(s) while in parallel enough PDXs are retained to be expanded for the next passage and drug set. Every serial passage undergoes several quality control assessments that serve as go/no-go criteria including pathology assessment, human:mouse DNA content assessment, and low pass whole genome sequencing to determine the average fraction of genome changed compared to the original donor material. If there is a QC failure, the PDX model is restarted from early passage cryo-material (passage 1-2). An additional quality control effort is to bookend the combination studies with the first set of agents to see if tumor response is similar across passages. To date, most of the models have demonstrated a high degree of stability, though a couple of models have moved toward murine content and have been restarted from early passage material so all drug combinations can be tested. DNA and RNA are retained from all passages so a full NGS evaluation can be performed at a later date. This effort has been ongoing for over a year and the first bookend studies are beginning to be tested to determine if response at first and last passage of the study are consistent with each other, given the constraints of the inherent heterogeneity of the models themselves. Single agent studies of drug combinations that demonstrated a response in 30%-50% of the models tested are also underway to determine which combinations have a more than additive effect compared to the single agents. Promising combinations will be moved forward to early phase clinical trials for these rare cancers.

Funded by NCI Contract No. HHSN261200800001E

Citation Format: Yvonne A. Evrard, Biswajit Das, Sergio Y. Alcoser, Suzanne Borgel, Devynn Breen, John Carter, Tiffanie Chase, Alice Chen, Lily Chen, Kristen Cooley, Emily Delaney, Raymond Divelbiss, Lyndsay Dutko, Thomas Forbes, Kyle Georgius, Michelle Gottholm-Ahalt, Tara Grinnage-Pulley, Sierra Hoffman, Chris Karlovich, Shahanawaz Jiwani, Justine Mills, Malorie Morris, Michael Mullendore, Dianne Newton, Rajesh Patidar, Gloryvee Rivera, Howard Stotler, Jesse Stottlemyer, Savanna Styers, Debbie Trail, Shannon Uzelac, Thomas Vilimas, Abigail Walke, Thomas Walsh, Nicole Walters, Peng Wang, P. Mickey Williams, Melinda Hollingshead, James H. Doroshow. Quality control efforts in a large-scale, preclinical trial of rare cancer PDXs by the National Cancer Institute's patient-derived models repository (NCI PDMR) [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5056.

Potential of the fluoroketolide RBx 14255 against Streptococcus pneumoniae, Neisseria meningitidis and Haemophilus influenzae in an experimental murine meningitis model

BACKGROUND

RBx 14255 is a fluoroketolide in pre-clinical evaluation with potent activity against MDR Gram-positive pathogens.

OBJECTIVES

To investigate the efficacy of RBx 14255 against bacterial meningitis caused by Streptococcus pneumoniae, Neisseria meningitidis or Haemophilus influenzae in an experimental murine meningitis model.

METHODS

In vitro activity of RBx 14255 was evaluated against clinical isolates of S. pneumoniae, N. meningitidis and H. influenzae. The in vivo efficacy of RBx 14255 was evaluated against bacterial meningitis, induced with S. pneumoniae 3579 erm(B), S. pneumoniae MA 80 erm(B), N. meningitidis 1852 and H. influenzae B1414 in a murine meningitis model.

RESULTS

RBx 14255 showed strong in vitro bactericidal potential against S. pneumoniae, N. meningitidis and H. influenzae with MIC ranges of 0.004-0.1, 0.03-0.5 and 1-4 mg/L, respectively. In a murine meningitis model, a 50 mg/kg dose of RBx 14255, q12h, resulted in significant reduction of bacterial counts in the brain compared with the pretreatment control. The concentration of RBx 14255 in brain tissue correlated well with the efficacy in this mouse model.

CONCLUSIONS

RBx 14255 showed superior bactericidal activity in time-kill assays in vitro and in vivo in an experimental murine meningitis model. RBx 14255 could be a promising candidate for future drug development against bacterial meningitis.

Quinacrine Based Gold Hybrid Nanoparticles Caused Apoptosis through Modulating Replication Fork in Oral Cancer Stem Cells

The presence of cancer stem cells (CSCs) in the tumor microenvironment is responsible for the development of chemoresistance and recurrence of cancer. Our previous investigation revealed the anticancer mechanism of quinacrine-based silver and gold hybrid nanoparticles (QAgNP and QAuNP) in oral cancer cells, but to avoid cancer recurrence, it is important to study the effect of these nanoparticles (NPs) on CSCs. Here, we developed an in vitro CSCs model using SCC-9 oral cancer cells and validated via FACS analysis. Then, 40-60% of cells were found to be CD44+/CD133+ and CD24-. QAuNP showed excellent anti-CSC growth potential against SCC-9-cancer stem like cells (IC₅₀ = 0.4 μg/mL) with the down-regulation of representative CSC markers. Prolonged exposure of QAuNP induced the S-phase arrest and caused re-replication shown by the extended G2/M population and apoptosis to SCC-9-CSC like cells. Up-regulation of BAX, PARP cleavage, and simultaneous down-regulation of Bcl-xL in prolonged treatment to CSCs suggested that the majority of the cells have undergone apoptosis. QAuNP treatment also caused a loss in DNA repair in CSCs. Mostly, the base excision repair (BER) components (Fen-1, DNA ligase-1, Pol-β, RPA, etc.) were significantly down-regulated after QAuNP treatment, which suggested its action against DNA repair machinery. The replication fork maintenance-related proteins, RAD 51 and BRCA-2, were also deregulated. Very surprisingly, depletion of WRN (an interacting partner for Pre-RC and Fen-1) and a significant increase in expression of fork-degrading nuclease MRE-11 in 96 h treated NPs were observed. Results suggest QAuNP treatment caused excessive DNA damage and re-replication mediated replication stress (RS) and stalling of the replication fork. Inhibition of BER components hinders the flap clearance activity of Fen-1, and it further caused RS and stopped DNA synthesis. Overall, QAuNP treatment led to irreparable replication fork movement, and the stalled replication fork might have degraded by MRE-11, which ultimately results in apoptosis and the death of the CSCs.

Tumor genomic analysis for biomarker identification in a phase I trial of the Wee 1 inhibitor adavosertib (AZD1775)

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Background: Adavosertib, a first-in-class Wee1 kinase inhibitor, abrogates G2/M cell cycle arrest causing premature mitosis and DNA replication stress, yielding enhanced DNA damage. Here we report on potential biomarkers of response from tumor genomic analysis in patients (pts) with solid tumors treated with adavosertib. Methods: Adavosertib was administered once daily on days 1-5 and 8-12 of a 21-day cycle. RECIST 1.1 was used to evaluate clinical response. Paired tumor biopsies were obtained for RNASeq gene expression profiling (GEP) and for whole-exome sequencing (WES) to evaluate gene mutation and copy number amplification (CNA). Fold change (FC) was calculated to define gene overexpression. To identify the frequency of CNA and mRNA overexpression for the genomic biomarkers of interest, cBioPortal analysis using TCGA and MSK-IMPACT datasets was performed. Differential GEP analysis of tumor and paired normal tissue was performed using the gene expression profiling interactive analysis (GEPIA) interface (Tang et al. 2017). Results: Out of 35 pts evaluable for response, 6 (17%) had partial response (PR; 4 ovarian carcinoma [OVC], 2 endometrial carcinoma [EC]). The median duration of response was 5.2 months (range 4.0-23.1). Eighteen pts (51.4%) had stable disease. Genomic analysis of tumor biopsies was available for 9 pts; 7 of these pts were evaluable for response, and 3 had PR (2 OVC, 1 EC). WES revealed TP53 mutations in 6 pts (66.6%; 3 pts with PR, 2 with progressive disease,1 not evaluable). On WES, tumor Cyclin E1 ( CCNE1) CNA was present in 1 of 3 PR pts while tumors from all 3 PR samples showed relatively high CCNE1 expression by RNAseq (FC = 4.07). In the MSK-IMPACT 2017 dataset, CCNE1 CNA was identified in 1.8% of pts (194 of 10336); of which, OVC (10.3%) and EC (8.7%) had the highest incidence of CCNE1 CNAs. In separate tumor-specific (OVC, EC) TCGA datasets having CCNE1 overexpression and/or CNA, overlap in CCNE1 overexpression with CCNE1 CNA was 35.5% (OVC) and 25.2% (EC). Compared to normal ovarian/ endometrial tissues, GEPIA analysis revealed significantly higher CCNE1 mRNA expression in OVC (FC = 3.5) and EC (FC = 3.8). Conclusions: CCNE1alterations (overexpression and/or CNA) tend to be enriched in OVC and EC with a limited fraction showing both overexpression and CNA. Tumor genomic analysis of additional OVC and EC pts treated with adavosertib is required to determine whether CCNE1 mRNA overexpression, regardless of CCNE1 CNA, is a potential biomarker of response to this drug in these tumor types. Funded by NCI contract No. HHSN261200800001E. Clinical trial information: NCT01748825 .

Genomic characterization of preclinical models derived from primary and metastatic sites from rapid autopsy patients in PDMR

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Background: The National Cancer Institute has developed a repository of preclinical models [Patient-Derived Models Repository (NCI PDMR, https://pdmr.cancer.gov )] including patient derived xenografts (PDXs), organoids (PDOrgs) and in vitro tumor cultures (PDCs) from patients with solid tumor cancer histologies. A subset of these preclinical models is derived from post-mortem collections from rapid autopsies representing the end point in disease progression. Clinical annotations and genomic datasets associated with these models provide a unique opportunity to study tumor evolution, mechanistic insights into the metastatic process, and treatment resistance. Methods: To date, 43 PDXs, 21 PDCs, and 23 PDOrgs using rapid autopsy specimens from 8 primary and 35 metastatic sites of 18 patients have been developed by the Biological Testing Branch (DTP, DCTD, NCI Frederick, MD) for the PDMR. Whole exome (WES) and total transcriptome (RNASeq) data were processed to generate mutation, copy number alteration (CNA) and gene expression data. Multi-model lineage trees were reconstructed based on putative somatic variants for all the models derived from all patients. The fraction of the genome affected by CNA was compared both within and across PDX models. Results: Most of the rapid autopsy PDX models (32/43) are derived from pancreatic adenocarcinoma (PAAD) patients (13/18), with metastatic specimens originating from sites including liver, colon, omentum, and lung. Driver mutations are present in all preclinical model specimens derived from the same patient. For instance, KRAS p.G12D is present in all patient-derived model specimens derived from PAAD patient 521955. The fraction of the genome affected by CNA remains stable within a PDX model across passages (n = 24, mean = 6.39%, sd = 5.90%). However, we found that this increased when comparing PDX models derived from metastatic sites versus the primary site (n = 19, mean = 16.92%, sd = 10.46%). This indicates presence of tumor heterogeneity between metastatic and primary sites. The lineage tree for models from patient 521955 indicates that one liver metastasis has a unique seeding event compared to the other 4 metastatic sites. Unsupervised clustering analysis on gene expression data also confirms the observed tumor site relationships. Conclusions: Our data demonstrate the potential use of these preclinical models available from the NCI PDMR. These models provide a unique resource for preclinical studies in tumor evolution, metastatic spread mediators, and drug resistance.

Stability of the negative ion of hydrogen in nonideal classical plasmas

The stability of the negative ion of hydrogen (H^{-}) embedded in nonideal classical plasma has been studied by computing the ground state energy of the ion quite accurately. The interactions among the charged particles in plasma have been modelled by a pseudopotential, derived from a solution of Bogolyubov's hierarchy equations. An extensive basis set is employed in Rayleigh-Ritz variational method to compute the ground state energy of H^{-} for various values of plasma parameters. Effects of nonideality of plasma on the stability of the ion have been investigated in detail for a wide range of nonideality. Particular emphasis is made to compute accurately the critical values of the plasma screening parameters.

Development and interlaboratory evaluation of a NIST Reference Material RM 8366 for EGFR and MET gene copy number measurements

Background The National Institute of Standards and Technology (NIST) Reference Material RM 8366 was developed to improve the quality of gene copy measurements of EGFR (epidermal growth factor receptor) and MET (proto-oncogene, receptor tyrosine kinase), important targets for cancer diagnostics and treatment. The reference material is composed of genomic DNA prepared from six human cancer cell lines with different levels of amplification of the target genes. Methods The reference values for the ratios of the EGFR and MET gene copy numbers to the copy numbers of reference genes were measured using digital PCR. The digital PCR measurements were confirmed by two additional laboratories. The samples were also characterized using Next Generation Sequencing (NGS) methods including whole genome sequencing (WGS) at three levels of coverage (approximately 1 ×, 5 ×  and greater than 30 ×), whole exome sequencing (WES), and two different pan-cancer gene panels. The WES data were analyzed using three different bioinformatic algorithms. Results The certified values (digital PCR) for EGFR and MET were in good agreement (within 20%) with the values obtained from the different NGS methods and algorithms for five of the six components; one component had lower NGS values. Conclusions This study shows that NIST RM 8366 is a valuable reference material to evaluate the performance of assays that assess EGFR and MET gene copy number measurements.